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DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter(More)
The molecular pathogenesis of renal cell carcinoma (RCC) is poorly understood. Whole-genome and exome sequencing followed by innovative tumorgraft analyses (to accurately determine mutant allele ratios) identified several putative two-hit tumor suppressor genes, including BAP1. The BAP1 protein, a nuclear deubiquitinase, is inactivated in 15% of clear cell(More)
SUMMARY An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio(More)
Gene transcription mediates many vital aspects of mammalian embryonic development. A comprehensive characterization of the dynamics of gene transcription in the embryo is therefore vital to our understanding of this process. We used microarrays to map transcription in the mouse embryo in the important period from embryonic day 8 (e8.0) to postnatal day 1(More)
Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: ACCESSION NUMBERS SNP and gene expression microarray data have been deposited in GEO (GSE25540 and GSE36895, respectively). Whole-genome and exome sequences for patients consenting(More)
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