Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations

Author:

Hou Kangcheng1ORCID,Gogarten Stephanie2ORCID,Kim Joohyun3,Hua Xing4,Dias Julie-Alexia5,Sun Quan6ORCID,Wang Ying7,Tan Taotao8, ,Adebamowo Sally,Adeyemo Adebowale,Auer Paul,Bensellak Taoufik,Berndt Sonja,Bhukar Rohan,Cao Hongyuan,Cario Clinton,Chatterjee Nilanjan,Chen Jiawen,Chikowore Tinashe,Choudhury Ananyo,Conomos Matthew,Conti David,Cullina Sinead,Darst Burcu,Ding Yi,Dong Ruocheng,Duan Rui,Fakim Yasmina,Franceschini Nora,Ge Tian,Ghoorah Anisah W,Gignoux Chris,Gogarten Stephanie,Hanchard Neil,Hanisch Rachel,Hauser Michael,Hazelhurst Scott,Hirbo Jibril,Hornsby Whitney,Hou Kangcheng,Hua Xing,Huerta Alicia,Hysong Micah,Jin Jin,Johar Angad,Judd Jon,Kachuri Linda,Kamiza Abram Bunya,Kenny Eimear,Khan Alyna,Kharitonova Elena,Kim Joohyun,Konigsberg Iain,Kooperberg Charles,Kosel Matt,Kullo Iftikhar,Lange Ethan,Li Yun,Li Qing,Liivrand Maria,Lohmueller Kirk,Lu Kevin,Mandla Ravi,Manning Alisa,Martin Iman,Martin Alicia,McDonnell Shannon,Mechanic Leah,Mercader Josep,Mester Rachel,Ng Maggie,Nguyen Kevin,Norland Kristján,Ockerman Franklin,Loohuis Loes Olde,Onyenobi Ebuka,Pasaniuc Bogdan,Patel Aniruddh,Petter Ella,Rice Kenneth,Rothstein Joseph,Rowan Bryce,Rowley Robb,Ruan Yunfeng,Sankararaman Sriram,Sartori Ambra,Schaid Dan,Shemirani Ruhollah,Shortt Jonathan,Sim Xueling,Smith Johanna L,Stanislawski Maggie,Stram Daniel,Sun Quan,Tayo Bamidele,Truong Buu,Tsuo Kristin,Urbut Sarah,Wang Ying,Wang Wallace Minxian,Wilson Riley,Witte John,Wojcik Genevieve,Zhang Jingning,Zhang Ruyue,Zhang Haoyu,Zhang Yuji,Zhong Michael,Zhou Laura,Atkinson Elizabeth G8,Martin Alicia7ORCID,Shortt Jonathan9,Hirbo Jibril10,Li Yun6,Pasaniuc Bogdan1,Zhang Haoyu4

Affiliation:

1. Bioinformatics Interdepartmental Program, University of California, Los Angeles , Los Angeles, CA, 90095, United States

2. Department of Biostatistics, University of Washington , Seattle, WA, 98195, United States

3. Vanderbilt Genetics Institute and Division of Genetic Medicine, Vanderbilt University Medical Center , Nashville, TN, 37232, United States

4. Division of Cancer Epidemiology and Genetics, National Cancer Institute , Bethesda, MD, 20892, United States

5. Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, MA, 02120, United States

6. Department of Biostatistics, University of North Carolina at Chapel Hill , Chapel Hill, NC, 27599, United States

7. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard , Cambridge, MA, 02142, United States

8. Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, 77030, United States

9. Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO, 80045, United States

10. Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center , Nashville, TN, 37232, United States

Abstract

Abstract Summary Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic studies of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations. Availability and implementation Admix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. Additionally, users can use the pipeline designed for admixed genotype simulation available at https://github.com/UW-GAC/admix-kit_workflow.

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

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