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Jessica Shea,
Vineeta Agarwala,
Anthony A Philippakis, Jared Maguire,
Eric Banks,
Mark Depristo,
Brian Thomson,
Candace Guiducci,
Robert C Onofrio,
Sekar Kathiresan,
Stacey Gabriel,
Noël P Burtt,
Mark J Daly,
Leif Groop,
David Altshuler
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ABSTRACT: Noncoding variants at human chromosome 9p21 near CDKN2A and CDKN2B are associated with type 2 diabetes, myocardial infarction, aneurysm, vertical cup disc ratio and at least five cancers. Here we compare approaches to more comprehensively assess genetic variation in the region. We carried out targeted sequencing at high coverage in 47 individuals and compared the results to pilot data from the 1000 Genomes Project. We imputed variants into type 2 diabetes and myocardial infarction cohorts directly from targeted sequencing, from a genotyped reference panel derived from sequencing and from 1000 Genomes Project low-coverage data. Polymorphisms with frequency >5% were captured well by all strategies. Imputation of intermediate-frequency polymorphisms required a higher density of tag SNPs in disease samples than is available on first-generation genome-wide association study (GWAS) arrays. Our association analyses identified more comprehensive sets of variants showing equivalent statistical association with type 2 diabetes or myocardial infarction, but did not identify stronger associations than the original GWAS signals.
Nature Genetics 01/2011; 43(8):801-5. · 35.53 Impact Factor
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Michael F Berger,
Joshua Z Levin,
Krishna Vijayendran,
Andrey Sivachenko,
Xian Adiconis, Jared Maguire,
Laura A Johnson,
James Robinson,
Roel G Verhaak,
Carrie Sougnez, [......],
David E Fisher,
Gad Getz,
Matthew Meyerson,
David B Jaffe,
Stacey B Gabriel,
Eric S Lander,
Reinhard Dummer,
Andreas Gnirke,
Chad Nusbaum,
Levi A Garraway
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ABSTRACT: Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. Using paired-end massively parallel sequencing of cDNA (RNA-seq) together with analyses of high-resolution chromosomal copy number data, we identified 11 novel melanoma gene fusions produced by underlying genomic rearrangements, as well as 12 novel readthrough transcripts. We mapped these chimeric transcripts to base-pair resolution and traced them to their genomic origins using matched chromosomal copy number information. We also used these data to discover and validate base-pair mutations that accumulated in these melanomas, revealing a surprisingly high rate of somatic mutation and lending support to the notion that point mutations constitute the major driver of melanoma progression. Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types.
Genome Research 02/2010; 20(4):413-27. · 13.61 Impact Factor
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Andreas Gnirke,
Alexandre Melnikov, Jared Maguire,
Peter Rogov,
Emily M LeProust,
William Brockman,
Timothy Fennell,
Georgia Giannoukos,
Sheila Fisher,
Carsten Russ,
Stacey Gabriel,
David B Jaffe,
Eric S Lander,
Chad Nusbaum
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ABSTRACT: Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA 'baits' to fish targets out of a 'pond' of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that approximately 60% of target bases in the exonic 'catch', and approximately 80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.
Nature Biotechnology 02/2009; 27(2):182-9. · 29.50 Impact Factor
