Research summary
The Genome Analysis Toolkit (GATK) was built as a MapReduce framework for next-generation DNA sequencing analysis, providing a programming structure that handles terabase-scale 1000 Genomes data and abstracts over the complexity of variant calling at scale [1]. The Exome Aggregation Consortium (ExAC) aggregated exomes from 60,706 individuals of diverse ancestries, finding roughly one variant every eight bases, providing direct evidence of widespread mutational recurrence, and supplying objective metrics of pathogenicity and gene-level selection [2]. ExAC was succeeded by the Genome Aggregation Database (gnomAD), which combined 125,748 exomes and 15,708 genomes to identify 443,769 high-confidence loss-of-function variants and to classify human protein-coding genes along a continuum of tolerance to inactivation, validated using model-organism and engineered-cell data and shown to boost gene-discovery power for both common and rare disease [3]. Earlier work on haplotype structure across 51 autosomal regions spanning 13 megabases in African, European, and Asian samples demonstrated that the human genome can be parsed objectively into haplotype blocks within which only a few common haplotypes occur, and that block boundaries and haplotype identities are highly correlated across populations [4]. Together these projects supply both the computational infrastructure (GATK) and the population-scale reference panels (ExAC, gnomAD) that underpin contemporary variant interpretation, and provide an empirical basis for haplotype-based association mapping.
Recent publications
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesDOI
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing dataDOI
- A framework for variation discovery and genotyping using next-generation DNA sequencing dataDOI
- PGC-1伪-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetesDOI
- Analysis of protein-coding genetic variation in 60,706 humansDOI
- The mutational constraint spectrum quantified from variation in 141,456 humansDOI
- Biological insights from 108 schizophrenia-associated genetic lociDOI
- MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populationsDOI
- LD Score regression distinguishes confounding from polygenicity in genome-wide association studiesDOI
- The Structure of Haplotype Blocks in the Human GenomeDOI
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External profiles
- ORCID: https://orcid.org/0000-0002-0949-8752
- OpenAlex: openalex.org
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