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Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry

Article scientifique 2016 Anglais

Résumé

To characterize the extent and impact of ancestry-related biases in precision genomic medicine, we use 642 whole-genome sequences from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) project to evaluate typical filters and databases. We find significant correlations between estimated African ancestry proportions and the number of variants per individual in all variant classification sets but one. The source of these correlations is highlighted in more detail by looking at the interaction between filtering criteria and the ClinVar and Human Gene Mutation databases. ClinVar's correlation, representing African ancestry-related bias, has changed over time amidst monthly updates, with the most extreme switch happening between March and April of 2014 (r=0.733 to r=-0.683). We identify 68 SNPs as the major drivers of this change in correlation. As long as ancestry-related bias when using these clinical databases is minimally recognized, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations.

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Kessler, M., Yerges-Armstrong, L., Taub, M., Shetty, A., Maloney, K., Jeng, L., Ruczinski, I., Levin, A., Williams, L., Beaty, T., Mathias, R., Barnes, K., Boorgula, M., Campbell, M., Chavan, S., Ford, J., Foster, C., Gao, L., Hansel, N., Horowitz, E., Huang, L., Ortiz, R., Potee, J., Rafaels, N., Vergara, C., Gao, J., Hu, Y., Johnston, H., Qin, Z., Padhukasahasram, B., Dunston, G., Faruque, M., Kenny, E., Gietzen, K., Hansen, M., Genuario, R., Bullis, D., Lawley, C., Deshpande, A., Grus, W., Locke, D., Foreman, M., Avila, P., Grammer, L., Kim, K., Kumar, R., Schleimer, R., Bustamante, C., Vega, F., Gignoux, C., Shringarpure, S., Musharoff, S., Wojcik, G., Burchard, E., Eng, C., Gourraud, P., Hernandez, R., Lizée, A., Pino‐Yanes, M., Torgerson, D., Szpiech, Z., Torres, R., Nicolae, D., Ober, C., Olopade, C., Olopade, O., Oluwole, O., Arinola, G., Song, W., Abecasis, G., 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., Pissamai, M., Trevor, M., 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. (2016). Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry. https://doi.org/10.1038/ncomms12521

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Auteur(s)

Michael D. Kessler Laura M. Yerges-Armstrong Margaret A. Taub Amol C. Shetty Kristin A. Maloney Linda Jo Bone Jeng Ingo Ruczinski Albert M. Levin L. Keoki Williams Terri H. Beaty Rasika A. Mathias Kathleen C. Barnes 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 Candelaria Vergara Jingjing Gao Yi‐Juan Hu H. Richard Johnston Zhaohui Qin Badri Padhukasahasram Georgia M. Dunston Mezbah U. Faruque Eimear E. Kenny Kimberly Gietzen Mark Hansen Rob Genuario Dave Bullis Cindy Lawley Aniket Deshpande Wendy E. Grus Devin P. Locke Marilyn G. Foreman Pedro C. Avila Leslie C. Grammer Kwang-YounA Kim Rajesh Kumar Robert P. Schleimer Carlos D. Bustamante Francisco M. De La Vega Chris Gignoux Suyash Shringarpure Shaila Musharoff Genevieve L. Wojcik Esteban Burchard Celeste Eng Pierre‐Antoine Gourraud Ryan D. Hernandez Antoine Lizée 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 Arinola Wei Song Gonçalo R. Abecasis Adolfo Correa Solomon K. Musani James G. Wilson Leslie A. Lange Joshua M. Akey Michael J. Bamshad Jessica X. Chong Wenqing Fu Deborah A. Nickerson Alexander P. Reiner Tina V. Hartert Lorraine B. Ware Eugene R. Bleecker Deborah Meyers Victor E. Ortega Maul R. N. Pissamai Maul R. N. Trevor 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

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