Novel genotyping algorithms for rare variants significantly improve the accuracy of Applied Biosystems™ Axiom™ array genotyping calls: Retrospective evaluation of UK Biobank array data
The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results, for almost 100,000 variants both directly gen...
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| Published in | PloS one Vol. 17; no. 11; p. e0277680 |
|---|---|
| Main Authors | , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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United States
Public Library of Science
17.11.2022
Public Library of Science (PLoS) |
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| Online Access | Get full text |
| ISSN | 1932-6203 1932-6203 |
| DOI | 10.1371/journal.pone.0277680 |
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| Abstract | The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results, for almost 100,000 variants both directly genotyped on the UK Biobank Axiom array and via whole exome sequencing. However, in a study using the exome sequencing results of the first 50k individuals as reference (truth), it was observed that the positive predictive value (PPV) decreased along with the number of heterozygous array calls per variant. We developed a novel addition to the genotyping algorithm, Rare Heterozygous Adjusted (RHA), to significantly improve PPV in variants with minor allele frequency below 0.01%. The improvement in PPV was roughly equal when comparing to the exome sequencing of 50k individuals, or to the more recent ~200k individuals. Sensitivity was higher in the 200k data. The improved calling algorithm, along with enhanced quality control of array probesets, significantly improved the positive predictive value and the sensitivity of array data, making it suitable for the detection of ultra-rare variants. |
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| AbstractList | The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results, for almost 100,000 variants both directly genotyped on the UK Biobank Axiom array and via whole exome sequencing. However, in a study using the exome sequencing results of the first 50k individuals as reference (truth), it was observed that the positive predictive value (PPV) decreased along with the number of heterozygous array calls per variant. We developed a novel addition to the genotyping algorithm, Rare Heterozygous Adjusted (RHA), to significantly improve PPV in variants with minor allele frequency below 0.01%. The improvement in PPV was roughly equal when comparing to the exome sequencing of 50k individuals, or to the more recent ~200k individuals. Sensitivity was higher in the 200k data. The improved calling algorithm, along with enhanced quality control of array probesets, significantly improved the positive predictive value and the sensitivity of array data, making it suitable for the detection of ultra-rare variants. The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results, for almost 100,000 variants both directly genotyped on the UK Biobank Axiom array and via whole exome sequencing. However, in a study using the exome sequencing results of the first 50k individuals as reference (truth), it was observed that the positive predictive value (PPV) decreased along with the number of heterozygous array calls per variant. We developed a novel addition to the genotyping algorithm, Rare Heterozygous Adjusted (RHA), to significantly improve PPV in variants with minor allele frequency below 0.01%. The improvement in PPV was roughly equal when comparing to the exome sequencing of 50k individuals, or to the more recent ~200k individuals. Sensitivity was higher in the 200k data. The improved calling algorithm, along with enhanced quality control of array probesets, significantly improved the positive predictive value and the sensitivity of array data, making it suitable for the detection of ultra-rare variants.The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results, for almost 100,000 variants both directly genotyped on the UK Biobank Axiom array and via whole exome sequencing. However, in a study using the exome sequencing results of the first 50k individuals as reference (truth), it was observed that the positive predictive value (PPV) decreased along with the number of heterozygous array calls per variant. We developed a novel addition to the genotyping algorithm, Rare Heterozygous Adjusted (RHA), to significantly improve PPV in variants with minor allele frequency below 0.01%. The improvement in PPV was roughly equal when comparing to the exome sequencing of 50k individuals, or to the more recent ~200k individuals. Sensitivity was higher in the 200k data. The improved calling algorithm, along with enhanced quality control of array probesets, significantly improved the positive predictive value and the sensitivity of array data, making it suitable for the detection of ultra-rare variants. |
| Author | Webster, Teresa A. Aull, Katherine H. Bivol, Adrian Woehrmann, Marcos H. Keeble, Sara M. Mittal, Anuradha Wong, Brant A. Gollub, Jeremy Mizrahi-Man, Orna Roter, Alan H. Schmidt, Jeanette P. |
| AuthorAffiliation | University of North Carolina at Chapel Hill, UNITED STATES Thermo Fisher Scientific, Santa Clara, CA, United States of America |
| AuthorAffiliation_xml | – name: University of North Carolina at Chapel Hill, UNITED STATES – name: Thermo Fisher Scientific, Santa Clara, CA, United States of America |
| Author_xml | – sequence: 1 givenname: Orna surname: Mizrahi-Man fullname: Mizrahi-Man, Orna – sequence: 2 givenname: Marcos H. surname: Woehrmann fullname: Woehrmann, Marcos H. – sequence: 3 givenname: Teresa A. surname: Webster fullname: Webster, Teresa A. – sequence: 4 givenname: Jeremy surname: Gollub fullname: Gollub, Jeremy – sequence: 5 givenname: Adrian surname: Bivol fullname: Bivol, Adrian – sequence: 6 givenname: Sara M. surname: Keeble fullname: Keeble, Sara M. – sequence: 7 givenname: Katherine H. surname: Aull fullname: Aull, Katherine H. – sequence: 8 givenname: Anuradha surname: Mittal fullname: Mittal, Anuradha – sequence: 9 givenname: Alan H. surname: Roter fullname: Roter, Alan H. – sequence: 10 givenname: Brant A. surname: Wong fullname: Wong, Brant A. – sequence: 11 givenname: Jeanette P. surname: Schmidt fullname: Schmidt, Jeanette P. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36395175$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright: © 2022 Mizrahi-Man et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 2022 Mizrahi-Man et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2022 Mizrahi-Man et al 2022 Mizrahi-Man et al |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Current address: BillionToOne, Menlo Park, CA, United States of America Current address: Sterne, Kessler, Goldstein & Fox, Furlong, Pennsylvania, United States of America Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: At the time of the study, all authors were employed by Thermo Fisher Scientific, which participated in the design of and manufactures the UK Biobank Axiom Array; AHR, AM, BAW, JG, JPS, KHA, MHW, OM, and TAW own Thermo Fisher Scientific stock or stock options; no other relationships or activities that could appear to have influenced the submitted work. This does not alter our adherence to PLOS ONE policies on sharing data and materials. |
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| SubjectTerms | Algorithms Arrays Biobanks Biological Specimen Banks Biology and Life Sciences Business metrics Exome Gene frequency Genotype Genotype & phenotype Genotyping High-Throughput Nucleotide Sequencing - methods Humans Polymorphism, Single Nucleotide Quality control Research and Analysis Methods Retrospective Studies Sensitivity United Kingdom Whole genome sequencing |
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| Title | Novel genotyping algorithms for rare variants significantly improve the accuracy of Applied Biosystems™ Axiom™ array genotyping calls: Retrospective evaluation of UK Biobank array data |
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