Tom Cooke (March 13th): “Next Gen Sequencing for cost-effective deep genotyping: Reduced representation sequencing in human and non-model organisms”

High-throughput reduced representation sequencing methods such as genotyping-by-sequencing (GBS), generate large numbers of randomly-distributed genetic markers that are useful for trait mapping, linkage map construction, selection scans, and demographic inference. The first part of the talk will focus on GBS in humans, and a statistical framework for correcting GBS-specific biases in genotype calling. The second part will focus on an ongoing project to map the genes responsible for pigmentation variation in budgerigar (common parakeet).

Seminar Title: WGS Seminar:Next Gen Sequencing for cost-effective deep genotyping: Reduced representation sequencing in human and non-model organisms
Speaker:  Tom Cooke
Location: Beckman Building, RM B-302 (DevBio Library)
Seminar Date: Thursday March 13
Time: 12:00 PM – 1:00 PM

WGS club flyer_Tom

Hinco Gierman (Feb 13th): “Whole Genome Sequencing of the World’s Oldest People”

Hey WGSers!!

You’ve heard him ask insightful questions the past two years… now for the
first time in WGS history, you can hear him speak!  :)   (And you can ask
him the hard questions…)

Thursday Hinco Gierman (postdoc in the lab of Stuart Kim), will talk about
analyzing the genomes of Supercentenarians. These are 110 year old
individuals, of which there are currently only 17 alive in the US. Besides
being the world’s oldest, these people are also extremely healthy, delaying
or even escaping most age-related diseases.
WGS club flyer_Hinco

Location: Beckman Building, RM B-302 (DevBio Library)
Seminar Date: Thursday Feb 13
Time: 12:00 PM – 1:00 PM
Free Pizza!


Systematic re-evaluation of pathogenic variant annotation

The current issue of Nature Genetics has an interesting paper on a massive evaluation/reclassification of (rare) pathogenic variants for Lynch Syndrome. The InSiGHT consortium revised over 12,000 variants from their database, using all available data like segregation analysis in pedigrees to evaluate the classification given to variants by original submitters. As a result, 1,370 variants that were not obviously pathogenic, have now been recognized as such and 24% of variants submitted as “pathogenic” turn out to have no hard evidence to substantiate this (see figure below).
Figure adapted from Thompson et al: The x-axis shows the variant annotation by submitter, the colors show the reclassified annotation from InSiGHT: class 1 is “not pathogenics” [purple] and class 5a/5b is “pathogenic” [green])

This is an important effort for reliable (clinical) evaluation of WGS data. And it allows for a data-driven discussion on the (presumed) error rate in pathogenic variant annotation, which holds important implications for (future) recommendations by the ACMG. The paper:

See also the editorial in Nature Genetics:

Russ Altman (Jan 23rd): “Applying Pharmacogenomics In A Whole Genome World (Or Genomes, Drugs And Rock & Roll)”

Russ Altman will kick off our third season of WGS Club seminars. No single drug works the same in all people and our DNA plays a large role in determing how people metabolize drugs differently. Hundreds of “pharmacogenomic” variants have been associated with differences in efficacy and or increased risk of adverse events. Russ Altman, Professor of Bioengineering, will discuss the Pharmacogenomic implications of having (many) sequenced genomes.

 We would like to thank the Stanford Center for Computational, Evolutionary and Human Genomics (CEHG) for sponsoring the WGS Club. As always, there is free pizza!
Date: Thursday January 23rdTime: 12:00 PM-1:00 PM
Location: Beckman Building, RM B-302 (DevBio Library)
Time: 12:00 PM – 1:00 PMWGS club flyer_Russ

FDA wants to regulate 23andMe

You might need to hurry up if you want to genotype yourself: The FDA sent 23andMe an enforcement letter this Monday, as it thinks their test is a class III medical diagnostic device, that needs to be tested and registered as such. You can read a piece on it and the actual FDA letter plus 23andMe’s response here:
Article on the decision:
FDA letter to 23andMe:
23andMe’s response:

Genomics X Prize sequencing competition cancelled


For the first time in its 18-year history, the X Prize Foundation is canceling one of its $10 million competitions for technological innovation: the Archon Genomics X Prize, which was designed to reward quick and accurate whole-genome sequencing.

The prize, established in 2006 with backing from multimillionaire philanthropist Stewart Blusson and his wife, Marilyn, would have been awarded to the first team that could rapidly and accurately sequence 100 whole human genomes to high resolution, at a cost of $10,000 or less per genome.

“What we realized is that genome sequencing technology is plummeting in cost and increasing in speed independent of our competition,” the foundation’s co-founder and chairman, Peter Diamandis, wrote in his Huffington Post column on Thursday. “Today, companies can do this for less than $5,000 per genome, in a few days or less — and are moving quickly towards the goals we set for the prize. For this reason, we have decided to cancel an X Prize for the first time ever.”

Source: NBC News (click to read more)

WGS Club Seminar Twitter feeds: #wgsclub

Thanks to Roxana Daneshjou, Konrad Karczewski and others for Tweeting on our latest WGS Club Seminar with Hank Greely and Kelly Ormond!

Roxana Daneshjou:

Konrad Karczewski:

Hank Greely:

Carlos Bustamante:

All #wgsclub Tweets:

wgsclub_Tweets2 HGreely_small KOrmond_small


US Supreme court limits gene patenting in Myriad case

The U.S. Supreme Court restricted the ability of companies to patent human genetic sequences, issuing a mixed ruling in a case that raised questions about thousands of biotechnology, agricultural and drug patents.

The justices unanimously ruled that parts of Myriad Genetics Inc. (MYGN)’s patents on genes linked to breast and ovarian cancer improperly covered natural phenomena. Other parts, the court said, involve enough human intervention to be eligible for legal protection.

The decision left both sides of the debate with grounds for claiming victory. It forces a change at the federal patent office, which has been awarding gene patents since 1982. That’s a victory for doctors’ groups and patient advocates that accused Myriad of using its patents to block clinical testing and research.

“Because of this ruling, patients will have greater access to genetic testing and scientists can engage in research on these genes without fear of being sued,” said Sandra Park, an attorney with the American Civil Liberties Union, which sued to challenge the Myriad patents.

At the same time, Myriad shares soared on news that parts of its patents had survived the high court case. Myriad rose 10 percent to $37.46 at 11:36 a.m. in New York, the highest since June 25, 2009.

Source & more information at: