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After GWAS studies, how to narrow the search for genes? -- ScienceDaily

Borrowing the machine-learning concept of "cross-validation," Benchmarker enables investigators to use the GWAS data itself as its own control. The idea is to take the GWAS dataset and single out one chromosome. The algorithm being benchmarked then uses the data from the remaining 21 chromosomes (all but X and Y) to make predictions about what genes on the single chromosome are most likely to contribute to the trait being investigated. As this process is repeated for each chromosome in turn, the genes that the algorithm has flagged are pooled. The algorithm is then validated by comparing this group of prioritized genes with the original GWAS results. "You train the algorithm on the GWAS with one chromosome withheld, then go back to that chromosome and ask whether those genes were actually associated with a strong p-value in the original GWAS results," explains Fine. "While these p-values don't represent the exact 'right answers,' they do tell you roughly where some true genetic associations are. The end product is an evaluation of how each algorithm performed."

A researcher with ALS wishes a polygenic analysis had warned him - STAT

Two years ago, had I been given even a tiny hint that my genes were tipping the scale for the development of a disease that would lock me into my body, unable to move or breath normally on my own, I would have been sad, and probably mad. But then I would have packed more hours into developing genetic analyses to help people solve diseases like ALS. So now I’m running as fast as I can — from my wheelchair.

Myriad Genetics to Acquire Counsyl for $375M | GenomeWeb

Myriad will merge Counsyl's reproductive health tests with its existing preventive care business unit into a new business unit called Myriad Women's Health, which will focus solely on OB-Gyns and reproductive healthcare providers. Myriad will also combine its women's health sales force of approximately 225 representatives with Counsyl's 80 sales professionals, enabling a threefold increase in physician reach for reproductive testing, according to Myriad.

An Expanded View of Complex Traits: From Polygenic to Omnigenic: Cell

In summary, many complex traits are driven by enormously large numbers of variants of small effects, potentially implicating most regulatory variants that are active in disease-relevant tissues. To explain these observations, we propose that disease risk is largely driven by genes with no direct relevance to disease and is propagated through regulatory networks to a much smaller number of core genes with direct effects. If this model is correct, then it implies that detailed mapping of cell-specific regulatory networks will be an essential task for fully understanding human disease biology.

An Expanded View of Complex Traits: From Polygenic to Omnigenic: Cell

core genes generally contribute just a small part of the total heritability and how most genes expressed in relevant cell types could make non-zero contributions to heritability. To resolve this, we propose that cell regulatory networks are highly interconnected to the extent that any expressed gene is likely to affect the regulation or function of core genes.

‘Omnigenic’ Model Suggests That All Genes Affect Every Complex Trait | Quanta Magazine

Starting about 15 years ago, geneticists began to collect DNA from thousands of people who shared traits, to look for clues to each trait’s cause in commonalities between their genomes, a kind of analysis called a genome-wide association study (GWAS). What they found, first, was that you need an enormous number of people to get statistically significant results — one recent GWAS seeking correlations between genetics and insomnia, for instance, included more than a million people. Second, in study after study, even the most significant genetic connections turned out to have surprisingly small effects. The conclusion, sometimes called the polygenic hypothesis, was that multiple loci, or positions in the genome, were likely to be involved in every trait, with each contributing just a small part. (A single large gene can contain several loci, each representing a distinct part of the DNA where mutations make a detectable difference.) on personal data ownership

Personal data needs to be regarded as a human right, just as access to water is a human right. The ability for people to own and control their data should be considered a central human value. The data itself should be treated like property and people should be fairly compensated for it.


Today, my gadgets may count my steps, but they aren’t seeing the big picture: what I ate, how I felt, what my blood pressure is. New services, built from the point of view of the consumer, will benefit me by sharing and interconnecting my own data, rather than selling it on. When more trust is established, my personal “agent” or “assistant” should merge relevant things together that are currently just disconnected data points.


A few state court cases have found patients own their medical records under specific circumstances.118 Unfortunately, the pertinent body of state medical records law generally applies in traditional healthcare settings and seemingly does not govern commercial providers of PHD devices and services, such as purveyors of medical and fitness devices. Courts do not recognize an individual property right in personal information such as one’s name, address, and social security number.119 Commercial databases that hold such information are generally treated as the property of the companies that compiled them.120 In a famous case121 where plaintiffs sought to block a company from disclosing their personal information by selling its mailing lists, Vera Bergelson notes an implicit judicial bias “that, to the extent personal information may be viewed as property, that property belongs to the one who collects it.”122 This bias— if it exists—is reminiscent of the ancient res nullius doctrine from natural resource law, which treated assets such as subsurface mineral deposits and wild animals as unowned until somebody discovers and captures (takes possession of) them.123 “Rarely used today, it let private owners stake claims as in the Klondike gold rush.”124


This article explores how these mechanisms, imbedded in major federal research and privacy regulations, enshrine institutional data holders—entities such as hospitals, research institutions, and insurers that store people’s health data—as the prime movers in assembling large-scale data resources for research and public health. They rely on approaches—such as de-identification of data and waivers of informed consent—that are increasingly unworkable going forward. They shower individuals with unwanted, paternalistic protections—such as barriers to access to their own research results—while denying them a voice in what will be done with their data.


Data resources are a central currency of twenty-first-century science, and the question is, “Who will control them?”

The F.D.A. vs. Personal Genetic Testing | The New Yorker

A fifty-five-year-old who is confused and depressed and learns that he carries two copies of the risk gene and stands an eighty-per-cent chance of getting Alzheimer’s might reach for a gun, which is the kind of scenario that some genetic counsellors worry about.

23andMe Is Sharing Genetic Data with Drug Giant - Scientific American

Only about 10,000 of the 1 million Americans with Parkinson’s disease have the disease because of LRRK2. So, GlaxoSmithKline has to test about 100 Parkinson’s patients to find just one potential candidate. However, 23andMe has already provided 250 Parkinson’s patients who have agreed to be re-contacted for GlaxoSmithKline’s clinical trials, which may help the pharmaceutical company develop the drug much faster, Forbes reported.

Full transcript: 23andMe CEO Anne Wojcicki answers genetics and privacy questions on Too Embarrassed to Ask - Recode

It’s hard because health care is spectacularly fragmented. An oncology team at Stanford doesn’t do the same things as an oncology team at Memorial Sloan Kettering and to protect it under the Practice of Medicine, and they have different ways that they engage with their patients. Everything is spectacularly fragmented. For us, one of the things that I’m really proud of that we saw is I have millions of people now on a single platform that I know are all interested in their DNA and their health. I think there’s a huge potential for us to help, again, engage all of our customers and potentially work with all of the innovative tech companies out here and give them a platform.