Biology subjects

Arthur, J. G.

Publications and source records attributed to Arthur, J. G..

4 recordsLinked to original sources

bioRxiv2018

Haplotype-resolved and integrated genome analysis of ENCODE cell line HepG2

The HepG2 cancer cell line is one of the most widely-used biomedical research and one of the main cell lines of ENCODE. Vast numbers of functional genomics and epigenomics datasets have been produced to characterize its biology. However, the correct interpretation such data requires an understanding of the cell lines genome sequence and genome structure. Using a variety of sequencing and analysis methods, we identified a wide spectrum of HepG2 genome characteristics: copy numbers of chromosomal segments, SNVs and Indels (corrected for aneuploidy), phased haplotypes extending to entire chromosome arms, loss of heterozygosity, retrotransposon insertions, structural variants (SVs) including complex and somatic genomic rearrangements. We also identified allele-specific expression and DNA methylation genome-wide and assembled an allele-specific CRISPR/Cas9 targeting map.\n\nSIGNIFICANCEHaplotype-resolved and comprehensive whole-genome analysis of a widely-used cell line for cancer research and ENCODE, HepG2, serves as an essential resource for unlocking complex cancer gene regulation using a genome-integrated framework and also provides genomic context for the analysis of ~1,000 functional datasets to date on ENCODE for biological discovery. We also demonstrate how deeper insights into genomic regulatory complexity are gained by adopting a genome-integrated framework.

genomics↗

bioRxiv2018

Sequencing of the Venter/HuRef genome using various strategies for the benchmarking of genome analysis tools

We produced an extensive collection of deep re-sequencing datasets for the Venter/HuRef genome using the Illumina massively-parallel DNA sequencing platform. The original Venter genome sequence is a very-high quality phased assembly based on Sanger sequencing. Therefore, researchers developing novel computational tools for the analysis of human genome sequence variation for the dominant Illumina sequencing technology can test and hone their algorithms by making variant calls from these Venter/HuRef datasets and then immediately confirm the detected variants in the Sanger assembly, freeing them of the need for further experimental validation. This process also applies to implementing and benchmarking existing genome analysis pipelines. We prepared and sequenced 200 bp and 350 bp short-insert whole-genome sequencing libraries (sequenced to 100x and 40x genomic coverages respectively) as well as 2 kb, 5 kb, and 12 kb mate-pair libraries (49x, 122x, and 145x physical coverages respectively). Lastly, we produced a linked-read library (128x physical coverage) from which we also performed haplotype phasing.

genomics↗

bioRxiv2017

Comprehensive, Integrated, and Phased Whole-Genome Analysis of the Primary ENCODE Cell Line K562

K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed. Such information is essential for the correct interpretation and understanding of the vast troves of existing functional genomics and epigenomics data for K562. We performed and integrated deep-coverage whole-genome (short-insert), mate-pair, and linked-read sequencing as well as karyotyping and array CGH analysis to identify a wide spectrum of genome characteristics in K562: copy numbers (CN) of aneuploid chromosome segments at high-resolution, SNVs and Indels (both corrected for CN in aneuploid regions), loss of heterozygosity, mega-base-scale phased haplotypes often spanning entire chromosome arms, structural variants (SVs) including small and large-scale complex SVs and non-reference retrotransposon insertions. Many SVs were phased, assembled, and experimentally validated. We identified multiple allele-specific deletions and duplications within the tumor suppressor gene FHIT. Taking aneuploidy into account, we re-analyzed K562 RNA-seq and whole-genome bisulfite sequencing data for allele-specific expression and allele-specific DNA methylation. We also show examples of how deeper insights into regulatory complexity are gained by integrating genomic variant information and structural context with functional genomics and epigenomics data. Furthermore, using K562 haplotype information, we produced an allele-specific CRISPR targeting map. This comprehensive whole-genome analysis serves as a resource for future studies that utilize K562 as well as a framework for the analysis of other cancer genomes.

genomics↗

bioRxiv2017

Detection of complex structural variation from paired-end sequencing data

Complex structural variants (cxSVs), e.g. inversions with flanking deletions or interspersed inverted duplications, are part of human genetic diversity but their characteristics are not well delineated. Because their structures are difficult to resolve, cxSVs have been largely excluded from genome analysis and population-scale association studies. To permit large-scale detection of cxSVs from paired-end whole-genome sequencing, we developed Automated Reconstruction of Complex Variants (ARC-SV) using a novel probabilistic algorithm and a machine learning approach that leverages the new Human Pangenome Reference Consortium diploid assemblies. Using ARC-SV, we resolved, across 4,262 human genomes spanning all continental super-populations, 8,493 cxSVs belonging to 12 subclasses. Some cxSVs with population-specific signatures are shared with Neanderthals. Overall cxSVs are significantly enriched in regions prone to recombination and germline de novo mutations. Many cxSVs mark phenotypic hotspots (each significantly associated with [≥] 20 traits) identified in genome-wide association studies (GWAS), and 46.4% of all significant GWAS-SNPs catalogued to date reside within {+/-}125 kb of at least one cxSV locus. Common SNPs near cxSVs show significant trait heritability enrichment. Genomic regions affected by cxSVs are enriched for bivalent chromatin states. Rare cxSVs are enriched in neural genes and loci undergoing rapid or accelerated evolution and recently evolved cis-regulatory regions for human corticogenesis. We also identified 41 fixed loci where divergence from our most recent common ancestor is via localized cxSV. Our method and analysis framework allow for the accurate, efficient, and automatic identification of cxSVs for future population-scale studies of human disease and genome biology.

bioinformatics↗