Accès ouvert

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

Article scientifique 2017 Anglais

Résumé

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

Citer ce document

Johnston, H., Hu, Y., Gao, J., O’Connor, T., Abecasis, G., Wojcik, G., Gignoux, C., Gourraud, P., Lizée, A., Genuario, R., Bullis, D., Lawley, C., Kenny, E., Bustamante, C., Beaty, T., Mathias, R., Barnes, K., Qin, Z., Boorgula, M., Campbell, M., Chavan, S., Ford, J., Foster, C., Gao, L., Hansel, N., Horowitz, E., Huang, L., Ortiz, R., Potee, J., Rafaels, N., Ruczinski, I., Scott, A., Taub, M., Vergara, C., Levin, A., Padhukasahasram, B., Williams, L., Dunston, G., Faruque, M., Gietzen, K., Deshpande, A., Grus, W., Locke, D., Foreman, M., Avila, P., Grammer, L., Kim, K., Kumar, R., Schleimer, R., Vega, F., Shringarpure, S., Musharoff, S., Burchard, E., Eng, C., Hernandez, R., Pino‐Yanes, M., Torgerson, D., Szpiech, Z., Torres, R., Nicolae, D., Ober, C., Olopade, C., Olopade, O., Oluwole, O., Arinola, G., Song, W., Correa, A., Musani, S., Wilson, J., Lange, L., Akey, J., Bamshad, M., Chong, J., Fu, W., Nickerson, D., Reiner, A., Hartert, T., Ware, L., Bleecker, E., Meyers, D., Ortega, V., Maul, P., Maul, T., Watson, H., Araújo, M., Oliveira, R., Caraballo, L., Marrugo, J., Martínez, B., Meza, C., Ayestas, G., Herrera-Paz, E., Landaverde-Torres, P., Erazo, S., Martinez, R., Mayorga, A., Mayorga, L., Mejia-Mejia, D., Ramos, H. (2017). Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. https://doi.org/10.1038/srep46398

Accès au document

Voir sur le dépôt source

Ce document est hébergé sur son dépôt institutionnel d'origine.

Auteur(s)

H. Richard Johnston Yi‐Juan Hu Jingjing Gao Timothy D. O’Connor Gonçalo R. Abecasis Genevieve L. Wojcik Christopher R. Gignoux Pierre‐Antoine Gourraud Antoine Lizée Rob Genuario Dave Bullis Cindy Lawley Eimear E. Kenny Carlos D. Bustamante Terri H. Beaty Rasika A. Mathias Kathleen C. Barnes Zhaohui Qin Meher Preethi Boorgula Monica Campbell Sameer Chavan Jean G. Ford Cassandra Foster Li Gao Nadia N. Hansel Edward A. Horowitz Lili Huang Romina Ortiz Joseph Potee Nicholas Rafaels Ingo Ruczinski Alan F. Scott Margaret A. Taub Candelaria Vergara Albert M. Levin Badri Padhukasahasram L. Keoki Williams Georgia M. Dunston Mezbah U. Faruque Kimberly Gietzen Aniket Deshpande Wendy E. Grus Devin P. Locke Marilyn G. Foreman Pedro C. Avila Leslie C. Grammer Kwang‐Youn A. Kim Rajesh Kumar R.P. Schleimer Francisco M. De La Vega Suyash Shringarpure Shaila Musharoff Esteban G. Burchard Celeste Eng Ryan D. Hernandez Maria Pino‐Yanes Dara G. Torgerson Zachary A. Szpiech Raúl Torres Dan L. Nicolae Carole Ober Christopher O. Olopade Olufunmilayo I. Olopade Oluwafemi Oluwole Ganiyu Olatunbosun Arinola Wei Song Adolfo Correa Solomon K. Musani James Wilson Leslie A. Lange Joshua M. Akey Michael J. Bamshad Jessica X. Chong Wenqing Fu Deborah A. Nickerson Alex P. Reiner Tina V. Hartert Lorraine B. Ware Eugene R. Bleecker Deborah A. Meyers Victor E. Ortega Pissamai Maul Trevor Maul Harold Watson Maria Ilma Araújo Ricardo Riccio Oliveira Luis Caraballo Javier Marrugo B. Martínez Catherine Meza Gerardo Ayestas Edwin Francisco Herrera-Paz Pamela Landaverde-Torres Said Omar Leiva Erazo Rosella Martinez Alvaro Mayorga L Mayorga Delmy-Aracely Mejia-Mejia Hector Ramos

Statistiques

Consultations : 2

Téléchargements : 0