Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Authors: Johnston Henry Richard , Hu Yi-Juan , Gao Jingjing , O’Connor Timothy D. , Abecasis Gonçalo R. , Wojcik Genevieve L , Gignoux Christopher R. , Gourraud Pierre-Antoine , Lizee Antoine , Hansen Mark , Genuario Rob , Bullis Dave , Lawley Cindy , Kenny Eimear E. , Bustamante Carlos , Beaty Terri H. , Mathias Rasika A. , Barnes Kathleen C. , Qin Zhaohui S. ,   CAAPA Consortium, Preethi Boorgula Meher , Campbell Monica , Chavan Sameer , Ford Jean G. , Foster Cassandra , Gao Li , Hansel Nadia N. , Horowitz Edward , Huang Lili , Ortiz Romina , Potee Joseph , Rafaels Nicholas , Ruczinski Ingo , Scott Alan F. , Taub Margaret A. , Vergara Candelaria , Levin Albert M. , Padhukasahasram Badri , Williams L. Keoki , Dunston Georgia M. , Faruque Mezbah U. , Gietzen Kimberly , Deshpande Aniket , Grus Wendy E. , Locke Devin P. , Foreman Marilyn G. , Avila Pedro C. , Grammer Leslie , Kim Kwang-Youn A. , Kumar Rajesh , Schleimer Robert , De La Vega Francisco M. , Shringarpure Suyash S. , Musharoff Shaila , Burchard Esteban G. , Eng Celeste , Hernandez Ryan D. , Pino-Yanes Maria , Torgerson Dara G. , Szpiech Zachary A. , Torres Raul , Nicolae Dan L. , Ober Carole , Olopade Christopher O , Olopade Olufunmilayo , Oluwole Oluwafemi , Arinola Ganiyu , Song Wei , Correa Adolfo , Musani Solomon , Wilson James G. , Lange Leslie A. , Akey Joshua , Bamshad Michael , Chong Jessica , Fu Wenqing , Nickerson Deborah , Reiner Alexander , Hartert Tina , Ware Lorraine B. , Bleecker Eugene , Meyers Deborah , Ortega Victor E. , Maul Pissamai , Maul Trevor , Watson Harold , Ilma Araujo Maria , Riccio Oliveira Ricardo , Caraballo Luis , Marrugo Javier , Martinez Beatriz , Meza Catherine , Ayestas Gerardo , Francisco Herrera-Paz Edwin , Landaverde-Torres Pamela , Erazo Said Omar Leiva , Martinez Rosella , Mayorga Alvaro , Mayorga Luis F. , Mejia-Mejia Delmy-Aracely , Ramos Hector , Saenz Allan , Varela Gloria , Marina Vasquez Olga , Ferguson Trevor , Knight-Madden Jennifer , Samms-Vaughan Maureen , Wilks Rainford J. , Adegnika Akim , Ateba-Ngoa Ulysse , Yazdanbakhsh Maria 
Published: April 2017

AbstractA primary goal of The C onsortium on A sthma among A frican-ancestry P opulations in the A mericas (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.