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Archive for the ‘Genomic Testing: Methodology for Diagnosis’ Category


scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

 

Present day technological advances have facilitated unprecedented opportunities for studying biological systems at single-cell level resolution. For example, single-cell RNA sequencing (scRNA-seq) enables the measurement of transcriptomic information of thousands of individual cells in one experiment. Analyses of such data provide information that was not accessible using bulk sequencing, which can only assess average properties of cell populations. Single-cell measurements, however, can capture the heterogeneity of a population of cells. In particular, single-cell studies allow for the identification of novel cell types, states, and dynamics.

 

One of the most prominent uses of the scRNA-seq technology is the identification of subpopulations of cells present in a sample and comparing such subpopulations across samples. Such information is crucial for understanding the heterogeneity of cells in a sample and for comparative analysis of samples from different conditions, tissues, and species. A frequently used approach is to cluster every dataset separately, inspect marker genes for each cluster, and compare these clusters in an attempt to determine which cell types were shared between samples. This approach, however, relies on the existence of predefined or clearly identifiable marker genes and their consistent measurement across subpopulations.

 

Although the aligned data can then be clustered to reveal subpopulations and their correspondence, solving the subpopulation-mapping problem by performing global alignment first and clustering second overlooks the original information about subpopulations existing in each experiment. In contrast, an approach addressing this problem directly might represent a more suitable solution. So, keeping this in mind the researchers developed a computational method, single-cell subpopulations comparison (scPopCorn), that allows for comparative analysis of two or more single-cell populations.

 

The performance of scPopCorn was tested in three distinct settings. First, its potential was demonstrated in identifying and aligning subpopulations from single-cell data from human and mouse pancreatic single-cell data. Next, scPopCorn was applied to the task of aligning biological replicates of mouse kidney single-cell data. scPopCorn achieved the best performance over the previously published tools. Finally, it was applied to compare populations of cells from cancer and healthy brain tissues, revealing the relation of neoplastic cells to neural cells and astrocytes. Consequently, as a result of this integrative approach, scPopCorn provides a powerful tool for comparative analysis of single-cell populations.

 

This scPopCorn is basically a computational method for the identification of subpopulations of cells present within individual single-cell experiments and mapping of these subpopulations across these experiments. Different from other approaches, scPopCorn performs the tasks of population identification and mapping simultaneously by optimizing a function that combines both objectives. When applied to complex biological data, scPopCorn outperforms previous methods. However, it should be kept in mind that scPopCorn assumes the input single-cell data to consist of separable subpopulations and it is not designed to perform a comparative analysis of single cell trajectories datasets that do not fulfill this constraint.

 

Several innovations developed in this work contributed to the performance of scPopCorn. First, unifying the above-mentioned tasks into a single problem statement allowed for integrating the signal from different experiments while identifying subpopulations within each experiment. Such an incorporation aids the reduction of biological and experimental noise. The researchers believe that the ideas introduced in scPopCorn not only enabled the design of a highly accurate identification of subpopulations and mapping approach, but can also provide a stepping stone for other tools to interrogate the relationships between single cell experiments.

 

References:

 

https://www.sciencedirect.com/science/article/pii/S2405471219301887

 

https://www.tandfonline.com/doi/abs/10.1080/23307706.2017.1397554

 

https://ieeexplore.ieee.org/abstract/document/4031383

 

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0927-y

 

https://www.sciencedirect.com/science/article/pii/S2405471216302666

 

 

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First Cost-Effectiveness Study of Multi-Gene Panel Sequencing in Advanced Non-Small Cell Lung Cancer Shows Moderate Cost-Effectiveness, Exposes Crucial Practice Gap

WASHINGTON (June 27, 2019) — The results of the first economic modeling study to estimate the cost-effectiveness of “multi-gene panel sequencing” (MGPS) as compared to standard-of-care, single-gene tests for patients with advanced non-small cell lung cancer (aNSCLC) show that the MGPS tests are moderately cost-effective but could deliver more value if patients with test results identifying actionable genetic mutations consistently received genetically guided treatments. The results of the study, which was commissioned by the Personalized Medicine Coalition (PMC), underline the need to align clinical practices with an era of personalized medicine in which physicians can use diagnostic tests to identify specific biological markers that inform targeted prevention and treatment plans.

The study, which was published yesterday in JCO Clinical Cancer Informatics, analyzed the clinical and economic value of using MGPS testing to identify patients with tumors that over-express genetic mutations that could be targeted by available therapies designed to inhibit the function of those genes — a mainstay of modern care for aNSCLC patients. Using data provided by Flatiron Health, researchers examined clinical and cost information associated with the care of 5,688 patients with aNSCLC treated between 2011 – 2016, separating them into cohorts who received MGPS tests that assess at least 30 genetic mutations at once and those who received only “single-marker genetic testing” (SMGT) of less than 30 genes.

Compared to SMGT, the MGPS testing strategy, including downstream treatment and monitoring of disease, incurred costs equal to $148,478 for each year of life that it facilitated, a level suggesting that MGPS is moderately cost-effective compared to commonly cited thresholds in the U.S., which range from $50,000 to $200,000 per life year (LY) gained.

The authors of the study point out, however, that physicians only prescribed a targeted therapy to some of the patients whose MGPS test results revealed actionable mutations. MGPS tests can only improve downstream patient outcomes if actionable results are used to put the patient on a targeted treatment regimen that is more effective than the therapy they would otherwise have been prescribed. It is therefore impossible for the cost of an MGPS test to translate into additional LYs if actionable results do not result in the selection of a targeted treatment regimen.

Although MGPS testing revealed actionable mutations in 30.1 percent of the patients in the study cohort, only 21.4 percent of patients who underwent MGPS testing received a targeted treatment.

The study’s authors calculated that if all MGPS-tested patients with actionable mutations had received a targeted therapy, MGPS testing would deliver measurably better value ($110,000 per LY gained).

“This research underlines the importance of ensuring that clinical practices keep pace with scientific progress in personalized medicine so that we can maximize the benefits of diagnostic tests that can improve patient care and make the health system more efficient by ensuring that safe and effective targeted therapies are prescribed to those patients who will benefit,” said PMC President Edward Abrahams.

The study’s authors include Dr. Lotte Steuten, Vice President and Head of Consulting, The Office of Health Economics, London, U.K., and Affiliate Associate Faculty Member, Hutchinson Institute for Cancer Outcomes Research, Fred Hutchinson Cancer Research Center; Dr. Bernardo Goulart, Associate Faculty Member, Hutchinson Institute for Cancer Outcomes Research, Fred Hutchinson Cancer Research Center; Dr. Neal Meropol, Vice President, Research Oncology, Flatiron Health; Dr. Daryl Pritchard, Senior Vice President, Science Policy, Personalized Medicine Coalition; and Dr. Scott Ramsey, Director, Hutchinson Institute for Cancer Outcomes Research, Fred Hutchinson Cancer Research Center.

###

About the Personalized Medicine Coalition:

The Personalized Medicine Coalition, representing innovators, scientists, patients, providers and payers, promotes the understanding and adoption of personalized medicine concepts, services and products to benefit patients and the health system. For more information, please visit www.personalizedmedicinecoalition.org.

SOURCE

From: Personalized Medicine Coalition <pmc@personalizedmedicinecoalition.org>

Reply-To: “Christopher Wells (PMC)” <cwells@personalizedmedicinecoalition.org>

Date: Thursday, June 27, 2019 at 9:32 AM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: First Cost-Effectiveness Study of MGPS in aNSCLC Shows Moderate Cost-Effectiveness, Exposes Crucial Practice Gap

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Tweets and Re-Tweets by @Pharma_BI ‏and @AVIVA1950 at 2019 Petrie-Flom Center Annual Conference: Consuming Genetics: Ethical and Legal Considerations of New Technologies, Friday, May 17, 2019 from 8:00 AM to 5:00 PM EDT @Harvard_Law

 

Tweets by @Pharma_BI ‏and @AVIVA1950

  1.   Retweeted

    AMAZING conference on Genomics and Ethics

  2. Amazing Conference LIVE 2019 Petrie-Flom Center Annual Conference: : and Considerations of New Technologies, Friday, May 17, 2019 from 8:00 AM to 5:00 PM EDT via

  3. Concluding remark cited by ⁦⁩ ⁦ Great Panel on the Impact of Genetic Information new conceptual approach prioritizing parental autonomy with restriction built in

  4. ⁩ ⁦ NIPT test for fetal sex blood type Trisonomy Whole Genome-wide analysis routinization of procedure READY at Birth impact intrafamilial discrimination babySeqProject G2P ⁦

  5. Leila Jamal, NIAID Pre- Test Genetic Counseling – information and testing need, indication for testing Post-Test Informational Burden low vs high: Likely pathogenic, Pathogenic benign – natural history data potentially high impact

  6. Leila Jamal, NIAID benefit the patient, positive autonomy, benefiesence – how potentially impactful is the Test Information Nondirectiveness – Why? distance from eugenics + abortion politics persons and patient autonomy

  7. Leila Jamal, NIAID Genetic and Genomics Testing: Prenata, Pediatric, Vancer, other: Cardiology, Neurology, Hematology, Infectious diseases, pharmaco genomics, DTC, Ancestry

  8. Emily Qian, Genetic Counselor, Veritas Genetics – Physician-Mediated Elective Whole Genome Sequencing Tests: Impacts on Informed Consent DTC Physician-initiated Genetic Testing Physician-initiated DTC Informed consent is a process

  9. ⁩ ⁦ Recommendation based on best evidence guidelines available

  10. Natalie RamGenetic Genealogy and the Problem of Familial Forensic Identification Familial Forensic Identification – Privacy for information held by Telephone companies Involuntarily Identification by genetic data genetic markers

  11. Natalie Ram, Assistant Professor of Law, University of Baltimore School of Law – Genetic Genealogy and the Problem of Familial Forensic Identification Opt in to share genetic data on the platforms opt in national DB

  12. Natalie Ram, Univ of Baltimore School of Law Genetic relatedness is stickier than social relations Voluntary sharing of genetic information – no other party can protect genetic information of any person, thu, if shared voluntarily

  13. ⁩ ⁦ gene APO-E e-2, e-3, e-4 If e-4 variant risk AD is 40% 23andMe since 2011 rest for e-4 unlock result # copies of e-4 are present little clinical value post diagnosis recommendation do not depend on e-4

  14. Jonathan Kahn, Precision Medicine and the Resurgence of Race in Genomic Medicineprecision medicine – classification of individuals into subpopulations that differ in their susceptability to a particular disease

  15. Kif Augustine-Adams, BYU Law School – Generational Failures of Law and Ethics: Rape, Mormon Orthodoxy, the Revelatory Power of Ancestry DNAComplex Sorrows: Anscestry DNA – 20 Millions records. Complete anonymity and privacy collapsed

  16. Regulating Consumer Genetic Technologies Conclusions: DTC policies are over the place, FDA poised to regulate Big Data, Human Genomics Somatic vs Germline are key distinctions NY Dept Health 3rd Party Certification in Genomics

  17. Scott Schweikart, Council on Ethical and Judicial Affairs, American Medical Association and Legal Editor, AMA Journal of Ethics – Human Gene Editing: An Ethical Analysis and Arguments for Regulatory Guidance National and Global Levels

  18. Catherine M. Sharkey, The Emerging Role of the FDA Genetic predisposition – BRCA I & II approved Testing Pharmaco-genetic Test authorization incorrect interpretation, incorrect action based on results False positive and False negative

  19. Scott Schweikart, AMA Ethical concernsTechnologiesCRISPR-Cas-9 Somatic vs GermlineAMA: Individual liberty (1) Autonomy & Gene Editing (2) Non-maleficence and Beneficence (3) Social Justice Treatment vs Enhancement National Regulations

  20. Patricia J. Zettler, Regulators can do: Promote self regulations vs restrict community labs Drugs: premarket approval by FDA 11/2017: any use of CRISPR is subjected to regulation Bio hacking materials are distributed outside channels

  21. Patricia J. Zettler, FDA agency – regulation can’t reach everything, Not seen wide range abuse, FDA encourage learning and information dissemination and Educate

  22. Maxwell J. Mehlman, Governing Non-Traditional Biology On-Line gene editing equipment CRISPR-Cas9 – IGEM – international Competition in community of Scientists Biological weapons – issues of Prior Art impeding patentability may come up

  23. Maxwell J. Mehlman Harm to subjects Biosafety Safety Phase I Gene drives in Human?? – Human gene editing: “Nanoparticle and liposomal delivery” and “Allelic drive using CRISPR”

  24. ⁩ ⁦ regulatory options: liabilities, legal requirements industry restrictions on access to material community labs, NTB IRBs self-governing bodies FBI surveillance

  25. Barbara J. Evans Is it FDA duty on Cosmetic enhancement Genome is Software, US is not good in regulating software The Harm Principle, Legal Paternalism benevolent vs non-benevolent Legal Moralism – no body is harmed but it’s just wrong

  26. Barbara J. Evans Multiple Agencies: In the 80’s on Future Products of Biotechnology: EPA, FDA, USDA, OSHA, CPSC, NIH, NEPA, ESA, APA Skepticism that compulsory regulation for compliance with norms

  27. Barbara J. Evans Regulatory Challenges Citizen Science and DIY Bio democratization of science and medicine narrative, new frontiers for institutional science narrative nostalgia narrative, political narrative: “hacker” portrayals

  28. in Preparing for Future Products of Biotechnology, NAS

  29. Seema Mohapatra, AAbolishing the Myth of “Anonymous” Gamete Donation in the Age of Direct-to-Consumer Genetic TestingAnonymous sperm donation Sell sperm $30 – $130 per sample – industry is thriving due to donor anonymity last 3 years,

  30. Seema Mohapatra, 2.6 million Ancestry DNA only to keep donor Anonymity Donor-Conceived Individuals at age 18 can identified the DonorLegal landscape ART – no federal laws regarding UT and WA [medical disclosure about the donor

  31. Nita Farahany, Professor Law, Philosophy Duke Law School need new Framework if anonymity is dead, most uses are diverted for medicinePrivacy is improving, ACA – protects from preexisting conditionsIndividual costs vs societal benefits

  32. Liza Vertinsky Courts: Pushing the boundaries: (1) Privacy (2) publicity rights (3) property (commodificationPresidential Figures: Infidelity gene, gambling geneLegal pathways Junk DNA Law enforcement databasesAlternative legal framing

  33. Kayte Spector-Bagdady, Data coming into Academia – Genetic data partnerships Academia (41% NIH funding) and Industry: Use of existing private data, company performs analysisPatients: using data and specimens in ways they do not wish

  34. Kayte Spector-Bagdady, to secondary research: stay anonymousPublic health covers Informed consent forms – conceptualize for secondary research protocols Transparency In BioBank Research 67% commercialization of biospecimens agree

  35. Property and Health Data: Excludability, Alienability and Divisibility, Valuation and compensation, Unstewarded and Orphan data, duration, tracking Propertization of medical information effect on biomedical research

  36. Genetic “Property” Statues: @CO – genetic information pertain to the individual health data – common law Personal Property vs Information as Property object

  37. direct consumer protection may get that by Claim of conversion – Common Law Genetic Testing companies are protected by three legal laws consumers as employees face genetic information been accessed by employers via Wellness Programs

  38. Courts shows a newfound openness to claims for genetic conversion claims will not stifle reaserch or create moral harms consumers genetics, claims for genetic conversion necessary to adequately protect people’s interests in their DNA

  39. ⁩ ⁦ three new regulations of ownership of genetic test information ownership even Dx of breast cancer Insurance may not cover BRCA testing

  40. ⁩ ⁦ employment law and genetic testing property ownership

  41. Family not in treatment relationship with the Researcher – Court rejected the claim family donated to research unfair benefir of the Hospital from the data and tissue donatedClaim of conversion – Common LawGene by Gene Family Tree DNA

  42. Insurance may or may not cover BRCA testing Law suit on that matter is pending

  43. Life insurance company initiated genetic testing: (a) Gatekeeping policy underwriting new comer applicants (b) Wellness Employer wellness programs incentivize healthy behavior Incorporate genetic testing into wellness Programs Testing

  44. wellness Programs Test for preventing genetic conditions Like BRCA, Lynch syndrome, preventable – win/win proposition –>>> Healthier employees. Studies show shift of cost from employer to employee and employer have access to genetic i

 

 

RE-TWEETS

 

  1.   Retweeted

    Max Mehlman thinks “DIYBio” is problematic b/c often team efforts; “biohacking” has negative connotations. Suggests “non-traditional biology.”

  2.   Retweeted

    In reviewing how reviewed various tests, Catherine Sharkey discusses how some were reviewed through De Novo and others through 510(k) pathway and benefits and drawbacks of each.

  3.   Retweeted

    . invokes THE CONE OF SILENCE. NO MORE DATA FROM THIS TALK! Medical/scientific publishing norms are weird.

  4.   Retweeted

    A very full house today (480 people registered!) for the Consuming Genetics conference . opening a day that promises to be fascinating. Kudos also for selecting hot topics and amazing speakers.

  5.   Retweeted

    Talking about her ⁦team’s ⁩ paper ⁦⁩ shows most patients want notification of commercial use of biospecimens, most are uncomfortable about profit from biospecimens, but feel better if reinvested in research.

  6.   Retweeted

    You don’t have to identify as a biohacker to understand their goals, interests, and culture.

  7.   Retweeted

    Blog post about about my upcoming presentation at Petrie-Flom Center’s upcoming Consumer Genetics conference this Friday, May 17.

  8.   Retweeted

    Incredibly difficult topic.

  9.   Retweeted

    I asked Maxwell Mehlman how he envisioned biohackers could form an IRB-style review process. One suggestion was to engage with insitutional IRBs. Raise your hand if you think an establishment IRB would approve enhancement experiments? (I don’t…)

  10.   Retweeted

    Gene editing has become cheaper, easier to do in community labs. Max Mehlman ⁦⁩ compares it to where Steve Jobs and Bill Gates began with the personal computer. But US gov has listed as a “weapon of mass destruction”

  11.   Retweeted

    Thanks to for hosting another great conference!

  12.   Retweeted

    “Diversity” means a LOT of different things–it’s very easy to slip back and forth (problematically) between molecular/genetic diversity and social constructs of race. Just using “diversity” elides and blurs important concepts. – Jonathan Kahn @

  13.   Retweeted

    Audience member during Q&A calls the first group of talks “very very interesting — and terrifying.” That’s what we’re here for, folks. These issues are real and we’re happy you’re here to talk about them with us.

  14.   Retweeted

    Just FYI my research showed you cannot waive statutory nondiscrim rights (under GINA or others) but can waive right to judicial forum to decide if there has been a violation (2009 Pyett v 14 Penn Plaza decision-ie case after GINA-overturned 30 years of precedence)

  15.   Retweeted

    FYI in Perlmutter & Peerenboom, the claim was not ownership in the DNA material. It was in the genetic information contained within it

  16.   Retweeted

    “If I want to edit my genes and make my skin glow green, whose business is that?” Barbara Evans on paternalism issues in our views of regulating DIYbio

  17.   Retweeted

    Takeaways from Regulating : Hazel: existing DTC genetic privacy policies are all over the place Sharkey: in an era of big data, FDA is poised to pose enhanced role as health information regulator Schweikart: in gene editing, somatic ≠ germline editing

  18.   Retweeted

    I have been waiting so long for this and is finally here!

  19.   Retweeted

    Many of the regulatory issues/possibilities raised by DIYbio will presented by (co-authors and ) “What can we do with what we’ve already got?”

  20.   Retweeted

    Moderators summary: In today’s panel we heard: -Property law won’t work -Anonymity is dead -Data is being commercialized and we don’t realize it -May be need for publicity rights for DNA. But there is hope. Good things are being done with this data.

  21.   Retweeted

    Is ⁦⁩ right, asks Vertinsky ⁦⁩,to be worried about “genetic ” publishing of information derived from your genetic information (especially discarded DNA). Or a presidential candidate ? What role for law?

  22.   Retweeted

    Interesting points by : Because many biohacking materials exchanges may not take place in traditional commercial contexts, attempting to regulate the trade of materials could prove difficult for FDA.

  23.   Retweeted

    We have not seen much FDA involvement in “genetic biohacking” says , but that might be a shame.Don’t need “harsh involvement” but “engagement” such as education — e.g., how long you can leave potato salad out at picnic, does not mean enforcement

  24.   Retweeted

    On genetic ownership and federalism. ⁦⁩ discusses the 5 states that have protected genetic property and skeptical about how well thought out the common law property approach has been. ⁩ ⁦

  25.   Retweeted

    “When you’re doing something that’s really high risk and cutting edge, maybe you SHOULD experiment on yourself–maybe that’s the most ethical way.” Barbara Evans talks up self-experimentation (reffing previous Nobels) @

  26.   Retweeted

    I feel simultanously very overwhelmed and very excited

  27.   Retweeted

    “Whatever the boundaries of FDA’s authority are [re: biohacking]…there are important questions about how it should use that authority.” @

  28.   Retweeted

    One person uploading info to a genetic database illuminates hundreds or thousands of other people–those people’s info isn’t “voluntarily” in datasets. Genetic databases familial searches aren’t voluntary. Natalie Ram @

  29.   Retweeted

    DIY gene therapy, CRISPR, etc. – failures likely to cause more harm (inadvertent) than successes. Speaker at analogizes to regulation of drones, beer, computer hacking many stakeholders with competing interests.

  30.   Retweeted

    Excellent talk by showing that in the face of clinicians can be legally damned if they do use revealed info and also damned if they don’t–potentially liable for patient’s misguided medical decisions

  31.   Retweeted

    “We need to rethink our Informed Consent methods for our secondary research protocols” – given all the confusion arising among Patients, their Doctors and the Researchers working with the data specimens about the use of the data, says – at Wasserstein Hall

  32.   Retweeted

    How do we deal with Publicity Rights in DNA? Thought-provoking talk by Professor Vertinsky of The “Genetic Paparazzi” conundrum – at Wasserstein Hall

  33.   Retweeted

    argues against recognizing Property Rights in personal health data: “A vast amount of ‘orphan Biomedical data’ is useless” – doesn’t help advance research in the field Other protections already available and more suitable

  34.   Retweeted

    Leading up to Friday’s Conference on Consuming Genetics () here’s a post about my topic: why law isn’t a good fit for health data.

  35.   Retweeted

    Professor Kif Augustine-Adams of says that individual privacy settings on Consumer Genetics testing have limited power; total anonymity is a myth. It is only a matter of time before the relational nature of DNA makes all connections identifiable. – at Wasserstein Hall

  36.   Retweeted

    “Wellness Programs” by Employers or Insurance underwriters – how should they deal with collecting genetic data? suggests Employers / Insurers only act as mediators between members and DTC genetic testing companies, and only get aggregate, anonymized data – at Harvard Law School

  37.   Retweeted

    Natalie Ram: there’s an idea of voluntariness re: searching & genetic information. THAT’S FICTION. Genetic relatedness is different–it’s sticky! “I could decline my aunt’s FaceBook request…but [she] can still serve as reliable-as-ever genetic informant on me.”

  38.   Retweeted

    A lot of thought-provoking posts this month from leading scholars in law, ethics, genetics. Get immersed in the issues before Friday’s conference!

  39.   Retweeted

    When employer “wellness programs” incentivize employees to use , consider what goes to , what to or , & what does employee have about any of this.

  40.   Retweeted

    Looking forward to joining this awesome line-up of speakers at ‘s conference & talking about ‘s, ‘s & my work. Thx to , & for organizing!

  41.   Retweeted

    It’s not every day that a serious conference on discusses Brad Pitt in a bath leaving behind sperm that later impregnates a woman and the legal challenges that emerge. Well done – you managed to get everyone’s attention 🙂

  42.   Retweeted

    Anguishing story told with elegance and grace. We are all utterly unprepared for generations of secrets unearthed by 26 million ++ kits sold to date.

  43.   Retweeted

    “Civilized societies are nearby, believe it or not!” explains how when is implemented in Canada, it means the government pays for it. (We are all v jealous about your developed country to the north, Vardit)

  44.   Retweeted

    Jonathan Kahn ⁦⁩ ⁦⁩ discusses the fall and rise of race in genetic medicine, its science and politics.

  45.   Retweeted

    Yes! And we should continue to strive to have racial and ethnic representation to ensure that genomic research and policy doesn’t continue to exacerbate racial disparities

  46.   Retweeted

    Fascinating discussions today at the conference

  47.   Retweeted

    Potential consequences are greater when editing germline compared with somatic cells, because its modification can allow for the generational transmission of altered genes. laying out priciplist bioethical concerns of

  48.   Retweeted

    Health information should not be treated as property to protect individuals, says . Instead, we should continue to enhance existing regulatory and liability rules to safeguard individual privacy and data security.

  49.   Retweeted

    There has been a relunctance by courts to recognize information as property, but that could change drastically when it comes to genetic data.

  50.   Retweeted

    Sir Wm. Blackstone is always a hit on the big screen — from my talk today on why health data isn’t property .

  51.   Retweeted

    FDA involvement with DTC tests hasn’t shut them down. Five have been approved, and FDA has been flexible in its approval pathway (4 de novo, 1 510(k)). – Catherine Sharkey @

  52.   Retweeted

    Emily Qian of is a genetic counselor and is co-author on one of the blog posts in our symposium:

  53.   Retweeted

    At the Ethics Conference on Consuming Genomics. There was a question about why patients decline participating in precision medicine research. Check out our paper on why patients decline genomic sequencing

  54.   Retweeted

    Great turnout at DTC genomics conference today. Tour de force discussion of the issues facing the personal genomics industry and consumers today.

  55.   Retweeted

    “Informed consent is a process” that should include: test’s purpose, possible results of the test, test’s limitations/consequences, confidentiality/privacy, risks of testing and familial implications, and voluntary participation.

  56.   Retweeted

    The amazing ⁦⁩ closes out the conference by discussing the ethics of non-invasive prenatal testing (NIPT), it’s ethical challenges, and how whole genome NIPT may make “the fetus transparent.”

  57.   Retweeted

    .: what about DNA vigilantes who upload information to databases explicitly to help law enforcement? Natalie Ram: BAM I ALREADY WROTE THAT ARTICLE CHECK IT OUT. (forthcoming , mayyyybe here? )

  58.   Retweeted

    23andMe does a pretty good job situating and contextualizing results, but APOE testing may have little benefit

  59.   Retweeted

    Is ⁦⁩ ‘s test for APOE associated with Alzheimer’s different ethically speaking from its other tests? ⁦⁩ ⁦⁩ discuss ⁦

  60.   Retweeted

    Ultrasound technology made the uterus transparent, so parents could see their child before it was born. In the future, could make the fetus itself transparent, so parents can see the whole genome. Many associated ethical challenges, both pre- and post-birth

  61.   Retweeted

    Great talk by one of the authors at on the need for laws and regulations to protect the privacy rights of genetic testing consumers and assuage concerns about information

  62.   Retweeted

    Johnathan on The Fall and Rise of Race in Genomics: – not a thing (2000) – a stepping stone to true targeting (2005) – useful to classify subpopulations (2011) – under-representation of ethnically diverse subpopulations are necessary for good data (2019)

  63.   Retweeted

    When tests allow the breach of anonymity and privacy of relatives who don’t want to be known–including in cases of rape–what should we do? Answers aren’t easy. -Kif Augustine-Adams

  64.   Retweeted

    Listening to the brilliant discuss the concept of non-directiveness in genetic counseling.

  65.   Retweeted

    Grateful for the opportunity to participate in the Annual Conference – thanks Carmel Sachar & Cristine Hutchison-Jones for a great line-up & planning- learned a lot & left with many more ?s to consider

  66.   Retweeted

    & : “The more jurisdictions that adopt a cautionary approach to their own regulations for genome editing (particularly heritable genome editing) the more likely negative world-wide consequences can be mitigated.”

  67.   Retweeted

    There’s no prospect of potentially suing because of the disclaimers and forced arbitration put into agreements by the company ⁦

  68.   Retweeted

    explains the ways employer wellness programs is only a “theoretical win-win.” Minimal results come at the cost at privacy, and all of which can also show up in insurace realms as well. (Ex: Life insurers also implementing wellness policies)

  69.   Retweeted

    Although increasing access to predictive/actionable genetic tests could theoretically be beneficial, we should be cautious about using third-parties, like life insurers, to disseminate these tests to their consumers without greater regulatory protections.

  70.   Retweeted

    . has examined for years whether we should own our genetic info. Three reactions: Lay: yeah, duh Lawyers: no, duh (see Moore v Regents of U of Cal) Clinicians/researchers: Good God No! Disaster! (Not live-tweeting b/c draft here: )

  71.   Retweeted

    Property Conversion in Genetic Property Rights – who owns the rights? “Researchers need to be transparent and use adequate informed consent” – claims for generic conversion should not stifle research or create moral harms, suggests – at Wasserstein Hall

  72.   Retweeted

    We’re so proud of our friend and Academic Fellowship alum ! ✨🕺🏻

  73.   Retweeted

    Why is most insurance typically a state issue? FYI – Congress essentially “blessed” and preserved a state regulatory system of the insurance industry with passage of the McCarran-Ferguson Act of 1945. It makes it politically difficult to push this at federal level

  74.   Retweeted

    DTC genetic testing customers lack legal protections. Genetic conversations might offer them some rights… ?

  75.   Retweeted

    . takeaway: Wellness programs aren’t necessarily bad, but question is what data goes to consumers, what data to employers and insurers, and what can they do with it?

  76.   Retweeted

    . takeaway: w/r/t liability, companies are essentially immune because of disclaimers & arbitration clauses; doctors may be on the hook.

  77.   Retweeted

    Q by : What do we tell GCs/trainees when we get a DTC result that needs to be confirmed but insurance won’t pay for confirmation? Answer: not very clear, but might be liable if we do nothing. Yikes!

  78.   Retweeted

    Major disconnect with the ideas of ways to convert health data into what we have traditionally considered property-like rights.

  79.   Retweeted

    Great point from about how to treat “control group” genetic data, from those without the indicative genetic information, in arguments for genetic ownership/remuneration arguments.

  80.   Retweeted

    The story of a mom who contacts her (donor conceived) five-year-old’s grandmother — then gets threatened by a sperm bank

  81.   Retweeted

    The ethical debate about anonymity is MOOT. There is no anonymity for sperm donors, nor are there any federal laws regarding anonymity of sperm donors. (Some states address medical information/disclosure but not anonymity)

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    Three observations: 1. Biomedical data/samples are governed by method of procurement 2. Contributors care about use 3. Specimens/data procured differently end up being used similarly (lots of mixing between academia & industry). ==>TENSION. – @

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    Rights to privacy or publicity – What will the courts decide? Well, it’s unclear because there are gaps in the existing laws. Liza Vertinsky also looking at the underlying implications of the choices of legal pathways

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    . is an active moderator! Asking excellent questions (including mine–how do we react to patients not ‘getting’ consent info?, and then ‘s on right not to be a genetic parent! Need to think on your feet w/ Nita around!)

  85.   Retweeted

  86.   Retweeted

    Wondering how panelists and fellow attendees feel about this lack of anonymity? and individuals conceived from egg or who want to know about their background never consented to anonymity of donors

  87.   Retweeted

    Yeah that looks simple! Barbara Evans on what the regulatory pathway issupposed to look like and what makes it challenging in the world of genetics using charts from 2017 reports. And an ode to the “pink golden retriever” we all want

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    You’re welcome!

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    Barbara Evans: Peer-review is no longer the threshold for good science it once was – grant review is. But if research is not funded…those protections aren’t there

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    How well are companies doing in complying with the privacy principles they themselves signed on to? James Hazel talks about the work he and Chris Slobogin ⁦⁩ ⁦⁩ have done. ⁦

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    Excellent talk by Barbara Evans expressing skepticism about a top down regulatory approach on biohacking (“If I want to turn my skin bright green who’s the FDA to tell me I can’t?), citing Lisa Ikemoto’s excellent DIY Bio Hacking article

  92.   Retweeted

    Terrific representation of women at ! Speakers: 14F, 6M Moderators: 4F, 2M Nicely done, folks.

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    Panel takeaways: * DTC privacy policies are all over the place, and Best practices are a good way forward. * FDA is poised to take an advanced role as a regulator in the field. * We must differentiate between germline and somatic editing for regulation

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    Catherine Sharkey asks us to consider the FDA may play in managing the conceptual risk and regulatory model for DTC genetic testing especially given the complexities that AI, machine learning, and big data add to this industry

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    You can hear a pin drop in the auditorium as Kif Augustine tells a very personal tale about how reveals a story of rape and a lost half sister. Secrets, lies, ancestry, DNA, and Mormon Orthodoxy in 1959 Utah.

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    And what does diversity mean? What does it do? Among other things, drives $$$$ funding in the research cycle.

  97.   Retweeted

    Health equity is due to structural and systemic racism in the field present from its beginnings. Seeking more diversity in the workforce will not solve this “health equity” issue. As Jonathan Khan notes, these d&i initiatives can be used to elide responsibility

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    Natalie Ram at talks about familial investigations for law enforcement. For a short, recent piece w/ & Amy McGuire: . Longer ago and longer (by far) in :

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    Natalie Ram uses her baby bump as the ultimate scholarly “flex” in showing the involuntary and immutable nature of informational revelation for the children we produce. How do these elements make the forensic use of that information different?

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    Ooh interesting! Natalie Ram argues that the involuntariness of familial info getting into databases means the Third Party Doctrine [which sucks anyway] shouldn’t apply. (here’s her piece, DNA by the Entirety: )

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    providing a range of policy/legal choices about how to address new forms of noninvasive prenatal testing

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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

 

RNA plays various roles in determining how the information in our genes drives cell behavior. One of its roles is to carry information encoded by our genes from the cell nucleus to the rest of the cell where it can be acted on by other cell components. Rresearchers have now defined how RNA also participates in transmitting information outside cells, known as extracellular RNA or exRNA. This new role of RNA in cell-to-cell communication has led to new discoveries of potential disease biomarkers and therapeutic targets. Cells using RNA to talk to each other is a significant shift in the general thought process about RNA biology.

 

Researchers explored basic exRNA biology, including how exRNA molecules and their transport packages (or carriers) were made, how they were expelled by producer cells and taken up by target cells, and what the exRNA molecules did when they got to their destination. They encountered surprising complexity both in the types of carriers that transport exRNA molecules between cells and in the different types of exRNA molecules associated with the carriers. The researchers had to be exceptionally creative in developing molecular and data-centric tools to begin making sense of the complexity, and found that the type of carrier affected how exRNA messages were sent and received.

 

As couriers of information between cells, exRNA molecules and their carriers give researchers an opportunity to intercept exRNA messages to see if they are associated with disease. If scientists could change or engineer designer exRNA messages, it may be a new way to treat disease. The researchers identified potential exRNA biomarkers for nearly 30 diseases including cardiovascular disease, diseases of the brain and central nervous system, pregnancy complications, glaucoma, diabetes, autoimmune diseases and multiple types of cancer.

 

As for example some researchers found that exRNA in urine showed promise as a biomarker of muscular dystrophy where current studies rely on markers obtained through painful muscle biopsies. Some other researchers laid the groundwork for exRNA as therapeutics with preliminary studies demonstrating how researchers might load exRNA molecules into suitable carriers and target carriers to intended recipient cells, and determining whether engineered carriers could have adverse side effects. Scientists engineered carriers with designer RNA messages to target lab-grown breast cancer cells displaying a certain protein on their surface. In an animal model of breast cancer with the cell surface protein, the researchers showed a reduction in tumor growth after engineered carriers deposited their RNA cargo.

 

Other than the above research work the scientists also created a catalog of exRNA molecules found in human biofluids like plasma, saliva and urine. They analyzed over 50,000 samples from over 2000 donors, generating exRNA profiles for 13 biofluids. This included over 1000 exRNA profiles from healthy volunteers. The researchers found that exRNA profiles varied greatly among healthy individuals depending on characteristics like age and environmental factors like exercise. This means that exRNA profiles can give important and detailed information about health and disease, but careful comparisons need to be made with exRNA data generated from people with similar characteristics.

 

Next the researchers will develop tools to efficiently and reproducibly isolate, identify and analyze different carrier types and their exRNA cargos and allow analysis of one carrier and its cargo at a time. These tools will be shared with the research community to fill gaps in knowledge generated till now and to continue to move this field forward.

 

References:

 

https://www.nih.gov/news-events/news-releases/scientists-explore-new-roles-rna

 

https://www.cell.com/consortium/exRNA

 

https://www.sciencedaily.com/releases/2016/06/160606120230.htm

 

https://www.pasteur.fr/en/multiple-roles-rnas

 

https://www.nature.com/scitable/topicpage/rna-functions-352

 

https://www.umassmed.edu/rti/biology/role-of-rna-in-biology/

 

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THE 3RD STAT4ONC ANNUAL SYMPOSIUM APRIL 25-27, 2019, HILTON, HARTFORD, CONNECTICUT, 315 Trumbull St, Hartford, CT 06103

Reporter: Stephen J. Williams, Ph.D.

SYMPOSIUM OBJECTIVES

The three-day symposium aims to bring oncologists and statisticians together to share new research, discuss novel ideas, ask questions and provide solutions for cancer clinical trials. In the era of big data, precision medicine, and genomics and immune-based oncology, it is crucial to provide a platform for interdisciplinary dialogues among clinical and quantitative scientists. The Stat4Onc Annual Symposium serves as a venue for oncologists and statisticians to communicate their views on trial design and conduct, drug development, and translations to patient care. To be discussed includes big data and genomics for oncology clinical trials, novel dose-finding designs, drug combinations, immune oncology clinical trials, and umbrella/basket oncology trials. An important aspect of Stat4Onc is the participation of researchers across academia, industry, and regulatory agency.

Meeting Agenda will be announced coming soon. For Updated Agenda and Program Speakers please CLICK HERE

The registration of the symposium is via NESS Society PayPal. Click here to register.

Other  2019 Conference Announcement Posts on this Open Access Journal Include:

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‘Direct-to-Consumer (DTC) Genetic Testing Market to hit USD 2.5 Bn by 2024’ by Global Market Insights

Requested Publishing in https://pharmaceuticalintelligence.com/

 

An industry news titled ‘Direct-to-Consumer (DTC) Genetic Testing Market to hit USD 2.5 Bn by 2024’ by Global Market Insights is relevant to your esteemed website https://pharmaceuticalintelligence.com/ . This email is a suggestion to publish this news (content attached in word format or can be picked from link mentioned below) on your website with an objective to share the information with your audiences.

 

News Link: https://www.gminsights.com/pressrelease/direct-to-consumer-dtc-genetic-testing-market

 

From: Jui Kate <jui.k@gminsights.com>

Date: Tuesday, February 12, 2019 at 7:29 AM

To: Aviva Lev-Ari <AvivaLev-Ari@alum.berkeley.edu>

Subject: Article Submission Request

Jui Kate| SEO Analyst

Global Market Insights

E-mail:jui.k@gminsights.com| Web: www.gminsights.com 

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Single-cell Genomics: Directions in Computational and Systems Biology – Contributions of Prof. Aviv Regev @Broad Institute of MIT and Harvard, Cochair, the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute

 

Curator: Aviva Lev-Ari, PhD, RN

 

Dana Pe’er, PhD, now chair of computational and systems biology at the Sloan Kettering Institute at the Memorial Sloan Kettering Cancer Center and a member of the Human Cell Atlas Organizing Committee,

what really sets Regev apart is the elegance of her work. Regev, says Pe’er, “has a rare, innate ability of seeing complex biology and simplifying it and formalizing it into beautiful, abstract, describable principles.”

Dr. Aviv Regev, an MIT biology professor who is also chair of the faculty of the Broad and director of its Klarman Cell Observatory and Cell Circuits Program, was reviewing a newly published white paper detailing how the Human Cell Atlas is expected to change the way we diagnose, monitor, and treat disease at a gathering of international scientists at Israel’s Weizmann Institute of Science, 10/2017.

For Regev, the importance of the Human Cell Atlas goes beyond its promise to revolutionize biology and medicine. As she once put it, without an atlas of our cells, “we don’t really know what we’re made of.”

Regev, turned to a technique known as RNA interference (she now uses CRISPR), which allowed her to systematically shut genes down. Then she looked at which genes were expressed to determine how the cells’ response changed in each case. Her team singled out 100 different genes that were involved in regulating the response to the pathogens—some of which weren’t previously known to be involved in immune function. The study, published in Science, generated headlines.

The project, the Human Cell Atlas, aims to create a reference map that categorizes all the approximately 37 trillion cells that make up a human. The Human Cell Atlas is often compared to the Human Genome Project, the monumental scientific collaboration that gave us a complete readout of human DNA, or what might be considered the unabridged cookbook for human life. In a sense, the atlas is a continuation of that project’s work. But while the same DNA cookbook is found in every cell, each cell type reads only some of the recipes—that is, it expresses only certain genes, following their DNA instructions to produce the proteins that carry out a cell’s activities. The promise of the Human Cell Atlas is to reveal which specific genes are expressed in every cell type, and where the cells expressing those genes can be found.

Regev says,

The final product, will amount to nothing less than a “periodic table of our cells,” a tool that is designed not to answer one specific question but to make countless new discoveries possible.

Sequencing the RNA of the cells she’s studying can tell her only so much. To understand how the circuits change under different circumstances, Regev subjects cells to different stimuli, such as hormones or pathogens, to see how the resulting protein signals change.

“the modeling step”—creating algorithms that try to decipher the most likely sequence of molecular events following a stimulus. And just as someone might study a computer by cutting out circuits and seeing how that changes the machine’s operation, Regev tests her model by seeing if it can predict what will happen when she silences specific genes and then exposes the cells to the same stimulus.

By sequencing the RNA of individual cancer cells in recent years—“Every cell is an experiment now,” she says—she has found remarkable differences between the cells of a single tumor, even when they have the same mutations. (Last year that work led to Memorial Sloan Kettering’s Paul Marks Prize for Cancer Research.) She found that while some cancers are thought to develop resistance to therapy, a subset of melanoma cells were resistant from the start. And she discovered that two types of brain cancer, oligodendroglioma and astrocytoma, harbor the same cancer stem cells, which could have important implications for how they’re treated.

As a 2017 overview of the Human Cell Atlas by the project’s organizing committee noted, an atlas “is a map that aims to show the relationships among its elements.” Just as corresponding coastlines seen in an atlas of Earth offer visual evidence of continental drift, compiling all the data about our cells in one place could reveal relationships among cells, tissues, and organs, including some that are entirely unexpected. And just as the periodic table made it possible to predict the existence of elements yet to be observed, the Human Cell Atlas, Regev says, could help us predict the existence of cells that haven’t been found.

This year alone it will fund 85 Human Cell Atlas grants. Early results are already pouring in.

  • In March, Swedish researchers working on cells related to human development announced they had sequenced 250,000 individual cells.
  • In May, a team at the Broad made a data set of more than 500,000 immune cells available on a preview site.

The goal, Regev says, is for researchers everywhere to be able to use the open-source platform of the Human Cell Atlas to perform joint analyses.

Eric Lander, PhDthe founding director and president of the Broad Institute and a member of the Human Cell Atlas Organizing Committee, likens it to genomics.

“People thought at the beginning they might use genomics for this application or that application,” he says. “Nothing has failed to be transformed by genomics, and nothing will fail to be transformed by having a cell atlas.”

“How did we ever imagine we were going to solve a problem without single-cell resolution?”

SOURCE

https://www.technologyreview.com/s/611786/the-cartographer-of-cells/?utm_source=MIT+Technology+Review&utm_campaign=Alumni-Newsletter_Sep-Oct-2018&utm_medium=email

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

 

University of California Santa Cruz’s Genomics Institute will create a Map of Human Genetic Variations

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2015/01/13/university-of-california-santa-cruzs-genomics-institute-will-create-a-map-of-human-genetic-variations/

 

Recognitions for Contributions in Genomics by Dan David Prize Awards

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/07/31/recognitions-for-contributions-in-genomics-by-dan-david-prize-awards/

 

ENCODE (Encyclopedia of DNA Elements) program: ‘Tragic’ Sequestration Impact on NHGRI Programs

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/09/18/encode-encyclopedia-of-dna-elements-program-tragic-sequestration-impact-on-nhgri-programs/

 

Single-cell Sequencing

Genomic Diagnostics: Three Techniques to Perform Single Cell Gene Expression and Genome Sequencing Single Molecule DNA Sequencing

Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/07/04/genomic-diagnostics-three-techniques-to-perform-single-cell-gene-expression-and-genome-sequencing-single-molecule-dna-sequencing/

 

LIVE – Real Time – 16th Annual Cancer Research Symposium, Koch Institute, Friday, June 16, 9AM – 5PM, Kresge Auditorium, MIT – See, Aviv Regev

REAL TIME PRESS COVERAGE & Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2017/03/13/16th-annual-cancer-research-symposium-koch-institute-friday-june-16-9am-5pm-kresge-auditorium-mit/

 

LIVE 11/3/2015 1:30PM @The 15th Annual EmTech MIT – MIT Media Lab: Top 10 Breakthrough Technologies & 2015 Innovators Under 35 – See, Gilead Evrony

REAL TIME PRESS COVERAGE & Reporter: Aviva Lev-Ari, PhD, RN
https://pharmaceuticalintelligence.com/2015/11/03/live-1132015-130pm-the-15th-annual-emtech-mit-mit-media-lab-top-10-breakthrough-technologies-2015-innovators-under-35/

 

Cellular Guillotine Created for Studying Single-Cell Wound Repair

Reporter: Irina Robu, PhD

https://pharmaceuticalintelligence.com/2017/06/29/cellular-guillotine-created-for-studying-single-cell-wound-repair/

 

New subgroups of ILC immune cells discovered through single-cell RNA sequencing

Reporter: Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/2016/02/17/new-subgroups-of-ilc-immune-cells-discovered-through-single-cell-rna-sequencing-from-karolinska-institute/

 

#JPM16: Illumina’s CEO on new genotyping array called Infinium XT and Bio-Rad Partnership for single-cell sequencing workflow

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2016/01/12/jpm16-illuminas-ceo-on-new-genotyping-array-called-infinium-xt-and-bio-rad-partnership-for-single-cell-sequencing-workflow/

 

Juno Acquires AbVitro for $125M: high-throughput and single-cell sequencing capabilities for Immune-Oncology Drug Discovery

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2016/01/12/juno-acquires-abvitro-for-125m-high-throughput-and-single-cell-sequencing-capabilities-for-immune-oncology-drug-discovery/

 

NIH to Award Up to $12M to Fund DNA, RNA Sequencing Research: single-cell genomics,  sample preparation,  transcriptomics and epigenomics, and  genome-wide functional analysis.

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2015/10/27/nih-to-award-up-to-12m-to-fund-dna-rna-sequencing-research-single-cell-genomics-sample-preparation-transcriptomics-and-epigenomics-and-genome-wide-functional-analysis/

 

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

https://pharmaceuticalintelligence.com/2012/08/07/genome-wide-single-cell-analysis-of-recombination-activity-and-de-novo-mutation-rates-in-human-sperm/

REFERENCES to Original studies

In Science, 2018

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

 See all authors and affiliations

Science  21 Apr 2017:
Vol. 356, Issue 6335, eaah4573
DOI: 10.1126/science.aah4573
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

See all authors and affiliations

Science  26 Apr 2018:
eaar3131
DOI: 10.1126/science.aar3131

In Nature, 2018 and 2017

How to build a human cell atlas

Aviv Regev is a maven of hard-core biological analyses. Now she is part of an effort to map every cell in the human body.

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