Category Archives: Genome

The era of the $1000 genome, which is all but upon us already, is a new era of predictive and personalized medicine during which the cost of full genome sequencing for an individual or patient drops to roughly $1,000.

Think about what personalized medicine can do: having access to your own genome information will open the doors to dozens of men and women wishing to find out if they have gene variants associated with Alzheimers, diabetes, heart disease or cancer. In some circumstances this genome map will also help your doctor determine which drugs you should consider taking and at what dosage, which if accurate enough would be much more efficient than the current approach. Sounds great doesnt it?

You probably heard something like this back in 2000 when Bill Clinton mentioned the completion of the Human Genome Project in a speech and suggested that humanity can cure any disease and reveal the secrets of our evolution. Well, back then we didnt have a clue what this 3 billion letter code would bring upon us in terms of storing and handling it and properly analysing it. Only the most savvy IT experts and bioinformaticians foresaw what the technical impact would be, and the side effect of the ensuing flood of data certainly didnt make revealing the secrets of evolution particularly easy.

Twelve years on, the target users of the $1000 genome are scientists at R&D companies and academic institutions, and the occasional wealthy businessman or celebrity such as Ozzy Ozbourne. But so far theyve all paid much more than $1000. Steve Jobs, for example paid $100,000 for his genome to be sequenced and analyzed, when he was fighting with cancer. Admittedly the higher price was a year or so ago, so with the continuing decline in sequencing costs you may well now get a number closer to the $1000 if it is just for sequencing, but without analysis.

If some analysis needs to be done, have a look at this article in Forbes which describes a $4000 genome scan but only covering a fraction 0.02% of the full genome. This type of sequencing is often used for sequencing targeted areas of cancer tissues in order to find the mutations which triggered the cancer.

The $1000 genome figure refers to a full genome scan, much more than what is covered in the Forbes example. Whole genome sequencing covers the complete genome, all 3 billion bases of it, 99.9% of which is identical to every other human, and indeed 99% identical to chimpanzees and bonobos.

Life Technologies announced this year that they can already scan the full genome for $1000, and another company called Geniachip claims to go beyond this and deliver the same results for just $100. It will be interesting to see how good the quality of this $100 genome is!

Given that 99.9% of the genome is identical in all individuals, full genome sequencing is largely unnecessary at least, if we believe that we are sure that all the information we need is in the remaining 0.1%. The recently published ENCODE project found some individually unique traits within that supposedly constant 99.9% genetic sequence which means that we definitely do not know as much about what makes each genome individual as we might have previously thought.

Exome sequencing is a lighter option which will cover only the 1% of your genome that is coding sequence i.e. translated into proteins within your body. This type of sequence will still not include the features that the ENCODE project suggests might exist in the non-coding regions, but it is suited well to current knowledge about the individual variations that can be found in humans. It is offered to the general public by 23andMe and other similar companies and can cost as little as $299 when offered as a commercial service.

To sequence the genome is just the start. Storing it and analysing it can turn out quite pricey. To store only the basic sequence data (no quality scores or ambiguous results) from your fully sequenced human genome you will need roughly 780MB. This can easily be stored on a DVD, which is not expensive at all, but for companies sequencing many human genomes, and certainly for any research where the quality information is as important as the sequence itself, they will need much bigger storage than a single DVD. In-house data centers are the default choice, but the growth in data is outpacing the growth in storage available in these facilities. That is why many of them have embraced the power of the cloud technologies, such as Amazon Web Services.

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The $1,000 Genome Is Almost Here- Are We Ready?

OTTAWA, ONTARIO--(Marketwire - Oct 12, 2012) - Genome Canada is pleased to announce the appointment of a new Chair of the Board of Directors - Lorne Hepworth - who is assuming the position effective immediately. Hepworth brings to the role considerable vision and experience relating to industrial and economic development, private sector innovation, government and stakeholder relations, research management and more.

"Mr. Hepworth is a highly seasoned individual in matters relating to economic advancement based on innovations that are powered by science," said Pierre Meulien, President and CEO, Genome Canada. "We are very much looking forward to the contributions he will make as our Chair in advancing the role of genomics in the development of an emerging bioeconomy that impacts all Canadians."

"I am pleased to be part of an endeavour that holds so much promise for boosting Canadian innovation, productivity and competitiveness," said Hepworth. "I feel honoured that such a seasoned, accomplished Board has expressed their support for my leadership. Together, we will work hard to advance the power and promise of genomics."

Hepworth has, since 1997, served as President of CropLife Canada, the trade association representing developers, manufacturers and distributors of plant science innovations for use in agriculture, urban and public health settings. He has been a member of the Canadian Agri- Food Research Council, the federal government''s Pest Management Advisory Committee and National Biotechnology Advisory Committee. He is currently a Board member with CARE Canada and the Canadian International Food Security Research Fund (CIFSRF) Scientific Advisory Committee. He has been a director of Genome Canada''s Board since June 2010.

A graduate of the Western College of Veterinary Medicine at the University of Saskatchewan (1971), Hepworth was a practicing veterinarian in Alberta and Saskatchewan until 1982, when he was elected to Saskatchewan''s Legislative Assembly for the Constituency of Weyburn. He subsequently served nine years in Cabinet, during which time he was appointed Minister of Agriculture, Education, Finance, and Energy and Mines.

From 1993 to 1997, he held several executive positions with the Canadian Agra group of companies specializing in agri-food/feed production, processing and marketing of such diverse products as wine, apple juice concentrate, canola oil and dehydrated alfalfa. While there, he also led the development of the International Division''s Agricultural Project in the People''s Republic of China.

Hepworth replaces Dr. C. Thomas Caskey, who is stepping down after a considerable tenure of serving on Genome Canada''s Board, including three years as its Chair.

Genome Canada is a catalyst for developing and applying genomic sciences that create economic wealth and social benefit for Canadians. We work in partnership to invest in and manage large-scale research and translate discoveries into commercial opportunities, new technologies, applications and solutions. We build bridges between government, academia and industry to forge a genomics-based public-private innovation focused on key life science sectors. For more information, visit http://www.genomecanada.ca

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Genome Canada Board Appoints New Chair

Laws to keep genetic information private are not strong enough -- a situation that could hinder progress in important research, according to a new high-level study Thursday on medical ethics.

As human genome sequencing becomes more and more affordable, researchers are finding new and important ways to use the data for research and at the clinical level.

This has the potential to lead to even more major advances in medicine and science, the Presidential Commission for the Study of Bioethical Issues said in its report.

But these advances depend on having available vast amounts of genetic information, coming from tens of thousands, or even millions of people, most of whom would not benefit directly from the research, emphasized commission chair Amy Gutmann.

And therein lies the potential for ethical dilemmas, the authors wrote, making a dozen recommendations on reinforcing regulations to protect the confidentiality of an individual's genetic information.

"Those who are willing to share some of the most intimate information about themselves for the sake of medical progress should be assured appropriate confidentiality," Gutmann said.

"The commission's goal was to find the most feasible ways of reconciling the enormous medical potential of whole genome sequencing with the pressing privacy and data access issues raised by the rapid emergence of low-cost whole genome sequencing," she added.

For instance, a person's genome may reveal a predisposition for diseases like Alzheimer's, diabetes, schizophrenia or heart problems. That information could be used in a negative way by employers or health insurance companies.

Without assurances that would not happen, many people may feel wary of volunteering for genome sequencing, the authors wrote.

And while genomic data are kept confidential in some situations, in others the rules are less clear.

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US panel calls for stronger privacy for genome data

Many U.S. states lack laws to protect people from harmful use of their whole DNA transcripts, or genomes, and should work with the federal government to provide consistent protection, presidential advisers said.

About half of states dont have legislation that would prevent someone from secretly analyzing another persons genome with the saliva from a used coffee cup, said Amy Gutmann, who led the Presidential Commission for the Study of Bioethical Issues panel that released a report today.

Variations in the human genome can spell the difference between health and disease for individuals, and the cost of a complete analysis has dropped from more than $1 million to about $4,500 in less than eight years. As genome sequencing becomes cheaper and more routine, the stakes are rising to keep vital information about a persons health private, Gutman said.

To make full use of whole genome sequencing, which holds out enormous promise for human health and medicine, were going to have to figure out how to protect peoples privacy and avoid the harm that come from misuse of this data, said Gutmann, who is also president of the Philadelphia-based University of Pennsylvania, in a telephone conference with reporters.

Existing federal laws, such as the Health Insurance Portability and Accountability Act, the Genetic Information Nondiscrimination Act, and the Common Rule that protects research subjects, offer some protections against unauthorized use of medical data, the panel said. Rewriting those rules might ensure that patients have some needed protections, said Anita Allen, a University of Pennsylvania law professor and a member of the commission.

Such a reform might be a very useful thing to do, and is likely to be taken up by Congress, Allen said.

As cost of sequencing falls, doctors may begin using whole genomes to assess patients risk of cancer, diabetes, heart disease, or other conditions, the report said. Scientists are clamoring for more genomes to add to data sets that can help clarify the impact of variations in the genome, it said.

Illumina Inc. (ILMN), based in San Diego, and Life Technologies Corp. (LIFE), based in Carlsbad, California, are the two biggest makers of DNA sequencers.

Many hospitals and medical centers are asking patients whether some of their genetic data, if not their whole genomes, can be used for such research, the report said.

Those who are willing to share some of the most intimate information about themselves for the sake of medical progress should be assured appropriate confidentiality, Gutmann said in a statement released by the commission.

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Inconsistent Genome Privacy Laws Need Toughening, Panel Says

STORRS

In what could further bolster hopes of making the state a hub for genomics research, a University of Connecticut researcher has received a $9.3 million grant as part of the massive international effort to better understand the human genome.

With the four-year grant, Brenton Graveley, a professor of genetics and developmental biology at the UConn Health Center, will study the functions of the genome that essentially turn genes "on" and "off" at certain times and the role this has on disease.

It's one of 15 grants awarded by the National Institutes of Health as part of the Encyclopedia Of DNA Elements (ENCODE), a worldwide project that involves hundreds of scientists and is designed to catalog all the functional elements of the genome and learn more about the genetic origins of several diseases.

"It's a big grant," said Dr. Marc Lalande, director UConn's Stem Cell Institute, adding that it's one of the largest the Health Center has received. "But more important than the money, it really boosts our reputation in genomics around the country. The other institutes that were recipients are the best places in the country."

Graveley previously worked on the modENCODE project, an extension of ENCODE, in which researchers mapped the functional elements of the genomes of the fruit fly and roundworm.

The previous phase of the ENCODE project also featured a major contribution from a Connecticut researcher. Mark Gerstein, professor of biomedical informatics at Yale, had received three NIH grants to study the molecular interactions of the genome and the complex networks they form. His research also shed light on the degree to which a mother and father each contribute to a genome. His findings, along with those of the rest of the phase of ENCODE were released in September.

Work in genomics began in earnest in the state in the 1990s, when Connecticut resident Jonathan Rothberg founded CuraGen, one of the first genomics start-up companies. Researchers at Yale, UConn and Wesleyan have since produced several important studies in the field.

The possibility that the state could be a major player in the field gained further ground last year, when state officials announced that Maine-based Jackson Laboratory planned to build a research facility on UConn's campus.

One of the hopes for genomics research is that it will produce an accessible form of personalized medicine which will allow doctors to precisely and quickly diagnose patients and with little trial and error administer effective treatment. It would also give patients a better understanding of their genetic risks for certain diseases.

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UConn Gets Grant For Genome Research

Peter Aldhous, San Francisco bureau chief In the era of the $1000 human genome, new rules will be needed to protect people's genetic privacy.

The US government and individual states should harmonize a mish-mash of laws to ensure a basic "floor" of genetic privacy protection across the nation, however the data information was obtained, the commission adds. For instance, if a volunteer has their genome sequenced for research, the information should have similar protection from prying eyes as if the analysis had been ordered by a doctor for diagnostic purposes.

Breaches in security of DNA sequence data held on computer systems are the most obvious threat. But in 2009, New Scientist pointed to another danger by simulating the surreptitious analysis of my genome: a colleague used commercially available services to extract DNA from a glass from which I had drunk, and analyse it for my genetic predispositions to disease.

We ordered a scan of about 1 million letters of my genetic code, but plummeting prices and advancing technology will soon make it feasible to obtain a full genome sequence in a similar way, at modest cost.

The new report comes down firmly against surreptitious genome sequencing:"[P]olicies should protect individual privacy by prohibiting unauthorized whole genome sequencing without the consent of the individual from whom the sample came."

This is part of a larger patchwork of regulation on genetic privacy that the bioethics commission wants to see overhauled.

Geneticists taking samples for research are not covered by HIPAA, but separate rules covering informed consent and the protection of research subjects. Researchers are usually careful to protect volunteers' privacy, but if breaches were to occur, those responsible would not be subject to the same criminal prosecution.

Without clear and consistent guidelines to protect personal genetic information, the bioethics commission fears that people could suffer harm - in part by keeping secret information that could help their doctors provide better treatment.

It was only when Grove developed a bout of pneumonia that she knew could lead to permanent lung damage for people with the condition that she broke down, explaining in a tearful phone call to a clinic why she needed an urgent prescription for antibiotics.

"If it's too difficult for those companies to operate, we may have a bottleneck in providing access to the patient who needs that information," she says.

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Cheap genome sequences demand new rules on privacy

ScienceDaily (Oct. 10, 2012) Whole genome sequencing -- spelling out all 3 billion letters in the human genome -- "is an obvious and powerful method for advancing our understanding of pancreatic cancer," according to a new study from TGen, Mayo Clinic and Scottsdale Healthcare published October 10.

The Translational Genomics Research Institute (TGen) demonstrated that the use of WGS "represents a compelling solution to obtaining detailed molecular information on tumor biopsies in order to provide guidance for therapeutic selection," concluded the study published by the journal PLOS ONE.

Examining three patients, the study spelled out the DNA of normal cells and compared that to the DNA of cells from biopsies of pancreatic adenocarcinoma (PAC), which makes up 95 percent of all pancreatic cancer tumors. Pancreatic cancer is the fourth leading cause of cancer death in the U.S.

Using next-generation sequencing, the study generated an average of 132 billion mappable bases, or data points, for each patient, resulting in the identification of 142 cellular genetic coding events, including mutations, insertions and deletions, and chromosomal copy number variants.

"This study is the first to report whole genome sequencing findings in paired tumor/normal samples collected from (three) separate PAC patients," said the report, which also was compiled with the collaboration of Mayo Clinic in Arizona, Arizona State University, and the Virginia G. Piper Cancer Center Clinical Trials at Scottsdale Healthcare, which is a partnership between TGen and Scottsdale Healthcare.

In all three case studies, the report found multiple potential therapeutic targets, highlighting the need to study the full spectrum of the genome and re-emphasizing the need to develop multiple avenues of therapeutics to match the specific medical challenges of each patient.

"Cancer, and specifically here pancreatic cancer, is a highly complex disease that ultimately will require a variety of treatment methods to control, and ultimately to cure," said Dr. Daniel Von Hoff, TGen's Physician-In-Chief, and Chief Scientific Officer for the Virginia G. Piper Cancer Center at Scottsdale Healthcare.

"This study shows that, as we continue to generate more information by sequencing the whole genomes of patients, we will continue to discover -- with ever more confidence -- the specific mechanisms that cause this cancer," said Dr. Von Hoff, one of the study's senior authors and one of the world's leading authorities on pancreatic cancer.

"We are very pleased to be working together with TGen in bringing hope and state of the art therapy to our patients at the Mayo Clinic Comprehensive Cancer Center," said Keith Stewart, M.B., Dean of Research at Mayo Clinic in Arizona, and the study's other senior author.

In the case of Patient 1, for example, genes previously associated with PAC were identified, including BRCA2, TP53, CDKN2A, MYC, SMAD4 and KRAS. But the study also made new discoveries. "Although BRCA2 mutations have been identified in PAC, the deletion we identify here in exon 10 of BRCA2 has not been previously reported," the study said.

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First whole genome sequencing of multiple pancreatic cancer patients has been outlined

Course Provides Opportunity for Students to Sequence, Analyze and Interpret Their Own Personal Genome Using Cutting-Edge Techniques

(PRWEB) October 08, 2012

The elective course, titled Practical Analysis of Your Personal Genome, is designed to address a gap in todays medical and graduate school education: to teach students how to understand and apply the wealth of information now available via whole genome sequencing, a laboratory process that reveals the unique genomic profile of each individual performed in the Genomics Core Facility at Mount Sinai. This course is offered through the Genetics and Genomic Sciences training area within the Graduate School of Biological Sciences.

Specifically, whole genome sequencing refers to full elucidation of an organisms DNA, which involves more than 3 billion nucleotide bases known as A,T, C, and G. It is an important part of a new era in modern medicinecalled precision medicinewhere precise knowledge of the molecular mechanism behind a patients condition would ultimately allow physicians to determine more individualized care. Recent technological advances have substantially lowered the cost of whole genome sequencing to where it can soon be applied in routine clinical care.

For precision medicine to become a routine in the medical clinic, we need to train the next great generation of physicians to harness sequencing-driven medical genetics, explained Dennis S. Charney, MD, Anne and Joel Ehrenkranz Dean of Mount Sinai School of Medicine and the Executive Vice President for Academic Affairs of The Mount Sinai Medical Center. We believe that an approach tailored to each individual patients diagnosis and treatment, informed by genomic information, will provide dramatic improvements in the quality of care. Practical Analysis of Your Personal Genome reflects Mount Sinais commitment to revolutionize the diagnosis and treatment of disease through the application of genomic information.

Andrew Kasarskis, PhD, Vice Chair, Department of Genetics and Genomic Sciences, said, "Unlike other courses that use commercial services to provide students with only a small portion of their genetic data, we decided to offer students in the course the unprecedented opportunity to do whole genome sequencing to view, analyze and interpret their entire genome." Dr. Kasarskis is also Co-Director, Mount Sinai Institute for Genomics and Multiscale Biology at Mount Sinai.

Students have the option to either sequence their own personal genome or that of an anonymous reference genome. When analyzing a complete genome, students will find greater than 4 million variants, many with known clinical significance, yet many with unclear significance. Students may find variants in their chosen genome related to ancestry, response to medications, the risk of developing diseases such as diabetes or cancer, and carrier status for single-gene disorders.

Mount Sinai also is conducting a questionnaire-based study to explore the degree to which course students who analyze their own genome demonstrate greater knowledge, as well as their perceptions regarding the utility of whole genome sequencing, and the impact on psychological wellbeing. This research will help faculty to learn how best to help students to interpret and analyze the wealth and complexity of genomic data, including potentially difficult findings such as risks of disease and carrier status. The results of the research study will be available after the course concludes in December.

The 20 students in the course represent a diverse collection of MD and PhD students, medical residents, genetic counseling students, and junior faculty. Though there was an emphasis on genetics, students were selected from a variety of backgrounds to reflect the interdisciplinary nature of applying genomic information to patient care, said Randi E. Zinberg, MS, CGC, Assistant Professor of Genetics and Genomic Sciences and of Obstetrics, Gynecology and Reproductive Science, and Director of the Graduate Program in Genetic Counseling at Mount Sinai School of Medicine.

We expect that courses such as ours will soon become an integral part of the curriculum at all medical schools. We look forward to sharing our learning from this course with other medical schools and graduate schools worldwide to help advance the breadth and depth of medical genetics education, Ms. Zinberg said.

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Mount Sinai School of Medicine Offers First-Ever Course with Whole Genome Sequencing

The concept of the $1,000 genome is "misleading," says Laura Hercher on the genetic counseling blog The DNA Exchange.

Hercher, a faculty member at Sarah Lawrence College, acknowledges that the cost of sequencing is dropping rapidly, but notes that the "$1,000 genome" doesn't mean that "getting your DNA sequenced will cost $1,000" because the number "covers only renewables those things like reagents and chips that are consumed in the process of sequencing. It does not include the cost of the sequencer or the cost of the tech who runs the sequencer. It does not cover overhead or profits. And most of all, it does not cover the costs associated with interpretation, without which a DNA sequence is merely an endless stream of A's, C's, T's and G's."

While much-hyped efforts like Mike Snyder's analysis of his own genome, which predicted that he had a high risk for diabetes, are commendable, "Snyder had available to him levels of expertise and medical care that are not in any way typical," Hercher says. "For much of America, paying for routine medical care is a challenge, and paying for acute or chronic medical care the most likely cause of personal bankruptcy."

Furthermore, she says, "Even people with money to spare don't usually get a sit-down with George Church to discuss their most disturbing sequence variants."

Hercher says that the $1,000 genome "is an enormous technical achievement" but warns that the scientific community should not "confuse people about what it means."

"The meme that represents the future of genetics should not be a bait-and-switch," she says.

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The $1,000 Genome: A Bait and Switch?

Raw genomic data are too complex for most physicians to use in the clinic.

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As DNA sequencing gets faster and cheaper, clinicians are clamouring to use it. A test for malfunctioning genes might show how to treat a tumour or help to diagnose the underlying causes of a disease. But sequencing data are too complex for most clinicians to analyse, and medical institutions are wary of transferring patient data to specialists elsewhere for analysis.

A genome-interpretation company is now offering its solution: a 1-metre-tall, 275-kilogram black box that carries enough storage and processing power to analyse one genome every day, picking out mutations with potential links to disease in theory, fast enough to inform treatment. But for some, the most important feature of the US$125,000 unit is that it is a self-contained object. In an era of cloud computing and global networks, a machine that keeps its information stubbornly local has growing appeal. There is a tremendous worry about privacy with sharing patient data, says Martin Tolar, chief executive of Knome, the company in Cambridge, Massachusetts, that produces the device. The institutions we approached said, We want to keep the system within our four walls.

Unveiled on 27 September, the Knome system, knoSYS 100, belongs to an emerging class of services and tools to help clinical researchers to catch up with advances in genome sequencing. That capability has made itself available faster than we are prepared to deal with, says Vincent Funari, director of the genomics core facility at Cedars-Sinai Medical Center in Los Angeles, California.

The core of Knomes system is not hardware, but software. The machine combs through a newly sequenced genome to find places where humans vary, and annotates them with existing knowledge. This process, known as genome interpretation, can winnow down the millions of variants found in any individuals genome to a handful that might explain a disease (see Super sifter). Our goal is to take these data and say, For this group of patients, these are the 510variants that are most likely to be implicated,explains Tolar. For now, the software is not meant for clinical diagnosis or medical advice. Clients include drug companies and medical centres researching how to use sequencing for clinical decisions.

Experts warn that genome interpretation is far from mature, and that its reliability depends on the quality of the sequences it analyses. Not all types of variants can be detected, and errors occur at every step before and during interpretation: in the sequencing of fragments of DNA; in matching those millions of fragments with their equivalents in the reference genome; and in detecting differences. The interpretation of variants is absolutely dependent on accurate variant identification, says Karl Voelkerding, medical director for genomics and bioinformatics at ARUP Laboratories, an assay facility in Salt Lake City, Utah.

Then there is the challenge of working out which detected variants are relevant to disease. The protocols are imperfect and the various annotation tools access different data in different ways and so supply a variety of answers. And all annotation tools uncover many variants of unknown significance,about which too little is known to assess whether or not they affect a persons health. Any variant that might be used to provide a diagnosis or guide patient care must be verified independently by separate experiments.

But just organizing information into a useful form is a big step forward, says George Church, a genomicist at Harvard Medical School in Boston, Massachusetts, and co-founder of Knome. The process, he says, is not about perfection. Its about delivering a high-quality interpretation based on current knowledge.

Knomes device may be well placed to tap a nascent clinical market in which data is preferentially kept on site, but sequencing companies are also making inroads with software that requires genomic data to be transferred elsewhere. For example, Illumina, based in San Diego, California, offers free data storage and variant identification for clients who upload sequencing data to its cloud-computing platform, which has an open programming interface. Illumina has contracts with a suite of other companies to develop data-analytic applications in the cloud. As more centres begin using sequencing data, it is expected that policies and procedures for using the cloud will mature.

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Genome interpreter vies for place in clinical market