Sequencing

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11th Annual Sequencing, Finishing, and Analysis in the Future Meeting EVOLUTION OF SEQUENCING IN THE ARIC COHORT TO REVEAL THE GENETIC ARCHITECTURE OF COMPLEX TRAITS Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.07) Ginger Metcalf 1 , Narayanan Veeraraghavan 1 , Harsha Doddapaneni 1 , Prof. Yi Han 1 , Bing Yu 2 , Simon White 1 , William Salerno 1 , Alanna Morrison 2 , Xiaoming Liu 2 , Andrew Carroll 3 , Darren Ames 3 , Donna Muzny 1 , Prof. Richard Gibbs 1 , Eric Boerwinkle 1 1 Human Genome Sequencing Center Baylor College of Medicine, 2 Human Genetics Center, University of Texas Health Science Center, 3 DNAnexus The Atherosclerosis Risk in the Community (ARIC) study is a flagship project of the HGSC seeking to identify susceptibility genes underlying well‐replicated GWAS findings for heart, lung, and blood diseases and their risk factors in combined analyses with the larger Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Early efforts involved a multiplexed capture sequencing approach targeting a 2.2 Mb region of the genome. While informative, analyses were limited to the loci selected from the GWAS findings and thus biased towards common variants. As sequencing platforms improved, more comprehensive applications of whole exome sequencing and low pass (6X) genomes became affordable, followed by 30X genomes on the Illumina Hiseq X. To date, the HGSC has sequenced 15K whole exome and 8K whole genome samples spanning 5 longitudinal cohort studies with extensive phenotypic and clinical data. These data have fueled considerable analytical work, forming the foundation for discovery of novel genes/loci influencing a number of chronic disease risk factors, but while an increased sample size increases the chance at discovery, it also introduces increased logistical challenges. The increasing footprint of genomic data creates challenges in data sharing, computational capability, and data storage. To address these complications we created an expansion of our local compute infrastructure as part of collaborations with DNAnexus and AWS. We built and validated our high throughput sequence processing and analysis framework into DNAnexus and staged the largest ever biomedical compute on the Amazon Cloud. Additionally a secure data commons was created whereby ARIC and CHARGE investigators from around the world could access the sequence data and run analysis tools on the cloud to achieve their individual study ai Analysis of 30X WGS data is underway in an effort to identify genomic regions influencing the human serum metabolome among ARIC members, with special emphasis on metabolites influencing risk of CVD. By focusing on proximal measures of physiologic processes we will optimize the size of a gene’s effect relative to corresponding risk factor level or disease endpoint. 41
11th Annual Sequencing, Finishing, and Analysis in the Future Meeting A NOVEL APPROACH FOR SELECTIVE ENRICHMENT OF GENE TARGETS Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.08) Andrew Barry 1 , Daniel Kraushaar 2 , Lynne Apone 1 , Sarah Bowman 2 , Kruti Patel 2 , Noa Henig 1 , Amy Emerman 2 , Theodore Davis 1 , Salvatore Russello 1 , Cynthia Hendrickson 2 1 New England Biolabs, Inc., 2 Directed Genomics Target enrichment of selected exonic regions for deep sequence analysis is a widely used practice for the discovery of novel variants, and identification and phenotypic association of known variants for a wide range of practical applications. Current available strategies for selective enrichment can be characterized as either hybridization‐based enrichment, where long synthetic oligonucleotides are used to selectively capture regions of interest, or multiplexed amplicon‐based, where pairs of short primer sequences leverage PCR to selectively amplify sequence targets. While hybridization‐based methods have proven to be a tractable approach for large panels scaling to whole exome, the approach presents challenges in a relatively high sample input requirement, longer workflows, and inability to scale to very focused panels. In contrast, multiplexed amplicon approaches have proven valuable for small, highly focused panels, yet suffer from inherent challenges including the inability to scale content, loss of specificity associated with PCR duplication, and difficulties annealing primer pairs to already degraded materials. The NEBNext DirectTM technology utilizes a novel approach to selectively enrich nucleic acid targets ranging from a single gene to several hundred genes, without sacrificing specificity. Further‐ more, intrinsic properties of the approach lend themselves to improved sensitivity and have proven amenable to challenging sample types including FFPE tissue and circulating tumor DNA (ctDNA). The result is a 1‐day protocol that enables the preparation of sequence‐ready libraries with high specificity, uniformity, and sensitivity for the discovery and identification of nucleic acid variants. 42
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Reliable solutions for focused NGS
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Sequencing

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