SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method
Abstract 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 i...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-22162-8 |
| _version_ | 1798029826404122624 |
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| author | Mikkel Meyer Andersen Steffan Noe Christiansen Jeppe Dyrberg Andersen Poul Svante Eriksen Niels Morling |
| author_facet | Mikkel Meyer Andersen Steffan Noe Christiansen Jeppe Dyrberg Andersen Poul Svante Eriksen Niels Morling |
| author_sort | Mikkel Meyer Andersen |
| collection | DOAJ |
| description | Abstract 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%. |
| first_indexed | 2024-04-11T19:30:32Z |
| format | Article |
| id | doaj.art-1fdcf1a8b2c345f6b1286b4e07d40eb0 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-11T19:30:32Z |
| publishDate | 2022-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-1fdcf1a8b2c345f6b1286b4e07d40eb02022-12-22T04:06:59ZengNature PortfolioScientific Reports2045-23222022-10-0112111110.1038/s41598-022-22162-8SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly methodMikkel Meyer Andersen0Steffan Noe Christiansen1Jeppe Dyrberg Andersen2Poul Svante Eriksen3Niels Morling4Department of Mathematical Sciences, Aalborg UniversitySection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenDepartment of Mathematical Sciences, Aalborg UniversityDepartment of Mathematical Sciences, Aalborg UniversityAbstract 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%.https://doi.org/10.1038/s41598-022-22162-8 |
| spellingShingle | Mikkel Meyer Andersen Steffan Noe Christiansen Jeppe Dyrberg Andersen Poul Svante Eriksen Niels Morling SNP allele calling of Illumina Infinium Omni5-4 data using the butterfly method Scientific Reports |
| 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 |
| url | https://doi.org/10.1038/s41598-022-22162-8 |
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