Accurate detection and genotyping of SNPs utilizing population sequencing data.

Next generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for SNP detection are designed to detect SNPs from single individual sequence datasets. Here we describe a novel method SNIP-Seq (Single Nucleotide polymorphism Identification from Population Sequence data) that leverages sequence data from a population of individuals to detect SNPs and assign genotypes to individuals. To evaluate our method, we utilized sequence data from a 200 kilobase region on chromosome 9p21 of the human genome. This region was sequenced in 48 individuals (5 sequenced in duplicate) using the Illumina GA platform. Using this dataset, we demonstrate that our method is highly accurate for detecting variants and can filter out false SNPs that are attributable to sequencing errors. The concordance of sequencing based genotype assignments between duplicate samples was 98.8%. The 200 kb region was independently sequenced to a high depth of coverage using two sequence pools containing the 48 individuals. Many of the novel SNPs identified by SNIP-Seq from the individual sequencing were validated by the pooled sequencing data and were subsequently confirmed by Sanger sequencing. We estimate that SNIP-Seq achieves a low false positive rate of ~2% improving upon the higher false positive rate for existing methods that do not utilize population sequence data. Collectively, these results suggest that analysis of population sequencing data is a powerful approach for the accurate detection of SNPs and the assignment of genotypes to individual samples.

from The Scripps Institute

MarketWatch: Sequencing Companies Dominate Investment

$400 the approximate cost of genetic testing to predict a patient’s response to the commonly prescribed blood thinner warfarin.

MIT Technology Review, March/April 2010, by Lauren Gravitz – The market for personalized medicine is growing: according to PricewaterhouseCoopers, the core market will reach $42 billion by 2015. However, that growth is not uniform. Some areas, such as genomic sequencing, are surging ahead; others, such as translating genetic data into clinically useful information, languish.

In this environment, startups developing sequencing technologies, such as Pacific Biosciences, Illumina, and Complete Genomics, have attracted sustained investor interest as they race to create ever cheaper ways to decode DNA (see “Faster Tools to Scrutinize the Genome“). In their most recent rounds of venture funding last summer, Pacific Biosciences and Complete Genomics received $68 million and $45 million, respectively.

Diagnostic technologies, too, are moving at a rapid pace. Startups from Boston to Silicon Valley have been pinning down disease-related genetic markers and creating many new tests that are already in the clinic or on their way. As these companies grow and bring more tests to market, large diagnostics companies are likely to acquire them, says venture capitalist Brook Byers of Kleiner Perkins Caufield and Byers.

One of the biggest undeveloped areas in personalized medicine, however, is the information technology needed to analyze and store the huge quantity of genetic data that is starting to pour forth (see “Drowning in Data“). Of the few bioinformatics companies working to digest the data, Proventys, based in Newton, MA, is among the furthest along. Its technology combines biomarkers and other information to make risk predictions about diseases.

Meanwhile, pharmaceutical companies are responding to the nascent market for personalized therapeutics in different ways. Pfizer, for example, is collaborating with existing biotech companies to develop drugs and diagnostics based on genetic testing. AstraZeneca recently announced a partnership with the Danish diagnostics company Dako, the first of many alliances it plans in a strategy for bringing genetic tests to market. Novartis is taking a different tack, dedicating a large portion of its own resources to developing personalized medicine.

In the United States, benefit management companies, which act as middlemen between patients and insurers or employers, are aggressively moving into the market. One of the largest, Medco, has established a personalized-medicine group to recommend which genetic tests insurers should pay for. In February it acquired DNA Direct, a firm that specializes in analyzing genetic diagnostics, to aid in this effort. One of its largest competitors, CVS Caremark, increased its stake in a similar company, Generation Health, last December. Because such companies serve millions of people, they will play a critical role in making genetic tests broadly available and educating doctors about the benefits of offering such tests to their patients.

A machine for DNA sequencing was invented by Leroy Hood and his colleagues at Caltech. In 1992, Hood and several others were granted U.S. patent 5,171,534 for an “Automated DNA Sequencing Technique.” Replacing slow and expensive manual methods, this is one of the most important pieces of intellectual property in biotechnology; explore this interactive analysis by IPVision of the patent’s impact on the innovation landscape.http://www.technologyreview.com/biomedicine/24593/page2/

Biotech & Genetics Industry Market Research, Statistics, Trends & Leading Companies

Plunkett’s Biotech and Genetics Industry Almanac 2009

Plunkett’s Biotech & Genetics Industry Almanac is a complete reference guide to the business side of biotechnology, genetics, proteomics and related services. This new book contains complete profiles of the leading biotech companies, in-depth chapters on trends in genetics, technologies, statistics and finances, a handy glossary and thorough indexes. Plunkett’s Biotech & Genetics Industry Almanac, our easy-to-understand reference to the biotech and genetics industry, is an absolutely vital addition to your office. For the first time, in one carefully-researched volume, you’ll get all of the data you need. Topics include: A Short History of Biotechnology; The State of the Biotechnology Industry Today; Biotechnology funding and investments; Patents; Biotech activities in Singapore and China; FDA; Gene Therapies; Personalized Medicine; Systems Biology; Drug Development; Clinical Trials; Controversy over Drug Prices; Stem Cells Research; Therapeutic Cloning; Regenerative Medicine Nanotechnology; Agricultural Biotechnology; Drug Delivery Systems; BioShield; Ethical Issues. The book also includes complete profiles on over 400 Biotech & Genetics companies, our own unique list of companies that are the leaders in biotechnology. These are the largest, most successful corporations in all facets of this exploding business. All of the corporate profile information is indexed and cross-indexed, including contact names, addresses, Internet addresses, fax numbers, toll-free numbers, plus growth and hiring plans, finances, research, marketing, technology, acquisitions and much more for each firm. Purchasers of either the book or PDF version can request a free copy of the company profiles database on CD-ROM, enabling export of contact names, addresses and more.

from

BiotechConnection.com

Cheap DNA sequencing will drive a revolution in health care

The dream of personalized medicine was one of the driving forces behind the 13-year, $3 billion Human Genome Project. Researchers hoped that once the genetic blueprint was revealed, they could create DNA tests to gauge individuals' risk for conditions like diabetes and cancer, allowing for targeted screening or preëmptive intervention. Genetic information would help doctors select the right drugs to treat disease in a given patient. Such advances would dramatically improve medicine and simultaneously lower costs by eliminating pointless treatments and reducing adverse drug reactions.

Delivering on these promises has been an uphill struggle. Some diseases, like Huntington's, are caused by mutations in a single gene. But for the most part, when our risk of developing a given condition depends on multiple genes, identifying them is difficult. Even when the genes linked to a condition are identified, using that knowledge to select treatments has proved tough (see "Drowning in Data"). We now have the 1.0 version of personalized medicine, in which relatively simple genetic tests can provide information on whether one patient will benefit from a certain cancer drug or how big a dose of blood thinner another should receive. But there are signs that personalized medicine will soon get more sophisticated. Ever cheaper genetic sequencing means that researchers are getting more and more genomic information, from which they can tease out subtle genetic variations that explain why two otherwise similar people can have very different medical destinies. Within the next few years, it will become cheaper to have your genome sequenced than to get an MRI (see "A Moore's Law for Genetics"). Figuring out how to use that information to improve your medical care is personalized medicine's next great challenge.

Pharmacogenomics: Personalized Medicine at the Corner Drugstore

MayoClinic.com, GoogleNews.com, February 24, 2010, by Carrie A. Zabel – Personalized medicine offered at your local drugstore?

Two large prescription drug companies have announced plans to offer genetic testing as part of the prescription-filling process. The testing will center on an emerging science, pharmacogenomics, which studies drug response based upon an individual’s genetic make-up. Pharmacogenomic testing is already used for some commonly prescribed drugs such as Tamoxifen and Warfarin.

The process would use a pharmacy benefits management company that would contract with large drugstore chains. When certain prescriptions come in, the company would contact the physician to let them know a genetic test is available, which may help them to more appropriately prescribe that medication. The individual may then be offered the genetic testing, but it wouldn’t be required.

Supporters say this will improve patient safety, health outcomes and decrease overall health care costs by using the right medications in the right patients. It may also provide an opportunity to advance the field of pharmacogenomics by collecting data on genetic testing results and drug effectiveness.

Others are concerned about the privacy of genetic testing information and say the science of pharmacogenomics is premature. Drug metabolism isn’t only based on our genetic make-up, but is affected by many additional factors, such as body size and age. And, since pharmacogenomics is a relatively new science, insurance companies may not reimburse for the cost of genetic testing.

Carrie A. Zabel, M.S., C.G.C., Genetic Counselor