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SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method

We introduce a within-sample SNP calling method, called the “butterfly method”, that improves the quality of SNP calling with the Illumina Infinium Omni5-4 SNP Kit. This was done by improving how no-calls are determined from allele signal intensities. High confidence of SNP allele calling is extreme...

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Autores principales: Andersen, Mikkel Meyer, Christiansen, Steffan Noe, Andersen, Jeppe Dyrberg, Eriksen, Poul Svante, Morling, Niels
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9556601/
https://www.ncbi.nlm.nih.gov/pubmed/36224332
http://dx.doi.org/10.1038/s41598-022-22162-8
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author Andersen, Mikkel Meyer
Christiansen, Steffan Noe
Andersen, Jeppe Dyrberg
Eriksen, Poul Svante
Morling, Niels
author_facet Andersen, Mikkel Meyer
Christiansen, Steffan Noe
Andersen, Jeppe Dyrberg
Eriksen, Poul Svante
Morling, Niels
author_sort Andersen, Mikkel Meyer
collection PubMed
description We introduce a within-sample SNP calling method, called the “butterfly method”, that improves the quality of SNP calling with the Illumina Infinium Omni5-4 SNP Kit. This was done by improving how no-calls are determined from allele signal intensities. High confidence of SNP allele calling is extremely important in forensic genetics and clinical diagnostics. This paper is accompanied by two open-source R packages, omni54manifest and snpbeadchip that make SNP calling easy by helping with bookkeeping and giving easy access to meta-information about the SNPs typed with the Illumina Infinium Omni5-4 Kit (including chromosome, probe type, and SNP bases). We compared the results from our method with those obtained with the Illumina GenomeStudio software (which does not provide sample and SNP specific genotype probabilities or other quality measures), and with whole-genome sequencing (WGS). Given the signal intensities, the SNP calling quality was optimised using a threshold for the a posteriori probability of a SNP belonging to a SNP cluster. By lowering the a posteriori probability threshold for no-calls, we obtained a higher call rate than GenomeStudio. Using a higher a posteriori probability threshold, we achieved a higher concordance with the WGS data than GenomeStudio. Our method had SNP call and concordance rates with WGS data of approximately 99%.
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spelling pubmed-95566012022-10-14 SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method Andersen, Mikkel Meyer Christiansen, Steffan Noe Andersen, Jeppe Dyrberg Eriksen, Poul Svante Morling, Niels Sci Rep Article We introduce a within-sample SNP calling method, called the “butterfly method”, that improves the quality of SNP calling with the Illumina Infinium Omni5-4 SNP Kit. This was done by improving how no-calls are determined from allele signal intensities. High confidence of SNP allele calling is extremely important in forensic genetics and clinical diagnostics. This paper is accompanied by two open-source R packages, omni54manifest and snpbeadchip that make SNP calling easy by helping with bookkeeping and giving easy access to meta-information about the SNPs typed with the Illumina Infinium Omni5-4 Kit (including chromosome, probe type, and SNP bases). We compared the results from our method with those obtained with the Illumina GenomeStudio software (which does not provide sample and SNP specific genotype probabilities or other quality measures), and with whole-genome sequencing (WGS). Given the signal intensities, the SNP calling quality was optimised using a threshold for the a posteriori probability of a SNP belonging to a SNP cluster. By lowering the a posteriori probability threshold for no-calls, we obtained a higher call rate than GenomeStudio. Using a higher a posteriori probability threshold, we achieved a higher concordance with the WGS data than GenomeStudio. Our method had SNP call and concordance rates with WGS data of approximately 99%. Nature Publishing Group UK 2022-10-12 /pmc/articles/PMC9556601/ /pubmed/36224332 http://dx.doi.org/10.1038/s41598-022-22162-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Andersen, Mikkel Meyer
Christiansen, Steffan Noe
Andersen, Jeppe Dyrberg
Eriksen, Poul Svante
Morling, Niels
SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
title SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
title_full SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
title_fullStr SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
title_full_unstemmed SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
title_short SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
title_sort snp allele calling of illumina infinium omni5-4 data using the butterfly method
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9556601/
https://www.ncbi.nlm.nih.gov/pubmed/36224332
http://dx.doi.org/10.1038/s41598-022-22162-8
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