دورية أكاديمية
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The Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection.

التفاصيل البيبلوغرافية
العنوان: The Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection.
المؤلفون: Hayeck TJ; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Li Y; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Mosbruger TL; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Bradfield JP; Quantinuum Research LLC, Philadelphia, PA, USA., Gleason AG; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Damianos G; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Shaw GT; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Duke JL; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA., Conlin LK; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Turner TN; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA., Fernández-Viña MA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA.; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, USA., Sarmady M; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Monos DS; Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
المصدر: Genome biology and evolution [Genome Biol Evol] 2024 Feb 01; Vol. 16 (2).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 101509707 Publication Model: Print Cited Medium: Internet ISSN: 1759-6653 (Electronic) Linking ISSN: 17596653 NLM ISO Abbreviation: Genome Biol Evol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford, UK : Oxford University Press
مواضيع طبية MeSH: Polymorphism, Single Nucleotide* , HLA-DQ Antigens*/genetics, Gene Frequency ; Linkage Disequilibrium ; Bayes Theorem ; Haplotypes
مستخلص: Regions under balancing selection are characterized by dense polymorphisms and multiple persistent haplotypes, along with other sequence complexities. Successful identification of these patterns depends on both the statistical approach and the quality of sequencing. To address this challenge, at first, a new statistical method called LD-ABF was developed, employing efficient Bayesian techniques to effectively test for balancing selection. LD-ABF demonstrated the most robust detection of selection in a variety of simulation scenarios, compared against a range of existing tests/tools (Tajima's D, HKA, Dng, BetaScan, and BalLerMix). Furthermore, the impact of the quality of sequencing on detection of balancing selection was explored, as well, using: (i) SNP genotyping and exome data, (ii) targeted high-resolution HLA genotyping (IHIW), and (iii) whole-genome long-read sequencing data (Pangenome). In the analysis of SNP genotyping and exome data, we identified known targets and 38 new selection signatures in genes not previously linked to balancing selection. To further investigate the impact of sequencing quality on detection of balancing selection, a detailed investigation of the MHC was performed with high-resolution HLA typing data. Higher quality sequencing revealed the HLA-DQ genes consistently demonstrated strong selection signatures otherwise not observed from the sparser SNP array and exome data. The HLA-DQ selection signature was also replicated in the Pangenome samples using considerably less samples but, with high-quality long-read sequence data. The improved statistical method, coupled with higher quality sequencing, leads to more consistent identification of selection and enhanced localization of variants under selection, particularly in complex regions.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
References: Mol Biol Evol. 2019 Jan 1;36(1):177-199. (PMID: 30380122)
PLoS Biol. 2006 Mar;4(3):e72. (PMID: 16494531)
Mol Biol Evol. 2019 May 1;36(5):1101-1109. (PMID: 30590560)
Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28. (PMID: 30395293)
Stat Med. 2015 Oct 15;34(23):3133-43. (PMID: 26011599)
Nat Rev Genet. 2010 Jan;11(1):17-30. (PMID: 19953080)
PLoS Comput Biol. 2016 Oct 28;12(10):e1005151. (PMID: 27792722)
Nat Rev Genet. 2020 Oct;21(10):597-614. (PMID: 32504078)
Trends Genet. 2005 Jan;21(1):30-2. (PMID: 15680511)
Nat Genet. 2018 Sep;50(9):1311-1317. (PMID: 30104759)
Mol Biol Evol. 2020 Nov 1;37(11):3267-3291. (PMID: 32462188)
Mol Biol Evol. 2016 Oct;33(10):2555-64. (PMID: 27436009)
Mol Biol Evol. 2019 Mar 1;36(3):632-637. (PMID: 30517680)
Nature. 2023 May;617(7960):312-324. (PMID: 37165242)
Genome Biol Evol. 2024 Feb 1;16(2):. (PMID: 38302106)
Am J Hum Genet. 1997 Feb;60(2):397-407. (PMID: 9012413)
PLoS Comput Biol. 2010 Dec 02;6(12):e1001025. (PMID: 21152010)
Int J Immunogenet. 2015 Dec;42(6):413-22. (PMID: 26456690)
Mol Biol Evol. 2017 Nov 1;34(11):2996-3005. (PMID: 28981714)
Int J Epidemiol. 2007 Feb;36(1):195-202. (PMID: 17329317)
PLoS Genet. 2013;9(8):e1003709. (PMID: 23990802)
Mol Biol Evol. 2014 May;31(5):1275-91. (PMID: 24554778)
Science. 2013 Mar 29;339(6127):1578-82. (PMID: 23413192)
PLoS Comput Biol. 2016 Mar 28;12(3):e1004845. (PMID: 27018908)
Nature. 2020 May;581(7809):434-443. (PMID: 32461654)
Mol Biol Evol. 2009 Dec;26(12):2755-64. (PMID: 19713326)
Mol Biol Evol. 2015 May;32(5):1186-96. (PMID: 25605789)
Blood. 2014 Dec 18;124(26):3996-4003. (PMID: 25323824)
Nature. 2007 Oct 18;449(7164):913-8. (PMID: 17943131)
Hum Immunol. 2021 Jul;82(7):505-522. (PMID: 34030896)
Transplantation. 2021 Mar 1;105(3):637-647. (PMID: 32301906)
Am J Epidemiol. 2018 Apr 1;187(4):864-870. (PMID: 29020135)
Genome Biol Evol. 2023 Mar 3;15(3):. (PMID: 36821771)
PLoS Comput Biol. 2017 Aug 28;13(8):e1005693. (PMID: 28846675)
Nat Rev Genet. 2008 Jun;9(6):477-85. (PMID: 18427557)
N Engl J Med. 2019 Jul 4;381(1):64-74. (PMID: 31269367)
Genetics. 1987 May;116(1):153-9. (PMID: 3110004)
Am J Hum Genet. 2011 Sep 9;89(3):424-31. (PMID: 21907013)
Genet Epidemiol. 2009 Jan;33(1):79-86. (PMID: 18642345)
Am J Hum Genet. 2005 Apr;76(4):634-46. (PMID: 15747258)
Clin Lab Med. 2018 Dec;38(4):679-693. (PMID: 30420061)
Nat Genet. 2012 Dec;44(12):1294-301. (PMID: 23104008)
Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012. (PMID: 30445434)
Eur J Hum Genet. 2020 May;28(5):627-635. (PMID: 31844174)
Genetics. 2004 Oct;168(2):1071-6. (PMID: 15514076)
Cell. 2020 Sep 3;182(5):1198-1213.e14. (PMID: 32888493)
PLoS Genet. 2018 Apr 5;14(4):e1007308. (PMID: 29621242)
Blood. 2010 Mar 4;115(9):1815-22. (PMID: 20018918)
Am J Hum Genet. 2007 Aug;81(2):208-27. (PMID: 17668372)
Nature. 2015 Oct 1;526(7571):68-74. (PMID: 26432245)
Sci Rep. 2019 Jun 27;9(1):9354. (PMID: 31249361)
Biometrics. 2003 Mar;59(1):92-9. (PMID: 12762445)
Genome Biol Evol. 2018 Mar 1;10(3):939-955. (PMID: 29608730)
Genome Biol Evol. 2020 Feb 1;12(2):3873-3877. (PMID: 32011695)
Genetics. 2022 May 31;221(2):. (PMID: 35385101)
Nucleic Acids Res. 2021 Jan 8;49(D1):D939-D946. (PMID: 33152070)
Transplantation. 2018 Aug;102(8):1338-1343. (PMID: 29443827)
Mol Ecol Resour. 2021 Nov;21(8):2706-2718. (PMID: 33749134)
Clin Transplant. 2021 Sep;35(9):e14406. (PMID: 34180101)
Nat Genet. 2006 Aug;38(8):904-9. (PMID: 16862161)
Nat Rev Immunol. 2005 Mar;5(3):201-14. (PMID: 15719024)
PLoS One. 2018 Mar 8;13(3):e0193614. (PMID: 29518122)
Am J Hum Genet. 2016 Mar 3;98(3):456-472. (PMID: 26924531)
Genome Biol. 2016 Jan 18;17:9. (PMID: 26781712)
Immunogenetics. 2018 Jan;70(1):5-27. (PMID: 28687858)
BMC Med Res Methodol. 2017 Feb 23;17(1):33. (PMID: 28231767)
Nat Ecol Evol. 2018 Apr;2(4):713-720. (PMID: 29459708)
Genetics. 1989 Nov;123(3):585-95. (PMID: 2513255)
J Biol Chem. 2014 Apr 4;289(14):10024-8. (PMID: 24550402)
Am J Hum Genet. 2019 Feb 7;104(2):299-309. (PMID: 30686509)
Mol Biol Evol. 2021 Apr 13;38(4):1356-1371. (PMID: 33185667)
PLoS Genet. 2014 Aug 21;10(8):e1004561. (PMID: 25144706)
Nat Commun. 2019 Nov 28;10(1):5436. (PMID: 31780650)
فهرسة مساهمة: Keywords: Bayesian; balancing selection; human leukocyte antigen genes; linkage disequilibriumhuman; population genetics; sequencing platform; statistical genetics
المشرفين على المادة: 0 (HLA-DQ Antigens)
تواريخ الأحداث: Date Created: 20240201 Date Completed: 20240214 Latest Revision: 20240703
رمز التحديث: 20240704
مُعرف محوري في PubMed: PMC10853003
DOI: 10.1093/gbe/evae009
PMID: 38302106
قاعدة البيانات: MEDLINE
الوصف
تدمد:1759-6653
DOI:10.1093/gbe/evae009