Cargando…
Scaling probabilistic models of genetic variation to millions of humans
A major goal of population genetics is to quantitatively understand variation of genetic polymorphisms among individuals. The aggregated number of genotyped humans is currently on the order millions of individuals, and existing methods do not scale to data of this size. To solve this problem we deve...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127768/ https://www.ncbi.nlm.nih.gov/pubmed/27819665 http://dx.doi.org/10.1038/ng.3710 |
_version_ | 1782470280593014784 |
---|---|
author | Gopalan, Prem Hao, Wei Blei, David M. Storey, John D. |
author_facet | Gopalan, Prem Hao, Wei Blei, David M. Storey, John D. |
author_sort | Gopalan, Prem |
collection | PubMed |
description | A major goal of population genetics is to quantitatively understand variation of genetic polymorphisms among individuals. The aggregated number of genotyped humans is currently on the order millions of individuals, and existing methods do not scale to data of this size. To solve this problem we developed TeraStructure, an algorithm to fit Bayesian models of genetic variation in structured human populations on tera-sample-sized data sets (10(12) observed genotypes, e.g., 1M individuals at 1M SNPs). TeraStructure is a scalable approach to Bayesian inference in which subsamples of markers are used to update an estimate of the latent population structure between samples. We demonstrate that TeraStructure performs as well as existing methods on current globally sampled data, and we show using simulations that TeraStructure continues to be accurate and is the only method that can scale to tera-sample-sizes. |
format | Online Article Text |
id | pubmed-5127768 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
record_format | MEDLINE/PubMed |
spelling | pubmed-51277682017-05-07 Scaling probabilistic models of genetic variation to millions of humans Gopalan, Prem Hao, Wei Blei, David M. Storey, John D. Nat Genet Article A major goal of population genetics is to quantitatively understand variation of genetic polymorphisms among individuals. The aggregated number of genotyped humans is currently on the order millions of individuals, and existing methods do not scale to data of this size. To solve this problem we developed TeraStructure, an algorithm to fit Bayesian models of genetic variation in structured human populations on tera-sample-sized data sets (10(12) observed genotypes, e.g., 1M individuals at 1M SNPs). TeraStructure is a scalable approach to Bayesian inference in which subsamples of markers are used to update an estimate of the latent population structure between samples. We demonstrate that TeraStructure performs as well as existing methods on current globally sampled data, and we show using simulations that TeraStructure continues to be accurate and is the only method that can scale to tera-sample-sizes. 2016-11-07 2016-12 /pmc/articles/PMC5127768/ /pubmed/27819665 http://dx.doi.org/10.1038/ng.3710 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Gopalan, Prem Hao, Wei Blei, David M. Storey, John D. Scaling probabilistic models of genetic variation to millions of humans |
title | Scaling probabilistic models of genetic variation to millions of humans |
title_full | Scaling probabilistic models of genetic variation to millions of humans |
title_fullStr | Scaling probabilistic models of genetic variation to millions of humans |
title_full_unstemmed | Scaling probabilistic models of genetic variation to millions of humans |
title_short | Scaling probabilistic models of genetic variation to millions of humans |
title_sort | scaling probabilistic models of genetic variation to millions of humans |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127768/ https://www.ncbi.nlm.nih.gov/pubmed/27819665 http://dx.doi.org/10.1038/ng.3710 |
work_keys_str_mv | AT gopalanprem scalingprobabilisticmodelsofgeneticvariationtomillionsofhumans AT haowei scalingprobabilisticmodelsofgeneticvariationtomillionsofhumans AT bleidavidm scalingprobabilisticmodelsofgeneticvariationtomillionsofhumans AT storeyjohnd scalingprobabilisticmodelsofgeneticvariationtomillionsofhumans |