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Home > ARRA Stories > At Least $145M in FY `09 NIH Stimulus Funding Goes to Sequencing; Disease-Focused Studies Dominate
At Least $145M in FY `09 NIH Stimulus Funding Goes to Sequencing; Disease-Focused Studies Dominate

By Julia Karow

October 20, 2009

The National Institutes of Health has awarded at least $145 million in funding from the 2009 American Recovery and Reinvestment Act to sequencing-related projects in fiscal year 2009, according to an analysis of award data by In Sequence.

Three-quarters of the funding went to a variety of sequencing projects that are using patient samples to study disease, including sequencing for the Cancer Genome Atlas project, followed by projects for sequencing technology development, computational development, metagenomics, gene regulation and sequencing instrumentation purchases (see charts below).

The analysis was conducted by a survey of project titles for stimulus-funded grants in NIH's RePORTER database, which was frozen as of Sept. 30, the end of the fiscal year. As such, it is likely to be incomplete.

In total, In Sequence identified 89 sequencing-related awards, which received $144.7 million in stimulus funding in fiscal year 2009. Sixty-four of these grants are for new projects, whereas 25 are supplemental awards for existing grants.

The number of awards represents just 0.7 percent of the 12,788 ARRA grants awarded by NIH in fiscal 2009, but around 3 percent of the $4.4 billion in total NIH stimulus funding this year.

The largest amount of stimulus funding for sequencing came from the National Human Genome Research Institute, which awarded $57.2 million for grants in this area — approximately half its total ARRA budget — in fiscal 2009, followed by $38.7 million from the National Heart, Lung, and Blood Institute; $18.3 million from the National Institute of Mental Health; $9.8 million from the National Institute of Diabetes and Digestive and Kidney Diseases; and $7.6 million from the National Institute of Allergy and Infectious Diseases (see charts below).

Focus on Disease

Projects focusing on harnessing sequencing to find genetic factors underlying a variety of diseases reaped the greatest benefit from the reinvestment act: overall, 40 such awards gathered a combined $86.3 million this year, excluding funding for TCGA (see table below).

The largest single award, $12.3 million from the National Heart, Lung, and Blood Institute, went to Eric Boerwinkle at the University of Texas Health Science Center for a project titled "Building on GWAS for NHLBI-diseases: the US CHARGE Consortium."

According to the grant abstract, the project aims to identify susceptibility genes, based on findings from genome-wide association studies for heart, lung and blood diseases in the CHARGE consortium. The consortium consists of several large cohort studies, including the Atherosclerosis Risk in Communities, or ARIC, study; the Cardiovascular Health Study; the Framingham Heart Study; and the Coronary Artery Risk Developments in Young Adults study.

The researchers plan to first resequence 60 genomic regions that influence 15 phenotypes, sequencing 400 cases and 400 controls for each phenotype. In addition, they want to sequence whole genomes of 230 African-American ARIC participants, selected from the top and bottom 10 percent of the HDL-cholesterol distribution, in order to identify the "the dark matter of unaccounted-for genetic variance" for the HDL cholesterol phenotype. Any sequencing-based discoveries will be validated by genotyping in additional samples.

The infrastructure for the project, according to the abstract, "is already in place," as a result of ongoing collaborations among genomic scientists, physicians, epidemiologists, and population and statistical geneticists.

Two other large NHLBI awards, for exome- and, in some cases, genome-wide sequencing of 10,000 well-phenotyped samples went to David Altshuler and Stacey Gabriel at the Broad Institute, who received $10.2 million in fiscal 2009, and to four researchers at the University of Washington, who received $11 million — $8.5 million from NHLBI and $2.5 million from the Office of the Director.

Both awards, which total $50 million over their lifetime, are part of a $64 million NHLBI project to sequence and analyze the exomes of participants in 12 long-term studies (see In Sequence 10/6/2009). Four related awards, for managing sample cohorts for the study, went to Rebecca Jackson and colleagues at Ohio State University Medical Center, Michael Bamshad and colleagues at the University of Washington, Timothy Graubert and colleagues at Washington University in St. Louis, and Stephen Rich at the University of Virginia Health System.

Altshuler and Michael Boehnke, of the University of Michigan, won another large-scale award for a separate project, from the National Institute of Diabetes and Digestive and Kidney Diseases, that totals $8.9 million in fiscal 2009. Entitled "Low-Pass Sequencing and High-Density SNP Genotyping for Type 2 Diabetes," the project proposes to use next-generation sequencing to study low-frequency variants in type-2 diabetes case-control samples.

According to the grant abstract, the study will compare three strategies for discovering genes involved in type-2 diabetes and other diseases: imputation and in silico association analysis using existing GWA data and data from the 1000 Genomes Project, employing next-generation high-density SNP arrays, and low-pass whole-genome sequencing. Each strategy will be used in 3,000 case-control samples from three GWA studies and will be evaluated "with regard to completeness of variant discovery, genotype accuracy and cost-effectiveness, providing guidance to other researchers in the field."

Several grants went to projects that seek to use sequencing to study neurological diseases, including autism, bipolar disorder and schizophrenia, Amyotrophic Lateral Sclerosis, and epilepsy.

Among them are five related awards, totaling almost $8 million in fiscal 2009, for a project to elucidate "the genetic architecture of autism by deep genomic sequencing," to groups at Vanderbilt University, the Broad Institute, Baylor College of Medicine, Mount Sinai School of Medicine and the University of Pennsylvania (see In Sequence 10/6/2009).

Other funded projects in the disease-focused category study Mendelian diseases, gout, myotonic dystrophy, myelodysplastic syndromes, human respiratory chain disease, SCID, B-cell lymphoma, HIV/AIDS, pancreatic cancer, hepatitis C and hyperplastic vasculomyopathy.

Sequencing for TCGA

Another large chunk of stimulus funding — $25 million in fiscal 2009 — went to the three genome centers that are funded by the National Human Genome Research Institute, in the form of supplements to their existing grants.

An NHGRI program officer confirmed this week that this funding will go toward sequencing and analysis for the Cancer Genome Atlas, a project that is jointly sponsored by the National Cancer Institute and the NHGRI.

Earlier this month, NCI said that TCGA had received $275 million in new funding, of which $175 million comes from the recovery act. Approximately $125 million of the total is allocated for sequencing, according to the program director (see In Sequence 10/6/2009).

For now, the Genome Center at Washington University School of Medicine received $10 million, the Broad Institute obtained $9 million, and the Baylor College of Medicine Human Genome Sequencing Center was awarded $6 million for sequencing and analysis under TCGA.

Sequencing Technology Development & Computational Tools

Projects seeking to develop new sequencing technology won a total of $13.7 million in fiscal 2009 stimulus funding, all awarded by NHGRI.

The awards are a mixture of newly funded projects and supplements to existing awards under NHGRI's "$1,000 Genome" grant program (see In Sequence 10/13/2009).

Another $10.7 million in fiscal 2009 stimulus funding went to about a dozen projects aiming to develop computational tools to handle as well as analyze high-throughput sequence data.

The largest such award is $4.8 million in supplemental funding to Mark Daly at the Broad Institute for SNP and CNV calling in sequence data from the 1000 Genomes Project.

Another award, for $1.1 million, went to researchers led by Gabor Marth at Boston College to build a data processing pipeline for the National Center for Biotechnology Information that can also be used "by scientists wishing to process and analyze large of amounts of next-generation sequence data."

Metagenomics & Gene Regulation

Eight projects in the areas of metagenomics as well as gene regulation analysis received a total of $7.9 million in fiscal 2009 stimulus funding.

Among them is a $4.6-million award that went to Bob Strausberg at the J. Craig Venter Institute to sequence 110 reference genome, of which 15 will be finished, for the Human Microbiome Project.

Another award, $900,000 to Kevin White at the University of Chicago, proposed to "systematically epitope-tag transcription and chromatin-associated factors for ChIP-seq" in order to "speed current large-scale mapping projects," such as the ENCODE project.

Sequencing Instrumentation

Three awards, totaling $1.1 million, were made under the National Center for Research Resources' Shared Instrumentation Program for the purchase of DNA sequencers (see In Sequence 7/28/2009).


Pie Chart Illustrating the Number of Sequencing ARRA Grants Awarded, FY 2009, by Category: Disease Studies (40); Genome Centers/TCGA (3); Tech Development (22). Computational (13); Metagenomics (3); Gene Regulation (5); Instrument Purchases (3)



Pie Chart Illustrating the Amount of Sequencing ARRA Funding, FY 2009, by Category ($M): Disease Studies ($86.3M); Genome Centers/TCGA ($25M); Tech Development ($13.7M); Computational ($10.7M); Metagenomics ($5.2M); Gene Regulation ($2.7M); Instrument Purchases ($1.1M)



Pie Chart Illustrating the Number of Sequencing ARRA Grants Awarded, FY 2009, by NIH Institute: NHGRI (42); NHLBI (10); NIMH (11); NIDDK (3); NIAID (3); NINDS (2); NCI (5); NCRR (4); Others (8)



Pie Chart Illustrating the Amount of Sequencing ARRA Funding, FY 2009, by NIH Institute ($M): NHGRI ($57.2M); NHLBI ($38.7M); NIMH ($18.3M); NIDDK ($9.8M); NIAID ($7.6M); NINDS ($2.9M); NCI ($2.5M); NCRR ($1.3M); Others ($6.4M)



Disease-Related Sequencing Projects Awarded by NIH in FY2009 Using Stimulus Funding
FY2009 Funding Organization Project Title Principal Investigators Admin IC
$12,281,613 University of Texas Health Science Center Building on GWAS for NHLBI-Disease: The CHARGE Consortium Eric Boerwinkle NHLBI
$10,157,633 Broad Institute Comprehensive Sequencing and Analysis of Variation in NHLBI Cohorts David Altshuler, Stacey Gabriel NHLBI
$8,951,229 University of Michigan Low-Pass Sequencing and High-Density SNP Genotyping for Type 2 Diabetes David Altshuler, Michael Boehnke NIDDK
$8,508,061 University of Washington Northwest Genomics Center Phillip Green, Deborah Nickerson, Mark Rieder, Jay Shendure NHLBI
$3,075,000 Broad Institute Whole Genome Sequencing of Bipolar Disorder and Schizophrenia Shaun Purcell, Pamela Sklar NIMH
$2,727,684 Network Biosystems Rapid Biothreat Identification in Clinical Samples by Multilocus Sequencing Richard Selden NIAID
$2,594,102 University of Washington ARRA - NHLBI Lung Cohorts Sequencing Project Michael Bamshad NHLBI
$2,500,000 University of Washington Northwest Genomics Center Phillip Green, Deborah Nickerson, Mark Rieder, Jay Shendure OD
$2,478,799 Vanderbilt University 5/5 - Elucidating the Genetic Architecture of Autism by Deep Genomic Sequencing James Sutcliffe NIMH
$2,474,114 Children's Hospital, Boston Human Autism Genetics and Activity - Dependent Gene Activation Christopher Walsh NIMH, OD
$2,442,659 Broad Institute 2/5 - Elucidating the Genetic Architecture of Autism by Deep Genomic Sequencing Mark Daly NIMH
$2,113,954 Ohio State University WHI Sequencing Project (WHISP) Christopher Carlson, Rebecca Jackson, Kari North, Ulrike Peters NHLBI
$2,000,000 Baylor College of Medicine 1/5 - Elucidating the Genetic Architecture of Autism by Deep Genomic Sequencing Richard Gibbs NIMH
$1,976,527 University of Washington Genetics of Lipid Levels: Draft Sequencing of 1000 Genomes Goncalo Rocha Abecasis NHGRI
$1,960,613 University of Washington Next Generation Mendelian Genetics Michael Bamshad, Deborah Nickerson, Wendy Raskind, Jay Shendure NHGRI
$1,804,409 University of Massachusetts Medical School Full Human Genome Sequencing in ALS Robert Brown NINDS
$1,671,247 Duke University Whole-Genome Sequencing for Rare Highly Penetrant Gene Variants in Schizophrenia David Goldstein NIMH
$1,483,107 Massachusetts Institute of Technology Deep Sequencing Analysis of mRNA Isoform Expression Changes in Myotonic Dystrophy Christopher Burge, Thomase Cooper, David Housman NHGRI
$1,384,503 Cold Spring Harbor Laboratory Deep Sequencing of Autism Candidate Genes in 2000 Families from the Simons Sample Richard McCombie, Michael Wigler NIMH
$1,317,671 University of Texas Health Science Center Next-Generation Medical Resequencing of Gout Disease Genes in the Aric Cohort James Hixon NHGRI
$1,224,842 Washington University Whole Genome Sequencing of Myelodysplastic Syndromes Timothy Graubert NHLBI
$1,183,908 Yale University Genomic Profiling and Functional Mutation Analysis in Autism Spectrum Disorders Matthew State NIMH
$1,099,524 Duke University Whole-Genome Sequencing in Multiplex Epilepsy Families David Goldstein, Ruth Ottman NINDS
$993,317 Massachusetts Institute of Technology Defining the Genetic Basis of Human Respiratory Chain Disease Vamsi Krishna Mootha NHGRI
$850,000 University of Washington Application of Ribotag-seq to Exploration of Tumor Microenvironments David Morris NCI
$817,287 University of Virginia Charlottesville Human Exome Sequencing in Six Well-Phenotyped NHLBI Cohorts Stephen Rich NHLBI
$810,738 University of Texas Austin Next-Gen Sequencing: Searching for Mechanisms of Alcohol and Nicotine Dependence Roy Mayfield NIAAA
$758,511 Dana-Farber Cancer Institute An Infrastructure for Cancer Virus Discovery for Next-Generation Sequencing Data Matthew Meyerson NCI
$571,568 Mount Sinai School of Medicine 3/5-Elucidating the Genetic Architecture of Autism by Deep Genome Sequencing Joseph Buxbaum NIMH
$564,301 California Institute of Technology RNA-seq Studies of Gene Expression in Cells and Networks in FI and ACC in Autism John Allman, Barbara Wold NIMH
$500,000 Duke University Identification of Disease-Causing Mutations in SCID Using Exome-Wide Sequencing Joseph Roberts NHLBI
$500,000 Scripps Research Institute Deep Sequencing of Small Regulatory RNAs in Diffuse Large B Cell Lymphoma Changchun Xiao NCI
$500,000 University of California Riverside Virus Discovery by Deep Sequencing and Assembly of Virus-Derived siRNAs Shou-Wei Ding NIGMS
$500,000 University of Chicago Genome-Wide Association and Exon Sequencing Study in IPF Naftali Kaminski, Dan Nicolae, Imre Noth NHLBI
$490,729 University of Michigan Exon Capture and Large-Scale Sequencing for Disease-Cause Identification, Early Detection Friedhelm Hildebrandt NIDDK
$482,846 University of Pennsylvania 4/5-Elucidating the Genetic Architecture of Autism by Deep Genome Sequencing Gerard David Schellenberg NIMH
$266,000 Brigham and Women's Hospital V3 Loop Characterization by Ultradeep Sequencing During CCR5 Antagonist Therapy Daniel Kuritzkes NIAID
$255,225 Johns Hopkins University High-Throughput Analysis of Pancreatic Cancer Mutations Scott Ken NCI
$12,537 Saint Louis University Role of HCV Sequence Variation in Pathology John Tavis NIDDK
$7,223 University of Texas Health Science Center Sequencing Candidate Genes for Hyperplastic Vasculomyopathy Diana Milewicz NHLBI

This article originally appeared on the GenomeWeb website. Reposted with permission.

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