Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

…, C Lee, L Clarke, A Auton, Y Erlich, RE Handsaker… - Nature …, 2016 - nature.com
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26
worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 …

The variant call format and VCFtools

…, E Banks, MA DePristo, RE Handsaker… - …, 2011 - academic.oup.com
The variant call format (VCF) is a generic format for storing DNA polymorphism data such as
SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is …

[HTML][HTML] An integrated map of structural variation in 2,504 human genomes

PH Sudmant, T Rausch, EJ Gardner, RE Handsaker… - Nature, 2015 - nature.com
Structural variants are implicated in numerous diseases and make up the majority of varying
nucleotides among human genomes. Here we describe an integrated set of eight structural …

[HTML][HTML] Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence

G Genovese, AK Kähler, RE Handsaker… - … England Journal of …, 2014 - Mass Medical Soc
Background Cancers arise from multiple acquired mutations, which presumably occur over
many years. Early stages in cancer development might be present years before cancers …

Schizophrenia risk from complex variation of complement component 4

…, V Van Doren, G Genovese, SA Rose, RE Handsaker… - Nature, 2016 - nature.com
Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms.
Schizophrenia’s strongest genetic association at a population level involves variation in the major …

Mapping copy number variation by population-scale genome sequencing

RE Mills, K Walter, C Stewart, RE Handsaker, K Chen… - Nature, 2011 - nature.com
Genomic structural variants (SVs) are abundant in humans, differing from other forms of
variation in extent, origin and functional impact. Despite progress in SV characterization, the …

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

AD Johnson, RE Handsaker, SL Pulit, MM Nizzari… - …, 2008 - academic.oup.com
The interpretation of genome-wide association results is confounded by linkage disequilibrium
between nearby alleles. We have developed a flexible bioinformatics query tool for single-…

[HTML][HTML] Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

…, S Kamoun, MC Zody, RHY Jiang, RE Handsaker… - Nature, 2009 - nature.com
Phytophthora infestans is the most destructive pathogen of potato and a model organism for
the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms …

A systematic survey of loss-of-function variants in human protein-coding genes

…, Q Ayub, MA DePristo, E Banks, M Hu, RE Handsaker… - Science, 2012 - science.org
Genome-sequencing studies indicate that all humans carry many genetic variants predicted
to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy …

Whole genome sequencing in psychiatric disorders: the WGSPD consortium

…, DC Glahn, DB Goldstein, RE Gur, RE Handsaker… - Nature …, 2017 - nature.com
As technology advances, whole genome sequencing (WGS) is likely to supersede other
genotyping technologies. The rate of this change depends on its relative cost and utility. …