Abstract
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.
Original language | English (US) |
---|---|
Article number | 46398 |
Journal | Scientific reports |
Volume | 7 |
DOIs | |
State | Published - 2017 |
Externally published | Yes |
ASJC Scopus subject areas
- General
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In: Scientific reports, Vol. 7, 46398, 2017.
Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
AU - Consortia CAAPA Consortium
AU - Johnston, Henry Richard
AU - Hu, Yi Juan
AU - Gao, Jingjing
AU - O'Connor, Timothy D.
AU - Abecasis, Gonçalo R.
AU - Wojcik, Genevieve L.
AU - Gignoux, Christopher R.
AU - Gourraud, Pierre Antoine
AU - Lizee, Antoine
AU - Hansen, Mark
AU - Genuario, Rob
AU - Bullis, Dave
AU - Lawley, Cindy
AU - Kenny, Eimear E.
AU - Bustamante, Carlos
AU - Beaty, Terri H.
AU - Mathias, Rasika A.
AU - Barnes, Kathleen C.
AU - Qin, Zhaohui S.
AU - Boorgula, Meher Preethi
AU - Campbell, Monica
AU - Chavan, Sameer
AU - Ford, Jean G.
AU - Foster, Cassandra
AU - Gao, Li
AU - Hansel, Nadia N.
AU - Horowitz, Edward
AU - Huang, Lili
AU - Ortiz, Romina
AU - Potee, Joseph
AU - Rafaels, Nicholas
AU - Ruczinski, Ingo
AU - Scott, Alan F.
AU - Taub, Margaret A.
AU - Vergara, Candelaria
AU - Levin, Albert M.
AU - Padhukasahasram, Badri
AU - Williams, L. Keoki
AU - Dunston, Georgia M.
AU - Faruque, Mezbah U.
AU - Gietzen, Kimberly
AU - Deshpande, Aniket
AU - Grus, Wendy E.
AU - Locke, Devin P.
AU - Foreman, Marilyn G.
AU - Avila, Pedro C.
AU - Grammer, Leslie
AU - Kim, Kwang Youn A.
AU - Bleecker, Eugene
AU - Meyers, Deborah
N1 - Funding Information: The authors gratefully acknowledge the contributions of Paul Levett, Anselm Hennis, P. Michele Lashley, Raana Naidu, Malcolm Howitt, and Timothy Roach (BAGS), Audrey Grant, Eduardo Viera Ponte, Alvaro A. Cruz, and Edgar Carvalho (BIAS), Susan Balcer-Whaley, Maria Stockton-Porter, and Mao Yang (GRAAD), Mario Meraz, Jaime Nuñez, Eileen Fabiani Herrera Mejía (HONDAS), Deanna Ashley (JAAS), Silvia Jimenez, Nathalie Acevedo, Dilia Mercado (PGCA), Ann Jedlicka (REACH), Addison K. May, Caroline Gilmore, Patricia Minton (Vanderbilt University), Qun Niu, (University of Chicago), Adeyinka Falusi, Abayomi Odetunde (University of Ibadan, Nigeria). The authors also acknowledge the support of John Jay Shannon (Cook County Health Systems) and Kevin Weiss (Northwestern University), Regina Miranda and the Indians Zenues guards (San Basilio de Palenque, Bolivar, Colombia), Ulysse Ateba Ngoa (Leiden University), and Charles Rotimi, Adeyemo Adebowale, Floyd J Malveaux, and Elena Reece (Howard University). We thank the numerous health care providers and community clinics and co-investigators who assisted in the phenotyping and collection of DNA samples, and the families and patients for generously donating DNA samples to BAGS, BIAS, BREATHE, CAG, GRAAD, HONDAS, REACH, SAGE II, VALID, SAPPHIRE, SARP, COPDGene, JAAS, GALA II, PGCA, and AEGS. Special thanks to community leaders, teachers, doctors and personnel from health centers at the Garifuna communities for organizing the medical brigades and to the medical students at Universidad Católica de Honduras, Campus San Pedro y San Pablo for their participation in the fieldwork related to HONDAS; study coordinator Sandra Salazar, and the recruiters in SAGE and GALA: Duanny Alva, MD, Gaby Ayala-Rodriguez, Ulysses Burley, Lisa Caine, Elizabeth Castellanos, Jaime Colon, Denise DeJesus, Iliana Flexas, Blanca Lopez, Brenda Lopez, MD, Louis Martos, Vivian Medina, Juana Olivo, Mario Peralta, Esther Pomares, MD, Jihan Quraishi, Johanna Rodriguez, Shahdad Saeedi, Dean Soto, Ana Taveras, Emmanuel Viera, Dr. Michael LeNoir, Dr. Kelley Meade, Mindy Jensen, and Adam Davis; and health liaisons and public health officers of the main Conde office, Adaliudes Conceição, Luciana Quintela, Ivanice Santos, Analú Lima, Benivaldo Valber Oliveira Silva, and Iraci Santos Araujo, and students from the Federal University of Bahia who assisted in data collection in BIAS: Rafael Santana, Roberta Barbosa, Ana Paula Santana, Charlton Barros, Marcele Brandão, Ludmila Almeida, Thiago Cardoso and Daniela Costa. We are grateful for the support from the international state governments and universities from Honduras, Colombia, Brazil, Gabon, Nigeria, Netherlands, Jamaica, Barbados and the United States who made this work possible. We also thank Robert Genuario for invaluable assistance in the whole genome sequencing at Illumina, Inc., Gonçalo Abecasis, William Cookson, Miriam Moffatt, for helpful discussions, Pat Oldewurtel and Murali Bopparaju for technical support, Shuai Yuan for software support, and Kit Rees and Cate Kiefe for artistic contributions. We thank Steven Salzberg and Alex Szalay for computing and data storage resources available on the Data-Scope instrument at the Institute for Data Intensive Science (IDIES), Johns Hopkins University. The authors also acknowledge the support from James Kiley, Susan Banks-Schlegel, and Weiniu Gan at the National Heart, Lung, and Blood Institute. Funding for this study was provided by National Institutes of Health (NIH) R01HL104608. Additional NIH funding includes NCI, R21CA178706 (RDH), U01CA161032, P50CA125183 (OO). NCRR, G12RR003048 (GMD), RR24975 (TH). NHGRI, R01HG007644, R21HG007233 (RDH), R21HG004751 (HRJ, JG, ZSQ), T32HG000044 (CRG). NHLBI, R01HL087699 (KCB), R01HL118267 (LKW), R01HL117004, R01HL088133, R01HL004464 (EGB), HL081332, HL112656 (LBW), R01HL69167, U01HL109164 (EB, DM), RC2HL101651, RC2HL101543, U01HL49596, R01HL072414 (CO), R01HL089897, R01HL089856, K01HL092601 (MGF), R01HL51492, R01HL/ AI67905 (JGF), HHSN268201300046C, HHSN268201300047C, HHSN268201300048C, HHSN268201300049C, HHSN268201300050C (JGW). NIAID, K08AI01582 (TH), R01AI079139 (LKW), U19AI095230 (CO). NIEHS, R01ES015794 (EGB). NIGMS, S06GM08016 (MUF), T32GM07175 (CRG). NIMHD, P60MD006902 (EGB), 8U54MD007588, P20MD0066881 (MGF). NSFGRF #1144247 (RT). Additional sources of funding include: American Asthma Foundation (LKW and EGB), American Lung Association Clinical Research Grant (TH), Colombian Government (Colciencias) 331–2004 and 680–2009 (LC), EDCTP:CT.2011.40200.025 (AAA), EU-IDEA HEALTH-F3-2009-241642 and EU-TheSchistoVac HEALTH-Fe-2009-242107 (MY), Ernest Bazley Fund (PCA, RK, LG, RS), and the Fund for Henry Ford Hospital (LKW). The Jamaica 1986 Birth Cohort Study was supported by grants from the Caribbean Health Research Council, Caribbean Cardiac Society, National Health Fund (Jamaica) and Culture Health Arts Sports and Education Fund (Jamaica). Study nurses were supported by the University Hospital of the West Indies (TF, JKM), Ralph and Marion Falk Medical Trust (COO, OO, OO, GA), UCSF Dissertation Year Fellowship (CRG), Universidad Católica de Honduras, San Pedro Sula (EHP), University of Cartagena (JM), Wellcome Trust 072405/Z/03/Z, 088862/Z/09/Z (PJC). The Jackson Heart Study is supported by contracts HHSN268201300046C, HHSN268201300047C, HHSN268201300048C, HHSN268201300049C, HHSN268201300050C from the NHLBI and the NIMHD. EGB was funded by Flight Attendant Medical Research Institute, RWJF Amos Medical Faculty Development Award and the Sandler Foundation; the Sloan Foundation to RDH; CRG was supported in part by the UCSF Chancellor’s Research Fellowship and Dissertation Year Fellowship. KCB was supported in part by the Mary Beryl Patch Turnbull Scholar Program. RAM was supported in part by the MOSAIC Initiative Awards from Johns Hopkins University. MP-Y was funded by a Postdoctoral Fellowship from Fundación Ramón Areces. MIA is an investigator supported by National Council for Scientific and Technological Development (CNPq). TVH was supported in part by K24 AI 77930, UL1 TR00445, and U19 AI95227. RO was funded by NHLBI Diversity Supplement R01HL104608.Funding for the cohorts was provided by the following: AEGS, BAGS, BIAS, BREATHE (K08AI001582, RR24975), CAG, COPDGene, GALA II, GRAAD, HONDAS, JAAS (The Jamaica 1986 Birth Cohort Study was supported by grants from the Caribbean Health Research Council, Caribbean Cardiac Society, National Health Fund (Jamaica) and Culture Health Arts Sports and Education Fund (Jamaica). The study nurses were supported by the University Hospital of the West Indies.), PGCA (University of Cartagena and Colciencias Contracts 183–2002, 680–2009), REACH, SAGE II, SAPPHIRE, SARP, SCAALA, VALID. Individual-level sequence data presented in this study are currently being prepared for deposition into dbGAP. Currently, these data are available through a data access agreement to respect the privacy of the participants for the transfer of genetic data, by contacting R.A.M. and K.C.B. and CAAPA (http://www.caapaproject.org). Funding Information: The authors gratefully acknowledge the contributions of Paul Levett, Anselm Hennis, P. Michele Lashley, Raana Naidu, Malcolm Howitt, and Timothy Roach (BAGS), Audrey Grant, Eduardo Viera Ponte, Alvaro A. Cruz, and Edgar Carvalho (BIAS), Susan Balcer-Whaley, Maria Stockton-Porter, and Mao Yang (GRAAD), Mario Meraz, Jaime Nuñez, Eileen Fabiani Herrera Mejía (HONDAS), Deanna Ashley (JAAS), Silvia Jimenez, Nathalie Acevedo, Dilia Mercado (PGCA), Ann Jedlicka (REACH), Addison K. May, Caroline Gilmore, Patricia Minton (Vanderbilt University), Qun Niu, (University of Chicago), Adeyinka Falusi, Abayomi Odetunde (University of Ibadan, Nigeria). The authors also acknowledge the support of John Jay Shannon (Cook County Health Systems) and Kevin Weiss (Northwestern University), Regina Miranda and the Indians Zenues guards (San Basilio de Palenque, Bolivar, Colombia), Ulysse Ateba Ngoa (Leiden University), and Charles Rotimi, Adeyemo Adebowale, Floyd J Malveaux, and Elena Reece (Howard University). We thank the numerous health care providers and community clinics and co-investigators who assisted in the phenotyping and collection of DNA samples, and the families and patients for generously donating DNA samples to BAGS, BIAS, BREATHE, CAG, GRAAD, HONDAS, REACH, SAGE II, VALID, SAPPHIRE, SARP, COPDGene, JAAS, GALA II, PGCA, and AEGS. Special thanks to community leaders, teachers, doctors and personnel from health centers at the Garifuna communities for organizing the medical brigades and to the medical students at Universidad Católica de Honduras, Campus San Pedro y San Pablo for their participation in the fieldwork related to HONDAS; study coordinator Sandra Salazar, and the recruiters in SAGE and GALA: Duanny Alva, MD, Gaby Ayala-Rodriguez, Ulysses Burley, Lisa Caine, Elizabeth Castellanos, Jaime Colon, Denise DeJesus, Iliana Flexas, Blanca Lopez, Brenda Lopez, MD, Louis Martos, Vivian Medina, Juana Olivo, Mario Peralta, Esther Pomares, MD, Jihan Quraishi, Johanna Rodriguez, Shahdad Saeedi, Dean Soto, Ana Taveras, Emmanuel Viera, Dr. Michael LeNoir, Dr. Kelley Meade, Mindy Jensen, and Adam Davis; and health liaisons and public health oficers of the main Conde ofice, Adaliudes Conceição, Luciana Quintela, Ivanice Santos, Analú Lima, Benivaldo Valber Oliveira Silva, and Iraci Santos Araujo, and students from the Federal University of Bahia who assisted in data collection in BIAS: Rafael Santana, Roberta Barbosa, Ana Paula Santana, Charlton Barros, Marcele Brandão, Ludmila Almeida, Tiago Cardoso and Daniela Costa. We are grateful for the support from the international state governments and universities from Honduras, Colombia, Brazil, Gabon, Nigeria, Netherlands, Jamaica, Barbados and the United States who made this work possible. We also thank Robert Genuario for invaluable assistance in the whole genome sequencing at Illumina, Inc., Gonçalo Abecasis, William Cookson, Miriam Mofatt, for helpful discussions, Pat Oldewurtel and Murali Bopparaju for technical support, Shuai Yuan for software support, and Kit Rees and Cate Kiefe for artistic contributions. We thank Steven Salzberg and Alex Szalay for computing and data storage resources available on the Data-Scope instrument at the Institute for Data Intensive Science (IDIES), Johns Hopkins University. The authors also acknowledge the support from James Kiley, Susan Banks-Schlegel, and Weiniu Gan at the National Heart, Lung, and Blood Institute. Funding for this study was provided by National Institutes of Health (NIH) R01HL104608. Additional NIH funding includes NCI, R21CA178706 (RDH), U01CA161032, P50CA125183 (OO). NCRR, G12RR003048 (GMD), RR24975 (TH). NHGRI, R01HG007644, R21HG007233 (RDH), R21HG004751 (HRJ, JG, ZSQ), T32HG000044 (CRG). NHLBI, R01HL087699 (KCB), R01HL118267 (LKW), R01HL117004, R01HL088133, R01HL004464 (EGB), HL081332, HL112656 (LBW), R01HL69167, U01HL109164 (EB, DM), RC2HL101651, RC2HL101543, U01HL49596, R01HL072414 (CO), R01HL089897, R01HL089856, K01HL092601 (MGF), R01HL51492, R01HL/AI67905 (JGF), HHSN268201300046C, HHSN268201300047C, HHSN268201300048C, HHSN268201300049C, HHSN268201300050C (JGW). NIAID, K08AI01582 (TH), R01AI079139 (LKW), U19AI095230 (CO). NIEHS, R01ES015794 (EGB). NIGMS, S06GM08016 (MUF), T32GM07175 (CRG). NIMHD, P60MD006902 (EGB), 8U54MD007588, P20MD0066881 (MGF). NSFGRF #1144247 (RT). Additional sources of funding include: American Asthma Foundation (LKW and EGB), American Lung Association Clinical Research Grant (TH), Colombian Government (Colciencias) 331-2004 and 680-2009 (LC), EDCTP:CT2011.40200.025 (AAA), EU-IDEA HEALTH-F3-2009-241642 and EU-TheSchistoVac HEALTH-Fe-2009-242107 (MY), Ernest Bazley Fund (PCA, RK, LG, RS), and the Fund for Henry Ford Hospital (LKW). The Jamaica 1986 Birth Cohort Study was supported by grants from the Caribbean Health Research Council, Caribbean Cardiac Society, National Health Fund (Jamaica) and Culture Health Arts Sports and Education Fund (Jamaica). Study nurses were supported by the University Hospital of the West Indies (TF, JKM), Ralph and Marion Falk Medical Trust (COO, OO, OO, GA), UCSF Dissertation Year Fellowship (CRG), Universidad Católica de Honduras, San Pedro Sula (EHP), University of Cartagena (JM), Wellcome Trust 072405/Z/03/Z, 088862/Z/09/Z (PJC). The Jackson Heart Study is supported by contracts HHSN268201300046C, HHSN268201300047C, HHSN268201300048C, HHSN268201300049C, HHSN268201300050C from the NHLBI and the NIMHD. EGB was funded by Flight Attendant Medical Research Institute, RWJF Amos Medical Faculty Development Award and the Sandler Foundation; the Sloan Foundation to RDH; CRG was supported in part by the UCSF Chancellor's Research Fellowship and Dissertation Year Fellowship. KCB was supported in part by the Mary Beryl Patch Turnbull Scholar Program. RAM was supported in part by the MOSAIC Initiative Awards from Johns Hopkins University. MP-Y was funded by a Postdoctoral Fellowship from Fundación Ramón Areces. MIA is an investigator supported by National Council for Scientific and Technological Development (CNPq). TVH was supported in part by K24 AI 77930, UL1 TR00445, and U19 AI95227. RO was funded by NHLBI Diversity Supplement R01HL104608. Funding for the cohorts was provided by the following: AEGS, BAGS, BIAS, BREATHE (K08AI001582, RR24975), CAG, COPDGene, GALA II, GRAAD, HONDAS, JAAS (Te Jamaica 1986 Birth Cohort Study was supported by grants from the Caribbean Health Research Council, Caribbean Cardiac Society, National Health Fund (Jamaica) and Culture Health Arts Sports and Education Fund (Jamaica). The study nurses were supported by the University Hospital of the West Indies.), PGCA (University of Cartagena and Colciencias Contracts 183-2002, 680-2009), REACH, SAGE II, SAPPHIRE, SARP, SCAALA, VALID. Individual-level sequence data presented in this study are currently being prepared for deposition into dbGAP. Currently, these data are available through a data access agreement to respect the privacy of the participants for the transfer of genetic data, by contacting R.A.M. and K.C.B. and CAAPA (http://www.caapaproject.org). Publisher Copyright: © The Author(s) 2017.
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85038807070&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85038807070&partnerID=8YFLogxK
U2 - 10.1038/srep46398
DO - 10.1038/srep46398
M3 - Article
C2 - 28429804
AN - SCOPUS:85038807070
SN - 2045-2322
VL - 7
JO - Scientific reports
JF - Scientific reports
M1 - 46398
ER -