Posts Tagged ‘human genome’

Reporter and Curator: Irina Robu, PhD

Monitoring cancer patients and evaluating their response to treatment can sometimes involve invasive procedures, including surgery.

The liquid biopsies have become something of a Holy Grail in cancer treatment among physicians, researchers and companies gambling big on the technology. Liquid biopsies, unlike traditional biopsies involving invasive surgery — rely on an ordinary blood draw. Developments in sequencing the human genome, permitting researchers to detect genetic mutations of cancers, have made the tests conceivable. Some 38 companies in the US alone are working on liquid biopsies by trying to analyze blood for fragments of DNA shed by dying tumor cells.

Premature research on the liquid biopsy has concentrated profoundly on patients with later-stage cancers who have suffered treatments, including chemotherapy, radiation, surgery, immunotherapy or drugs that target molecules involved in the growth, progression and spread of cancer. For cancer patients undergoing treatment, liquid biopsies could spare them some of the painful, expensive and risky tissue tumor biopsies and reduce reliance on CT scans. The tests can rapidly evaluate the efficacy of surgery or other treatment, while old-style biopsies and CT scans can still remain inconclusive as a result of scar tissue near the tumor site.

As recently as a few years ago, the liquid biopsies were hardly used except in research. At the moment, thousands of the tests are being used in clinical practices in the United States and abroad, including at the M.D. Anderson Cancer Center in Houston; the University of California, San Diego; the University of California, San Francisco; the Duke Cancer Institute and several other cancer centers.

With patients for whom physicians cannot get a tissue biopsy, the liquid biopsy could prove a safe and effective alternative that could help determine whether treatment is helping eradicate the cancer. A startup, Miroculus developed a cheap, open source device that can test blood for several types of cancer at once. The platform, called Miriam finds cancer by extracting RNA from blood and spreading it across plates that look at specific type of mRNA. The technology is then hooked up at a smartphone which sends the information to an online database and compares the microRNA found in the patient’s blood to known patterns indicating different type of cancers in the early stage and can reduce unnecessary cancer screenings.

Nevertheless, experts warn that more studies are essential to regulate the accuracy of the test, exactly which cancers it can detect, at what stages and whether it improves care or survival rates.


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

Liquid Biopsy Chip detects an array of metastatic cancer cell markers in blood – R&D @Worcester Polytechnic Institute, Micro and Nanotechnology Lab

Reporters: Tilda Barliya, PhD and Aviva Lev-Ari, PhD, RN

Liquid Biopsy Assay May Predict Drug Resistance

Curator: Larry H. Bernstein, MD, FCAP

One blood sample can be tested for a comprehensive array of cancer cell biomarkers: R&D at WPI

Curator: Marzan Khan, B.Sc




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Sequence the Human Genome

Curator: Larry H Bernstein, MD, FCAP



Geneticist Craig Venter helped sequence the human genome. Now he wants yours.


If you enter Health Nucleus, a new facility in San Diego cofounded by J. Craig Venter, one of the world’s best-known living scientists, you will get a telling glimpse into the state of medical science in 2015.

Your entire genome will be sequenced with extraordinary resolution and accuracy. Your body will be scanned in fine, three-dimensional detail. Thousands of compounds in your blood will be measured. Even the microbes that live inside you will be surveyed. You will get a custom-made iPad app to navigate data about yourself. Also, your wallet will be at least $25,000 lighter.

Venter, who came to the world’s attention in the 1990s when he led a campaign to produce the first draft of a human genome, launched Health Nucleus last month as part of his new company, Human Longevity. He has made clear that his aim is just as lofty as it was when he and his team sequenced the human genome or built a flu vaccine from a genetic sequence delivered to them over the Internet.

“We’re trying to show the value of actual scientific data that can change people’s lives,” Venter told STAT in some of his most extensive remarks yet about the project. “Our goal is to interpret everything in the genome that we can.”

Still, the initiative is drawing deep suspicion among some doctors who question whether Venter’s existing tests can tell patients anything meaningful at all. In interviews, they said they see Health Nucleus as the latest venture that could lead consumers to believe that more testing means improved health. That notion, they say, could drive customers to get procedures they don’t need, which might even be harmful.

“I think there is absolutely no evidence that any of those tests have any benefit for healthy people,” Dr. Rita Redberg, a cardiologist at the University of California at San Diego and the editor-in-chief of JAMA Internal Medicine, said when asked about Venter’s new project.

Venter has a black belt in media savvy — he can make the details of molecular biology alluring for viewers of 60 Minutes and TED talks alike — but off screen he has earned a reputation even from his critics for serious scientific achievements. His non-profit J. Craig Venter Institute, which he founded in 1992, now has a staff of 300. Scientists at the institute have explored everything from the ocean’s biodiversity to the Ebola virus.

Last year, at age 67, Venter cofounded Human Longevity, a company based in San Diego with branches in Mountain View, Calif., and Singapore that is building the largest human genome-sequencing operation on Earth, equipped with massive computing resources to analyze the data being generated. The firm’s database now contains highly accurate genome sequences from 20,000 people; another 3,000 genomes are being added each month.

Franz Och, the former head of Google Translate and an expert on machine learning, is leading a team that’s teaching computers to recognize patterns in the company’s databases that scientists themselves may not be able to see. To demonstrate the power of this approach, Human Longevity researchers are using machine learning to discover how genetic variations shape the human face.

“We can determine a good resemblance of your photograph straight from your genetic code,” said Venter.

Venter and his colleagues will be publishing the results of that study soon — most likely generating another round of headlines. But headlines don’t pay the bills, and at a company that’s got $70 million in funding from private investors, bills matter. The company is now exploring a number of avenues for generating income from its database. It has partnered with Discovery, an insurance company in England and South Africa, to read the DNA of their clients. For $250 apiece, it will sequence the protein-coding regions of the genome, known as exomes, and offer an interpretation of the data.

Health Nucleus could become yet another source of income for Human Longevity. The San Diego facility can handle eight to 12 people a day. There are plans to open more sites both in the United States and abroad. “You can do the math,” Venter said.

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Saudi Human Genome Program, International Barcode of Life Project

Reporter: Aviva Lev-Ari, PhD, RN

Life Tech Becomes Partner in Saudi Human Genome Program, International Barcode of Life Project

December 09, 2013

NEW YORK, GenomeWeb − Life Technologies has become a partner in two research projects, the Saudi Human Genome Program and the International Barcode of Life (iBOL) project, the company said this week. The projects will employ the firm’s Ion Proton, capillary electrophoresis, and PGM sequencing technologies.

The goal of the Saudi Human Genome Project, led by Saudi Arabia’s national funding agency, the King Abdulaziz City for Science and Technology (KACST), is to study the genetic basis of disease in Saudi Arabia and the Middle East.

Over the next five years, the project aims to sequence 100,000 genomes from individuals from the region using Life Tech’s Ion Proton technology. Sequencing will be initially conducted at 10 genome centers across Saudi Arabia, with five additional centers to be created in the future.

Life Tech will design and equip the centers, and provide “end-to-end solutions” and services for operations and informatics. Integrated Gulf Biosystems, Life Tech’s distributor in the Middle East, said it played a “pivotal role” in bringing Life Tech’s technology to KACST.

Results from the project will be used to build a Saudi-specific database, providing the basis for future personalized medicine in the Kingdom. Specifically, the information is expected to help with premarital and prenatal screening for rare genetic diseases, as well as for population studies.



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Curator: Aviva Lev-Ari, PhD, RN

In their discussion, the researchers argue that the U.S. Supreme Court now has a chance to shape the balance between the medical good versus inventor protection, adding that, in their opinion, the court should limit the patenting of existing nucleotide sequences, due to their broad scope and non-specificity in the human genome.

“I am extremely pro-patent, but I simply believe that people should not be able to patent a product of nature,” Dr. Mason says. “Moreover, I believe that individuals have an innate right to their own genome, or to allow their doctor to look at that genome, just like the lungs or kidneys. Failure to resolve these ambiguities perpetuates a direct threat to genomic liberty, or the right to one’s own DNA.”

Supreme Court May Decide Whether We Own Our Genes

March 26, 2013
Image Credit:

Brett Smith for – Your Universe Online

They may be responsible for everything in your life, from conception to death, they may be inside every living cell in your body – but you do not own your own genes, legally speaking.

According to a report in Genome Medicine, patents essentially cover the entire human genome, hampering research and raising the question of “genomic liberty.”

The legal standing of genomic patents could change next month when the Supreme Court reviews patent rights for two key breast and ovarian cancer genes, BRCA1 and BRCA2, which include segments of genetic code as small as 15 nucleotides, known as 15mers.

“This is, so to speak, patently ridiculous,” said report co-author Dr. Christopher E. Mason of Weill Cornell Medical College. “If patent claims that use these small DNA sequences are upheld, it could potentially create a situation where a piece of every gene in the human genome is patented by a phalanx of competing patents.”

In their report, Mason and Dr. Jeffrey Rosenfeld, an assistant professor of medicine at the University of Medicine & Dentistry of New Jersey, looked at patents for two different categories of DNA fragments:

  • long and
  • short.

They revealed 41 percent of the human genome is covered by “long” DNA patents that can include whole genes. Because many genes share similar sequences within their code that are patented, the combination of all these “short” DNA patents covers 100 percent of the genome.

“This demonstrates that short patent sequences are extremely non-specific and that a 15mer claim from one gene will always cross-match and patent a portion of another gene as well,” Mason said. “This means it is actually impossible to have a 15mer patent for just one gene.”

To reach their conclusions, the researchers first looked at small sequences within BRCA1 and noticed one of the company’s BRCA1 patents also covered almost 690 other human genes. Some of these genes are unrelated to breast cancer – instead being associated with brain development and heart functioning.

Next, researchers determined how many known genes are covered by 15mers in current patent claims. They found 58 patents covered at least ten percent of all bases of all human genes. The broadest patent claim matched 91.5 percent of human genes. When the team took patented 15mers and matched them to known genes, they found 100 percent of known genes are patented.

Finally, the team also looked at “long” DNA sequences from existing gene patents, ranging from a few dozen to thousands of base pairs. They found these long sequences added up to 41 percent of known human genes.

“There is a real controversy regarding gene ownership due to the overlap of many competing patent claims. It is unclear who really owns the rights to any gene,” Rosenfeld said. “While the Supreme Court is hearing one case concerning just the BRCA1 patent, there are also many other patents whose claims would cover those same genes.

“Do we need to go through every gene to look at who made the first claim to that gene, even if only one small part? If we resort to this rule, then the first patents to be granted for any DNA will have a vast claim over portions of the human genome,” he added.

Another legal question surrounds patented DNA sequences that cross species boundaries. The researchers found one company has the rights to 84 percent of all human genes for a patent they received for cow breeding.

Source: Brett Smith for – Your Universe Online

Topics: Health Medical PharmaGeneticsGene patentBiologyGeneLiving modified organismAssociation for Molecular Pathology v. U.S. Patent and Trademark OfficeBRCA1DNASupreme CourtHuman genome


Human Genome: Name Your Price

Posted March 27, 2013 – 12:51 by a staff writer

Weill Cornell Medical College researchers have issued a warning that, according to the patent system, the vast majority of humans on the planet don’t ‘own’ their own genes, and in fact their biological make-up is being exploited for profit. Even seemingly innocent research into cow breeding can cover human genetic make-up.

As spotted by a Slashdot user, two researchers combing through patents on human DNA discovered that over 40,000 patents on DNA molecules have effectively declared the human genome for profit. A report in medical journal Genome Medicine said that humans may be losing their grip on “individual genomic liberty”.

Looking at two kinds of patented DNA sequences, or long and short fragments, 41 percent of the human genome is covered by DNA patents that can cover entire genes. According to the research, if all of the short sequence patents were allowed in aggregate they could cover 100 percent of the human genome.

Lead author Dr Christopher E Mason and co-author Dr Jeffrey Rosenfeld warned that short sequences from patents cover “virtually the entire genome, even outside of genes”. A Weill Cornell assistant professor asked: “How is it possible that my doctor cannot look at my DNA without being concerned about patent infringement?”

There will be a Supreme Court hearing about genomic patent rights next month that will debate the morality of a molecular diagnostic company claiming patents on key cancer genes, as well as on any small sequence of code within the BRCA1 gene. Cornell explained that at present, genes are able to be patented by researchers working in companies and institutions who discover genes that have potentially useful applications, like in testing for cancer risks. Because the patents can be held by companies or organisations, it is possible for the patent owner to charge doctors thousands of dollars for each diagnostic test.

The authors pointed out that in their studies, while engaged in research, it is common to come across a gene that’s patented “almost every day”. Their paper promises to examine how genes may have been impacted by held patents, and the extent of intellectual property on the genome. Gene patents can also relate between different species – for example, a company may have a patent for breeding cows that also covers a large percentage of human genes. They cited one company that owns 84 percent of all human genes because of a patent for cow breeding.

“There is a real controversy regarding gene ownership due to the overlap of many competing patent claims. It is unclear who really owns the rights to any gene,” Dr Rosenfeld said. “Do we need to go through every gene to look at who made the first claim to that gene, even if only one small part? If we resort to this rule, then the first patents to be granted for any DNA will have a vast claim over portions of the human genome.”

Lead author Dr Mason insisted he is pro-patent, but believes people “should not be able to patent a product of nature”.

“I believe that individals have an innate right to their own genome,” he said. 

Other related articles on Genomics and Ethics on this Open Access Online Scientific Journal include the following:

Aviva Lev-Ari, PhD, RN

20.2 Understanding the Role of Personalized Medicine

Larry H Bernstein, MD, FACP

20.3 Attitudes of Patients about Personalized Medicine

Larry H Bernstein, MD, FACP

20.4  Genome Sequencing of the Healthy

Larry H. Bernstein, MD, FACP and Aviva Lev-Ari, PhD, RN

20.5   Genomics in Medicine – Tomorrow’s Promise

Larry H. Bernstein, MD, FACP

20.6  The Promise of Personalized Medicine

Larry H. Bernstein, MD, FACP

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Curators: Aviva Lev-Ari, PhD, RN and Larry Bernstein, MD, FACP

The essence of the message is summarized by Larry Bernstein, MD, FACP, as follows:

[1] we employ a massively parallel reporter assay (MPRA) to measure the transcriptional levels induced by 145bp DNA segments centered on evolutionarily-conserved regulatory motif instances and found in enhancer chromatin states
[2] We find statistically robust evidence that (1) scrambling, removing, or disrupting the predicted activator motifs abolishes enhancer function, while silent or motif-improving changes maintain enhancer activity; (2) evolutionary conservation, nucleosome exclusion, binding of other factors, and strength of the motif match are all associated with wild-type enhancer activity; (3) scrambling repressor motifs leads to aberrant reporter expression in cell lines where the enhancers are usually not active.
[3] Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale experimental manipulation, and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to generate and test predictive models of gene expression.

Manolis Kellis and co-authors from the Massachusetts Institute of Technology and the Broad Institute describe a massively parallel reporter assay that they used to systematically study regulatory motifs falling within thousands of predicted enhancer sequences in the human genome. Using this assay, they examined 2,104 potential enhancers in two human cell lines, along with another 3,314 engineered enhancer variants. “Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale experimental manipulation,” they write, “and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to generate and test predictive models of gene expression.”


Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay

  1. Pouya Kheradpour1,
  2. Jason Ernst1,
  3. Alexandre Melnikov2,
  4. Peter Rogov2,
  5. Li Wang2,
  6. Xiaolan Zhang2,
  7. Jessica Alston2,
  8. Tarjei S Mikkelsen2 and
  9. Manolis Kellis1,3

+Author Affiliations

  1. 1 MIT;

  2. 2 Broad Institute
  1. * Corresponding author; email:


Genome-wide chromatin maps have permitted the systematic mapping of putative regulatory elements across multiple human cell types, revealing tens of thousands of candidate distal enhancer regions. However, until recently, their experimental dissection by directed regulatory motif disruption has remained unfeasible at the genome scale, due to the technological lag in large-scale DNA synthesis. Here, we employ a massively parallel reporter assay (MPRA) to measure the transcriptional levels induced by 145bp DNA segments centered on evolutionarily-conserved regulatory motif instances and found in enhancer chromatin states. We select five predicted activators (HNF1, HNF4, FOXA, GATA, NFE2L2) and two predicted repressors (GFI1, ZFP161) and measure reporter expression in erythroleukemia (K562) and liver carcinoma (HepG2) cell lines. We test 2,104 wild-type sequences and an additional 3,314 engineered enhancer variants containing targeted motif disruptions, each using 10 barcode tags in two cell lines and 2 replicates. The resulting data strongly confirm the enhancer activity and cell type specificity of enhancer chromatin states, the ability of 145bp segments to recapitulate both, the necessary role of regulatory motifs in enhancer function, and the complementary roles of activator and repressor motifs. We find statistically robust evidence that (1) scrambling, removing, or disrupting the predicted activator motifs abolishes enhancer function, while silent or motif-improving changes maintain enhancer activity; (2) evolutionary conservation, nucleosome exclusion, binding of other factors, and strength of the motif match are all associated with wild-type enhancer activity; (3) scrambling repressor motifs leads to aberrant reporter expression in cell lines where the enhancers are usually not active. Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale experimental manipulation, and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to generate and test predictive models of gene expression.

  • Received June 26, 2012.
  • Accepted March 14, 2013.

This manuscript is Open Access.

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at


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Gene Sequencing – to the Bedside

Reporter: Larry H Bernstein, MD, FCAP

Gene sequencing leaves the laboratory

Maturing technology speeds medical diagnoses.
Erika Check Hayden  19 February 2013
The steep fall in the cost of sequencing a genome has, for the moment, slowed. Yet researchers attending this year’s Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida, on 20–23 February are not complaining. At a cost as low as US$5,000–10,000 per human genome, sequencing has become cheap and reliable enough that researchers are not waiting for the next sequencing machine to perfect new applications in medicine.
Single-cell genomics is allowing fertility clinics to screen embryos for abnormalities more cheaply.
Human genome to genes

Human genome to genes (Photo credit: Wikipedia)

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CRACKING THE CODE OF HUMAN LIFE: Milestones along the Way – Part IIA

Curator: Larry H Bernstein, MD, FCAP

Introduction and purpose

This material goes beyond the Initiation Phase of Molecular Biology, Part I.
Part II reviews the Human Genome Project and the decade beyond.

In a three part series:
Part IIA.  CRACKING THE CODE OF HUMAN LIFE: Milestones along the Way
Part IIB.  CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics & Computational Genomics
Part IIC.  CRACKING THE CODE OF HUMAN LIFE: Recent Advances in Genomic Analysis and Disease

Part III will conclude with Ubiquitin, it’s Role in Signaling and Regulatory Control.
Part I reviewed the huge expansion of the biological research enterprise after the Second World War. It concentrated on the

  • discovery of cellular structures,
  • metabolic function, and
  • creation of a new science of Molecular Biology.

Part II follows the race to delineation of the Human Genome, discovery methods and fundamental genomic patterns that are ancient in both animal and plant speciation. But it explores both the complexity and the systems view of the architecture that underlies and understanding of the genome.

These articles review a web-like connectivity between inter-connected scientific discoveries, as significant findings have led to novel hypotheses and many expectations over the last 75 years. This largely post WWII revolution has driven our understanding of biological and medical processes at an exponential pace owing to successive discoveries of

  • chemical structure,
  • the basic building blocks of DNA  and proteins,
  • nucleotide and protein-protein interactions,
  • protein folding, allostericity,
  • genomic structure,
  • DNA replication,
  • nuclear polyribosome interaction, and
  • metabolic control.

In addition, the emergence of methods for

  • copying,
  • removal,
  • insertion,
  • improvements in structural analysis
  • developments in applied mathematics that have transformed the research framework.

Part IIA:


Milestones along the Way

A NOVA interview with Francis Collins (NHGRI) (FC), J. Craig Venter (CELERA)(JCV), and Eric Lander (EL).
RK: For the past ten years, scientists all over the world have been painstakingly trying to read the tiny instructions buried inside our DNA. And now, finally, the “Human Genome” has been decoded.
EL: The genome is a storybook that’s been edited for a couple billion years.
The following will address the odd similarity of genes between man and yeast

EL: In the nucleus of your cell the DNA molecule resides that is about 10 angstroms wide curled up, but the amount of curling is limited by the negative charges that repel one another, but there are folds upon folds. If the DNA is stretched the length of the DNA would be thousands of feet.
EL: We have known for 2000 years that your kids look a lot like you. Well it’s because you must pass them instructions that give them the eyes, the hair color, and the nose shape they have. RK: Cracking the code of those minuscule differences in DNA that influence health and illness is what the Human Genome Project is all about. Since 1990, scientists all over the world have been involved in the effort to read all three billion As, Ts, Gs, and Cs of human DNA.  It took 10 years to find the one genetic mistake that causes cystic fibrosis. Another 10 years to find the gene for Huntington’s disease. Fifteen years to find one of the genes that increase the risk for breast cancer. One letter at a time, painfully slowly…     And then came the revolution. In the last ten years the entire process has been computerized. The computations can do a thousand every second and that has made all the difference. EL: This is basically a parts list with a lot of parts. If you take an airplane, a Boeing 777, I think it has like 100,000 parts. If I gave you a parts list for the Boeing 777 in one sense you’d know 100,000 components, screws and wires and rudders and things like that.  But you wouldn’t know how to put it together, or why it flies. We now have a parts list, and that’s not enough to understand why it flies.

The Human Genome

The Human Genome (Photo credit: dullhunk)

A Quest For Clarity

Tracy Vence is a senior editor of Genome Technology
Tracy Vence @GenomeTechMag
Projects supported by the US National Institutes of Health will have produced 68,000 total human genomes — around 18,000 of those whole human genomes — through the end of this year, National Human Genome Research Institute estimates indicate. And in his book, The Creative Destruction of Medicine, the Scripps Research Institute’s Eric Topol projects that 1 million human genomes will have been sequenced by 2013 and 5 million by 2014.
Daniel MacArthur, a group leader in Massachusetts General Hospital’s Analytic and Translational Genetics Unit estimates that “From a capacity perspective … millions of genomes are not that far off. If you look at the rate that we’re scaling, we can certainly achieve that.”    The prospect of so many genomes has brought clinical interpretation into focus. But there is an important distinction to be made between the interpretation of an apparently healthy person’s genome and that of an individual who is already affected by a disease.
In an April Science Translational Medicine paper, Johns Hopkins University School of Medicine‘s Nicholas Roberts and his colleagues reported that personal genome sequences for healthy monozygotic twin pairs are not predictive of significant risk for 24 different diseases in those individuals. The researchers concluded that whole-genome sequencing was not likely to be clinically useful. Ambiguities have clouded even the most targeted interpretation efforts.

  • Technological challenges,
  • meager sample sizes,
  • a need for increased,
  • fail-safe automation and most important
  • a lack of community-wide standards for the task.

have hampered researchers’ attempts to reliably interpret the clinical significance of genomic variation.

How signals from the cell surface affect transcription of genes in the nucleus.

James Darnell, Jr., MD, Astor Professor, Rockefeller
After graduation from Washington University School of Medicine he worked with Francois Jacob at the Pasteur Institute in Paris and served as Vice President for Academic Affairs at Rockefeller in 1990-91. He is the coauthor with S.E. Luria of General Virology and the founding author with Harvey Lodish and David Baltimore of Molecular Cell Biology, now in its sixth edition. His book RNA, Life’s Indispensable Molecule was published in July 2011 by Cold Spring Harbor Laboratory Press. A member of the National Academy of Sciences since 1973, recipient of  numerous awards, including the 2003 National Medal of Science, the 2002 Albert Lasker Award.
Using interferon as a model cytokine, the Darnell group discovered that cell transcription was quickly changed by binding of cytokines to the cell surface. The bound interferon led to the tyrosine phosphorylation of latent cytoplasmic proteins now called STATs (signal transducers and activators of transcription) that dimerize by

  • reciprocal phosphotyrosine-SH2 interchange.
  • accumulate in the nucleus,
  • bind DNA and drive transcription.

This pathway has proved to be of wide importance with seven STATs now known in mammals that take part in a wide variety of developmental and homeostatic events in all multicellular animals. Crystallographic analysis defined functional domains in the STATs, and current attention is focused on two areas:

  • how the STATs complete their cycle of  activation and inactivation, which requires regulated tyrosine dephosphorylation; and how
  • persistent activation of STAT3 that occurs in a high proportion of many human cancers contributes to blocking apoptosis in cancer cells.

Current efforts are devoted to inhibiting STAT3 with modified peptides that can enter cells.

Cell cycle regulation and the cellular response to genotoxic stress

Stephen J Elledge, PhD, Gregor Mendel Professor of Genetics and Medicine, Investigator, Howard Hughes Medical Institute, Harvard Medical School
As a postdoctoral fellow at Stanford working on eukaryotic homologous recombination, he serendipitously found a family of genes known as ribonucleotide reductases. He subsequently showed that

  • these genes are activated by DNA damage and
  • could serve as tools to help scientists dissect the signaling pathways
  • through which cells sense and respond to DNA damage and replication stress.

At Baylor College of Medicine he made a second major breakthrough with the discovery of the cyclin-dependent kinase 2 gene (Cdk2), which

  • controls the G1-to-S cell cycle transition,
  • an entry checkpoint for the cell proliferation cycle and
  • a critical regulatory step in tumorigenesis.

From there, using a novel “two-hybrid” cloning method he developed, Elledge and Wade Harper, PhD, proceeded to

  • isolate several members of the Cdk2-inhibitory family.

Their discoveries included the p21 and p57 genes, mutations in the latter (responsible for Beckwith-Wiedemann syndrome), characterized by somatic overgrowth and increased cancer risk. Elledge is also recognized for his work in understanding

  • proteome remodeling through ubiquitin-mediated proteolysis.
  • they identified F-box proteins that regulate protein degradation in the cell by
  1. binding to specific target protein sequences and then
  2. marking them with ubiquitin for destruction by the cell’s proteasome machinery.

This breakthrough resulted in

  • the elucidation of the cullin ubiquitin ligase family,
  • which controls regulated protein stability in eukaryotes.

nature10774-f5.2  nature10774-f3.2   ubiquitin structures  Rn1  Rn2

Elledge’s recent research has focused on the cellular mechanisms underlying DNA damage detection and cancer using genetic technologies. In collaboration with Cold Spring Harbor Laboratory researcher Gregory Hannon, PhD, Elledge has generated complete human and mouse short hairpin RNA (shRNA) libraries for genome-wide loss-of-function studies. Their efforts have led to

  • the identification of a number of tumor suppressor proteins
  • genes upon which cancer cells uniquely depend for survival.

This work led to the development of the “non-oncogene addiction” concept. This is noted as follows:

  • proteome remodeling through ubiquitin-mediated proteolysis
  • F-box proteins regulate protein degradation in the cell by binding to specific target protein sequences
  • and then marking them with ubiquitin for destruction by the cell’s proteasome machinery
  • elucidation of the cullin ubiquitin ligase family, which controls regulated protein stability in eukaryotes

Playing the dual roles of inventor and investigator, Elledge developed original techniques to define

  • what drives the cell cycle and
  • how cells respond to DNA damage.

By using these tools, he and his colleagues have identified multiple genes involved in cell-cycle regulation.

Elledge’s work has earned him many awards, including a 2001 Paul Marks Prize for Cancer Research and a 2003 election to the National Academy of Sciences. In his Inaugural Article (1), published in this issue of PNAS, Elledge and his colleagues describe the function of Fbw7, a protein involved in controlling cell proliferation (see below). Elledge studied the error-prone DNA repair mechanism in E-Coli (Escherichia coli) called SOS mutagenesis for his PhD thesis at MIT. His work identified  and described

  • the regulation of a group of enzymes now known as error-prone polymerases,
  • the first members of which were the umuCD genes in E. coli.

It was then that he developed a new cloning tool. Elledge invented a technique that allowed him to approach future cloning problems of this type with great rapidity. With the new technique, “you could make large libraries in lambda that behave like plasmids. We called them `phasmid’ vectors, like plasmid and phage together”. The phasmid cloning method was an early cornerstone for molecular biology research.

Elledge began working on homologous recombination in postdoctoral fellowship at Stanford University, an important niche in the field of eukaryotic genetics. Working with the yeast genome, Elledge searched for rec A, a gene that allows DNA to recombine homologously. Although he never located rec A, he discovered a family of genes known as ribonucleotide reductases (RNRs), which are involved in DNA production. Rec A and RNRs share the same last 4 amino acids, which caused an antibody crossreaction in one of Elledge’s experiments. Initially disappointed with the false positives in his hunt for rec A, Elledge was later delighted with his luck. He found that

  • RNRs are turned  on by DNA damage, and
  • these genes are regulated by the cell cycle.

Prior to leaving Stanford, Elledge attended a talk at the University of California, San Francisco, by Paul Nurse, a leader in cell-cycle research who would later win the 2001 Nobel Prize in medicine. Nurse described his success in isolating the homolog of a key human cell-cycle kinase gene, Cdc2, by using a mutant strain of yeast (8). Although Nurse’s methods were primitive, Elledge was struck by the message he carried: that

  • cell-cycle regulation was functionally conserved, and
  • many human genes could be isolated by looking for complimentary genes in yeast.

Elledge then took advantage of his past successes in building phasmid vectors to build a versatile human cDNA library that could be expressed in yeast. After setting up a laboratory at Baylor, he introduced this library into yeast, screening for complimentary cell-cycle genes.  He quickly identified the same Cdc2 gene isolated by Nurse. However, Elledge also discovered a related gene known as Cdk2. Elledge subsequently found that

  • Cdk2 controlled the G1 to S cell-cycle transition, a step that often goes awry in cancer. These results were published in the EMBO Journal in 1991.

He then continued to use

  • RNRs to perform genetic screens to
  • identify genes involved in sensing and responding to DNA damage.

He subsequently worked out the

  • signal transduction pathways in both yeast and humans that recognize damaged DNA and replication problems.

These “checkpoint” pathways are central to the

  • prevention of genomic instability and a key to understanding tumorigenesis.

This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on April 29, 2003.

Defective cardiovascular development and elevated cyclin E and Notch proteins in mice lacking the Fbw7 F-box protein.

Tetzlaff MT, Yu W, Li M, Zhang P, Finegold M, Mahon K , Harper JW, Schwartz RJ, and SJ Elledge. PNAS 2004; 101(10): 3338-3345. cgi doi 10.1073.  pnas.0307875101

The mammalian F-box protein Fbw7 and its Caenorhabditis elegans counterpart Sel-10 have been implicated in

  • the ubiquitin-mediated turnover of cyclin E
  • as well as the Notch Lin-12 family of transcriptional activators. Both unregulated
  1. Notch and cyclin E
  2. promote tumorigenesis, and
  3. inactivate mutations in human

Fbw7 studies suggest that it may be a tumor suppressor. To generate an in vivo system to assess the consequences of such unregulated signaling, we generated mice deficient for Fbw7.  Fbw7-null mice die around 10.5 days post coitus because of a combination of deficiencies in hematopoietic and vascular development and heart chamber mutations. The absence of Fbw7 results in elevated levels of cyclin E, concurrent with inappropriate DNA replication in placental giant trophoblast cells. Moreover, the levels of both Notch 1 and Notch 4 intracellular domains were elevated, leading to stimulation of downstream transcriptional pathways involving Hes1, Herp1, and Herp2. These data suggest essential functions for Fbw7 in controlling cyclin E and Notch signaling pathways in the mouse.

Science as an Adventure


Prof. Avram Hershko – Science as an Adventure
Prof. Avram Hershko shared the 2004 Nobel Prize in Chemistry with Aaron Ciechanover and Irwin Rose for “for the discovery of ubiquitin-mediated protein degradation.”

Gene Switches

Nipam Patel is a professor in the Departments of Molecular and Cell Biology and Integrative Biology at UC Berkeley and runs a research laboratory that studies the role, during embryonic development, of homeotic genes (the genetic switches described in this feature). “Ghost in Your Genes” focuses on epigenetic “switches” that turn genes “on” or “off.” But not all switches are epigenetic; some are genetic. That is, other genes within the chromosome turn genes on or off. In an animal’s embryonic stage, these gene switches play a predominant role in laying out the animal’s basic body plan and perform other early functions;

  • the epigenome begins to take over during the later stages of embryogenesis.

Beginning as a fertilized single egg that egg becomes many different kinds of cells.  Altogether, multicellular organisms like humans have thousands of differentiated cells. Each is optimized for use in the brain, the liver, the skin, and so on. Remarkably, the DNA inside all these cells is exactly the same. What makes the cells differ from one another is that different genes in that DNA are either turned on or off in each type of cell.

Take a typical cell, such as a red blood cell. Each gene within that cell has a coding region that encodes the information used to make a particular protein. (Hemoglobin shuttles oxygen to the tissues and carbon dioxide back out to the lungs—or gills, if you’re a fish.) But another region of the gene, called “regulatory DNA,” determines whether and when the gene will be expressed, or turned on, in a particular kind of cell. This precise transcribing of genes is handled by proteins known as transcription factors, which bind to the regulatory DNA, thereby generating instructions for the coding region.

One important class of transcription factors is encoded by the so called homeotic, or Hox, genes. Found in all animals, Hox genes act to “regionalize” the body along the embryo’s anterior-to-posterior (head-to-tail) axis. In a fruit fly, for example, Hox genes lay out the various main body segments—the head, thorax, and abdomen. Amazingly, all animals, from fruit flies to mice to people, rely on the same basic Hox-gene complex. Using different-colored antibody stains, we can see exactly where and to what degree Hox genes are expressed. Each Hox gene is expressed in a specific region along the anterior-to-posterior axis of the embryo.

A fly’s body has three main divisions: head, thorax, and abdomen. We’ll focus on the thorax, which itself has three main segments. In a normal adult fly, the second thoracic segment features a pair of wings, while the third thoracic segment has a pair of small, balloon-shaped structures called halteres. A modified second wing, the haltere serves as a flight stabilizer. In order for the pair of wings and the pair of halteres (as well as all other parts of the fly) to develop properly, the fly’s suite of

  • Hox genes must be expressed in a precise way and at precise times.

During development, the fly’s two wings grow from a structure in the larva known as the wing imaginal disk. (An imago is an insect in its final, adult state.) The haltere grows from the larval haltere imaginal disk. Remember the Ubx Hox gene? Using staining again, we can detect the gene product of Ubx. This reveals that

  • the Ubx gene is naturally “off” in the wing disk—
  • and is “on” in the haltere disk.
  • Now you’ll see what happens when the Ubx gene—just one of a large number of Hox genes—is turned off in the haltere disk. What if a genetic mutation caused the Ubx gene to be turned off, during the larval stage, in the third thoracic segment, the segment that normally produces the haltere? Instead of a pair of halteres, the fly has a second set of wings. With the switch of that single Hox gene, Ubx, from on to off, the third thoracic segment becomes an additional second thoracic segment and the pair of halteres became a second pair of wings. This illustrates the remarkable ability of transcription factors like Ubx to control patterning as well as cell type during development.


A. Data Suggests “Gene” Redefinition

As part of a huge collaborative effort called ENCODE (Encyclopedia of DNA Elements), a research team led by Cold Spring Harbor Laboratory (CSHL) Professor Thomas Gingeras, PhD, publishes a genome-wide analysis of RNA messages, called transcripts, produced within human cells.
Their analysis—one component of a massive release of research results by ENCODE teams from 32 institutes in 5 countries, with 30 papers appearing in 3 different high-level scientific journals—shows that three-quarters of the genome is capable of being transcribed.  This indicates that nearly all of our genome is dynamic and active.  It stands in marked contrast to consensus views prior to ENCODE’s comprehensive research efforts, which suggested that

  • only the small protein-encoding fraction of the genome was transcribed.

The vast amount of data generated with advanced technologies by Gingeras’ group and others in the ENCODE project changes the prevailing understanding of what defines a gene. The current outstanding question concerns

  • the nature and range of those functions.  It is thought that these
  • “non-coding” RNA transcripts act something like components of a giant, complex switchboard, controlling a network of  many events in the cell by
  1. regulating the processes of
  2. replication,
  3. transcription
  4. and translation

– that is, the copying of DNA and the making of proteins is based on information carried by messenger RNAs.  With the understanding that so much of our DNA can be transcribed into RNA comes the realization that there is much less space between what we previously thought of as genes, Gingeras points out.

The full ENCODE Consortium data sets can be freely accessed through

  • the ENCODE project portal as well as at the University of California at Santa Cruz genome browser,
  • the National Center for Biotechnology Information, and
  • the European Bioinformatics Institute.

Topic threads that run through several different papers can be explored via the ENCODE microsite page at    Date: September 5, 2012   Source: Cold Spring Harbor Laboratory

1000 Genomes Project Team Reports on Variation Patterns

(from Phase I Data) October 31, 2012 GenomeWeb

In a study appearing online today in Nature, members of the 1000 Genomes Project Consortium presented an integrated haplotype map representing the genomic variation present in more than 1,000 individuals from 14 human populations.  Using data on 1,092 individuals tested by

  • low-coverage whole-genome sequencing,
  • deep exome sequencing, and/or
  • dense genotyping,

the team looked at the nature and extent of the rare and common variation present in the genomes of individuals within these populations. In addition to population-specific differences in common variant profiles, for example, the researchers found distinct rare variant patterns within populations from different parts of the world — information that is expected to be important in interpreting future disease studies. They also encountered a surprising number of the variants that are expected to impact gene function, such as

  • non-synonymous changes,
  • loss-of-function variants, and, in some cases,
  • potentially damaging mutations.

ENCODE was designed to pick up where the Human Genome Project left off.
Although that massive effort revealed the blue­print of human biology, it quickly became clear that the instruction manual for reading the blueprint was sketchy at best. Researchers could identify in its 3 billion letters many of the regions that code for proteins, but they make up little more than 1% of the genome, contained in around 20,000 genes. ENCODE, which started in 2003, is a massive data-collection effort designed to catalogue the

  • ‘functional’ DNA sequences,
  • learn when and in which cells they are active and
  • trace their effects on how the genome is
  1. packaged,
  2. regulated and
  3. read.

After an initial pilot phase, ENCODE scientists started applying their methods to the entire genome in 2007. That phase came to a close with the publication of 30 papers, in Nature, Genome Research and Genome Biology. The consortium has assigned some sort of function to roughly 80% of the genome, including

  • more than 70,000 ‘promoter’ regions — the sites, just upstream of genes, where proteins bind to control gene expression —
  • and nearly 400,000 ‘enhancer’ regions that regulate expression of  distant genes (see page 57)1. But the job is far from done.

Junk DNA? What Junk DNA?

New data reveals that at least 80% of the human genome encodes elements that have some sort of biological function. [© Gernot Krautberger –] Far from containing vast amounts of junk DNA between its protein-coding genes, at least 80% of the human genome encodes elements that have some sort of biological function, according to newly released data from the Encyclopedia of DNA Elements (Encode) project, a five-year initiative that aims to delineate all functional elements within human DNA. The massive international project, data from which are published in 30 different papers in Nature, Genome Research, Genome Biology, the Journal of Biological Chemistry, Science, and Cell, has identified four million gene switches, effectively

  • regulatory regions in the genome where
  • proteins interact with the DNA to control gene expression.

Overall, the Encode data define regulatory switches that are scattered all over the three billion nucleotides of the genome. In fact, the data suggests,

  • the regions that lie between gene-coding sequences contain a wealth of previously unrecognized functional elements,Including
  • nonprotein-coding RNA transcribed sequences,
  • transcription factor binding sites,
  • chromatin structural elements, and
  • DNA methylation sites.

The combined results suggest that 95% of the genome lies within 8 kb of a DNA-protein interaction, and 99% lies within 1.7 kb of at least one of the biochemical events, the researchers say. Importantly, given the complex three-dimensional nature of DNA, it’s also apparent that

  • a regulatory element for one gene may be located quite some ‘linear’ distance from the gene itself.

“The information processing and the intelligence of the genome reside in the regulatory elements,” explains Jim Kent, director of the University of California, Santa Cruz Genome Browser project and head of the Encode Data Coordination Center. “With this project, we probably went from understanding less than 5% to now around 75% of them.”
The ENCODE results also identified SNPs within regulatory regions that are associated with a range of diseases, providing new insights into the roles that

  • noncoding DNA plays in disease development.

“As much as nine out of 10 times, disease-linked genetic variants are not in protein-coding regions,” comments Mike Pazin, Encode program director at the National Human Genome Research Institute.  “Far from being junk DNA, this regulatory DNA clearly makes important contributions to human disease.”

Other Related Articles on this Open Access Online Scientific Journal, include the following: 

Big Data in Genomic Medicine LHB

BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair S Saha

Computational Genomics Center: New Unification of Computational Technologies at Stanford A Lev-Ari

Personalized medicine gearing up to tackle cancer ritu saxena

Differentiation Therapy – Epigenetics Tackles Solid Tumors sj Williams

Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment A Lev-Ari

The Molecular pathology of Breast Cancer Progression tilde barliya`

Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1 ( A Lev-Ari

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2 A Lev-Ari

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3 A Lev-Ari

Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ ALA Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders/

GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico effect of the inhibitor in its “virtual clinical trial” A Lev-Ari

Recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes in serous endometrial tumors S Saha

Personalized medicine-based cure for cancer might not be far away ritu saxena

Human Variome Project: encyclopedic catalog of sequence variants indexed to the human genome sequence A Lev-Ari

Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition sjwilliams

Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics A Lev-Ari

The “Cancer establishments” examined by James Watson, co-discoverer of DNA w/Crick, 4/1953 A Lev-Ari

Directions for genomics in personalized medicine lhb

How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis. SJwilliams

Mitochondria: More than just the “powerhouse of the cell” eritu saxena

Mitochondrial fission and fusion: potential therapeutic targets? Ritu saxena

Mitochondrial mutation analysis might be “1-step” away ritu saxena

mRNA interference with cancer expression lhb

Expanding the Genetic Alphabet and linking the genome to the metabolome LHB

Breast Cancer, drug resistance, and biopharmaceutical targets lhb

Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression Analysis A Lev-Ari

Gastric Cancer: Whole-genome reconstruction and mutational signatures A Lev-Ari

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis lhb

Genomic Analysis: FLUIDIGM Technology in the Life Science and Agricultural Biotechnology A Lev-Ari

Reveals from ENCODE project will invite high synergistic collaborations to discover specific targets A. Sarkar

ENCODE: the key to unlocking the secrets of complex genetic diseases R. Saxena

Impact of evolutionary selection on functional regions: The imprint of evolutionary selection on ENCODE regulatory elements is manifested between species and within human populations s Saha

ENCODE Findings as Consortium A Lev-Ari

Genomics Orientations for Personalized Medicine SJH, ALA, LHB

2013 Genomics: The Era Beyond the Sequencing of the Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

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