jeudi 25 mars 2010
Personal Genomes meeting, Cold Spring Harbor Laboratory, September 2009
Personal Genomes meeting, Cold Spring Harbor Laboratory, September 2009
jeudi 11 mars 2010
Disease Cause Is Pinpointed With Genome
By NICHOLAS WADE
The New York Times, March 10, 2010
Two research teams have independently decoded the entire genome of patients to find the exact genetic cause of their diseases. The approach may offer a new start in the so far disappointing effort to identify the genetic roots of major killers like heart disease, diabetes and Alzheimer’s.
In the decade since the first full genetic code of a human was sequenced for some $500 million, less than a dozen genomes had been decoded, all of healthy people.
Geneticists said the new research showed it was now possible to sequence the entire genome of a patient at reasonable cost and with sufficient accuracy to be of practical use to medical researchers. One subject’s genome cost just $50,000 to decode.
“We are finally about to turn the corner, and I suspect that in the next few years human genetics will finally begin to systematically deliver clinically meaningful findings,” said David B. Goldstein, a Duke University geneticist who has criticized the current approach to identifying genetic causes of common diseases.
Besides identifying disease genes, one team, in Seattle, was able to make the first direct estimate of the number of mutations, or changes in DNA, that are passed on from parent to child. They calculate that of the three billion units in the human genome, 60 per generation are changed by random mutation — considerably less than previously thought.
The three diseases analyzed in the two reports, published online Wednesday, are caused by single, rare mutations in a gene.
In one case, Richard A. Gibbs of the Baylor College of Medicine sequenced the whole genome of his colleague Dr. James R. Lupski, a prominent medical geneticist who has a nerve disease, Charcot-Marie-Tooth neuropathy.
In the second, Leroy Hood and David J. Galas of the Institute for Systems Biology in Seattle have decoded the genomes of two children with two rare genetic diseases, and their parents.
More common diseases, like cancer, are thought to be caused by mutations in several genes, and finding the causes was the principal goal of the $3 billion human genome project. To that end, medical geneticists have invested heavily over the last eight years in an alluring shortcut.
But the shortcut was based on a premise that is turning out to be incorrect. Scientists thought the mutations that caused common diseases would themselves be common. So they first identified the common mutations in the human population in a $100 million project called the HapMap. Then they compared patients’ genomes with those of healthy genomes. The comparisons relied on ingenious devices called SNP chips, which scan just a tiny portion of the genome. (SNP, pronounced “snip,” stands for single nucleotide polymorphism.) These projects, called genome-wide association studies, each cost around $10 million or more.
The results of this costly international exercise have been disappointing. About 2,000 sites on the human genome have been statistically linked with various diseases, but in many cases the sites are not inside working genes, suggesting there may be some conceptual flaw in the statistics. And in most diseases the culprit DNA was linked to only a small portion of all the cases of the disease. It seemed that natural selection has weeded out any disease-causing mutation before it becomes common.
The finding implies that common diseases, surprisingly, are caused by rare, not common, mutations. In the last few months, researchers have begun to conclude that a new approach is needed, one based on decoding the entire genome of patients.
The new reports, though involving only single-gene diseases, suggest that the whole-genome approach can be developed into a way of exploring the roots of the common multigene diseases.
“We need a way of assessing rare variants better than the genomewide association studies can do, and whole-genome sequencing is the only way to do that,” Dr. Lupski said.
With 10 genomes of healthy humans sequenced, Dr. Gibbs, a specialist in DNA sequencing, decided it was time to decode the genome of someone with a genetic disease and asked his colleague Dr. Lupski to volunteer.
Mutations in any of 39 genes can cause Charcot-Marie-Tooth, a disease that impairs nerves to the hands and feet and causes muscle weakness.
Fifty thousand dollars later, Dr. Lupski turned out to have mutations in an obscure gene called SH3TC2. The copy of the gene he inherited from his father is mutated in one place, and the copy from his mother in a second.
Both his parents had one good copy of the gene in addition to the mutated one. A single good copy can generate enough, or nearly enough, of the gene’s product for the nerves to work properly. Dr. Lupski’s mother was free of the disease and his father had only mild symptoms.
In the genetic lottery that is human procreation, two of their eight children inherited good copies of SH3TC2 from each parent; two inherited the mother’s mutation but the father’s good copy and are free of the disease; and four siblings including Dr. Lupski inherited mutated copies from both parents. These four all have Charcot-Marie-Tooth disease. The results are reported in The New England Journal of Medicine.
In Seattle, Dr. Hood and Dr. Galas have also applied whole-genome sequencing to disease. They analyzed the genome of a family of four, in which the two children each have two single-gene diseases, called Miller syndrome and ciliary dyskinesia. With four related genomes available, the researchers could identify the causative genes. They also improved the accuracy of the sequencing because DNA changes that did not obey Mendel’s rules of inheritance could be classed as errors in the decoding process.
The Seattle team believes whole-genome sequencing can be applied to the study of the common multigene diseases and plans to sequence more than 100 genomes next year, starting with multigenerational families.
The family whose genomes they report in Science were sequenced by a company with a new DNA sequencing method, Complete Genomics of Mountain View, Calif., at a cost of $25,000 each. Clifford Reid, the chief executive, said that the company was scaling up to sequence 500 genomes a month and that for large projects the price per genome would soon drop below $10,000. “We are on our way to the $5,000 genome,” he said.
Dr. Reid said the HapMap and genomewide association studies were not a mistake but “the best we could do at the time.” But they have not yet revolutionized medicine, “which we are on the verge of doing,” he said.
Dr. Goldstein, of Duke University, said the whole-genome sequencing approach that was now possible should allow rapid progress. “I think we are finally headed where we have long wanted to go,” he said.
The New York Times, March 10, 2010
Two research teams have independently decoded the entire genome of patients to find the exact genetic cause of their diseases. The approach may offer a new start in the so far disappointing effort to identify the genetic roots of major killers like heart disease, diabetes and Alzheimer’s.
In the decade since the first full genetic code of a human was sequenced for some $500 million, less than a dozen genomes had been decoded, all of healthy people.
Geneticists said the new research showed it was now possible to sequence the entire genome of a patient at reasonable cost and with sufficient accuracy to be of practical use to medical researchers. One subject’s genome cost just $50,000 to decode.
“We are finally about to turn the corner, and I suspect that in the next few years human genetics will finally begin to systematically deliver clinically meaningful findings,” said David B. Goldstein, a Duke University geneticist who has criticized the current approach to identifying genetic causes of common diseases.
Besides identifying disease genes, one team, in Seattle, was able to make the first direct estimate of the number of mutations, or changes in DNA, that are passed on from parent to child. They calculate that of the three billion units in the human genome, 60 per generation are changed by random mutation — considerably less than previously thought.
The three diseases analyzed in the two reports, published online Wednesday, are caused by single, rare mutations in a gene.
In one case, Richard A. Gibbs of the Baylor College of Medicine sequenced the whole genome of his colleague Dr. James R. Lupski, a prominent medical geneticist who has a nerve disease, Charcot-Marie-Tooth neuropathy.
In the second, Leroy Hood and David J. Galas of the Institute for Systems Biology in Seattle have decoded the genomes of two children with two rare genetic diseases, and their parents.
More common diseases, like cancer, are thought to be caused by mutations in several genes, and finding the causes was the principal goal of the $3 billion human genome project. To that end, medical geneticists have invested heavily over the last eight years in an alluring shortcut.
But the shortcut was based on a premise that is turning out to be incorrect. Scientists thought the mutations that caused common diseases would themselves be common. So they first identified the common mutations in the human population in a $100 million project called the HapMap. Then they compared patients’ genomes with those of healthy genomes. The comparisons relied on ingenious devices called SNP chips, which scan just a tiny portion of the genome. (SNP, pronounced “snip,” stands for single nucleotide polymorphism.) These projects, called genome-wide association studies, each cost around $10 million or more.
The results of this costly international exercise have been disappointing. About 2,000 sites on the human genome have been statistically linked with various diseases, but in many cases the sites are not inside working genes, suggesting there may be some conceptual flaw in the statistics. And in most diseases the culprit DNA was linked to only a small portion of all the cases of the disease. It seemed that natural selection has weeded out any disease-causing mutation before it becomes common.
The finding implies that common diseases, surprisingly, are caused by rare, not common, mutations. In the last few months, researchers have begun to conclude that a new approach is needed, one based on decoding the entire genome of patients.
The new reports, though involving only single-gene diseases, suggest that the whole-genome approach can be developed into a way of exploring the roots of the common multigene diseases.
“We need a way of assessing rare variants better than the genomewide association studies can do, and whole-genome sequencing is the only way to do that,” Dr. Lupski said.
With 10 genomes of healthy humans sequenced, Dr. Gibbs, a specialist in DNA sequencing, decided it was time to decode the genome of someone with a genetic disease and asked his colleague Dr. Lupski to volunteer.
Mutations in any of 39 genes can cause Charcot-Marie-Tooth, a disease that impairs nerves to the hands and feet and causes muscle weakness.
Fifty thousand dollars later, Dr. Lupski turned out to have mutations in an obscure gene called SH3TC2. The copy of the gene he inherited from his father is mutated in one place, and the copy from his mother in a second.
Both his parents had one good copy of the gene in addition to the mutated one. A single good copy can generate enough, or nearly enough, of the gene’s product for the nerves to work properly. Dr. Lupski’s mother was free of the disease and his father had only mild symptoms.
In the genetic lottery that is human procreation, two of their eight children inherited good copies of SH3TC2 from each parent; two inherited the mother’s mutation but the father’s good copy and are free of the disease; and four siblings including Dr. Lupski inherited mutated copies from both parents. These four all have Charcot-Marie-Tooth disease. The results are reported in The New England Journal of Medicine.
In Seattle, Dr. Hood and Dr. Galas have also applied whole-genome sequencing to disease. They analyzed the genome of a family of four, in which the two children each have two single-gene diseases, called Miller syndrome and ciliary dyskinesia. With four related genomes available, the researchers could identify the causative genes. They also improved the accuracy of the sequencing because DNA changes that did not obey Mendel’s rules of inheritance could be classed as errors in the decoding process.
The Seattle team believes whole-genome sequencing can be applied to the study of the common multigene diseases and plans to sequence more than 100 genomes next year, starting with multigenerational families.
The family whose genomes they report in Science were sequenced by a company with a new DNA sequencing method, Complete Genomics of Mountain View, Calif., at a cost of $25,000 each. Clifford Reid, the chief executive, said that the company was scaling up to sequence 500 genomes a month and that for large projects the price per genome would soon drop below $10,000. “We are on our way to the $5,000 genome,” he said.
Dr. Reid said the HapMap and genomewide association studies were not a mistake but “the best we could do at the time.” But they have not yet revolutionized medicine, “which we are on the verge of doing,” he said.
Dr. Goldstein, of Duke University, said the whole-genome sequencing approach that was now possible should allow rapid progress. “I think we are finally headed where we have long wanted to go,” he said.
lundi 25 janvier 2010
Into the Personal Genomics Fray
GenomeWeb, January 25, 2010
Counsyl, a Stanford University start-up, has announced its Universal Genetic Test that allows prospective parents to determine whether their child would be at risk for more than 100 genetic diseases.
The company’s press release says that the test “is free with insurance for more than 100 million Americans” and “is now offered by physicians at more than 100 prestigious medical centers.”
At Genetic Future, Daniel MacArthur, who has used a free kit from Counsyl, says he is intrigued by its approach, especially that it is covered by some insurance companies and that it will likely face question about the ethics of screening for carriers.
“Counsyl's offering is intensely focused: the goal is simply to pick up as many known serious disease-associated mutations as possible,” he writes.
Counsyl, a Stanford University start-up, has announced its Universal Genetic Test that allows prospective parents to determine whether their child would be at risk for more than 100 genetic diseases.
The company’s press release says that the test “is free with insurance for more than 100 million Americans” and “is now offered by physicians at more than 100 prestigious medical centers.”
At Genetic Future, Daniel MacArthur, who has used a free kit from Counsyl, says he is intrigued by its approach, especially that it is covered by some insurance companies and that it will likely face question about the ethics of screening for carriers.
“Counsyl's offering is intensely focused: the goal is simply to pick up as many known serious disease-associated mutations as possible,” he writes.
jeudi 14 janvier 2010
New Machine From San Diego’s Illumina Intensifies Race for Faster, Cheaper Genome Decoder
Denise Gellene 1/14/10, xconomy.com
The cost of sequencing a person’s genome continues to fall. Illumina this week introduced a machine that can sequence an individual’s genome for under $10,000.
That is one percent of the $1 million it cost to decode a human genome three years ago (2007).
The announcement pushes San Diego-based Illumina to the forefront in an intense race to develop faster and cheaper genome-decoding equipment. The next-cheapest technology costs five times more.
Illumina, which unveiled its HiSeq 2000 at the JP Morgan Healthcare Conference in San Francisco, clearly believes the machine will establish its leadership in the gene-sequencing category.
“Other companies are talking about future products, but we’re talking about products that are going to ship next month,” CEO Jay Flatley told Forbes.
Illumina says its first customer is BGI, formerly known as the Bejing Genomics Institute, which has ordered 128 of the new gene-sequencers for its new genome center in Hong Kong.
The HiSeq 2000, which can sequence two genomes simultaneously, is priced at $690,000.
Flatley said during Illumina’s R&D Day presentation today that the purchase will make BGI the world’s largest genome center.
In a statement issued by Illumina, BGI’s president says it is focused on using genetic analysis to enhance agriculture and food production and to develop the personal genomics field in China.
It will be interesting to see how the competition shapes up from here. Complete Genomics of Mountain View, CA, which Luke profiled in 2008, has a stated goal of sequencing individual genomes for $5,000 each. It has a different business model from Illumina.
Rather than selling sequencing machines, Complete Genomics does the genome decoding in-house and sends clients the results. In November 2009, the company published a “proof of principle” in the journal Science that demonstrated it could sequence and analyze a person’s genome for $8,005 to $1,726.
Another competitor is Helicos Biosciences of Cambridge, MA, which announced last year that it had sequenced the genome of one of its founders for $50,000. That is about the same price Illumina set in August 2009 for its sequencing service aimed at consumers.
Cheaper sequencing will enable more researchers to examine genomes from large numbers of individuals for differences linked to health risks or disease.
Some believe that the information will lead to personalized medical care, based on an individual’s genetic information. No one knows how low the cost of genome sequencing can go. But it’s probably fair to say we haven’t seen the bottom.
Denise Gellene is a former Los Angeles Times science writer and regular contributor to Xconomy. You can reach her at dgellene@xconomy.com
The cost of sequencing a person’s genome continues to fall. Illumina this week introduced a machine that can sequence an individual’s genome for under $10,000.
That is one percent of the $1 million it cost to decode a human genome three years ago (2007).
The announcement pushes San Diego-based Illumina to the forefront in an intense race to develop faster and cheaper genome-decoding equipment. The next-cheapest technology costs five times more.
Illumina, which unveiled its HiSeq 2000 at the JP Morgan Healthcare Conference in San Francisco, clearly believes the machine will establish its leadership in the gene-sequencing category.
“Other companies are talking about future products, but we’re talking about products that are going to ship next month,” CEO Jay Flatley told Forbes.
Illumina says its first customer is BGI, formerly known as the Bejing Genomics Institute, which has ordered 128 of the new gene-sequencers for its new genome center in Hong Kong.
The HiSeq 2000, which can sequence two genomes simultaneously, is priced at $690,000.
Flatley said during Illumina’s R&D Day presentation today that the purchase will make BGI the world’s largest genome center.
In a statement issued by Illumina, BGI’s president says it is focused on using genetic analysis to enhance agriculture and food production and to develop the personal genomics field in China.
It will be interesting to see how the competition shapes up from here. Complete Genomics of Mountain View, CA, which Luke profiled in 2008, has a stated goal of sequencing individual genomes for $5,000 each. It has a different business model from Illumina.
Rather than selling sequencing machines, Complete Genomics does the genome decoding in-house and sends clients the results. In November 2009, the company published a “proof of principle” in the journal Science that demonstrated it could sequence and analyze a person’s genome for $8,005 to $1,726.
Another competitor is Helicos Biosciences of Cambridge, MA, which announced last year that it had sequenced the genome of one of its founders for $50,000. That is about the same price Illumina set in August 2009 for its sequencing service aimed at consumers.
Cheaper sequencing will enable more researchers to examine genomes from large numbers of individuals for differences linked to health risks or disease.
Some believe that the information will lead to personalized medical care, based on an individual’s genetic information. No one knows how low the cost of genome sequencing can go. But it’s probably fair to say we haven’t seen the bottom.
Denise Gellene is a former Los Angeles Times science writer and regular contributor to Xconomy. You can reach her at dgellene@xconomy.com
mardi 12 janvier 2010
mardi 13 octobre 2009
Kaiser, UCSF awarded $25 million from NIH to build resource for genetic research
October 13, 2009 UCSF News
The Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) and the University of California, San Francisco (UCSF) have been awarded $24.8 million over two years by the National Institutes of Health (NIH) to create a new resource for studying disease, health, and aging.
With this support, Kaiser Permanente’s RPGEH and UCSF will conduct a genome-wide analysis of DNA samples from 100,000 Kaiser Permanente members from Northern California who have volunteered to join the RPGEH. This new and detailed genetic information – which has never before been generated on such a large and diverse population – will be linked to decades of historical clinical and other health-related information on these participants, taken from health surveys and the Kaiser Permanente electronic health record, the world’s largest civilian electronic health record. Environmental information will also be included in the new resource, such as information about air and water quality, proximity to parks and healthy foods, and much more. The resulting resource will give researchers an entirely new platform for studying genetic and environmental influences over time on a wide variety of health conditions, across diverse populations.
The National Institute on Aging (NIA), part of the NIH, was the key driver for the grant, in part because the average age of those whose DNA will be genotyped is 65. “A body of research tells us that both genes and environmental factors influence how we age,” explains NIA director Richard J. Hodes, MD. ”We are very excited about the opportunity to develop this extraordinary database in an older population, to facilitate studies of gene-environment interaction as determinants of health, disease, and longevity.”
The UCSF Institute for Human Genetics is the partner on the project and will perform the actual genotyping. Grant funds will be shared by both institutions.
“This investment of federal dollars will provide researchers with access to a uniquely rich resource for research on genetic and environmental effects on health, aging, and disease,” says Cathy Schaefer, PhD, executive director of the RPGEH. “Providing access to genome-wide genetic data on such a large population, combined with rich clinical and environmental data, is without precedent.”
For example, the genetic information generated by the project will include new data regarding drug metabolism and drug response, information that may help researchers to discover genetic factors that explain differences between people in response to medications. This would in turn help doctors provide patients with the best medicines for them individually, with less trial and error, based on their genetic background. It may also help researchers understand why some patients with cancer or heart disease, for example, develop certain symptoms and other patients do not, insights that may lead to new treatments and, in some cases, new ways to lessen the severity or even prevent disease.
Neil Risch, Ph.D., co-director of the RPGEH, director of the UCSF Institute for Human Genetics, and co-chair of the Department of Epidemiology and Biostatistics at UCSF, will share lead investigator responsibilities for the grant with Schaefer. The genotyping will be performed at the UCSF Genomics Core Facility, part of the Institute for Human Genetics, under the director of Pui-Yan Kwok, MD, Ph.D., a co-investigator on the grant and the Henry Bachrach Distinguished Professor at UCSF.
“This award represents a landmark in the development of the RPGEH resource, and fulfillment of years of planning,” says Risch. “Following the human genome project, the development of very efficient and inexpensive high-density assays of genetic variation spanning the entire human genome is what has enabled this study to move forward. The marriage of this technology with the unrivaled comprehensive longitudinal health information in the Kaiser Permanente databases on a very large number of subjects provides an unprecedented opportunity to revolutionize genetic epidemiology research. We are delighted that the NIH shares in this vision, in addition to our prior funders.”
The two-year grant was awarded by the NIH with funds from the American Recovery and Reinvestment Act (ARRA). Funding for the grant came from three NIH sources: the Office of the Director, the National Institute on Aging, and the National Institute of Mental Health.
“This grant is recognition of the excellence of research that Kaiser Permanente is able to do. No other research institution can match the size of the genetic data base which we are developing through the RPGEH,” says Robert Pearl, MD, executive director and CEO of The Permanente Medical Group. “I am optimistic that the combination of quality research, physician excellence and technology will allow our nation to solve the healthcare challenges it faces today and in the future.”
Following several years of planning and development, Kaiser Permanente Northern California Division of Research launched the RPGEH in 2005 and initiated enrollment of participants from the Northern California region’s three million Kaiser Permanente members in 2007. The research program has already obtained biospecimens from more than 110,000 members for its biobank, as part of plans to collect DNA samples and health surveys from 500,000 Kaiser Permanente members in Northern California by 2013, which will make it one of the largest and most diverse population-based biobanks in the world.
This new NIH grant builds on an $8.6 million grant awarded in December 2008 by the Robert Wood Johnson Foundation’s Pioneer Portfolio (RWJF) that is funding the collection and storage of the first 200,000 DNA samples into the RPGEH, as well as the building of the secure health and environmental databases needed to power this groundbreaking genetic resource.
“The unequaled size and power of this biorepository will enable researchers to analyze genetic, environmental and other health data in ways that were never before possible. The findings they generate will help us target effective prevention and treatment strategies that dramatically improve people’s health and the quality of their care,” said RWJF President and CEO Risa Lavizzo-Mourey, MD, MBA. “We’re excited that this substantial new NIH funding positions the RPGEH to take major leaps forward toward realizing this vision.”
Research at Kaiser Permanente is funded almost entirely from grants, such as those from the National Institutes of Health and private foundations. Generous grants to support the RPGEH have also come from the Wayne and Gladys Valley Foundation and the Ellison Medical Foundation. Kaiser Permanente’s Community Benefit Program has also provided financial support for the RPGEH.
Participation in the RPGEH is completely voluntary. An individual’s genetic information is not used in genetic research studies without his or her written consent.
As with all studies carried out by the Division of Research, protecting confidentiality and security of member information is a first priority. The Division of Research maintains separate information and databases from the Kaiser Permanente health plan and members’ medical records.
Only Kaiser Permanente members in Northern California may participate in the RPGEH. Those who are interested in joining the RPGEH should look for information about the program in the U.S. mail from Kaiser Permanente.
The Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) and the University of California, San Francisco (UCSF) have been awarded $24.8 million over two years by the National Institutes of Health (NIH) to create a new resource for studying disease, health, and aging.
With this support, Kaiser Permanente’s RPGEH and UCSF will conduct a genome-wide analysis of DNA samples from 100,000 Kaiser Permanente members from Northern California who have volunteered to join the RPGEH. This new and detailed genetic information – which has never before been generated on such a large and diverse population – will be linked to decades of historical clinical and other health-related information on these participants, taken from health surveys and the Kaiser Permanente electronic health record, the world’s largest civilian electronic health record. Environmental information will also be included in the new resource, such as information about air and water quality, proximity to parks and healthy foods, and much more. The resulting resource will give researchers an entirely new platform for studying genetic and environmental influences over time on a wide variety of health conditions, across diverse populations.
The National Institute on Aging (NIA), part of the NIH, was the key driver for the grant, in part because the average age of those whose DNA will be genotyped is 65. “A body of research tells us that both genes and environmental factors influence how we age,” explains NIA director Richard J. Hodes, MD. ”We are very excited about the opportunity to develop this extraordinary database in an older population, to facilitate studies of gene-environment interaction as determinants of health, disease, and longevity.”
The UCSF Institute for Human Genetics is the partner on the project and will perform the actual genotyping. Grant funds will be shared by both institutions.
“This investment of federal dollars will provide researchers with access to a uniquely rich resource for research on genetic and environmental effects on health, aging, and disease,” says Cathy Schaefer, PhD, executive director of the RPGEH. “Providing access to genome-wide genetic data on such a large population, combined with rich clinical and environmental data, is without precedent.”
For example, the genetic information generated by the project will include new data regarding drug metabolism and drug response, information that may help researchers to discover genetic factors that explain differences between people in response to medications. This would in turn help doctors provide patients with the best medicines for them individually, with less trial and error, based on their genetic background. It may also help researchers understand why some patients with cancer or heart disease, for example, develop certain symptoms and other patients do not, insights that may lead to new treatments and, in some cases, new ways to lessen the severity or even prevent disease.
Neil Risch, Ph.D., co-director of the RPGEH, director of the UCSF Institute for Human Genetics, and co-chair of the Department of Epidemiology and Biostatistics at UCSF, will share lead investigator responsibilities for the grant with Schaefer. The genotyping will be performed at the UCSF Genomics Core Facility, part of the Institute for Human Genetics, under the director of Pui-Yan Kwok, MD, Ph.D., a co-investigator on the grant and the Henry Bachrach Distinguished Professor at UCSF.
“This award represents a landmark in the development of the RPGEH resource, and fulfillment of years of planning,” says Risch. “Following the human genome project, the development of very efficient and inexpensive high-density assays of genetic variation spanning the entire human genome is what has enabled this study to move forward. The marriage of this technology with the unrivaled comprehensive longitudinal health information in the Kaiser Permanente databases on a very large number of subjects provides an unprecedented opportunity to revolutionize genetic epidemiology research. We are delighted that the NIH shares in this vision, in addition to our prior funders.”
The two-year grant was awarded by the NIH with funds from the American Recovery and Reinvestment Act (ARRA). Funding for the grant came from three NIH sources: the Office of the Director, the National Institute on Aging, and the National Institute of Mental Health.
“This grant is recognition of the excellence of research that Kaiser Permanente is able to do. No other research institution can match the size of the genetic data base which we are developing through the RPGEH,” says Robert Pearl, MD, executive director and CEO of The Permanente Medical Group. “I am optimistic that the combination of quality research, physician excellence and technology will allow our nation to solve the healthcare challenges it faces today and in the future.”
Following several years of planning and development, Kaiser Permanente Northern California Division of Research launched the RPGEH in 2005 and initiated enrollment of participants from the Northern California region’s three million Kaiser Permanente members in 2007. The research program has already obtained biospecimens from more than 110,000 members for its biobank, as part of plans to collect DNA samples and health surveys from 500,000 Kaiser Permanente members in Northern California by 2013, which will make it one of the largest and most diverse population-based biobanks in the world.
This new NIH grant builds on an $8.6 million grant awarded in December 2008 by the Robert Wood Johnson Foundation’s Pioneer Portfolio (RWJF) that is funding the collection and storage of the first 200,000 DNA samples into the RPGEH, as well as the building of the secure health and environmental databases needed to power this groundbreaking genetic resource.
“The unequaled size and power of this biorepository will enable researchers to analyze genetic, environmental and other health data in ways that were never before possible. The findings they generate will help us target effective prevention and treatment strategies that dramatically improve people’s health and the quality of their care,” said RWJF President and CEO Risa Lavizzo-Mourey, MD, MBA. “We’re excited that this substantial new NIH funding positions the RPGEH to take major leaps forward toward realizing this vision.”
Research at Kaiser Permanente is funded almost entirely from grants, such as those from the National Institutes of Health and private foundations. Generous grants to support the RPGEH have also come from the Wayne and Gladys Valley Foundation and the Ellison Medical Foundation. Kaiser Permanente’s Community Benefit Program has also provided financial support for the RPGEH.
Participation in the RPGEH is completely voluntary. An individual’s genetic information is not used in genetic research studies without his or her written consent.
As with all studies carried out by the Division of Research, protecting confidentiality and security of member information is a first priority. The Division of Research maintains separate information and databases from the Kaiser Permanente health plan and members’ medical records.
Only Kaiser Permanente members in Northern California may participate in the RPGEH. Those who are interested in joining the RPGEH should look for information about the program in the U.S. mail from Kaiser Permanente.
mardi 7 octobre 2008
OVP, Enterprise Partners See Big Opportunity in $5,000 Human Genome Sequencing
Luke Timmerman 10/7/08, xconomy.com
It’s getting cheaper by the day to sequence the entire string of 6 billion chemical units of DNA that make up an individual human being.
Yesterday, Complete Genomics of Mountain View, CA unveiled plans for what amounts to a democratization of genomics. It will offer a service to sequence full human genomes for just $5,000, beginning in the second quarter of 2009.
At Xconomy.com, we normally focus on companies based in Boston, Seattle, and San Diego, but we couldn’t resist digging into this one, because it has multiple connections to our network cities.
Complete Genomics raised its seed capital in 2006 from OVP Venture Partners in Kirkland, WA, and Enterprise Partners in San Diego. It also counts a pair of Xconomists, Leroy Hood of the Institute for Systems Biology in Seattle, and George Church of Harvard Medical School, as scientific advisers.
So we tracked down OVP managing director (and Xconomist) Chad Waite to find out why he decided to invest in this technology versus all the other sophisticated instruments made by companies like Applied Biosystems, Illumina, 454 Life Sciences, and Helicos Biosciences. (He proudly pointed out that his Harvard Business School connection to CEO Clifford Reid gave him the inside track on this investment, and he invited Drew Senyei of Enterprise in on the action, but more on that later.)
It turns out Waite was sold on Complete Genomics because it has a fundamentally different vision of the market from its rivals.
Instead of trying to sell a machine to pharmaceutical companies and top academic labs for hundreds of thousands of dollars, Complete Genomics plans to keep the work in-house on its own proprietary machines and offer sequencing as a service.
The company plans to open 10 sequencing centers around the world over the next five years, with the capacity to sequence 1 million complete human genomes.
It will have enough bandwidth to sequence an entire genome for $5,000 in about four days, compared with $100,000 and six weeks to six months on currently marketed instruments, Waite says.
“We’re disruptive on technology, and on the business model,” Waite continues. “We’re not going out and trying to sell million-dollar machines. Is there really a competitive advantage for a pharmaceutical company to have the machine? The advantage for them is in the data. They want the data.”
So how might that be really useful for companies or academics?
At that high speed and low price, it’s conceivable that drug companies will want to sequence every patient who enters a clinical trial to provide clues as to why some patients respond differently than others to experimental drugs, Waite says.
Or, they might want to run big experiments that compare the genomes of 1,000 patients with diabetes to 1,000 other people as healthy controls, to look for tiny genetic variations that might offer clues.
They could look at a bunch of prostate cancer tumor samples to try to find genomic markers that explain why the disease spreads more quickly in some people than in others, Waite says.
These concepts are truly mind-boggling when you look at the recent history of gene sequencing.
Back in 1991, when many scientists were skeptical the full human genome could ever be sequenced, Congress was told it would cost $3 billion to sequence the human genome and it would be done by 2005.
It was actually done by 2003, at a cost of $2.7 billion, according to the National Institutes of Health.
Five years later, thanks to big improvements in sequencing technology, it can now generally be done for about $100,000, depending on how you account for the expense of labor to run the machines, Waite says.
Even at that high degree of efficiency, only a couple dozen human genomes have been fully sequenced, according to this report in the New York Times.
Complete Genomics hasn’t published its methods in a top peer-reviewed journal like Science or Nature, although it has double-checked its machine for accuracy against competitors internally, and plans to publish the work soon, Waite says.
The paper hasn’t come out yet, so the following comes with a grain of salt, but the company says it achieves its lower costs by using much less of chemical reagents than existing tools. It also uses ultra high-density DNA tests that can be read with commercial imaging equipment that keeps those costs down.
The company will need that validation to convince scientists and others that they are getting their money’s worth by getting sequences done at Complete Genomics.
Before the paper comes out, though, the company hopes to receive some validation already from two very prominent early partners—the Institute for Systems Biology in Seattle, and Genentech, the biotech industry’s No. 1 company by market value.
Complete Genomics’ partnership with the ISB is expected to sequence 100 individual genomes in 2009, and 2,000 more in 2010.
The new low-cost tool “will allow us to gain a more complete understanding of the genetic components and molecular processes of diseases in order to better manage, treat and prevent human disease and better understand human health,” Hood said in a statement.
Waite and Senyei invested together in Seattle-based Corixa back in the 1990s, so it was natural that they would go in together on Complete Genomics, Waite says.
Both OVP and Enterprise Partners have participated in all three rounds of funding in Complete Genomics, while Prospect Venture Partners led the second round and Highland Capital Management led the third, according to DowJones VentureSource data that my colleague in San Diego, Bruce Bigelow, found. The company has raised about $46.5 million since its founding, and has 100 employees.
People have been talking about the dream of the $1,000 genome, so I asked Waite how low can this sequencing really go. “We think it can go lower, but we’re not really going to talk about that,” Waite says. “But this is really exciting on many levels.”
Luke Timmerman is the National Biotechnology Editor for Xconomy. You can e-mail him at ltimmerman@xconomy.com, call 206-624-2374, or follow him on Twitter at http://twitter.com/ldtimmerman.
It’s getting cheaper by the day to sequence the entire string of 6 billion chemical units of DNA that make up an individual human being.
Yesterday, Complete Genomics of Mountain View, CA unveiled plans for what amounts to a democratization of genomics. It will offer a service to sequence full human genomes for just $5,000, beginning in the second quarter of 2009.
At Xconomy.com, we normally focus on companies based in Boston, Seattle, and San Diego, but we couldn’t resist digging into this one, because it has multiple connections to our network cities.
Complete Genomics raised its seed capital in 2006 from OVP Venture Partners in Kirkland, WA, and Enterprise Partners in San Diego. It also counts a pair of Xconomists, Leroy Hood of the Institute for Systems Biology in Seattle, and George Church of Harvard Medical School, as scientific advisers.
So we tracked down OVP managing director (and Xconomist) Chad Waite to find out why he decided to invest in this technology versus all the other sophisticated instruments made by companies like Applied Biosystems, Illumina, 454 Life Sciences, and Helicos Biosciences. (He proudly pointed out that his Harvard Business School connection to CEO Clifford Reid gave him the inside track on this investment, and he invited Drew Senyei of Enterprise in on the action, but more on that later.)
It turns out Waite was sold on Complete Genomics because it has a fundamentally different vision of the market from its rivals.
Instead of trying to sell a machine to pharmaceutical companies and top academic labs for hundreds of thousands of dollars, Complete Genomics plans to keep the work in-house on its own proprietary machines and offer sequencing as a service.
The company plans to open 10 sequencing centers around the world over the next five years, with the capacity to sequence 1 million complete human genomes.
It will have enough bandwidth to sequence an entire genome for $5,000 in about four days, compared with $100,000 and six weeks to six months on currently marketed instruments, Waite says.
“We’re disruptive on technology, and on the business model,” Waite continues. “We’re not going out and trying to sell million-dollar machines. Is there really a competitive advantage for a pharmaceutical company to have the machine? The advantage for them is in the data. They want the data.”
So how might that be really useful for companies or academics?
At that high speed and low price, it’s conceivable that drug companies will want to sequence every patient who enters a clinical trial to provide clues as to why some patients respond differently than others to experimental drugs, Waite says.
Or, they might want to run big experiments that compare the genomes of 1,000 patients with diabetes to 1,000 other people as healthy controls, to look for tiny genetic variations that might offer clues.
They could look at a bunch of prostate cancer tumor samples to try to find genomic markers that explain why the disease spreads more quickly in some people than in others, Waite says.
These concepts are truly mind-boggling when you look at the recent history of gene sequencing.
Back in 1991, when many scientists were skeptical the full human genome could ever be sequenced, Congress was told it would cost $3 billion to sequence the human genome and it would be done by 2005.
It was actually done by 2003, at a cost of $2.7 billion, according to the National Institutes of Health.
Five years later, thanks to big improvements in sequencing technology, it can now generally be done for about $100,000, depending on how you account for the expense of labor to run the machines, Waite says.
Even at that high degree of efficiency, only a couple dozen human genomes have been fully sequenced, according to this report in the New York Times.
Complete Genomics hasn’t published its methods in a top peer-reviewed journal like Science or Nature, although it has double-checked its machine for accuracy against competitors internally, and plans to publish the work soon, Waite says.
The paper hasn’t come out yet, so the following comes with a grain of salt, but the company says it achieves its lower costs by using much less of chemical reagents than existing tools. It also uses ultra high-density DNA tests that can be read with commercial imaging equipment that keeps those costs down.
The company will need that validation to convince scientists and others that they are getting their money’s worth by getting sequences done at Complete Genomics.
Before the paper comes out, though, the company hopes to receive some validation already from two very prominent early partners—the Institute for Systems Biology in Seattle, and Genentech, the biotech industry’s No. 1 company by market value.
Complete Genomics’ partnership with the ISB is expected to sequence 100 individual genomes in 2009, and 2,000 more in 2010.
The new low-cost tool “will allow us to gain a more complete understanding of the genetic components and molecular processes of diseases in order to better manage, treat and prevent human disease and better understand human health,” Hood said in a statement.
Waite and Senyei invested together in Seattle-based Corixa back in the 1990s, so it was natural that they would go in together on Complete Genomics, Waite says.
Both OVP and Enterprise Partners have participated in all three rounds of funding in Complete Genomics, while Prospect Venture Partners led the second round and Highland Capital Management led the third, according to DowJones VentureSource data that my colleague in San Diego, Bruce Bigelow, found. The company has raised about $46.5 million since its founding, and has 100 employees.
People have been talking about the dream of the $1,000 genome, so I asked Waite how low can this sequencing really go. “We think it can go lower, but we’re not really going to talk about that,” Waite says. “But this is really exciting on many levels.”
Luke Timmerman is the National Biotechnology Editor for Xconomy. You can e-mail him at ltimmerman@xconomy.com, call 206-624-2374, or follow him on Twitter at http://twitter.com/ldtimmerman.
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