Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations
Kangcheng Hou, Stephanie M. Gogarten, Joohyun Kim, Xing Hua, Julie‐Alexia Dias, Quan Sun, Ying Wang, Taotao Tan, Sally N. Adebamowo, Adebowale Adeyemo, Paul L. Auer, Taoufik Bensellak, Sonja I. Berndt, Rohan Bhukar, Hongyuan Cao, Clinton L. Cario, Nilanjan Chatterjee, Jiawen Chen, Tinashe Chikowore, Ananyo Choudhury, Matthew P. Conomos, David V. Conti, Sinéad Cullina, Burcu F. Darst, Yi Ding, Ruocheng Dong, Rui Duan, Yasmina Jaufeerally Fakim, Nora Franceschini, Tian Ge, Anisah W. Ghoorah, Chris Gignoux, Stephanie M. Gogarten, Neil A. Hanchard, Rachel Hanisch, Michael A. Hauser, Scott Hazelhurst, Jibril Hirbo, Whitney Hornsby, Kangcheng Hou, Xing Hua, Alicia Huerta, Micah R. Hysong, Jin Jin, Angad Johar, Jon Judd, Linda Kachuri, Abram Bunya Kamiza, Eimear Kenny, Alyna Khan, E. P. Kharitonova, Joohyun Kim, Iain R. Konigsberg, Charles Kooperberg, Matt Kosel, Iftikhar J. Kullo, Ethan M. Lange, Yun Li, Qing Li, Maria Bouvy‐Liivrand, Kirk E. Lohmueller, Kevin GuoKai Lu, Ravi Mandla, Alisa K. Manning, Iman K. Martin, Alicia R. Martin, Shannon K. McDonnell, Leah E. Mechanic, Josep Mercader, Rachel Mester, Maggie C. Y. Ng, Kevin T. Nguyen, Kristján Norland, Franklin P Ockerman, Loes M. Olde Loohuis, Ebuka Onyenobi, Bogdan Paşaniuc, Aniruddh D. Patel, Ella Petter, Kenneth Rice, Joseph H. Rothstein, Bryce Rowan, Robb Rowley, Yunfeng Ruan, Sriram Sankararaman, Ambra Sartori, Dan Schaid, Ruhollah Shemirani, Jonathan Shortt, Xueling Sim, Johanna L. Smith, Maggie A. Stanislawski, Daniel O. Stram, Quan Sun, Bamidele O. Tayo, Buu Truong, Kristin Tsuo, Sarah Urbut, Ying Wang, Wallace Minxian Wang
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.