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NGS Leaders Blog

Genome in a Bottle Project

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Justin Zook of the National Institute of Standards and Technology (NIST) discussed the progress and future goals of the Genome in a Bottle project, which aims to create near-perfectly characterized human genome sequences for use as reference standards. Members of the Genome in a Bottle Consortium have chosen several human DNA samples to repeatedly sequence on multiple technologies and bioinformatics pipelines, aiming to capture variants from single-nucleotide polymorphisms (SNPs) to massive structural changes with very high accuracy. The NIST could then distribute the same samples to outside organizations for resequencing, to help identify genomic regions or types of variants that tend to be called incorrectly. 
Read the full article from Bio-IT World, covering the Next Generation DxSummit.

Edico Genome Makes First Sale of NGS Processor

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The year of the thousand-dollar genome just got a little more interesting as Edico Genome, which makes a data processor called the DRAGEN for next generation sequencing (NGS) data, made its first sale to Sequenom, Inc. 

Read the full article from Bio-IT World.

New Things Coming to NGS Leaders

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NGS Leaders is now part of Bio-IT World, which means we have lots of great things coming soon!  If you have any suggestions for how you would like to see us improve NGS Leaders, let us know!

In the meantime, we are now accepting speaking proposals for the upcoming Bio-IT World Conference & Expo.  The 2015 event is taking place April 21-23 in Boston.  For more information, visit: Bio-ITWorldexpo.com

Celebrating the 10th Anniversary of the Human Genome Project

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genomicMay 1, 2013
Kevin Davies :  On DNA Day, April 25, a parade of leading genome scientists gathered at NIH to celebrate the 10th anniversary of the completion of the Human Genome Project (HGP). NIH assembled an outstanding list of speakers, including NIH Director Francis Collins, ENCODE project leader Ewan Birney, Princeton geneticist David Botstein, cancer geneticist Levi Garraway and experts in evolutionary and population genetics and healthcare.

I was honored (and a little petrified) to be included in the line-up. After all, my most significant contribution to biomedical research was hanging up my lab coat 25 years ago to seek refuge in the cramped, dilapidated offices of Nature magazine in London.

I was asked to speak on public perceptions of the HGP and the inexorable march of sequencing technology towards the $1,000 genome. Preparations did not go smoothly: despite the lack of coffee (a victim of the sequester), I managed to procure a cup, only to spill the contents down my jacket mid-morning. Hopefully it's not evindent in the video…

The talk was enjoyable (for me anyway): Along the way, I worked in a plug for the new film Decoding Annie Parker, on which I served as a genetics consultant; showed off a little Welsh; and had a little fun at the expense of current NIH Director, whose next book almost certainly will not be entitled The Language of Love – or 46 Shades of Grey - for that matter.

The video of my talk is below and is below and the entire set of event videos can be viewed at the NHGRI Genome TV channel.  



Nancy Kelley Steps Down as New York Genome Center Executive Director

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March 18, 2013 

Bio-IT World Staff : Nancy KelleyNancy J. Kelley, the founding executive director of the New York Genome Center (NYGC) and the person most responsible for conceiving and bringing the ambitious institute to fruition, is stepping down from her leadership role.

She will remain an advisor and a member of the Board of Directors.

“Working with the New York Genome Center and all of its supporters and partners has been an extraordinary experience,” said Kelley in a statement released today. “This is an exciting time in science and medicine. The Center is now well positioned to become a world-class collaborative center for translational genomic research under the strong leadership of [Bob] Darnell… I will always value my experience there.”

Kelley “was instrumental in nurturing NYGC from an idea to a reality, to the inestimable benefit of scientific research and New York City,” said Russ Carson and Ivan Seidenberg, co-chairs of the NYGC Board of Directors, in a statement. “We are extremely appreciative of her vision, persistence, and accomplishments, and we look forward to continuing to work with her as an advisor and a member of NYGC’s Board of Directors."

As Kelley detailed in a lengthy interview with Bio-IT World in 2011, she saw the faintest possibility of building a world-class genomics institute in the middle of Manhattan and ran with it. Working with Columbia University professor Tom Maniatis and a number of key administrative and philanthropic supporters, Kelley forged a coalition of 11 founding institutions, including most of the major research and clinical centers in and around New York City.

NYGC was officially launched in 2011. Many of the center’s foundational elements, including its Pilot Laboratory at Rockefeller University, the NYGC Innovation Center, and key technology partnerships, were established under her leadership. Kelley also oversaw the selection and build out of NYGC’s permanent facility at 101 Avenue of the Americas in New York City, which is scheduled to open this summer.

Late last year, NYGC appointed Rockefeller University physician scientist Robert Darnell as president and scientific Director.

Reached by Bio-IT World, Kelley declined to comment on the record other than to say she is looking forward to taking some time off. It is unlikely that NYGC will be her last contribution to the biomedical enterprise.

Ed Note: The Bio-IT World Conference in April 2013 will include a session on building out the IT infrastructure at NYGC.  

Putting Science on Screen: The Perfect 46

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 Editor’s Note: We are pleased to share a guest post submitted by Brett Bonowicz, Author and Director of "The Perfect 46". 

March 5, 2013 :  “The Perfect 46” is a film about the CEO of a personal genetics company and what happens when he creates a website that pairs individuals with their ideal genetic match for children. The CEO – Jesse Darden – bares some similarities to the brilliant game-changing innovators such as Steve Jobs or Mark Zuckerberg, and ties that entrepreneurial spirit to the fascinating world of direct-to-consumer (DTC) personal genomics. 

What would happen if a personality so tied to the identity of his company had the chance to change the nature of our relationships. What if facebook started telling us who we should be with? The script is written and is pretty good – of course, as the author, I’m a little biased. If we can raise enough money, we aim to start shooting this May and all going well, release the film later in 2013. 

As I begin to promote the film and raise funding, I have some trepidation about reaching out to the scientific community. Why should people that work incredibly hard to create the wonderful reality of tomorrow care about someone making fictional art?   

My best answer is that the reflection they might see of themselves in the film might spark debate. And perhaps not just within the scientific community, but with an entirely different audience that wouldn’t normally be engaged in such a discussion. theperfect46 

I started to think about where the film could go and where the two subjects – the genetics visionary and the social networking aspect -- might begin to overlap. As I began to formulate the film in my outline, I read a lot about the field of personal genomics. I found myself highlighting pages in books that came right out of my outline. Ideas that I thought might be science fiction were already becoming reality.

I seemed to be on the right track with the story, and every time I started to veer off into subject matter that was fantasy I would reign it back in because sticking closer to the reality was always more interesting. I discovered fascinating facts about eugenics and the very American history of how it began at the beginning of the 20th century.

By making the film as factually accurate as possible, the conversation that the film creates should, I think, spark something that a more futuristic, fantastic treatment perhaps cannot. The topics we cover in the film -- genetics, eugenics, the moral and ethical implications of a consumer genetics service, and the role of government vs. a DTC model -- are discussions that deserve to be out in the public. This is a film of the moment. We have an amazing opportunity to make something right on the cutting edge of what is possible in personal genetics.

Science is rarely, if ever, treated well in film. Outside the realm of documentaries, it is hard to find more than a handful of films that truly respect the scientific community. I am frustrated with that fact, and I cannot be alone in thinking that works like this have an audience and that they deserve to be made and to be seen.

I read the works of Arthur C. Clarke and I wonder why they never made it to the screen? I read the wonderful literature of George Dyson, and I can imagine a perfect film coming from the story of Project Orion. But where is it? Where are those films? If an audience can be found, I guarantee those films will start to crop up.

It’s been over 15 years since Andrew Niccol’s excellent, thought-provoking film Gattaca (tagline “There is no gene for the human spirit”) came to theatres. A lot of our perceptions about genetics have changed in those years. What we’re making can be looked at as a sort of prequel to Gattaca. We’re looking at the moment when society might begin to shift. We’re looking at the discussions and the realities of a service of this kind.

Please help us get the word out about this film. We are using the popular crowd-sourcing model via a website called Indiegogo to raise some modest funding to begin shooting the movie.

The fund-raising campaign is for 46 days, with the goal of raising $46 thousand. Please take a look at what we've been creating at: www.theperfect46.com 

Okay, You've Sequenced My Genome: Are You Sure You Got it Right?

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Editor’s Note: We are pleased to share a guest post submitted by Justin Zook and Marc Salit from the National Institute of Standards and Technology. 

January 3, 2013 : Clinical application of “Next-Generation Sequencing” for hereditary genetic diseases, oncology, and other purposes is rapidly growing.  At present, there are no widely accepted genomic standards or quantitative performance metrics for confidence in variant calling. These are needed to achieve the confidence in measurement results expected for sound, reproducible research and regulated applications in the clinic.  On April 13, 2012, the National Institute of Standards and Technology (NIST) convened the workshop Genome in a Bottle to initiate a consortium to develop the reference materials, reference methods, and reference data needed to assess confidence in human whole genome variant calls. A principal motivation for this consortium is to develop widely accepted reference materials and accompanying performance metrics to provide a strong scientific foundation for the development of regulations and professional standards for clinical sequencing.

The consortium has four working groups with the listed responsibilities:

  • Reference Material (RM) Selection and Design
  • Select appropriate cell lines for whole genome RMs and design synthetic DNA constructs that could be spiked-in to samples
  • Measurements for Reference Material Characterization,
  • Design and carry out experiments to characterize the RMs using multiple sequencing methods, other methods, and validation of selected variants using orthogonal technologies
  • Bioinformatics, Data Integration, and Data Representation
  • Develop methods to analyze and integrate the data for each RM, as well as select appropriate formats to represent the data
  • Performance Metrics and Figures of Merit
  • Develop useful performance metrics and figures of merit that can be obtained through measurement of the RMs

The products of these working groups will be a set of well-characterized whole genome and synthetic DNA RMs along with the methods (documentary standards) and reference data necessary for use of the RMs. These products will be designed to help enable translation of whole genome sequencing to clinical applications by providing widely accepted materials, methods, and data for performance assessment.

An open meeting was held August 16-17, 2012 at NIST in Gaithersburg, MD to receive public comment on this proposed work plan for the “Genome in a Bottle” Consortium.  Each working group developed a more detailed work plan, which is available in the slides and summary of the workshop. 

Since the workshop, there has been considerable discussion about what is an appropriate informed consent for whole genome Reference Materials from NIST. The consortium has decided to use the extensive existing data fromHapMap/CEPH/Utah Genetic Repository sample NA12878 and her pedigree for bioinformatics methods development, and NIST is seeking guidance from its IRB regarding the propriety of the current consent for a NIST Reference Material.  In parallel, the consortium has selected three father-mother-child trios with a more recent open consent from the Personal Genome Project for an initial set of NIST Reference Materials. When cell lines for these trios are available (hopefully in the next few months), the consortium will begin sequencing them with multiple sequencing technologies and library preparation methods. Over the next year, the consortium plans to select five additional trios from the Personal Genome Project as additional ethnic groups may choose to enroll.

On March 21, 2013 at 8:30am, the Genome in a Bottle Consortium is planning a morning session co-located with the XGen Congress in San Diego, CA. Each working group will present their progress and work plans and NIST will present its work forming consensus variant calls from multiple datasets on a single genome, followed by an open panel discussion with questions from the audience. All are welcome to attend this event free of charge, and we hope to see many of you there.  More information about the consortium can be found on the website www.genomeinabottle.org, and the consortium is always open to new members from public, private, and academic sectors. To receive updates, you can register and choose to receive newsletters by email on the website.

I-Study: Genomic Interpretation - Who Will Pay?
During this webinar, members of the study review team present preliminary findings of the I-Study, conducted at the Harvard Medical School's 2011 Personalized Medicine Conference.
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