Haplotype estimation for biobank scale datasets
By Jared O’Connell, Kevin Sharp, N. Shrine, L. Wain, I. Hall, Martin D. Tobin, Jean-François Zagury, Olivier Delaneau, Jonathan Marchini. 2016
226 citations recorded by the source corpus.
The UK Biobank (UKB) has recently released genotypes on 152,328 individuals together with extensive phenotypic and lifestyle information. We present a new phasing method, SHAPEIT3, that can handle such biobank-scale data sets and results in switch error rates as low as ∼0.3%. The method exhibits O(NlogN) scaling with sample size N, enabling fast and accurate phasing of even larger cohorts.
Subfields: Genetics, Molecular Biology
How researchers see this paper
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In Genetics
- Jonathan Marchini
- Olivier Delaneau
- G. McVean
- Peter Donnelly
- Stephen Leslie
- Desislava Petkova
- Sharon R. Browning
- Matthew Stephens
In Molecular Biology
- Jonathan Marchini
- G. McVean
- Peter Donnelly
- Olivier Delaneau
- Matthew Stephens
- Julio Rozas
- Paul Scheet
Citations in the corpus
- Genome-wide genetic data on ~500,000 UK Biobank participants (2017, methodology): “Phasing on the autosomes was carried out using SHAPEIT3 [46] in chunks of 15,000 markers, with an overlap of 250 markers between chunks.”
- Allelic Landscape of Human Blood Cell Trait Variation and Links (2016, unknown): “9 (Chang et al., 2015) https://www.cog-genomics.org/plink2 SHAPEIT3 (O’Connell et al., 2016) https://jmarchini.org/software/ PBWT (Durbin, 2014) https://imputation.sanger.ac.uk/ BOLT-LMM (Loh et al., 2015) https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ METAL (Willer et al., 2010)…”
- WhatsHap: fast and accurate read-based phasing (2016, unknown): “The accuracy of such methods crucially depends on the size of the panel and recent progress has been made to scale them up to panels of more than 100 000 haplotypes [10, 11].”