As one of the NHGRI Centers for Common Disease Genomics, NYGC plans to sequence at least 2500 whole human genomes this year, focused on families with simplex autism. As outlined in our original proposal, we plan to apply multiple methods to call single nucleotide variants (SNVs), copy number variants (CNVs), and other structural variants (SVs) in these genomes. Our goal over the span of the project is to develop a comprehensive view of the genomic architecture of autism (and other disease projects taken on over the course of the project). However, while our data analysis pipeline is already well suited to this application, as we believe those of other CCDGs are well suited to their studies, these pipelines do not currently produce functionally identical results. We believe, as laid out in the GSP Data Working Group proposal ?Accelerated Genome Aggregation and Joint Variant Calling Effort?, that generating functionally identical primary processing and uniform variant call sets across all the CCDG sequencing efforts will provide significant value to the CCDGs, the CCDG analysis centers, and the broader genomic research community. These efforts are completely consistent with the original proposal, as the standardized pipeline results and uniform call sets will be directly applicable our downstream analysis of autism samples. Further, this will add greater value to the entire data set by allowing use of common controls across multiple disease working groups. Finally, we propose to work with the other sequencing centers and the coordinating center to build a common cloud data repository for data exchange, long term storage, and potentially cloud-based analysis.
As one of the NHGRI Centers for Common Disease Genomics, NYGC plans to sequence at least 2500 whole human genomes this year, focused on families with simplex autism. As outlined in our original proposal, we plan to apply multiple methods to call single nucleotide variants (SNVs), copy number variants (CNVs), and other structural variants (SVs) in these genomes. Our goal over the span of the project is to develop a comprehensive view of the genomic architecture of autism (and other disease projects taken on over the course of the project).
| Castel, Stephane E; Cervera, Alejandra; Mohammadi, Pejman et al. (2018) Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk. Nat Genet 50:1327-1334 |
| Jereb, Saša; Hwang, Hun-Way; Van Otterloo, Eric et al. (2018) Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. Elife 7: |
| Regier, Allison A; Farjoun, Yossi; Larson, David E et al. (2018) Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nat Commun 9:4038 |
| Yuan, Yuan; Xie, Shirley; Darnell, Jennifer C et al. (2018) Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons. Genome Biol 19:117 |
| Mak, Angel C Y; White, Marquitta J; Eckalbar, Walter L et al. (2018) Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med 197:1552-1564 |
| Mohammadi, Pejman; Castel, Stephane E; Brown, Andrew A et al. (2017) Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. Genome Res 27:1872-1884 |
| GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group et al. (2017) Genetic effects on gene expression across human tissues. Nature 550:204-213 |
| Stoeckius, Marlon; Hafemeister, Christoph; Stephenson, William et al. (2017) Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14:865-868 |
| Hwang, Hun-Way; Saito, Yuhki; Park, Christopher Y et al. (2017) cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation. Neuron 95:1334-1349.e5 |
| Willems, Thomas; Zielinski, Dina; Yuan, Jie et al. (2017) Genome-wide profiling of heritable and de novo STR variations. Nat Methods 14:590-592 |
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