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Archive for the ‘Genome Biology’ Category

The Human Genome Gets Fully Sequenced: A Simplistic Take on Century Long Effort

 

Curator: Stephen J. Williams, PhD

Ever since the hard work by Rosalind Franklin to deduce structures of DNA and the coincidental work by Francis Crick and James Watson who modeled the basic building blocks of DNA, DNA has been considered as the basic unit of heredity and life, with the “Central Dogma” (DNA to RNA to Protein) at its core.  These were the discoveries in the early twentieth century, and helped drive the transformational shift of biological experimentation, from protein isolation and characterization to cloning protein-encoding genes to characterizing how the genes are expressed temporally, spatially, and contextually.

Rosalind Franklin, who’s crystolagraphic data led to determination of DNA structure. Shown as 1953 Time cover as Time person of the Year

Dr Francis Crick and James Watson in front of their model structure of DNA

 

 

 

 

 

 

 

 

 

Up to this point (1970s-mid 80s) , it was felt that genetic information was rather static, and the goal was still to understand and characterize protein structure and function while an understanding of the underlying genetic information was more important for efforts like linkage analysis of genetic defects and tools for the rapidly developing field of molecular biology.  But the development of the aforementioned molecular biology tools including DNA cloning, sequencing and synthesis, gave scientists the idea that a whole recording of the human genome might be possible and worth the effort.

How the Human Genome Project  Expanded our View of Genes Genetic Material and Biological Processes

 

 

From the Human Genome Project Information Archive

Source:  https://web.ornl.gov/sci/techresources/Human_Genome/project/hgp.shtml

History of the Human Genome Project

The Human Genome Project (HGP) refers to the international 13-year effort, formally begun in October 1990 and completed in 2003, to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. Another project goal was to determine the complete sequence of the 3 billion DNA subunits (bases in the human genome). As part of the HGP, parallel studies were carried out on selected model organisms such as the bacterium E. coli and the mouse to help develop the technology and interpret human gene function. The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project.

 

Please see the following for goals, timelines, and funding for this project

 

History of the Project

It is interesting to note that multiple government legislation is credited for the funding of such a massive project including

Project Enabling Legislation

  • The Atomic Energy Act of 1946 (P.L. 79-585) provided the initial charter for a comprehensive program of research and development related to the utilization of fissionable and radioactive materials for medical, biological, and health purposes.
  • The Atomic Energy Act of 1954 (P.L. 83-706) further authorized the AEC “to conduct research on the biologic effects of ionizing radiation.”
  • The Energy Reorganization Act of 1974 (P.L. 93-438) provided that responsibilities of the Energy Research and Development Administration (ERDA) shall include “engaging in and supporting environmental, biomedical, physical, and safety research related to the development of energy resources and utilization technologies.”
  • The Federal Non-nuclear Energy Research and Development Act of 1974 (P.L. 93-577) authorized ERDA to conduct a comprehensive non-nuclear energy research, development, and demonstration program to include the environmental and social consequences of the various technologies.
  • The DOE Organization Act of 1977 (P.L. 95-91) mandated the Department “to assure incorporation of national environmental protection goals in the formulation and implementation of energy programs; and to advance the goal of restoring, protecting, and enhancing environmental quality, and assuring public health and safety,” and to conduct “a comprehensive program of research and development on the environmental effects of energy technology and program.”

It should also be emphasized that the project was not JUST funded through NIH but also Department of Energy

Project Sponsors

For a great read on Dr. Craig Ventnor with interviews with the scientist see Dr. Larry Bernstein’s excellent post The Human Genome Project

 

By 2003 we had gained much information about the structure of DNA, genes, exons, introns and allowed us to gain more insights into the diversity of genetic material and the underlying protein coding genes as well as many of the gene-expression regulatory elements.  However there was much uninvestigated material dispersed between genes, the then called “junk DNA” and, up to 2003 not much was known about the function of this ‘junk DNA’.  In addition there were two other problems:

  • The reference DNA used was actually from one person (Craig Ventor who was the lead initiator of the project)
  • Multiple gaps in the DNA sequence existed, and needed to be filled in

It is important to note that a tremendous amount of diversity of protein has been realized from both transcriptomic and proteomic studies.  Although about 20 to 25,000 coding genes exist the human proteome contains about 600,000 proteoforms (due to alternative splicing, posttranslational modifications etc.)

This expansion of the proteoform via alternate splicing into isoforms, gene duplication to paralogs has been shown to have major effects on, for example, cellular signaling pathways (1)

However just recently it has been reported that the FULL human genome has been sequenced and is complete and verified.  This was the focus of a recent issue in the journal Science.

Source: https://www.science.org/doi/10.1126/science.abj6987

Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

 

The current human reference genome was released by the Genome Reference Consortium (GRC) in 2013 and most recently patched in 2019 (GRCh38.p13) (1). This reference traces its origin to the publicly funded Human Genome Project (2) and has been continually improved over the past two decades. Unlike the competing Celera effort (3) and most modern sequencing projects based on “shotgun” sequence assembly (4), the GRC assembly was constructed from sequenced bacterial artificial chromosomes (BACs) that were ordered and oriented along the human genome by means of radiation hybrid, genetic linkage, and fingerprint maps. However, limitations of BAC cloning led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes. As a result, several GRC assembly gaps are unsolvable because of incompatible structural polymorphisms on their flanks, and many other repetitive and polymorphic regions were left unfinished or incorrectly assembled (5).

 

Fig. 1. Summary of the complete T2T-CHM13 human genome assembly.
(A) Ideogram of T2T-CHM13v1.1 assembly features. For each chromosome (chr), the following information is provided from bottom to top: gaps and issues in GRCh38 fixed by CHM13 overlaid with the density of genes exclusive to CHM13 in red; segmental duplications (SDs) (42) and centromeric satellites (CenSat) (30); and CHM13 ancestry predictions (EUR, European; SAS, South Asian; EAS, East Asian; AMR, ad-mixed American). Bottom scale is measured in Mbp. (B and C) Additional (nonsyntenic) bases in the CHM13 assembly relative to GRCh38 per chromosome, with the acrocentrics highlighted in black (B) and by sequence type (C). (Note that the CenSat and SD annotations overlap.) RepMask, RepeatMasker. (D) Total nongap bases in UCSC reference genome releases dating back to September 2000 (hg4) and ending with T2T-CHM13 in 2021. Mt/Y/Ns, mitochondria, chrY, and gaps.

Note in Figure 1D the exponential growth in genetic information.

Also very important is the ability to determine all the paralogs, isoforms, areas of potential epigenetic regulation, gene duplications, and transposable elements that exist within the human genome.

Analyses and resources

A number of companion studies were carried out to characterize the complete sequence of a human genome, including comprehensive analyses of centromeric satellites (30), segmental duplications (42), transcriptional (49) and epigenetic profiles (29), mobile elements (49), and variant calls (25). Up to 99% of the complete CHM13 genome can be confidently mapped with long-read sequencing, opening these regions of the genome to functional and variational analysis (23) (fig. S38 and table S14). We have produced a rich collection of annotations and omics datasets for CHM13—including RNA sequencing (RNA-seq) (30), Iso-seq (21), precision run-on sequencing (PRO-seq) (49), cleavage under targets and release using nuclease (CUT&RUN) (30), and ONT methylation (29) experiments—and have made these datasets available via a centralized University of California, Santa Cruz (UCSC), Assembly Hub genome browser (54).

 

To highlight the utility of these genetic and epigenetic resources mapped to a complete human genome, we provide the example of a segmentally duplicated region of the chromosome 4q subtelomere that is associated with facioscapulohumeral muscular dystrophy (FSHD) (55). This region includes FSHD region gene 1 (FRG1), FSHD region gene 2 (FRG2), and an intervening D4Z4 macrosatellite repeat containing the double homeobox 4 (DUX4) gene that has been implicated in the etiology of FSHD (56). Numerous duplications of this region throughout the genome have complicated past genetic analyses of FSHD.

The T2T-CHM13 assembly reveals 23 paralogs of FRG1 spread across all acrocentric chromosomes as well as chromosomes 9 and 20 (Fig. 5A). This gene appears to have undergone recent amplification in the great apes (57), and approximate locations of FRG1 paralogs were previously identified by FISH (58). However, only nine FRG1 paralogs are found in GRCh38, hampering sequence-based analysis.

Future of the human reference genome

The T2T-CHM13 assembly adds five full chromosome arms and more additional sequence than any genome reference release in the past 20 years (Fig. 1D). This 8% of the genome has not been overlooked because of a lack of importance but rather because of technological limitations. High-accuracy long-read sequencing has finally removed this technological barrier, enabling comprehensive studies of genomic variation across the entire human genome, which we expect to drive future discovery in human genomic health and disease. Such studies will necessarily require a complete and accurate human reference genome.

CHM13 lacks a Y chromosome, and homozygous Y-bearing CHMs are nonviable, so a different sample type will be required to complete this last remaining chromosome. However, given its haploid nature, it should be possible to assemble the Y chromosome from a male sample using the same methods described here and supplement the T2T-CHM13 reference assembly with a Y chromosome as needed.

Extending beyond the human reference genome, large-scale resequencing projects have revealed genomic variation across human populations. Our reanalyses of the 1KGP (25) and SGDP (42) datasets have already shown the advantages of T2T-CHM13, even for short-read analyses. However, these studies give only a glimpse of the extensive structural variation that lies within the most repetitive regions of the genome assembled here. Long-read resequencing studies are now needed to comprehensively survey polymorphic variation and reveal any phenotypic associations within these regions.

Although CHM13 represents a complete human haplotype, it does not capture the full diversity of human genetic variation. To address this bias, the Human Pangenome Reference Consortium (59) has joined with the T2T Consortium to build a collection of high-quality reference haplotypes from a diverse set of samples. Ideally, all genomes could be assembled at the quality achieved here, but automated T2T assembly of diploid genomes presents a difficult challenge that will require continued development. Until this goal is realized, and any human genome can be completely sequenced without error, the T2T-CHM13 assembly represents a more complete, representative, and accurate reference than GRCh38.

 

This paper was the focus of a Time article and their basis for making the lead authors part of their Time 100 people of the year.

From TIME

The Human Genome Is Finally Fully Sequenced

Source: https://time.com/6163452/human-genome-fully-sequenced/

 

The first human genome was mapped in 2001 as part of the Human Genome Project, but researchers knew it was neither complete nor completely accurate. Now, scientists have produced the most completely sequenced human genome to date, filling in gaps and correcting mistakes in the previous version.

The sequence is the most complete reference genome for any mammal so far. The findings from six new papers describing the genome, which were published in Science, should lead to a deeper understanding of human evolution and potentially reveal new targets for addressing a host of diseases.

A more precise human genome

“The Human Genome Project relied on DNA obtained through blood draws; that was the technology at the time,” says Adam Phillippy, head of genome informatics at the National Institutes of Health’s National Human Genome Research Institute (NHGRI) and senior author of one of the new papers. “The techniques at the time introduced errors and gaps that have persisted all of these years. It’s nice now to fill in those gaps and correct those mistakes.”

“We always knew there were parts missing, but I don’t think any of us appreciated how extensive they were, or how interesting,” says Michael Schatz, professor of computer science and biology at Johns Hopkins University and another senior author of the same paper.

The work is the result of the Telomere to Telomere consortium, which is supported by NHGRI and involves genetic and computational biology experts from dozens of institutes around the world. The group focused on filling in the 8% of the human genome that remained a genetic black hole from the first draft sequence. Since then, geneticists have been trying to add those missing portions bit by bit. The latest group of studies identifies about an entire chromosome’s worth of new sequences, representing 200 million more base pairs (the letters making up the genome) and 1,956 new genes.

 

NOTE: In 2001 many scientists postulated there were as much as 100,000 coding human genes however now we understand there are about 20,000 to 25,000 human coding genes.  This does not however take into account the multiple diversity obtained from alternate splicing, gene duplications, SNPs, and chromosomal rearrangements.

Scientists were also able to sequence the long stretches of DNA that contained repeated sequences, which genetic experts originally thought were similar to copying errors and dismissed as so-called “junk DNA”. These repeated sequences, however, may play roles in certain human diseases. “Just because a sequence is repetitive doesn’t mean it’s junk,” says Eichler. He points out that critical genes are embedded in these repeated regions—genes that contribute to machinery that creates proteins, genes that dictate how cells divide and split their DNA evenly into their two daughter cells, and human-specific genes that might distinguish the human species from our closest evolutionary relatives, the primates. In one of the papers, for example, researchers found that primates have different numbers of copies of these repeated regions than humans, and that they appear in different parts of the genome.

“These are some of the most important functions that are essential to live, and for making us human,” says Eichler. “Clearly, if you get rid of these genes, you don’t live. That’s not junk to me.”

Deciphering what these repeated sections mean, if anything, and how the sequences of previously unsequenced regions like the centromeres will translate to new therapies or better understanding of human disease, is just starting, says Deanna Church, a vice president at Inscripta, a genome engineering company who wrote a commentary accompanying the scientific articles. Having the full sequence of a human genome is different from decoding it; she notes that currently, of people with suspected genetic disorders whose genomes are sequenced, about half can be traced to specific changes in their DNA. That means much of what the human genome does still remains a mystery.

The investigators in the Telomere to Telomere Consortium made the Time 100 People of the Year.

Michael Schatz, Karen Miga, Evan Eichler, and Adam Phillippy

Illustration by Brian Lutz for Time (Source Photos: Will Kirk—Johns Hopkins University; Nick Gonzales—UC Santa Cruz; Patrick Kehoe; National Human Genome Research Institute)

BY JENNIFER DOUDNA

MAY 23, 2022 6:08 AM EDT

Ever since the draft of the human genome became available in 2001, there has been a nagging question about the genome’s “dark matter”—the parts of the map that were missed the first time through, and what they contained. Now, thanks to Adam Phillippy, Karen Miga, Evan Eichler, Michael Schatz, and the entire Telomere-to-Telomere Consortium (T2T) of scientists that they led, we can see the full map of the human genomic landscape—and there’s much to explore.

In the scientific community, there wasn’t a consensus that mapping these missing parts was necessary. Some in the field felt there was already plenty to do using the data in hand. In addition, overcoming the technical challenges to getting the missing information wasn’t possible until recently. But the more we learn about the genome, the more we understand that every piece of the puzzle is meaningful.

I admire the

T2T group’s willingness to grapple with the technical demands of this project and their persistence in expanding the genome map into uncharted territory. The complete human genome sequence is an invaluable resource that may provide new insights into the origin of diseases and how we can treat them. It also offers the most complete look yet at the genetic script underlying the very nature of who we are as human beings.

Doudna is a biochemist and winner of the 2020 Nobel Prize in Chemistry

Source: https://time.com/collection/100-most-influential-people-2022/6177818/evan-eichler-karen-miga-adam-phillippy-michael-schatz/

Other articles on the Human Genome Project and Junk DNA in this Open Access Scientific Journal Include:

 

International Award for Human Genome Project

 

Cracking the Genome – Inside the Race to Unlock Human DNA – quotes in newspapers

 

The Human Genome Project

 

Junk DNA and Breast Cancer

 

A Perspective on Personalized Medicine

 

 

 

 

 

 

 

Additional References

 

  1. P. Scalia, A. Giordano, C. Martini, S. J. Williams, Isoform- and Paralog-Switching in IR-Signaling: When Diabetes Opens the Gates to Cancer. Biomolecules 10, (Nov 30, 2020).

 

 

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Lessons on the Frontier of Gene & Cell Therapy – The Disruptive Dozen 12 #GCT Breakthroughs that are revolutionizing Healthcare

Reporter: Aviva Lev-Ari, PhD, RN

Mass General Brigham Innovation

@MGBInnovation

Read key takeaways from the 2022 World Medical Innovation Forum in this report from the Bank of America Institute. #WMIF2022

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Bank of America News

@BofA_News

· May 6

What are the 12 emerging #GeneAndCellTherapy technologies with the greatest potential to transform #healthcare? Read our report for key takeaways from #WMIF2022. @MassGenBrigham

4:30 PM · May 6, 2022·Twitter Web App

Mass General Brigham Innovation

@MGBInnovation

Read key takeaways from the 2022 World Medical Innovation Forum in this report from the Bank of America Institute. #WMIF2022

Quote Tweet

Bank of America News

@BofA_News

· May 6

What are the 12 emerging #GeneAndCellTherapy technologies with the greatest potential to transform #healthcare? Read our report for key takeaways from #WMIF2022. @MassGenBrigham

4:30 PM · May 6, 2022·Twitter Web App

The Disruptive Dozen 12 #GCT Breakthroughs that are revolutionizing Healthcare

Liz Everett Krisberg, Head of the Bank of America Institute

The Disruptive Dozen 12 GCT breakthroughs that are revolutionizing healthcare 05 May 2022 Key Takeaways • Gene and cell therapy (GCT) is widely recognized as a transformational opportunity in medicine, with the potential to stop or slow the effects of disease by targeting it at the genetic level. • The “Disruptive Dozen” identifies 12 emerging GCT technologies with the greatest potential to transform healthcare over the next several years • These breakthroughs range from restoration of sight and increasing the supply of donor organs, to treating brain cancer, hearing loss and autoimmune diseases that currently lack few or any treatment alternatives. Gene and cell therapy (GCT) technologies are transforming medicine and the approach to severe diseases like cancer, hereditary conditions including Huntington Disease and Sickle Cell, as well as rare disorders that currently have no treatment alternatives. GCT has the potential to stop or slow the effects of disease by targeting it at the genetic level, either replacing, inactivating or modifying the genetic material or by transferring live or intact cells into a patient to treat or cure disease. Even in cases where the GCT approach does not fully cure a condition, GCT has the potential to be life changing. This is because GCT treatments are often “one and done,” only requiring a single administration, which may enable a patient to manage their disease without onerous ongoing treatment cycles. While some of the first GCT applications were focused on rare and orphan diseases, recent advancements show tremendous potential opportunity for use cases with more broad applications. Beyond the messenger ribonucleic acid or mRNA vaccines that protect against infectious disease including COVID-19, GCT technologies exhibit promise to address prevalent chronic diseases such as diabetes and hearing loss, as well as central nervous system (CNS) disorders and Alzheimer’s. This week, Bank of America joined Mass General Brigham to present the World Medical Innovation Forum in Boston, where over 1,000 clinical experts, industry leaders and investors explored how to advance GCT technologies that may lead to breakthrough medical advancements and solutions. We highlight the twelve emerging GCT technologies – the “Disruptive Dozen” – with the greatest potential to impact and transform healthcare in the next several years. These breakthroughs range from restoration of sight and increasing the supply of donor organs, to treating brain cancer, hearing loss and autoimmune diseases. Restoring sight by mending broken genes Roughly 200 genes are directly linked to vision disorders. In the last several years, groundbreaking new gene therapies have emerged that can compensate for faulty genes in the eye by adding new, healthy copies — a molecular fix that promises to restore sight to those who have lost it. The approach, known as CRISPR-Cas-9 gene editing, could open the door to treating genetic forms of vision loss that are not suited to conventional gene therapy, and a host of other medical conditions. A clinical trial is now underway to evaluate a CRISPR-Cas 9 gene-editing therapy for a severe form of childhood blindness for which there currently are no treatments. Although this treatment is still experimental, it is already historic — it is the first medicine based on CRISPR-Cas-9 to be delivered in vivo, or inside a patient’s body. Similar gene-editing therapies are also under development that correct genes within blood cells. A gene editing solution to increase the supply of donor organs In the U.S. alone, more than 100,000 people need a life-saving organ transplant. But the supply of donor organs is quite limited, and every day, patients die waiting for a donor organ. One way to address this crisis is xenotransplantation — harvesting organs from animals and placing them into human patients. Advances in gene editing technology make it possible to remove, insert, or replace genes with relative ease and precision. This molecular engineering can sidestep the human immune system, which is highly adept at recognizing foreign tissues and triggering rejection. Over the last 20 years, scientists have been working to devise successful gene editing strategies that will render pig organs compatible with humans. The field has taken another major step forward in the past year: transplanting gene-edited pig organs, including the heart and kidney, into humans. While extensive clinical testing is needed before xenotransplantation becomes a reality, that future now seems within reach. I NSTI TUTE Accessible version 2 05 May 2022 I NSTI TUTE Cell therapies to conquer common forms of blindness The eye has been a proving ground for pioneering gene therapies and is also fueling new cell-based therapies than can restore sight, offering a functional cure by replacing critical cells that have been lost or injured. One approach involves stem cells from the retina that can give rise to light-sensitive cells, called photoreceptors, which are required for healthy vision. Scientists are harnessing retinal stem cells to develop treatments for incurable eye diseases, including retinitis pigmentosa. Because the immune system doesn’t patrol the eye as aggressively as other parts of the body, retinal stem cells from unrelated, healthy donors can be transplanted into patients with vision disorders. Other progress includes cell therapies that harness patients’ own cells, for example, from blood or skin, that can be converted into almost any cell type in the body, including retinal cells. Another novel treatment being tested utilizes stem cells from a patient’s healthy eye to repair the affected cornea of the other eye. Harnessing the power of RNA to treat brain cancer RNA is widely known for its helper functions, carrying messages from one part of a cell to another to make proteins. But scientists now recognize that RNA plays a more central role in biology and are tapping its hidden potential to create potent new therapies for a range of diseases, including a devastating form of brain cancer called glioblastoma. This cancer is extremely challenging to treat and highly adaptable. New approaches that either target RNA or mimic its activity could hold promise, including an intriguing class of RNA molecules called microRNAs. One team identified a trio of microRNAs that plays important roles in healthy neurons but is lost when brain cancer develops. These microRNAs can be stitched together into a single unit and delivered into the brain using a virus. Initial studies in mice reveal that this therapeutic can render tumors more vulnerable to existing treatments, including chemotherapy. Another team is also exploring a microRNA called miR-10b. Blocking its activity causes tumor cells to die. Now, scientists are working to develop a targeted therapeutic against miR-10b that can be tested in clinical trials. Realizing the promise of gene therapy for brain disorders Gene therapy holds enormous promise for serious and currently untreatable diseases, including those of the brain and central nervous system. But some big obstacles remain. For example, a commonly-used vehicle for gene therapy — a virus called AAV — cannot penetrate a major biological roadblock, the blood-brain barrier. Now, researchers are engineering new versions of AAV that can cross the blood-brain barrier. Using various molecular strategies, a handful of teams have modified the protein shell that surrounds the virus so it can gain entry and become broadly distributed within the brain. These modified viral vectors are now under development and could begin clinical testing within a few years. Scientists are also tinkering with the inner machinery of AAV to sidestep potential toxicities. With a safe, effective method for accessing the brain, researchers will be able to devise gene therapies for a range of neurological conditions, including neurodegenerative diseases, cancers, and devastating rare diseases that lack any treatment. A flexible, programmable approach to fighting viruses The COVID-19 pandemic has laid bare the tremendous need for rapidly deployable therapies to counteract emerging viruses. Scientists are now developing a novel form of anti-viral therapy that can be programmed to target a range of different viruses — from well-known human pathogens, such as hepatitis C, to those less familiar, such as the novel coronavirus SARS-CoV-2. This new approach harnesses a popular family of gene editing tools, known as CRISPR-Cas. While CRISPR-based systems have gained attention for their capacity to modify human genes, their original purpose in nature was to defend bacteria from viral infections. As a throwback to these early roots, scientists are now adapting CRISPR tools to tackle a variety of viruses that infect humans. Researchers are studying the potential of these programmable anti-viral agents in the context of several different viruses, including ones that pose significant threats to global health, such as SARS-CoV-2, hepatitis C, and HIV. On the move: Cell therapies to restore gut motility The human digestive tract — or “gut” — has its own nervous system. This second brain, known as the enteric nervous system, is comprised of neurons and support cells that carry out critical tasks, like moving food through the gut. When enteric neurons are missing or injured, gut motility can be impaired. Now, scientists are developing an innovative cell replacement therapy to treat diseases of gut motility. Donor cells can be isolated from a patient’s own gut or from a more readily available source, such as subcutaneous fat. These cells are then cultivated in the laboratory and coaxed to form the progenitors that give rise to enteric neurons. Researchers are also devising “off-the-shelf” approaches, which could create a supply of donor cells that are shielded from the immune system and can therefore be transplanted universally across different patients. Early research shows that transplanted enteric neurons can also take up residence in the brain. That means these forays in cell therapy for the gut could also help pave a path toward cell therapies for the brain and spinal cord. CAR-T cell therapies take aim at autoimmune diseases CAR-T cells have emerged as powerful treatments for some forms of cancer, especially blood cancers. By harnessing the same underlying concept — rewiring patients’ own T cells to endow them with therapeutic properties — scientists are working to develop novel CAR-T therapies for a variety of autoimmune diseases. Several research teams are engineering CAR-T cells so they can seek out and destroy harmful immune cells, such as those that produce auto-antibodies — immune proteins that help coordinate the attack on the body’s own tissues. For example, one team is using CAR-T cells to destroy certain immune cells, called B cells, as a potential treatment for lupus, a serious autoimmune disease that mainly affects women. Scientists are also 05 May 2022 3 I NSTI TUTE developing CAR-T therapies that take aim at other rogue members of the immune system. These efforts could yield novel treatments for multiple sclerosis and type 1 diabetes. Regrowing cells in the inner ear to treat hearing loss In the U.S. alone, some 37 million people suffer from a hearing deficit. Currently, there are no drugs that can halt, prevent, or even reverse hearing loss. Scientists are working on a novel regenerative approach that could restore the cells in the inner ear required for normal hearing, offering hope to millions of patients who grapple with hearing loss. Healthy hearing requires specialized cells in the inner ear called hair cells, which have fine, hair-like projections. If the cells are damaged or lost, which often happens with age or after repeated exposure to loud sounds, the body cannot repair them. But researchers have discovered a potential workaround that can stimulate existing cells in the ear to proliferate and give rise to new hair cells. Scientists are now working to convert this molecular strategy, which is being studied in animal models, into a therapeutic that is safe and effective for hearing loss patients. New technologies for delivering gene therapies A formidable challenge in the field of gene therapy is delivery — getting gene-based therapeutics into the body and into the right target cells. Researchers are exploring the potential of new delivery methods that could expand the reach of gene therapy, including microneedles. When applied to the skin, a microneedle patch can penetrate the outermost layer with minimal pain and discomfort. This novel delivery method can readily access the legion of immune cells that reside in the skin — important targets for vaccines as well as for the treatment of various diseases, including cancer and autoimmune conditions. Another emerging technology involves an implantable device made of biodegradable materials. When placed inside the body, this device can provide localized, sustained release of therapeutics with few side effects. The approach is now being tested for the first time in cancer patients using standard chemotherapy drugs administered directly at tumor sites. In the future, this method could be customized for the delivery of gene therapy payloads, an advance that could revolutionize cancer treatment, particularly for difficult-to-treat forms like pancreatic cancer. Engineering cancer-killing cells that target solid tumors CAR-T cells are a revolutionary form of cell therapy that has yielded some remarkable cures of difficult-to-treat blood cancers. But the outcomes in other cancers have been lackluster. Now, scientists are enhancing this technology to enable new ways of treating solid tumors. One approach involves making CAR-T cells more like computers, relying on simple logic to decide which cells are cancer — and should be destroyed — and which cells are healthy and should be spared. By building several logic gates and combining them together, researchers are hoping to pave the way toward targeting new tumor types. Scientists are also devising other groundbreaking forms of cancer-killing cell therapy, including one that uses cancer cells themselves. This approach exploits a remarkable feature: once disseminated within the body, cancer cells can migrate back to the original tumor. Researchers are now harnessing this rehoming capability and, with the help of gene editing, turning tumor cells into potent cancer killers. An early version of this technology uses patients’ own cells. Now, the scientists are developing an off-the-shelf version that can be universally applied to patients. Reawakening the X-chromosome: a therapeutic strategy for devastating neurodevelopmental diseases The X chromosome is one of two sex-determining chromosomes in humans, and it carries hundreds of disease-causing genes. These diseases often affect males and females differently. In females, one X chromosome is naturally, and randomly, chosen and rendered inactive. Although X-inactivation was once thought to be permanent, scientists are uncovering ways to reverse it. Scientists are now exploiting this unusual biology to reawaken the dormant X chromosome — a strategy that could yield muchneeded treatments for a group of rare, yet devastating neurodevelopmental disorders, which predominantly affect females. This new approach could hold promise for females with Rett syndrome, a severe X-linked disorder. A similar strategy could also hold promise for other serious X-linked disorders, including fragile X syndrome and CDKL5 syndrome.

SOURCE

https://business.bofa.com/content/dam/flagship/bank-of-america-institute/transformation/world-innovation-forum-takeaways-may-2022.pdf

Other related articles published in this Open Access Online Scientific Journal include the following:

UPDATED on 5/7/2022

Tweets at #WMIF2022 by @pharma_BI & @AVIVA1950 and All Retweets of these Tweets – 2022 World Medical Innovation Forum, GENE & CELL THERAPY • MAY 2–4, 2022 • BOSTON

Real Time coverage: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2022/05/07/tweets-at-wmif2022-by-pharma_bi-aviva1950-and-all-retweets-of-these-tweets-2022-world-medical-innovation-forum-gene-cell-therapy-may-2-4-2022/

 

2022 World Medical Innovation Forum, GENE & CELL THERAPY • MAY 2–4, 2022 • BOSTON • IN-PERSON

https://pharmaceuticalintelligence.com/2022/05/01/2022-world-medical-innovation-forum-gene-cell-therapy-may-2-4-2022-boston-in-person/

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2022 World Medical Innovation Forum, GENE & CELL THERAPY • MAY 2–4, 2022 • BOSTON • IN-PERSON

Reporter: Aviva Lev-Ari, PhD, RN

World Medical Innovation Forum as we bring together global leaders to assess the latest opportunities and challenges, from the investment landscape to key technology developments to manufacturing and regulatory barriers. Gain first-hand insights on medicine’s ultimate game changer.

https://worldmedicalinnovation.org/

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World Medical Innovation Forum will be held June 12 – 14 in Boston, MA. We hope you’ll join us for #WMIF2023!

From: “Rieck, Lucy (BOS-WSW)” <LRieck@webershandwick.com>
Date: Tuesday, April 12, 2022 at 10:25 AM
To: Aviva Lev-Ari <avivalev-ari@alum.berkeley.edu>
Subject: You’re Invited: Mass General Brigham’s World Medical Innovation Forum

Hi Aviva,

I’m reaching out to extend free registration for you or a colleague to the 8th annual World Medical Innovation Forum (WMIF), taking place May 2-4 at the Westin Copley Place in Boston. This year’s event, co-sponsored with Bank of America, will explore gene and cell therapies (GCT), including the latest opportunities and challenges – from the investment landscape to key technology developments to manufacturing and regulatory barriers.

The event will feature 200 speakers – including CEOs of leading companies in the GCT and biotech fields, investors, entrepreneurs, Harvard clinicians and scientists, government officials and other key influencers – who discover, invest in, and cultivate GCT breakthroughs. Notable speakers include:

  • Peter Marks: Director, Center for Biologics Evaluation and Research at the FDA
  • Brian Moynihan: CEO, Bank of America
  • Anne Klibansky: President & CEO, Mass General Brigham
  • Senior executives from biopharma and academic institutions of all sizes (including Novartis, BMS, Takeda, Verve, UPenn)

 

You can view the full list of speakers here and the program agenda here.

WMIF is hosted by the Mass General Brigham health system, which comprises 14 hospitals, including two world-renowned medical centers: Mass General and Brigham & Women’s. Since 2015, the Forum has brought together global leaders to assess medical breakthroughs, the investment landscape and technology developments that have the potential to transform the industry.

In addition to a packed agenda, the 2022 “Disruptive Dozen” – 12 breakthrough technologies most likely to have significant impact on gene and cell therapy in the next 18 months – will also be announced.

Please let me know if you would be interested in attending.

Best,

Lucy 

Lucy Rieck

Senior Associate, Healthcare

C: +1 203-331-7894

33 Arch Street

Boston, MA, 02109

webershandwick.com

Ad Age Agency A-List (2020)

Ad Age Best Place to Work (2019)

PRovoke Global Agency of the Decade (2020)

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www.linkedin.com/in/lucyrieck

AGENDA

7:00 AM – 5:00 PMAmerica Foyer
7:00 AM – 8:00 AMAmerica Foyer
8:00 AM – 9:30 AMAmerica Ballroom

FIRST LOOK

First Look: 8 rapid fire presentations on Mass General Brigham’s new GCT technologies

New Gene and Cell Therapy technologies

Moderators:
Meredith Fisher, PhD
  • Partner, Mass General Brigham Ventures
Roger Kitterman
  • VP, Mass General Brigham Ventures
Presenters:
Bakhos Tannous, PhD
  • Director, Experimental Therapeutics Unit, Director, Viral Vector Core, MGH
  • Professor of Neurology, HMS
Vijaya Ramesh, PhD
  • Co-Director of Neuroscience, Associate Geneticist in Neurology, MGH
  • Professor of Neurology, HMS
Anna Krichevsky, PhD
  • Associate Professor of Neurology, BWH, HMS
Nerea Zabaleta, PhD
  • Principal Investigator, Grousbeck Gene Therapy Center, Mass Eye and Ear
  • Instructor in Ophthalmology, HMS
Francisco Quintana, PhD
  • Professor, Neurology, Ann Romney Center for Neurologic Diseases, BWH
  • Kuchroo Weiner Distinguished Professor of Neuroimmunology, BWH
Stephen Haggarty, PhD
  • Director, Chemical Neurobiology Laboratory, Center for Genomic Medicine, MGH
  • Associate Professor of Neurology, HMS
Michael Young, PhD
  • Director, Minda de Gunzburg Center for Retinal Regeneration, Associate Scientist, Schepens Eye Research Institute, Mass Eye and Ear
  • Associate Professor of Ophthalmology, Co-Director, Ocular Regenerative Medicine Institute, HMS
Max Jan, MD, PhD
  • Principal Investigator, Center for Cancer Research, MGH
  • Assistant Professor of Pathology, HMS
9:30 AM – 9:45 AM
9:45 AM – 11:15 AMAmerica Ballroom

FIRST LOOK

First Look: 8 rapid fire presentations on Mass General Brigham’s new GCT technologies

New Gene and Cell Therapy technologies

Moderators:
Meredith Fisher, PhD
  • Partner, Mass General Brigham Ventures
Roger Kitterman
  • VP, Mass General Brigham Ventures
Presenters:
Choi-Fong Cho, PhD
  • Assistant Professor of Neurosurgery, BWH, HMS
Yulia Grishchuk, PhD
  • Assistant Investigator, Center for Genomic Medicine, MGH
  • Assistant Professor of Neurology, HMS
Lynn Bry, MD, PhD
  • Director, Massachusetts Host-Microbiome Center, BWH
  • Associate Professor of Pathology, HMS
David Corey, PhD
  • Bertarelli Professor of Translational Medical Science, Neurobiology, HMS
Anil Chandraker, MD
  • Medical Director of Kidney and Pancreas Transplantation, BWH
  • Associate Professor of Medicine, HMS
Ole Isacson, MD, PhD
  • Director, Neuroregeneration Research Institute, McLean
  • Professor of Neurology & Neuroscience, HMS
Marco Mineo, PhD
  • Instructor in Neurosurgery, BWH, HMS
Susan Cotman, PhD
  • Assistant in Neuroscience, Center for Genomic Medicine, MGH
  • Assistant Professor of Neurology, HMS
11:15 AM – 11:45 AM
11:45 AM – 12:45 PM3rd Floor and 7th Floor

DR. IS IN

Dr. Is In Sessions

Understanding long-term Gene and Cell Therapy investment complexities requires a keen awareness of where the science and the markets are headed. That’s why “The Doctor is In” in these updates on the latest GCT technologies. Presented by Mass General Brigham clinicians and innovators from the front lines of care, the sessions are co-hosted by expert analysts from Bank of America and include interactive discussion and Q&A.

1:00 PM – 1:30 PMAmerica Ballroom

Opening Remarks

Introducer:
Scott Sperling
  • Co-Chief Executive Officer, Thomas H. Lee Partners
  • Chairman of the Board of Directors, Mass General Brigham
Panelists:
Anne Klibanski, MD
  • President & CEO, Mass General Brigham
  • Laurie Carrol Guthart Professor of Medicine, HMS
Brian Moynihan
  • Chair & CEO, Bank of America
1:30 PM – 2:00 PMAmerica Ballroom

Co-Chair Kick Off

Moderator:
Susan Hockfield, PhD
  • President Emerita, MIT
Panelists:
Miceal Chamberlain
  • President of Massachusetts, Northeast Region Executive, Bank of America
Marcela Maus, MD, PhD
  • Director, Cellular Immunotherapy Program, Cancer Center, MGH
  • Associate Professor, Medicine, HMS
Geoff Meacham, PhD
  • Managing Director, Global Research, BofA Securities
Ravi Thadhani, MD
  • Chief Academic Officer, Mass General Brigham
2:00 PM – 2:40 PMAmerica Ballroom

GCT’s Historic Potential | Priorities and Trade Offs

This panel features industry leaders who will discuss what the future may hold for gene and cell therapy. Which applications are likely to have the greatest impact? What are the key hurdles to be overcome? What specific platforms and technologies may enable optimal solutions? In what disease areas? Learn more about these and other questions as the panelists discuss the future potential of GCT.

Moderator:
Jean-François Formela, MD
  • Partner, Atlas Venture
Panelists:
Pablo Cagnoni, MD
  • CEO, Rubius Therapeutics
Kristen Hege, MD
  • Senior Vice President, Early Clinical Development, Hematology/Oncology & Cell Therapy, Bristol Myers Squibb
Andrew Plump, MD, PhD
  • President, R&D, Takeda
Catherine Stehman-Breen, MD
  • CEO, Chroma Medicine
2:40 PM – 3:20 PMAmerica Ballroom

Manufacturing | Process Control

Manufacturing quality and cost are critical for enabling rapid growth in GCT. Panelists will explore a variety of critical questions in this space. For example, are there historic parallels that can be drawn between GCT manufacturing and other groundbreaking technologies? How do key manufacturing concerns in GCT differ from those for more conventional pharmaceutical? What are the long-term opportunities for non-viral vectors? Will manufacturing capacity be a limiting factor in GCT growth over the next 5 to 10 years?

Moderator:
John Bishai, PhD
  • Managing Director, Global Investment Banking, BofA Securities
Panelists:
Christopher Murphy
  • Vice President Viral Vector Services, Thermo Fisher
Michael Paglia
  • COO, ElevateBio BaseCamp, ElevateBio
Rahul Singhvi, ScD
  • CEO, National Resilience, Inc.
Ran Zheng
  • CEO, Landmark Bio
3:20 PM – 3:40 PM
3:40 PM – 4:05 PMAmerica Ballroom

FIRESIDE

Regulatory Perspectives on Gene and Cell Therapy: Past Lessons, Current Challenges, Future Directions

At the end of 2021, roughly 410 novel drugs had been approved in the past decade. On average, there were 40 approvals per year with over 150 of them being between 2018 and 2020. What has changed in the approval process and what is the vision of the future state? What will happen over the next 1–3 years? What does the new iteration of the Prescription Drug User Fees Act (PDUFA) need to do in this area and which fields show the greatest potential for innovation in CGT?

Moderator:
Luk Vandenberghe, PhD
  • Grousbeck Associate Professor in Gene Therapy, Mass General Brigham (on leave)
Panelist:
Peter Marks, MD, PhD
  • Director, Center for Biologics Evaluation and Research, FDA
4:10 PM – 4:50 PMAmerica Ballroom

Clinical GCT Trial Design | Regulatory | Strategy, Innovation and Future Direction | Risk vs Hype

This panel will delve into clinical trials for GCT. How do these trials differ from those for conventional therapeutics? What are the key lessons learned from completed GCT trials? How is the regulatory landscape shifting and what will that mean for the future of GCT?

Moderator:
Angela Shen, MD
  • Vice President, Strategic Innovation Leaders, Mass General Brigham Innovation
Panelists:
Laura Aguilar, MD, PhD
  • Co-Founder, Candel Therapeutics
Matthew Frigault, MD
  • Clinical Director, Cellular Immunotherapy Program, MGH
  • Assistant Professor of Medicine, HMS
Arati Rao, MD
  • Senior Vice President, Clinical Development, PACT Pharma
John Rossi
  • VP Head of Translational Medicine, Syncopation Life Sciences
4:50 PM – 5:15 PMAmerica Ballroom

FIRESIDE

mRNA Opportunities: Lessons Learned, Priorities, and the Future of GCT

Dr. Bourla will share what Pfizer has learned from its leadership on mRNA and the development of the Covid vaccine that can be extrapolated to other R&D.

Moderator:
Geoff Meacham, PhD
  • Managing Director, Global Research, BofA Securities
Panelist:
Albert Bourla, PhD
  • CEO, Pfizer Inc.
5:15 PM – 6:15 PMAmerica Foyer

#WMIF2022

@MGBInnovation

@MassGenBrigham

@pharma_BI

@AVIVA1950

7:00 AM – 5:00 PMAmerica Foyer
7:00 AM – 8:00 AMAmerica Foyer

Breakfast

Sponsored by Bayer

7:45 AM – 8:00 AMAmerica Ballroom

Opening Remarks

Introducer:
Chris Coburn
  • Chief Innovation Officer, Mass General Brigham
8:00 AM – 8:25 AMAmerica Ballroom

FIRESIDE

1:1 Fireside Chat: Robert Califf, MD, Commissioner Food and Drugs, FDA

Moderators:
Tazeen Ahmad
  • Managing Director, Global Research, BofA Securities
J. Keith Joung, MD, PhD
  • Robert B. Colvin, M.D. Endowed Chair in Pathology & Pathologist, MGH
  • Professor of Pathology, HMS
Panelist:
Robert Califf, MD
  • Commissioner of Food and Drugs, US Food and Drug Administration
8:25 AM – 9:05 AMAmerica Ballroom

Living with COVID | Lessons Learned and Looking Ahead

As we enter the third year of the coronavirus pandemic, the world is shifting to a new strategy: living with and managing COVID as a part of our everyday lives. What will the coming year look like? How will mitigation measures differ in this new phase? What about treatment strategies? Should we be bracing for another surge?

Introducer:
Jonathan Kraft
  • President, The Kraft Group
  • Chairman of the Board of Trustees, MGH
Moderator:
David Brown, MD
  • President, Massachusetts General Hospital
  • Executive Vice President, Mass General Brigham
Panelists:
Paul Biddinger, MD
  • Chief Preparedness and Continuity Officer, Mass General Brigham
  • Associate Professor of Emergency Medicine, HMS
Helen Branswell
  • Senior Writer, STAT
Daniel Kuritzkes, MD
  • Chief, Division of Infectious Diseases, BWH
  • Harriet Ryan Albee Professor of Medicine, HMS
Erica Shenoy, MD, PhD
  • Associate Chief, Infection Control Unit, MGH
  • Associate Professor of Medicine, HMS
9:05 AM – 9:45 AMAmerica Ballroom

The Global Biotech Epicenter | New England Now and in 2030

This panel will feature a discussion of global biotech clusters with a deep dive into the New England/Boston area. How does the capital availability, scale, and density of New England drive local growth in GCT? Also, the influx of large biopharmaceutical companies into the region has fueled global outcomes. What is the future impact of these investments and when will they peak? How will the biopharmaceutical landscape in New England appear in 2030?

Moderator:
Anne Finucane
  • Chairman of the Board, Bank of America Europe
Panelists:
Seth Ettenberg, PhD
  • President & CEO, BlueRock Therapeutics
Joel Marcus
  • Executive Chairman & Founder, Alexandria Real Estate Equities, Inc.
Terry McGuire
  • Founding Partner, Polaris Partners
Vicki Sato, PhD
  • Chairman of the Board, Vir Biotechnology
  • Chairman, Denali Therapeutics
Phillip Sharp, PhD
  • Institute Professor and Professor of Biology, Koch Institute for Integrative Cancer Research at MIT
  • Co-Founder, Alnylam Pharmaceuticals, Inc.
9:45 AM – 10:05 AM
10:10 AM – 10:50 AMAmerica Ballroom

The Patient Experience

The role of patients and their experiences are critical as the promise of GCT unfolds. This panel will discuss the patient experience and explore the challenges different patient populations face, both in rare diseases and more common conditions. Panelists will also discuss financial considerations, clinical trial access, and the role of advocacy groups in GCT.

Moderator:
Merit Cudkowicz, MD
  • Chair, Dept of Neurology, MGH
  • Julieanne Dorn Professor of Neurology, HMS
Panelist:
James Beck, PhD
  • CSO, Parkinson’s Foundation
Monica Coenraads
  • CEO, Rett Syndrome Research Trust
Annie Ganot
  • VP, Head of Patient Advocacy, Solid Biosciences
Staci Kallish, DO
  • President, Board of Directors, National Tay Sachs and Allied Diseases
  • Medical Geneticist, Associate Professor of Clinical Medicine, Penn Medicine
Rebecca Oberman, PhD
  • Executive Director, Mucolipidosis Type IV (ML4) Foundation
10:50 AM – 11:15 AMAmerica Ballroom

FIRESIDE

Meeting the Moment: The Next Wave of Innovation in Cancer and Cardiology

As many countries begin to turn the corner on COVID-19, they face a resurgence of chronic illnesses, such as cancer and cardiovascular disease, that were not adequately addressed during the pandemic, and for which new treatments are urgently needed. Population aging – and the resulting increase in chronic diseases associated with aging – has compounded the challenge. There’s never been a greater need for biopharmaceutical innovation – or, fortunately, a greater ability to innovate. Amgen is investing in new discovery research capabilities that portend a revolution in drug design and development.

Moderator:
Geoff Meacham, PhD
  • Managing Director, Global Research, BofA Securities
Panelist:
Robert Bradway
  • CEO, Amgen
11:15 AM – 11:20 AMAmerica Ballroom

First Look Award Presentation

Presenters:
Miceal Chamberlain
  • President of Massachusetts, Northeast Region Executive, Bank of America
Nino Chiocca, MD, PhD
  • Neurosurgeon-in-Chief and Chairman, Neurosurgery, BWH
  • Harvey W. Cushing Professor of Neurosurgery, HMS
11:20 AM – 11:30 AMAmerica Ballroom
11:30 AM – 11:45 AM
11:45 AM – 12:45 PM3rd Floor and 7th Floor

DR. IS IN

Dr. Is In Sessions

Lunch Sponsored by Astellas

Understanding long-term Gene and Cell Therapy investment complexities requires a keen awareness of where the science and the markets are headed. That’s why “The Doctor is In” in these updates on the latest GCT technologies. Presented by Mass General Brigham clinicians and innovators from the front lines of care, the sessions are co-hosted by expert analysts from Bank of America and include interactive discussion and Q&A.

  • Personalizing Cancer Care through RNA Therapies

    11:45 AM – 12:45 PM

    In this session, Dr. Peruzzi will discuss how RNA for cancer therapy is a versatile of a tool for a protean problem.

    Moderator:
    Jason Gerberry
    • Managing Director, Global Research, BofA Securities
    Panelist:
    Pierpaolo Peruzzi, MD, PhD
    • Neurosurgeon and Principal Investigator, BWH
    • Assistant Professor of Neurosurgery, HMS
  • Designing for Success: Clinical Trial Approaches for Rare and Ultra-Rare Diseases

    11:45 AM – 12:45 PM

    In this session, Dr. Vavvas will discuss examples of clinical trials in rare diseases and share insights into how clinical trials should be approached for rare and ultra-rare diseases and how study design is not a one-size fits all.

    Moderator:
    Tazeen Ahmad
    • Managing Director, Global Research, BofA Securities
    Panelist:
    Demetrios Vavvas, MD, PhD
    • Associate Director of the Retina Service, Mass Eye and Ear
    • Solman and Libe Friedman Professor of Ophthalmology, Co-Director Ocular Regenerative Medical Institute, HMS
  • A New Hope: Cell Therapy and Transplantation for Parkinson’s Disease

    11:45 AM – 12:45 PM

    In this session, hear experts weigh in on the possibilities of cell therapy development and transplantation for the treatment of Parkinson’s Disease. What does the futures hold and how do we get there?

    Moderator:
    Greg Harrison
    • Vice President, Global Research, BofA Securities
    Panelist:
    Bob Carter, MD, PhD
    • Chairman, Department of Neurosurgery, MGH
    • William and Elizabeth Sweet Professor of Neurosurgery, HMS
    Todd Herrington, MD, PhD
    • Director, Deep Brain Stimulation Program, MGH
    • Assistant Professor of Neurology, HMS
    Kwang-Soo Kim, PhD
    • Director, Molecular Neurobiology Laboratory, McLean
    • Professor of Neuroscience and Psychiatry, HMS
    Jeffrey Schweitzer, MD, PhD
    • Neurosurgeon, MGH
    • Assistant Professor of Neurosurgery, HMS
  • The Inner Workings of Gene Therapy Manufacturing

    11:45 AM – 12:45 PM

    In this session, Dr. Nikiforow will provide insights into the world of gene therapy manufacturing and the complexities of scaling, costs and insurance reimbursement.

    Moderator:
    Michael Ryskin
    • Director, Global Research, BofA Securities
    Panelist:
    Sarah Nikiforow, MD, PhD
    • Medical Director, Cell Manipulation Core Facility, Technical Director, Immune Effector Cell Therapy Program, DFCI
    • Assistant Professor, HMS
  • The Road Ahead: Regulatory Challenges for Gene and Cell Therapy

    11:45 AM – 12:45 PM

    In this session, Dr. Marks will discuss the ins and outs of regulatory challenges for biological products and therapies in gene and cell therapy and the responsibility to assure safety and effectiveness.

    Moderator:
    Geoff Meacham, PhD
    • Managing Director, Global Research, BofA Securities
    Panelist:
    Peter Marks, MD, PhD
    • Director, Center for Biologics Evaluation and Research, FDA
  • The Mysterious Dark Genome

    11:45 AM – 12:45 PM

    Dark genome, accounting for ~98.5% of the human genome and containing the non-coding part, offers unprecedented opportunity to look for novel elements that could play a role in human health. This non-coding region consists of repeat elements, enhancers, regulatory sequences and non-coding RNAs. This session will explore this exciting new frontier in biology and how to translate this so called “junk” and previously ignored genome into potential novel therapeutics.

    Moderators:
    Angela Shen, MD
    • Vice President, Strategic Innovation Leaders, Mass General Brigham Innovation
    Richard Young, PhD
    • Professor, Whitehead Institute, MIT
    Panelists:
    Rosana Kapeller, MD, PhD
    • Co-Founder, President & CEO, ROME Therapeutics
    Josh Mandel-Brehm
    • President & CEO, CAMP4 Therapeutics
    Amir Nashat, PhD
    • Managing Partner, Polaris Ventures
    Issi Rozen
    • Venture Partner, GV
1:00 PM – 1:40 PMAmerica Ballroom

Capital Formation | Shaping Innovation

Panelists will discuss the life sciences capital markets environment with particular emphasis on private and public fundraising for GCT companies. What trends do panelists observe that will impact the availability and cost of capital for GCT? Are there novel fundraising structures that will serve GCT in the future?

Moderator:
Greg Butz
  • Managing Director, Head of Life Sciences Investment Banking, BofA Securities
Sumit Mukherjee
  • Managing Director & Head of Healthcare in Equity Capital Markets, BofA Securities
Panelists:
Shelley Chu, MD, PhD
  • Partner, Lightspeed
Stephen Knight, MD
  • President & Managing Partner, F-Prime Capital
Adam Koppel, MD, PhD
  • Managing Director, Bain Capital Life Sciences
Daniel Krizek
  • Portfolio Manager, Citadel
1:40 PM – 2:05 PMAmerica Ballroom

FIRESIDE

Ending Cancer as We Know It: The Game Changing Potential of GCT

50 years after the nation’s War on Cancer was launched, do new treatment innovations have us at a turning point to end cancer “as we know it”.

Moderator:
Erin Harris
  • Chief Editor, Cell & Gene
Panelists:
David Scadden, MD
  • Director, Center for Regenerative Medicine, MGH
  • Gerald and Darlene Jordan Professor of Medicine, HMS
Norman Sharpless, MD
  • Former Director, National Cancer Institute
2:05 PM – 2:30 PMAmerica Ballroom

FIRESIDE

Vision and Execution: Curing Disease with Cell Therapies

As one of the foremost researchers of CAR-T cancer treatments, Dr. June will share what he believes is the next wave of cell-and-gene based oncology research and how his work set the stage for breakthrough developments in cancer.

Moderators:
Marcela Maus, MD, PhD
  • Director, Cellular Immunotherapy Program, Cancer Center, MGH
  • Associate Professor, Medicine, HMS
Ravi Thadhani, MD
  • Chief Academic Officer, Mass General Brigham
Panelist:
Carl June, MD
  • Richard W. Vague Professor in Immunotherapy, Director, Center for Cellular Immunotherapies, Director, Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine
2:30 PM – 3:10 PMAmerica Ballroom

GCT Development Centers | Academia’s Unique Contribution

This panel will examine the role of academia in driving the promise of GCT. How does academic innovation contribute to the success of GCT? What are the risks and opportunities? Which models have proven most successful and what is the impact on clinical translation? How can these partnerships be accelerated?

Moderator:
Ravi Thadhani, MD
  • Chief Academic Officer, Mass General Brigham
Panelists:
Carl June, MD
  • Richard W. Vague Professor in Immunotherapy, Director, Center for Cellular Immunotherapies, Director, Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine
Maria Millan, MD
  • President & CEO, California Institute for Regenerative Medicine
Richard Mulligan, PhD
  • Mallinckrodt Professor of Genetics, Emeritus, HMS
  • Executive Vice Chairman, Sana Biotechnology, Inc
Norman Sharpless, MD
  • Former Director, National Cancer Institute
3:10 PM – 3:30 PM
3:30 PM – 3:55 PMAmerica Ballroom

FIRESIDE

1:1 Fireside Chat: Marc Casper

Moderator:
Derik de Bruin, PhD
  • Managing Director, Global Research, BofA Securities
Panelist:
Marc Casper
  • CEO, ThermoFisher
3:55 PM – 4:35 PMAmerica Ballroom

Gene and Cell Therapy | The World Speaks

This panel will bring together gene and cell therapy leaders from across the world to discuss the latest opportunities and challenges in the field, from the investment landscape to key technology developments to manufacturing and regulatory barriers. These global experts will offer first-hand insights on the systemic complexity of this advancing field and its therapeutic promise.

Moderator:
Christine Fox
  • President, Novartis Gene Therapies
Panelists:
Christopher Baum, MD
  • Chairman of the Board of Directors, Berlin Institute of Health
Nicholas Galakatos, PhD
  • Global Head of Life Sciences, Blackstone
Luigi Naldini, MD, PhD
  • Director, San Raffaele Telethon Institute for Gene Therapy
Kendra Rose, PhD
  • VP, Head of New Platforms, Ophthalmology and Hemophilia, Bayer
4:35 PM – 5:15 PMAmerica Ballroom

Control or Mitigation of the Effects of Chronic Neuroinflammation

Chronic inflammation in the brain is now recognized as a contributor to many neurodegenerative diseases, ranging from Parkinson’s disease to multiple sclerosis to Alzheimer’s disease. Are solutions to these historically intractable neurological diseases imminent or several years away? Are market-making platforms identifiable for neurological diseases? Are there novel genetic targets that can be explored? What are the prospects for cell therapies?

Moderator:
Ole Isacson, MD, PhD
  • Director, Neuroregeneration Research Institute, McLean
  • Professor of Neurology & Neuroscience, HMS
Panelists:
Colin Hill
  • CEO, GNS Healthcare
Spyros Papapetropoulos, MD, PhD
  • CMO, Vigil Neuroscience
Richard Ransohoff, MD
  • CMO, Abata Therapeutics
  • Venture Partner, Third Rock Ventures
Beth Stevens, PhD
  • HHMI Investigator, F.M. Kirby Neurobiology Research Program, Boston Children’s Hospital
  • Associate Professor of Neurology, HMS
Rudolph Tanzi, PhD
  • Vice-Chair, Neurology, Director, Genetics and Aging Research Unit, MGH
  • Joseph P. and Rose F. Kennedy Professor of Neurology, HMS
5:15 PM – 6:15 PMAmerica Foyer

Attendee Networking Reception

Sponsored by Novartis

#WMIF2022

@MGBInnovation

@MassGenBrigham

@pharma_BI

@AVIVA1950

7:00 AM – 12:00 PMAmerica Foyer
7:00 AM – 8:00 AMAmerica Foyer
8:05 AM – 8:45 AMAmerica Ballroom

The Cell Therapy Landscape | CAR-T to Stem Cells

Cell therapies, ranging from CAR-T cells to stem-cell-based approaches, are emerging as a transformative therapeutic modality. Panelists will examine this emerging landscape and discuss a range of key topics. What drives differentiation in this space given the high number of competing technologies? How will the uptake of autologous cell therapies and allogeneic versions evolve? When will the regenerative medicine market mature?

Moderator:
Marcela Maus, MD, PhD
  • Director, Cellular Immunotherapy Program, Cancer Center, MGH
  • Associate Professor, Medicine, HMS
Panelists:
Christina Coughlin, MD, PhD
  • CEO, Cytoimmune
Rachel Haurwitz, PhD
  • President & CEO, Caribou Biosciences
Nick Leschly
  • CEO, 2seventy bio
Dhvanit Shah, PhD
  • President & CEO, Garuda Therapeutics
Rusty Williams, MD, PhD
  • Chairman & CEO, Walking Fish Therapeutics
8:50 AM – 9:30 AMAmerica Ballroom

Disrupting Interventions

This panel will explore how GCT technology could lead to disruptions in other areas of medicine, including surgery and medical devices, over the next several years. Could cell replacement therapy in diabetes advance enough to reduce the need for diabetes pumps or insulin? Will stem-cell-based methods for regenerating cartilage advance rapidly enough to disrupt the number of patients seeking hip and knee replacements? How is GCT driving innovations in surgical techniques?

Introducer:
John Fish
  • Chairman & CEO, Suffolk
  • Chair, Brigham and Women’s Hospital
Moderator:
Robert Higgins, MD
  • President, Brigham and Women’s Hospital
  • Executive Vice President, Mass General Brigham
Panelists:
Irina Antonijevic, MD, PhD
  • CMO and Head of R&D, Triplet Therapeutics, Inc.
Rachel McMinn, PhD
  • Founder & CEO, Neurogene
Harith Rajagopalan, MD, PhD
  • CEO & Co-Founder, Fractyl Health
Bastiano Sanna, PhD
  • EVP, Chief of Cell & Gene Therapies and VCGT Site Head, Vertex Pharmaceuticals
Jeffrey Schweitzer, MD, PhD
  • Neurosurgeon, MGH
  • Assistant Professor of Neurosurgery, HMS
9:30 AM – 9:55 AMAmerica Ballroom

FIRESIDE

1:1 Fireside Chat: Dan Skovronsky

Moderator:
Geoff Meacham, PhD
  • Managing Director, Global Research, BofA Securities
Panelist:
Daniel Skovronsky, MD, PhD
  • Chief Scientific and Medical Officer, Eli Lilly and Company
9:55 AM – 10:20 AMAmerica Ballroom

FIRESIDE

Reimagining GCT Production

What is the new generation of approaches to gene therapy manufacturing and delivery? What are the lessons learned from Covid and how can it be applied to custom disease response and the ability to custom design biologic organisms?

Moderator:
Derik de Bruin, PhD
  • Managing Director, Global Research, BofA Securities
Panelist:
Jason Kelly, PhD
  • Co-Founder & CEO, Ginkgo Bioworks
10:20 AM – 11:00 AMAmerica Ballroom

Gene and Cell Therapy Safety | Enduring Framework Required

This panel will feature an in-depth discussion of the safety of gene and cell therapies. What are the unique safety concerns in this field, both acute and potential long-term risks? Which of these concerns are supported by clinical data versus the presumption of theoretical risk? What are the key issues for AAV-based gene therapies? Will redosing become feasible? What are the predominant safety concerns for in vivo versus ex vivo GCT modalities, including base editing?

Moderator:
Christine Seidman, MD
  • Director, Cardiovascular Genetics Center, BWH
  • Smith Professor of Medicine & Genetics, HMS
Panelists:
Rick Fair
  • President & CEO, Bellicum
Alexandria Forbes, PhD
  • President & CEO, MeiraGTx
Sekar Kathiresan, MD
  • CEO, Verve Therapeutics
Rick Modi
  • CEO, Affinia Therapeutics
11:00 AM – 11:40 AMAmerica Ballroom

RNA Therapeutics | Lessons Learned

The label “RNA” encompasses a wide array of biologically active agents spanning therapeutic modalities, vaccines, non-coding controls, and other forms. In this panel we will discuss a number of these forms, discuss examples of recent developments and illustrate why RNA developments represent a promising source of novel therapies and therapeutic approaches.

Moderator:
Janet Wu
  • Anchor/Reporter, Bloomberg
Panelists:
Sarah Boyce
  • President & CEO, Avidity Biosciences, Inc.
Jim Burns, PhD
  • CEO, Locanabio
Jeannie Lee, MD, PhD
  • Molecular Biologist, MGH
  • Professor of Genetics, HMS
Laura Sepp-Lorenzino, PhD
  • Chief Scientific Officer, Executive Vice President, Intellia Therapeutics
11:40 AM – 12:40 PMAmerica Ballroom

Disruptive Dozen: 12 Technologies That Will Reinvent GCT in the Next Five Years

The Disruptive Dozen identifies and ranks the GCT technologies that Mass General Brigham faculty feel will break through over the next one to five years to significantly improve health care.

Moderators:
Nino Chiocca, MD, PhD
  • Neurosurgeon-in-Chief and Chairman, Neurosurgery, BWH
  • Harvey W. Cushing Professor of Neurosurgery, HMS
Susan Slaugenhaupt, PhD
  • Scientific Director and Elizabeth G. Riley and Daniel E. Smith Jr. Endowed Chair, Mass General Research Institute
  • Professor, Neurology, HMS
Ravi Thadhani, MD
  • Chief Academic Officer, Mass General Brigham
Panelists:
Galit Alter, PhD
  • Principal Investigator, Ragon Institute, MGH
  • Professor of Medicine, HMS
Natalie Artzi, PhD
  • Assistant Professor of Medicine, HMS
Fengfeng Bei, PhD
  • Principal Investigator, Department of Neurosurgery, BWH
  • Assistant Professor of Neurosurgery, HMS
Zheng-Yi Chen, DPhil
  • Associate Scientist, Eaton-Peabody Laboratories, Mass Eye and Ear
  • Associate Professor of Otolaryngology Head and Neck Surgery, HMS
Matthew Frigault, MD
  • Clinical Director, Cellular Immunotherapy Program, MGH
  • Assistant Professor of Medicine, HMS
Michael Gilmore, PhD
  • Chief Scientific Officer, Mass Eye and Ear
  • Sir William Osler Professor of Ophthalmology, HMS
Allan Goldstein, MD
  • Chief of Pediatric Surgery, MGH
  • Surgeon-in-Chief, MassGeneral for Children
Anna Krichevsky, PhD
  • Associate Professor of Neurology, BWH, HMS
Jeannie Lee, MD, PhD
  • Molecular Biologist, MGH
  • Professor of Genetics, HMS
James Markmann, MD, PhD
  • Chief, Division of Transplant Surgery, MGH
  • Claude E. Welch Professor of Surgery, HMS
Khalid Shah, PhD
  • Vice Chairman of Research, Department of Neurosurgery, BWH
  • Professor, HMS
Demetrios Vavvas, MD, PhD
  • Associate Director of the Retina Service, Mass Eye and Ear
  • Solman and Libe Friedman Professor of Ophthalmology, Co-Director Ocular Regenerative Medical Institute, HMS

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Three Expert Opinions on “The alarming rise of complex genetic testing in human embryo selection”

Reporter: Aviva Lev-Ari, PhD, RN

Based on this articles three expert opinions where formed by the following domain knowledge experts and are presented, below.

Expert Opinions on rise of complex genetic testing in human embryo selection

ttps://www.nature.com/articles/d41586-022-00787-z

Domain Knowledge Experts:

Prof. Marc Feldman, Genetics, Stanford University

Dr. Shraga Rottem, MD, D.Sc., Fetal OB

Prof. Steven J. Williams, Biological Sciences, Temple University

 

First expert opinion by Prof. Marcus W. Feldman

The recent publication in Nature Medicine on genetic risk prediction in pre-implementation embryos(1) has already engendered heated discussion.(2,3) Kumar et al.(1) advocate the integration of polygenic risk scores (PRS) derived from pre-implantation genetic testing (PGT) with standard monogenic prediction. The paper focuses primarily on BRCA1 (and breast cancer) and APC (and colon cancer). Genetic tests for inherited disorders such as Tay-Sachs disease and breast cancers caused by BRCA1 and BRCA2 have been approved, but these are potentially devastating conditions with relatively simple inheritance; in most counseling situations the risks are straightforward to calculate.

The limitation on the amount and quality of DNA available from early embryo biopsies has made it difficult to produce genomic profiles of embryos in the IVF situation. Kumar et al. genotyped more than one-hundred embryos at hundreds of thousands of nucleotide sites and combined these genotype data with whole genome sequences of the prospective parents to produce reconstructed embryo genomes. These genomes were compared with those of ten born siblings and polygenic risk scores (PRS) were calculated for twelve conditions related to diseases. The PRS were claimed to be 97–99 percent accurate.

The primary market for this procedure would be couples seeking IVF, and Kumar and his colleagues, most of whom are employees of biotech companies, show that it is feasible to calculate a PRS for an embryo. The authors do present several caveats for the use of their procedure for PGT. For example, if a couple has a family history of a disease, they “may unintentionally prioritize” a mutant embryo for PGT-based only on PRS. They also acknowledge that results from research cohorts may not generalize to sibling embryos in IVF, which could limit the clinical utility of their approach. Kumar et al. also acknowledge the “portability” problem, namely PRSs have limited predictive accuracy in people with non-European ancestry(2,3) or of different ages or socioeconomic status.(4,5) They also mention the issue of unequal access to IVF technology in general.(2)

It is also important, However, to stress the limited predictive utility of PRS for common traits, not only diseases. There is increasing use of PRS among social scientists for characteristics such as years of education, which have heritabilities in the 10–15 percent range. Such studies, and potentially this one by Kumar et al., can lead to reduced emphasis on environmental and social associations with diseases or other traits. For omnigenic traits, such as height or body mass index (BMI), that have hundreds or thousands of associated nucleotide polymorphisms, and high heritability, the public might receive the mistaken impression that PGT or other genomic interventions can allow parents to choose their offspring’s phenotype.

For example, a recent study(6) of BMI in 881 subjects from Quebec found that PRS could explain only between 1.2 percent and 7.5 percent of the variance in BMI of these participants. Even when PRSs are statistically significant, their predictive value is too weak to be applied. The use of polygenic risk scores to select embryos, abbreviated ESPS for embryo selection based on polygenic scores, has been criticized before.(7) One of the important points raised by Turley et al.(7) concerns the environmental context of the children of IVG customers, which may be quite different from that of the sample of people from which the PRS was calculated. Because of gene-environment interactions, the predictive power of PRS for any complex trait is limited. As pointed out by Turley et al. (p. 79), “the predictive power of a polygenic score is maximized when the person is from the same environment as the research participants from whom the polygenic scores were derived. But this will never be the case in ESPS.”

PGT and ESPS raise ethical issues beyond IVG that more generally concern designer babies.(7,8) PRSs have been calculated for non-disease related traits such as educational attainment, income, or IQ, and it is conceivable that some prospective parents might regard these as important enough for intervention. There are also traits related to social constructs of race including skin pigmentation or facial features, and parental choice based on these phenotypes could enhance racial prejudices.

 

References

 

  1. Kumar, A., K. Im, M. Banjevic, P.C. Ng, T. Tunstall, G. Garcia, L. Galhardo, J. Sun,O.N. Schaedel, B. Levy, D. Hongo, D. Kijacic, M. Kiehl, N.D. Tran, P.C. Klatsky, and M. Rabinowitz. 2022. Whole-genome risk prediction of common diseases in human preimplantation embryos. Nature Medicine 28: 514–516. doi: 10.1038/s41591-022-01735-0.
  2. Johnston, J., and L.J. Matthews. 2022. Polygenic embryo testing: understated ethics, unclear utility. Nature Medicine 28: 445–451. doi: 10.1038/s41591-022-01743-0.
  3. Nature editorial. 2022. The alarming rise of complex genetic testing in human embryo testing. Nature 603: 549–550. doi: 10.1038/d41586-022-00787-z.
  4. Rosenberg, N., M. Edge, J. Pritchard, and M. Feldman. 2019. Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences. Evol. Med. Public Health 2019: 26–34. doi: 10.1093/emph/eoy036.
  5. Duncan, L.E., H. Shen, B. Gelaye, J. Meijsen, K.J. Ressler, M.W. Feldman, R.E. Peterson, and B.W. Domingue. 2019. Analysis of polygenic score usage and performance in diverse human populations. Nat. Comm. 10: 3328. doi: 10.1038/s41467-019-11112-0.
  6. De Toro-Martin, J.E., F. Guenard, C. Bouchard, A. Tremblay, L. Perusse, and M.-C. Vohl. 2019. The challenge of stratifying obesity: attempts in the Quebec family study. Front. Genet. 10:994. doi: 10.3389/fgene.2019.00994.
  7. Turley, P., M.N. Meyer, N. Wang, D. Cesarini, E. Hammonds, A.R. Martin, B.M. Neale, H.L. Rehm, L. Wilkins-Haug, D.J. Benjamin, S. Hyman, D. Laibson, and P.M. Visscher. 2021. Problems with using polygenic scores to select embryos. N. Engl. J. Med 385(1): 78–86.
  8. Forzano, F., O. Antonova, A. Clarke, G. de Wert, S. Hentze, Y. Jamshidi, Y. Moreau, M. Perola, I. Prokopenko, A. Read, A. Reymond, V. Stefansdottir, C. van El, and M. Genuardi. 2021. The use of polygenic risk scores in pre-implantation genetic testing: an unproven, unethical practice. European Journal of Human Genetics. doi: 10.1038/s41431-021-01000-x.

 

 

Second expert opinion by Dr. Shraga Rottem, MD, D.Sc., Fetal OB

PENDING

Third expert opinion by Prof. Steven J. Williams, Biological Sciences, Temple University

There has been much opinion, either as commentary in literature, meeting proceedings, or communiques from professional societies warning that this type of “high-impact” genetic information should not be given directly to the consumer as consumers will not fully understand the information presented to them, be unable to make proper risk-based decisions, results could cause panic and inappropriate action such as prophylactic oophorectomy or unwarranted risk-reduction mastectomy, or false reassurance in case of negative result and reduced future cancer screening measures taken by the consumer.  However, there have been few studies to investigate these concerns. 

The article by Kumar The alarming rise of complex genetic testing in human embryo selection

discusses the common trend of DTC (direct to consumer) and other genetic consutancy groups to offer disease risk assesment based on genetic predispostion genetic information in preimplantation embryos upon in vitro fertilization.  Although this editorial discusses some caveats and potential ethical issues the opinion of this reviewer feels a certain number of key issues points have not been addressed (which will be discussed below) including:

  1. the underlying risk of disclosure of all parties involved in decision making based on genetic testing including other family members
  2. complicating ethical issues not addressed through proper guideline establishment and regulation as seen in countries that allow such advances to go without proper review board
  3. a lack of discussion of the health disparities which may result of this type of genetic information or “selection” where groups of people would be shut out of such services due to socioeconomic status

Although the editorial highlights the issue that most genome wide association studies, on which most of the genetic counseling is based upon is from cohorts of European descent (and misses a large cohort which is Asian or African descent), there is little attention given to the issue that most panels of these agreed upon risk associated variants have not been validated in larger GWAS studies or that these panels only focus on the most common variants. An example of this would be BRCA1/2 and assumed future breast cancer risk.

In the related article The uncertain science of preimplantation and prenatal genetic testing

Gleicher al state

PGS and PGT-A
diagnoses have been built on biologically
incorrect assumptions and on unvalidated
guidelines dating back to 2016. These
guidelines, which remain influential to this
day, were published without a description
of methods, without peer review, with no
author identification, and without any
references1
. The guidelines changed the
binary diagnosis of euploid and aneuploid
to normal, mosaic and aneuploid.

 

In fact most family risk assesment programs are more effective upon counseling of young women, not at the embryonic stage where genetic risk factors may not be evident or resulting from epigenetic changes or accumulated somatic mutation.

  1.  Lack of communication to all related and involved parties

     Many times it is women, who having undergone these testings, have problems in communicating these risk findings to their children and family members, resulting in familial strains.

For instance, some women who discover they have the BRCA gene mutation, which puts them at higher risk for breast cancer, choose to tell their children about it before the children are old enough to understand the significance or deal with it, a new study found.

“Parents with the BRCA mutation are discussing their genetic test results with their offspring often many years before the offspring would need to do anything,” said study author Dr. Angela Bradbury, director of the Fox Chase Cancer Center’s Family Risk Assessment Program, in Philadelphia.

According to Bradbury, more than half of parents she surveyed told their children about genetic test results. Some parents reported that their children didn’t seem to understand the significance of the information, and some had initial negative reactions to the news.

“A lot of genetic information is being shared within families and there hasn’t been a lot of guidance from health-care professionals,” Bradbury said. “While this genetic risk may be shared accurately, there is risk of inaccurate sharing.”

In the study, Bradbury’s team interviewed 42 women who had the BRCA mutation. The researchers found that 55 percent of parents discussed the finding and the risk of breast cancer with at least one of their children who was under 25.

Also, most of the women didn’t avail themselves of the services of a doctor or genetic counselor in helping to tell their children, Bradbury’s group found.

The identification of familial risk factors can have very stressful impacts on the affected and their family however an IVF selection might even augment that familial stress.  More research is needed on the psychological impact of such testing and a patient’s choice.

2. Lack of health disparity considerations in IVF selection research or guidelines

     Another major concern, which has been highlighted in multiple articles on this site, is the growing health disparities between those who can obtain access to quality health care and those who are left out in the void of the medical system, either for economic or sociological reasons.  This has been very apparent in the cancer treatment and personalized medicine world (for example the disparities of health care access for cancer treatment in the southern poorer rural parts of the US versus metropolitan areas and the gaping disparities seen between rich and poor countries in Africa).   These health disparities have been also apparant in the genetic testing market, and although the DTC market meant to make genetic  testing more affordable, interestingly these disparities still exist in this niche market.

3. Lack of proper establishment of Institutional Review Board oversight in countries allowing this technique have been problematic with regard to addressing bioethical concerns

The third concern is, of course, a bioethical concern on the use of advanced genetic technologies in the human and clinical setting.  It has come to many people’s attention at the speed at which countries that do not seem to have strong bioethical review boards readily allow this type of research to be carried out without regulatory oversight or consequence. A prime example of this included the shunned Chinese research carried out to produce cloned humans, which was rapidly condemmed in the biomedical world however this research was conducted nonetheless.  This lack of attention is addressed in Kumar’s article yet little guidance is given as to best practices to establish review boards overseeing such work and or research.

SOURCE

https://www.nature.com/articles/d41586-022-00787-z

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Bipolar Disorder now understood by Markers Identified of the Gene Expression for this Diagnosis

Reporter: Aviva Lev-Ari, PhD, RN

Published: 

Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways

Abstract

Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression is altered in BD and how genetic risk for BD may contribute to these alterations. Here, we obtained transcriptomes from subgenual anterior cingulate cortex and amygdala samples from post-mortem brains of individuals with BD and neurotypical controls, including 511 total samples from 295 unique donors. We examined differential gene expression between cases and controls and the transcriptional effects of BD-associated genetic variants. We found two coexpressed modules that were associated with transcriptional changes in BD: one enriched for immune and inflammatory genes and the other with genes related to the postsynaptic membrane. Over 50% of BD genome-wide significant loci contained significant expression quantitative trait loci (QTL) (eQTL), and these data converged on several individual genes, including SCN2A and GRIN2A. Thus, these data implicate specific genes and pathways that may contribute to the pathology of BP.

SOURCE

https://www.nature.com/articles/s41593-022-01024-6

Gene Expression Markers for Bipolar Disorder Pinpointed

The work was led by researchers at Johns Hopkins’ Lieber Institute for Brain Development. The findings, published this week in Nature Neuroscience, represent the first time that researchers have been able to apply large-scale genetic research to brain samples from hundreds of patients with bipolar disorder (BD). They used 511 total samples from 295 unique donors.

“This is the first deep dive into the molecular biology of the brain in people who died with bipolar disorder—studying actual genes, not urine, blood or skin samples,” said Thomas Hyde of the Lieber Institute and a lead author of the paper. “If we can figure out the mechanisms behind BD, if we can figure out what’s wrong in the brain, then we can begin to develop new targeted treatments of what has long been a mysterious condition.”

Bipolar disorder is characterized by extreme mood swings, with episodes of mania alternating with episodes of depression. It usually emerges in people in their 20s and 30s and remains with them for life. This condition affects approximately 2.8% of the adult American population, or about 7 million people. Patients face higher rates of suicide, poorer quality of life, and lower productivity than the general population. Some estimates put the annual cost of the condition in the U.S. alone at $219.1 billion.

While drugs can be useful in treating BD, many patients find they have bothersome side effects, and for some patients, current medications don’t work at all.

In this study, researchers measured levels of messenger RNA in the brain samples. They observed almost eight times more differentially expressed gene features in the sACC versus the amygdala, suggesting that the sACC may play an especially prominent role—both in mood regulation in general and BD specifically.

In patients who died with BD, the researchers found abnormalities in two families of genes: one containing genes related to the synapse and the second related to immune and inflammatory function.

“There finally is a study using modern technology and our current understanding of genetics to uncover how the brain is doing,” Hyde said. “We know that BD tends to run in families, and there is strong evidence that there are inherited genetic abnormalities that put an individual at risk for bipolar disorder. Unlike diseases such as sickle-cell anemia, bipolar disorder does not result from a single genetic abnormality. Rather, most patients have inherited a group of variants spread across a number of genes.”

“Bipolar disorder, also known as manic-depressive disorder, is a highly damaging and paradoxical condition,” said Daniel R. Weinberger, chief executive and director of the Lieber Institute and a co-author of the study. “It can make people very productive so they can lead countries and companies, but it can also hurl them into the meat grinder of dysfunction and depression. Patients with BD may live on two hours of sleep a night, saving the world with their abundance of energy, and then become so self-destructive that they spend their family’s fortune in a week and lose all friends as they spiral downward. Bipolar disorder also has some shared genetic links to other psychiatric disorders, such as schizophrenia, and is implicated in overuse of drugs and alcohol.”

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@MIT Artificial intelligence system rapidly predicts how two proteins will attach: The model called Equidock, focuses on rigid body docking — which occurs when two proteins attach by rotating or translating in 3D space, but their shapes don’t squeeze or bend

Reporter: Aviva Lev-Ari, PhD, RN

This paper introduces a novel SE(3) equivariant graph matching network, along with a keypoint discovery and alignment approach, for the problem of protein-protein docking, with a novel loss based on optimal transport. The overall consensus is that this is an impactful solution to an important problem, whereby competitive results are achieved without the need for templates, refinement, and are achieved with substantially faster run times.
28 Sept 2021 (modified: 18 Nov 2021)ICLR 2022 SpotlightReaders:  Everyone Show BibtexShow Revisions
 
Keywords:protein complexes, protein structure, rigid body docking, SE(3) equivariance, graph neural networks
AbstractProtein complex formation is a central problem in biology, being involved in most of the cell’s processes, and essential for applications such as drug design or protein engineering. We tackle rigid body protein-protein docking, i.e., computationally predicting the 3D structure of a protein-protein complex from the individual unbound structures, assuming no three-dimensional flexibility during binding. We design a novel pairwise-independent SE(3)-equivariant graph matching network to predict the rotation and translation to place one of the proteins at the right location and the right orientation relative to the second protein. We mathematically guarantee that the predicted complex is always identical regardless of the initial placements of the two structures, avoiding expensive data augmentation. Our model approximates the binding pocket and predicts the docking pose using keypoint matching and alignment through optimal transport and a differentiable Kabsch algorithm. Empirically, we achieve significant running time improvements over existing protein docking software and predict qualitatively plausible protein complex structures despite not using heavy sampling, structure refinement, or templates.
One-sentence SummaryWe perform rigid protein docking using a novel independent SE(3)-equivariant message passing mechanism that guarantees the same resulting protein complex independent of the initial placement of the two 3D structures.
 
SOURCE
 

MIT researchers created a machine-learning model that can directly predict the complex that will form when two proteins bind together. Their technique is between 80 and 500 times faster than state-of-the-art software methods, and often predicts protein structures that are closer to actual structures that have been observed experimentally.

This technique could help scientists better understand some biological processes that involve protein interactions, like DNA replication and repair; it could also speed up the process of developing new medicines.

Deep learning is very good at capturing interactions between different proteins that are otherwise difficult for chemists or biologists to write experimentally. Some of these interactions are very complicated, and people haven’t found good ways to express them. This deep-learning model can learn these types of interactions from data,” says Octavian-Eugen Ganea, a postdoc in the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) and co-lead author of the paper.

Ganea’s co-lead author is Xinyuan Huang, a graduate student at ETH Zurich. MIT co-authors include Regina Barzilay, the School of Engineering Distinguished Professor for AI and Health in CSAIL, and Tommi Jaakkola, the Thomas Siebel Professor of Electrical Engineering in CSAIL and a member of the Institute for Data, Systems, and Society. The research will be presented at the International Conference on Learning Representations.

Significance of the Scientific Development by the @MIT Team

EquiDock wide applicability:

  • Our method can be integrated end-to-end to boost the quality of other models (see above discussion on runtime importance). Examples are predicting functions of protein complexes [3] or their binding affinity [5], de novo generation of proteins binding to specific targets (e.g., antibodies [6]), modeling back-bone and side-chain flexibility [4], or devising methods for non-binary multimers. See the updated discussion in the “Conclusion” section of our paper.

 

Advantages over previous methods:

  • Our method does not rely on templates or heavy candidate sampling [7], aiming at the ambitious goal of predicting the complex pose directly. This should be interpreted in terms of generalization (to unseen structures) and scalability capabilities of docking models, as well as their applicability to various other tasks (discussed above).

 

  • Our method obtains a competitive quality without explicitly using previous geometric (e.g., 3D Zernike descriptors [8]) or chemical (e.g., hydrophilic information) features [3]. Future EquiDock extensions would find creative ways to leverage these different signals and, thus, obtain more improvements.

   

Novelty of theory:

  • Our work is the first to formalize the notion of pairwise independent SE(3)-equivariance. Previous work (e.g., [9,10]) has incorporated only single object Euclidean-equivariances into deep learning models. For tasks such as docking and binding of biological objects, it is crucial that models understand the concept of multi-independent Euclidean equivariances.

  • All propositions in Section 3 are our novel theoretical contributions.

  • We have rewritten the Contribution and Related Work sections to clarify this aspect.

   


Footnote [a]: We have fixed an important bug in the cross-attention code. We have done a more extensive hyperparameter search and understood that layer normalization is crucial in layers used in Eqs. 5 and 9, but not on the h embeddings as it was originally shown in Eq. 10. We have seen benefits from training our models with a longer patience in the early stopping criteria (30 epochs for DIPS and 150 epochs for DB5). Increasing the learning rate to 2e-4 is important to speed-up training. Using an intersection loss weight of 10 leads to improved results compared to the default of 1.

 

Bibliography:

[1] Protein-ligand blind docking using QuickVina-W with inter-process spatio-temporal integration, Hassan et al., 2017

[2] GNINA 1.0: molecular docking with deep learning, McNutt et al., 2021

[3] Protein-protein and domain-domain interactions, Kangueane and Nilofer, 2018

[4] Side-chain Packing Using SE(3)-Transformer, Jindal et al., 2022

[5] Contacts-based prediction of binding affinity in protein–protein complexes, Vangone et al., 2015

[6] Iterative refinement graph neural network for antibody sequence-structure co-design, Jin et al., 2021

[7] Hierarchical, rotation-equivariant neural networks to select structural models of protein complexes, Eismann et al, 2020

[8] Protein-protein docking using region-based 3D Zernike descriptors, Venkatraman et al., 2009

[9] SE(3)-transformers: 3D roto-translation equivariant attention networks, Fuchs et al, 2020

[10] E(n) equivariant graph neural networks, Satorras et al., 2021

[11] Fast end-to-end learning on protein surfaces, Sverrisson et al., 2020

SOURCE

https://openreview.net/forum?id=GQjaI9mLet

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Debbie Nickerson Dies

Reporter: Aviva Lev-Ari, PhD, RN

Jan 03, 2022 | staff reporter

From

https://www.genomeweb.com/scan/debbie-nickerson-dies?adobe_mc=MCMID%3D34480469763973098982318083811122311334%7CMCORGID%3D138FFF2554E6E7220A4C98C6%2540AdobeOrg%7CTS%3D1641234870&CSAuthResp=1%3A%3A618831%3A273%3A24%3Asuccess%3A1AF77CF7470112199AEA1647462A9EDB#.YdNBvhPMKLo

Debbie Nickerson, a leader of human genome sequencing and its application in precision medicine, has died at the age of 67, according to the University of Washington, where she was a professor in the Department of Genome Sciences.

“Always pushing the existing boundaries with an infectious mix of creativity, vision, impatience, and a wicked sense of humor, Debbie exhorted herself and everyone around her to do more than they thought they could,” Francis Collins, former director of the National Institutes of Health, tells UW. “Her imprint on genomic medicine is profound, and she will be sorely missed.”

At the time of her death, from abdominal cancer, Nickerson was director of UW’s Center for Mendelian Genomics and a principal contributor to the NIH All of Us Research Program. During her career, she published more than 350 original research papers.

She was also a forceful advocate for women in science. “She fought for a culture that would not require women to sacrifice their personal lives to pursue careers in science,” UW writes. “In parallel, she advanced the training of young scientists from underrepresented minority backgrounds.”

Nickerson, who hailed from Mineola, New York, had been at UW since 1992. “Her former students and postdocs are now a powerful force in human genetics and genomics,” the university notes.

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New studies link cell cycle proteins to immunosurveillance of premalignant cells

Curator: Stephen J. Williams, Ph.D.

The following is from a Perspectives article in the journal Science by Virinder Reen and Jesus Gil called “Clearing Stressed Cells: Cell cycle arrest produces a p21-dependent secretome that initaites immunosurveillance of premalignant cells”. This is a synopsis of the Sturmlechener et al. research article in the same issue (2).

Complex organisms repair stress-induced damage to limit the replication of faulty cells that could drive cancer. When repair is not possible, tissue homeostasis is maintained by the activation of stress response programs such as apoptosis, which eliminates the cells, or senescence, which arrests them (1). Cellular senescence causes the arrest of damaged cells through the induction of cyclin-dependent kinase inhibitors (CDKIs) such as p16 and p21 (2). Senescent cells also produce a bioactive secretome (the senescence-associated secretory phenotype, SASP) that places cells under immunosurveillance, which is key to avoiding the detrimental inflammatory effects caused by lingering senescent cells on surrounding tissues. On page 577 of this issue, Sturmlechner et al. (3) report that induction of p21 not only contributes to the arrest of senescent cells, but is also an early signal that primes stressed cells for immunosurveillance.Senescence is a complex program that is tightly regulated at the epigenetic and transcriptional levels. For example, exit from the cell cycle is controlled by the induction of p16 and p21, which inhibit phosphorylation of the retinoblastoma protein (RB), a transcriptional regulator and tumor suppressor. Hypophosphorylated RB represses transcription of E2F target genes, which are necessary for cell cycle progression. Conversely, production of the SASP is regulated by a complex program that involves super-enhancer (SE) remodeling and activation of transcriptional regulators such as nuclear factor κB (NF-κB) or CCAAT enhancer binding protein–β (C/EBPβ) (4).

Senescence is a complex program that is tightly regulated at the epigenetic and transcriptional levels. For example, exit from the cell cycle is controlled by the induction of p16 and p21, which inhibit phosphorylation of the retinoblastoma protein (RB), a transcriptional regulator and tumor suppressor. Hypophosphorylated RB represses transcription of E2F target genes, which are necessary for cell cycle progression. Conversely, production of the SASP is regulated by a complex program that involves super-enhancer (SE) remodeling and activation of transcriptional regulators such as nuclear factor κB (NF-κB) or CCAAT enhancer binding protein–β (C/EBPβ) (4).

Sturmlechner et al. found that activation of p21 following stress rapidly halted cell cycle progression and triggered an internal biological timer (of ∼4 days in hepatocytes), allowing time to repair and resolve damage (see the figure). In parallel, C-X-C motif chemokine 14 (CXCL14), a component of the PASP, attracted macrophages to surround and closely surveil these damaged cells. Stressed cells that recovered and normalized p21 expression suspended PASP production and circumvented immunosurveillance. However, if the p21-induced stress was unmanageable, the repair timer expired, and the immune cells transitioned from surveillance to clearance mode. Adjacent macrophages mounted a cytotoxic T lymphocyte response that destroyed damaged cells. Notably, the overexpression of p21 alone was sufficient to orchestrate immune killing of stressed cells, without the need of a senescence phenotype. Overexpression of other CDKIs, such as p16 and p27, did not trigger immunosurveillance, likely because they do not induce CXCL14 expression.In the context of cancer, senescent cell clearance was first observed following reactivation of the tumor suppressor p53 in liver cancer cells. Restoring p53 signaling induced senescence and triggered the elimination of senescent cells by the innate immune system, prompting tumor regression (5). Subsequent work has revealed that the SASP alerts the immune system to target preneoplastic senescent cells. Hepatocytes expressing the oncogenic mutant NRASG12V (Gly12→Val) become senescent and secrete chemokines and cytokines that trigger CD4+ T cell–mediated clearance (6). Despite the relevance for tumor suppression, relatively little is known about how immunosurveillance of oncogene-induced senescent cells is initiated and controlled.

Source of image: Reen, V. and Gil, J. Clearing Stressed Cells. Science Perspectives 2021;Vol 374(6567) p 534-535.

References

2. Sturmlechner I, Zhang C, Sine CC, van Deursen EJ, Jeganathan KB, Hamada N, Grasic J, Friedman D, Stutchman JT, Can I, Hamada M, Lim DY, Lee JH, Ordog T, Laberge RM, Shapiro V, Baker DJ, Li H, van Deursen JM. p21 produces a bioactive secretome that places stressed cells under immunosurveillance. Science. 2021 Oct 29;374(6567):eabb3420. doi: 10.1126/science.abb3420. Epub 2021 Oct 29. PMID: 34709885.

More Articles on Cancer, Senescence and the Immune System in this Open Access Online Scientific Journal Include

Bispecific and Trispecific Engagers: NK-T Cells and Cancer Therapy

Natural Killer Cell Response: Treatment of Cancer

Issues Need to be Resolved With ImmunoModulatory Therapies: NK cells, mAbs, and adoptive T cells

New insights in cancer, cancer immunogenesis and circulating cancer cells

Insight on Cell Senescence

Immune System Stimulants: Articles of Note @pharmaceuticalintelligence.com

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Reporter: Stephen J. Williams, Ph.D.

From: Heidi Rheim et al. GA4GH: International policies and standards for data sharing across genomic research and healthcare. (2021): Cell Genomics, Volume 1 Issue 2.

Source: DOI:https://doi.org/10.1016/j.xgen.2021.100029

Highlights

  • Siloing genomic data in institutions/jurisdictions limits learning and knowledge
  • GA4GH policy frameworks enable responsible genomic data sharing
  • GA4GH technical standards ensure interoperability, broad access, and global benefits
  • Data sharing across research and healthcare will extend the potential of genomics

Summary

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

In order for genomic and personalized medicine to come to fruition it is imperative that data siloes around the world are broken down, allowing the international collaboration for the collection, storage, transferring, accessing and analying of molecular and health-related data.

We had talked on this site in numerous articles about the problems data siloes produce. By data siloes we are meaning that collection and storage of not only DATA but intellectual thought are being held behind physical, electronic, and intellectual walls and inacessible to other scientisits not belonging either to a particular institituion or even a collaborative network.

Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson and others

Standardization and harmonization of data is key to this effort to sharing electronic records. The EU has taken bold action in this matter. The following section is about the General Data Protection Regulation of the EU and can be found at the following link:

https://ec.europa.eu/info/law/law-topic/data-protection/data-protection-eu_en

Fundamental rights

The EU Charter of Fundamental Rights stipulates that EU citizens have the right to protection of their personal data.

Protection of personal data

Legislation

The data protection package adopted in May 2016 aims at making Europe fit for the digital age. More than 90% of Europeans say they want the same data protection rights across the EU and regardless of where their data is processed.

The General Data Protection Regulation (GDPR)

Regulation (EU) 2016/679 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data. This text includes the corrigendum published in the OJEU of 23 May 2018.

The regulation is an essential step to strengthen individuals’ fundamental rights in the digital age and facilitate business by clarifying rules for companies and public bodies in the digital single market. A single law will also do away with the current fragmentation in different national systems and unnecessary administrative burdens.

The regulation entered into force on 24 May 2016 and applies since 25 May 2018. More information for companies and individuals.

Information about the incorporation of the General Data Protection Regulation (GDPR) into the EEA Agreement.

EU Member States notifications to the European Commission under the GDPR

The Data Protection Law Enforcement Directive

Directive (EU) 2016/680 on the protection of natural persons regarding processing of personal data connected with criminal offences or the execution of criminal penalties, and on the free movement of such data.

The directive protects citizens’ fundamental right to data protection whenever personal data is used by criminal law enforcement authorities for law enforcement purposes. It will in particular ensure that the personal data of victims, witnesses, and suspects of crime are duly protected and will facilitate cross-border cooperation in the fight against crime and terrorism.

The directive entered into force on 5 May 2016 and EU countries had to transpose it into their national law by 6 May 2018.

The following paper by the organiztion The Global Alliance for Genomics and Health discusses these types of collaborative efforts to break down data silos in personalized medicine. This organization has over 2000 subscribers in over 90 countries encompassing over 60 organizations.

Enabling responsible genomic data sharing for the benefit of human health

The Global Alliance for Genomics and Health (GA4GH) is a policy-framing and technical standards-setting organization, seeking to enable responsible genomic data sharing within a human rights framework.

he Global Alliance for Genomics and Health (GA4GH) is an international, nonprofit alliance formed in 2013 to accelerate the potential of research and medicine to advance human health. Bringing together 600+ leading organizations working in healthcare, research, patient advocacy, life science, and information technology, the GA4GH community is working together to create frameworks and standards to enable the responsible, voluntary, and secure sharing of genomic and health-related data. All of our work builds upon the Framework for Responsible Sharing of Genomic and Health-Related Data.

GA4GH Connect is a five-year strategic plan that aims to drive uptake of standards and frameworks for genomic data sharing within the research and healthcare communities in order to enable responsible sharing of clinical-grade genomic data by 2022. GA4GH Connect links our Work Streams with Driver Projects—real-world genomic data initiatives that help guide our development efforts and pilot our tools.

From the article on Cell Genomics GA4GH: International policies and standards for data sharing across genomic research and healthcare

Source: Open Access DOI:https://doi.org/10.1016/j.xgen.2021.100029PlumX Metrics

The Global Alliance for Genomics and Health (GA4GH) is a worldwide alliance of genomics researchers, data scientists, healthcare practitioners, and other stakeholders. We are collaborating to establish policy frameworks and technical standards for responsible, international sharing of genomic and other molecular data as well as related health data. Founded in 2013,3 the GA4GH community now consists of more than 1,000 individuals across more than 90 countries working together to enable broad sharing that transcends the boundaries of any single institution or country (see https://www.ga4gh.org).In this perspective, we present the strategic goals of GA4GH and detail current strategies and operational approaches to enable responsible sharing of clinical and genomic data, through both harmonized data aggregation and federated approaches, to advance genomic medicine and research. We describe technical and policy development activities of the eight GA4GH Work Streams and implementation activities across 24 real-world genomic data initiatives (“Driver Projects”). We review how GA4GH is addressing the major areas in which genomics is currently deployed including rare disease, common disease, cancer, and infectious disease. Finally, we describe differences between genomic sequence data that are generated for research versus healthcare purposes, and define strategies for meeting the unique challenges of responsibly enabling access to data acquired in the clinical setting.

GA4GH organization

GA4GH has partnered with 24 real-world genomic data initiatives (Driver Projects) to ensure its standards are fit for purpose and driven by real-world needs. Driver Projects make a commitment to help guide GA4GH development efforts and pilot GA4GH standards (see Table 2). Each Driver Project is expected to dedicate at least two full-time equivalents to GA4GH standards development, which takes place in the context of GA4GH Work Streams (see Figure 1). Work Streams are the key production teams of GA4GH, tackling challenges in eight distinct areas across the data life cycle (see Box 1). Work Streams consist of experts from their respective sub-disciplines and include membership from Driver Projects as well as hundreds of other organizations across the international genomics and health community.

Figure thumbnail gr1
Figure 1Matrix structure of the Global Alliance for Genomics and HealthShow full caption


Box 1
GA4GH Work Stream focus areasThe GA4GH Work Streams are the key production teams of the organization. Each tackles a specific area in the data life cycle, as described below (URLs listed in the web resources).

  • (1)Data use & researcher identities: Develops ontologies and data models to streamline global access to datasets generated in any country9,10
  • (2)Genomic knowledge standards: Develops specifications and data models for exchanging genomic variant observations and knowledge18
  • (3)Cloud: Develops federated analysis approaches to support the statistical rigor needed to learn from large datasets
  • (4)Data privacy & security: Develops guidelines and recommendations to ensure identifiable genomic and phenotypic data remain appropriately secure without sacrificing their analytic potential
  • (5)Regulatory & ethics: Develops policies and recommendations for ensuring individual-level data are interoperable with existing norms and follow core ethical principles
  • (6)Discovery: Develops data models and APIs to make data findable, accessible, interoperable, and reusable (FAIR)
  • (7)Clinical & phenotypic data capture & exchange: Develops data models to ensure genomic data is most impactful through rich metadata collected in a standardized way
  • (8)Large-scale genomics: Develops APIs and file formats to ensure harmonized technological platforms can support large-scale computing

For more articles on Open Access, Science 2.0, and Data Networks for Genomics on this Open Access Scientific Journal see:

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Icelandic Population Genomic Study Results by deCODE Genetics come to Fruition: Curation of Current genomic studies

eScientific Publishing a Case in Point: Evolution of Platform Architecture Methodologies and of Intellectual Property Development (Content Creation by Curation) Business Model 

UK Biobank Makes Available 200,000 whole genomes Open Access

Systems Biology Analysis of Transcription Networks, Artificial Intelligence, and High-End Computing Coming to Fruition in Personalized Oncology

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UK Biobank Makes Available 200,000 whole genomes Open Access

Reporter: Stephen J. Williams, Ph.D.

The following is a summary of an article by Jocelyn Kaiser, published in the November 26, 2021 issue of the journal Science.

To see the full article please go to https://www.science.org/content/article/200-000-whole-genomes-made-available-biomedical-studies-uk-effort

The UK Biobank (UKBB) this week unveiled to scientists the entire genomes of 200,000 people who are part of a long-term British health study.

The trove of genomes, each linked to anonymized medical information, will allow biomedical scientists to scour the full 3 billion base pairs of human DNA for insights into the interplay of genes and health that could not be gleaned from partial sequences or scans of genome markers. “It is thrilling to see the release of this long-awaited resource,” says Stephen Glatt, a psychiatric geneticist at the State University of New York Upstate Medical University.

Other biobanks have also begun to compile vast numbers of whole genomes, 100,000 or more in some cases (see table, below). But UKBB stands out because it offers easy access to the genomic information, according to some of the more than 20,000 researchers in 90 countries who have signed up to use the data. “In terms of availability and data quality, [UKBB] surpasses all others,” says physician and statistician Omar Yaxmehen Bello-Chavolla of the National Institute for Geriatrics in Mexico City.

Enabling your vision to improve public health

Data drives discovery. We have curated a uniquely powerful biomedical database that can be accessed globally for public health research. Explore data from half a million UK Biobank participants to enable new discoveries to improve public health.

Data Showcase

Future data releases

This UKBB biobank represents genomes collected from 500,000 middle-age and elderly participants for 2006 to 2010. The genomes are mostly of a European descent. Other large scale genome sequencing ventures like Iceland’s DECODE, which collected over 100,000 genomes, is now a subsidiary of Amgen, and mostly behind IP protection, not Open Access as this database represents.

UK Biobank is a large-scale biomedical database and research resource, containing in-depth genetic and health information from half a million UK participants. The database is regularly augmented with additional data and is globally accessible to approved researchers undertaking vital research into the most common and life-threatening diseases. It is a major contributor to the advancement of modern medicine and treatment and has enabled several scientific discoveries that improve human health.

A summary of some large scale genome sequencing projects are show in the table below:

BiobankCompleted Whole GenomesRelease Information
UK Biobank200,000300,000 more in early 2023
TransOmics for
Precision Medicien
161,000NIH requires project
specific request
Million Veterans
Program
125,000Non-Veterans Affairs
researchers get first access
100,000 Genomes
Project
120,000Researchers must join Genomics
England collaboration
All of Us90,000NIH expects to release 2022

Other Related Articles on Genome Biobank Projects in this Open Access Online Scientific Journal Include the Following:

Icelandic Population Genomic Study Results by deCODE Genetics come to Fruition: Curation of Current genomic studies

Exome Aggregation Consortium (ExAC), generated the largest catalogue so far of variation in human protein-coding regions: Sequence data of 60,000 people, NOW is a publicly accessible database

Systems Biology Analysis of Transcription Networks, Artificial Intelligence, and High-End Computing Coming to Fruition in Personalized Oncology

Diversity and Health Disparity Issues Need to be Addressed for GWAS and Precision Medicine Studies

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