Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data
Segments of indentity-by-descent (IBD) detected from high-density genetic data are useful for many applications, including long-range phase determination, phasing family data, imputation, IBD mapping, and heritability analysis in founder populations. We present Refined IBD, a new method for IBD segm...
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ftpubmed:oai:pubmedcentral.nih.gov:3664855 2023-05-15T17:42:36+02:00 Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data Browning, Brian L. Browning, Sharon R. 2013-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664855 http://www.ncbi.nlm.nih.gov/pubmed/23535385 https://doi.org/10.1534/genetics.113.150029 en eng Genetics Society of America http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664855 http://www.ncbi.nlm.nih.gov/pubmed/23535385 http://dx.doi.org/10.1534/genetics.113.150029 Copyright © 2013 by the Genetics Society of America Available freely online through the author-supported open access option. Investigations Text 2013 ftpubmed https://doi.org/10.1534/genetics.113.150029 2013-09-05T00:17:00Z Segments of indentity-by-descent (IBD) detected from high-density genetic data are useful for many applications, including long-range phase determination, phasing family data, imputation, IBD mapping, and heritability analysis in founder populations. We present Refined IBD, a new method for IBD segment detection. Refined IBD achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement) evaluates candidate segments with a probabilistic approach to assess the evidence for IBD. Like GERMLINE, Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses. To investigate the properties of Refined IBD, we simulate SNP data from a model with recent superexponential population growth that is designed to match United Kingdom data. The simulation results show that Refined IBD achieves a better power/accuracy profile than fastIBD or GERMLINE. We find that a single run of Refined IBD achieves greater power than 10 runs of fastIBD. We also apply Refined IBD to SNP data for samples from the United Kingdom and from Northern Finland and describe the IBD sharing in these data sets. Refined IBD is powerful, highly accurate, and easy to use and is implemented in Beagle version 4. Text Northern Finland PubMed Central (PMC) Genetics 194 2 459 471 |
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Investigations Browning, Brian L. Browning, Sharon R. Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data |
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Investigations |
description |
Segments of indentity-by-descent (IBD) detected from high-density genetic data are useful for many applications, including long-range phase determination, phasing family data, imputation, IBD mapping, and heritability analysis in founder populations. We present Refined IBD, a new method for IBD segment detection. Refined IBD achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement) evaluates candidate segments with a probabilistic approach to assess the evidence for IBD. Like GERMLINE, Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses. To investigate the properties of Refined IBD, we simulate SNP data from a model with recent superexponential population growth that is designed to match United Kingdom data. The simulation results show that Refined IBD achieves a better power/accuracy profile than fastIBD or GERMLINE. We find that a single run of Refined IBD achieves greater power than 10 runs of fastIBD. We also apply Refined IBD to SNP data for samples from the United Kingdom and from Northern Finland and describe the IBD sharing in these data sets. Refined IBD is powerful, highly accurate, and easy to use and is implemented in Beagle version 4. |
format |
Text |
author |
Browning, Brian L. Browning, Sharon R. |
author_facet |
Browning, Brian L. Browning, Sharon R. |
author_sort |
Browning, Brian L. |
title |
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data |
title_short |
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data |
title_full |
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data |
title_fullStr |
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data |
title_full_unstemmed |
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data |
title_sort |
improving the accuracy and efficiency of identity-by-descent detection in population data |
publisher |
Genetics Society of America |
publishDate |
2013 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664855 http://www.ncbi.nlm.nih.gov/pubmed/23535385 https://doi.org/10.1534/genetics.113.150029 |
genre |
Northern Finland |
genre_facet |
Northern Finland |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664855 http://www.ncbi.nlm.nih.gov/pubmed/23535385 http://dx.doi.org/10.1534/genetics.113.150029 |
op_rights |
Copyright © 2013 by the Genetics Society of America Available freely online through the author-supported open access option. |
op_doi |
https://doi.org/10.1534/genetics.113.150029 |
container_title |
Genetics |
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194 |
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2 |
container_start_page |
459 |
op_container_end_page |
471 |
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1766144495818113024 |