Search

Your search keyword '"Hirbo, Jibril B."' showing total 25 results
Start Over Author "Hirbo, Jibril B."
25 results on '"Hirbo, Jibril B."'

1. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H, Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B, Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N, Faro, Valeria Lo, Lopera-Maya, Esteban A, Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J, Chapman, Sinéad B, Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M, Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A, Guare, Lindsay A, Gignoux, Christopher R, Graham, Sarah E, Hornsby, Whitney E, Ingold, Nathan, Ismail, Said I, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y, Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H, Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M, Thani, Asma Al, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H, Damrauer, Scott M, Douville, Nicholas J, Finer, Sarah, Fritsche, Lars G, Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J, Guo, Yu, Hunt, Karen A, Ioannidis, Alexander, Jansonius, Nomdo M, Konuma, Takahiro, Lee, Ming Ta Michael, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E, Moatamed, Babak, Nava-Aguilar, Marco A, Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A, Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C, Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K, Franke, Lude, Gamazon, Eric R, Ganna, Andrea, Gaunt, Tom R, Ge, Tian, Huang, Hailiang, and Huffman, Jennifer

Subjects
Human Genome, Genetics, Biotechnology, Generic health relevance, Good Health and Well Being, Biobank of the Americas, Biobank Japan Project, BioMe, BioVU, CanPath - Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center for Personalized Medicine, deCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank of Korea, Penn Medicine BioBank, Qatar Biobank, QSkin Sun and Health Study, Taiwan Biobank, HUNT Study, UCLA ATLAS Community Health Initiative, Uganda Genome Resource, UK Biobank, GWAS, ancestry diversity, biobank, genetic association studies, meta-analysis, phenotype harmonization
Abstract

Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)-a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.

Published
2022

4. Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H., Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B., Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N., Lo Faro, Valeria, Lopera-Maya, Esteban A., Läll, Kristi, Favé, Marie-Julie, Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Mutaamba, Maasha, Partanen, Juulia J., Brumpton, Ben M., Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Palta, Priit, Pandit, Anita, Preuss, Michael H., Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Zawistowski, Matthew, Zhong, Xue, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H., Douville, Nicholas J., Finer, Sarah, Fritsche, Lars G., Griffiths, Christopher J., Guo, Yu, Hunt, Karen A., Konuma, Takahiro, Marioni, Riccardo E., Nomdo, Jansonius, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Shortt, Jonathan A., Straub, Peter, Tao, Ran, Vanderwerff, Brett, Barnes, Kathleen C., Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K., Franke, Lude, Gamazon, Eric R., Ganna, Andrea, Gaunt, Tom R., Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Koskela, Jukka T., Lajonchere, Clara, Law, Matthew H., Li, Liming, Lindgren, Cecilia M., Loos, Ruth J.F., MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M., Porteous, David J., Shavit, Jordan A., Snieder, Harold, Trembath, Richard C., Vonk, Judith M., Whiteman, David, Wicks, Stephen J., Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Cox, Nancy J., Geschwind, Daniel H., Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E., Lin, Yen-Feng, Mägi, Reedik, Martin, Hilary C., Medland, Sarah E., Okada, Yukinori, Palotie, Aarno V., Pasaniuc, Bogdan, Sanna, Serena, Smoller, Jordan W., Stefansson, Kari, van Heel, David A., Walters, Robin G., Zöllner, Sebastian, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., Neale, Benjamin M., Lopera, Esteban, Kerminen, Sini, Wu, Kuan-Han, Bhatta, Laxmi, Brumpton, Ben, Deelen, Patrick, Murakami, Yoshinori, Willer, Cristen, and Hirbo, Jibril

Published
2023
Full Text
View/download PDF

5. Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H., Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B., Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N., Lo Faro, Valeria, Lopera-Maya, Esteban A., Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J., Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M., Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A., Guare, Lindsay A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Ismail, Said I., Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H., Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M., Al Thani, Asma, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, de Bock, Geertruida H., Damrauer, Scott M., Douville, Nicholas J., Finer, Sarah, Fritsche, Lars G., Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J., Guo, Yu, Hunt, Karen A., Ioannidis, Alexander, Jansonius, Nomdo M., Konuma, Takahiro, Michael Lee, Ming Ta, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E., Moatamed, Babak, Nava-Aguilar, Marco A., Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A., Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C., Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K., Franke, Lude, Gamazon, Eric R., Ganna, Andrea, Gaunt, Tom R., Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Katsanis, Nicholas, Koskela, Jukka T., Lajonchere, Clara, Law, Matthew H., Li, Liming, Lindgren, Cecilia M., Loos, Ruth J.F., MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M., Porteous, David J., Shavit, Jordan A., Snieder, Harold, Takano, Tomohiro, Trembath, Richard C., Vonk, Judith M., Whiteman, David C., Wicks, Stephen J., Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Bustamante, Carlos D., Cox, Nancy J., Fatumo, Segun, Geschwind, Daniel H., Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E., Lee, Seunggeun, Lin, Yen-Feng, Mbarek, Hamdi, Mägi, Reedik, Martin, Hilary C., Medland, Sarah E., Okada, Yukinori, Palotie, Aarno V., Pasaniuc, Bogdan, Rader, Daniel J., Ritchie, Marylyn D., Sanna, Serena, Smoller, Jordan W., Stefansson, Kari, van Heel, David A., Walters, Robin G., Zöllner, Sebastian, Biobank of the Americas, Biobank Japan Project, BioMe, BioVU, CanPath - Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center for Personalized Medicine, deCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank of Korea, Penn Medicine BioBank, Qatar Biobank, The Qskin Sun and Health Study, Taiwan Biobank, The Hunt Study, Ucla Atlas Community Health Initiative, Uganda Genome Resource, Uk Biobank, Martin, Alicia R., Willer, Cristen J., Daly, Mark J., Neale, Benjamin M., and Elzur, Roy

Published
2022
Full Text
View/download PDF

6. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics

Author

Partanen, Juulia J., Häppölä, Paavo, Zhou, Wei, Lehisto, Arto A., Ainola, Mari, Sutinen, Eva, Allen, Richard J., Stockwell, Amy D., Leavy, Olivia C., Oldham, Justin M., Guillen-Guio, Beatriz, Cox, Nancy J., Hirbo, Jibril B., Schwartz, David A., Fingerlin, Tasha E., Flores, Carlos, Noth, Imre, Yaspan, Brian L., Jenkins, R. Gisli, Wain, Louise V., Ripatti, Samuli, Pirinen, Matti, Laitinen, Tarja, Kaarteenaho, Riitta, Myllärniemi, Marjukka, Daly, Mark J., and Koskela, Jukka T.

Published
2022
Full Text
View/download PDF

7. Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Author

Wang, Ying, Namba, Shinichi, Lopera-Maya, Esteban A., Kerminen, Sini, Tsuo, Kristin, Läll, Kristi, Kanai, Masahiro, Zhou, Wei, Wu, Kuan Han H., Favé, Marie Julie, Bhatta, Laxmi, Awadalla, Philip, Brumpton, Ben M., Deelen, Patrick, Hveem, Kristian, Lo Faro, Valeria, Mägi, Reedik, Murakami, Yoshinori, Sanna, Serena, Smoller, Jordan W., Uzunovic, Jasmina, Wolford, Brooke N., Rasheed, Humaira, Hirbo, Jibril B., Bhattacharya, Arjun, Zhao, Huiling, Surakka, Ida, Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Mutaamba, Maasha, Partanen, Juulia J., Chavan, Sameer, Chen, Tzu Ting, Daya, Michelle, Ding, Yi, Feng, Yen Chen A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Loos, Ruth J.F., Wang, Ying, Namba, Shinichi, Lopera-Maya, Esteban A., Kerminen, Sini, Tsuo, Kristin, Läll, Kristi, Kanai, Masahiro, Zhou, Wei, Wu, Kuan Han H., Favé, Marie Julie, Bhatta, Laxmi, Awadalla, Philip, Brumpton, Ben M., Deelen, Patrick, Hveem, Kristian, Lo Faro, Valeria, Mägi, Reedik, Murakami, Yoshinori, Sanna, Serena, Smoller, Jordan W., Uzunovic, Jasmina, Wolford, Brooke N., Rasheed, Humaira, Hirbo, Jibril B., Bhattacharya, Arjun, Zhao, Huiling, Surakka, Ida, Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Mutaamba, Maasha, Partanen, Juulia J., Chavan, Sameer, Chen, Tzu Ting, Daya, Michelle, Ding, Yi, Feng, Yen Chen A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., and Loos, Ruth J.F.

Abstract

Polygenic risk scores (PRSs) have been widely explored in precision medicine. However, few studies have thoroughly investigated their best practices in global populations across different diseases. We here utilized data from Global Biobank Meta-analysis Initiative (GBMI) to explore methodological considerations and PRS performance in 9 different biobanks for 14 disease endpoints. Specifically, we constructed PRSs using pruning and thresholding (P + T) and PRS-continuous shrinkage (CS). For both methods, using a European-based linkage disequilibrium (LD) reference panel resulted in comparable or higher prediction accuracy compared with several other non-European-based panels. PRS-CS overall outperformed the classic P + T method, especially for endpoints with higher SNP-based heritability. Notably, prediction accuracy is heterogeneous across endpoints, biobanks, and ancestries, especially for asthma, which has known variation in disease prevalence across populations. Overall, we provide lessons for PRS construction, evaluation, and interpretation using GBMI resources and highlight the importance of best practices for PRS in the biobank-scale genomics era.

Published
2023

8. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan-Han H, Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B, Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N, Lo Faro, Valeria, Lopera-Maya, Esteban A, Läll, Kristi, Favé, Marie-Julie, Partanen, Juulia J, Chapman, Sinéad B, Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M, Chavan, Sameer, Chen, Tzu-Ting, Daya, Michelle, Ding, Yi, Feng, Yen-Chen A, Guare, Lindsay A, Gignoux, Christopher R, Graham, Sarah E, Hornsby, Whitney E, Ingold, Nathan, Ismail, Said I, Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y, Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H, Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Zhong, Xue, Afifi, Nahla, Al-Dabhani, Kawthar M, Al Thani, Asma, Bradford, Yuki, Campbell, Archie, Crooks, Kristy, De Bock, Geertruida H, Damrauer, Scott M, Douville, Nicholas J, Finer, Sarah, Fritsche, Lars G, Fthenou, Eleni, Gonzalez-Arroyo, Gilberto, Griffiths, Christopher J, Guo, Yu, Hunt, Karen A, Ioannidis, Alexander, Jansonius, Nomdo M, Konuma, Takahiro, Lee, Ming Ta Michael, Lopez-Pineda, Arturo, Matsuda, Yuta, Marioni, Riccardo E, Moatamed, Babak, Nava-Aguilar, Marco A, Numakura, Kensuke, Patil, Snehal, Rafaels, Nicholas, Richmond, Anne, Rojas-Muñoz, Agustin, Shortt, Jonathan A, Straub, Peter, Tao, Ran, Vanderwerff, Brett, Vernekar, Manvi, Veturi, Yogasudha, Barnes, Kathleen C, Boezen, Marike, Chen, Zhengming, Chen, Chia-Yen, Cho, Judy, Smith, George Davey, Finucane, Hilary K, Franke, Lude, Gamazon, Eric R, Ganna, Andrea, Gaunt, Tom R, Ge, Tian, Huang, Hailiang, Huffman, Jennifer, Katsanis, Nicholas, Koskela, Jukka T, Lajonchere, Clara, Law, Matthew H, Li, Liming, Lindgren, Cecilia M, Loos, Ruth JF, MacGregor, Stuart, Matsuda, Koichi, Olsen, Catherine M, Porteous, David J, Shavit, Jordan A, Snieder, Harold, Takano, Tomohiro, Trembath, Richard C, Vonk, Judith M, Whiteman, David C, Wicks, Stephen J, Wijmenga, Cisca, Wright, John, Zheng, Jie, Zhou, Xiang, Awadalla, Philip, Boehnke, Michael, Bustamante, Carlos D, Cox, Nancy J, Fatumo, Segun, Geschwind, Daniel H, Hayward, Caroline, Hveem, Kristian, Kenny, Eimear E, Lee, Seunggeun, Lin, Yen-Feng, Mbarek, Hamdi, Mägi, Reedik, Martin, Hilary C, Medland, Sarah E, Okada, Yukinori, Palotie, Aarno V, Pasaniuc, Bogdan, Rader, Daniel J, Ritchie, Marylyn D, Sanna, Serena, Smoller, Jordan W, Stefansson, Kari, Van Heel, David A, Walters, Robin G, Zöllner, Sebastian, Biobank Of The Americas, Biobank Japan Project, BioMe, BioVU, CanPath-Ontario Health Study, China Kadoorie Biobank Collaborative Group, Colorado Center For Personalized Medicine, DeCODE Genetics, Estonian Biobank, FinnGen, Generation Scotland, Genes & Health Research Team, LifeLines, Mass General Brigham Biobank, Michigan Genomics Initiative, National Biobank Of Korea, Penn Medicine BioBank, Qatar Biobank, QSkin Sun And Health Study, Taiwan Biobank, HUNT Study, UCLA ATLAS Community Health Initiative, Uganda Genome Resource, UK Biobank, Martin, Alicia R, Willer, Cristen J, Daly, Mark J, Neale, Benjamin M, Namba, Shinichi [0000-0002-7486-3146], Guare, Lindsay A [0000-0001-6988-5319], Palta, Priit [0000-0001-9320-7008], de Bock, Geertruida H [0000-0003-3104-4471], Finer, Sarah [0000-0002-2684-4653], Jansonius, Nomdo M [0000-0002-6495-6568], Rojas-Muñoz, Agustin [0000-0001-7594-0599], Gamazon, Eric R [0000-0003-4204-8734], Ganna, Andrea [0000-0002-8147-240X], Koskela, Jukka T [0000-0002-0154-7222], MacGregor, Stuart [0000-0001-6731-8142], Palotie, Aarno V [0000-0002-2527-5874], and Apollo - University of Cambridge Repository

Subjects
biobank, meta-analysis, genetic association studies, GWAS, ancestry diversity, phenotype harmonization
Abstract

Funder: Biogen, Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)-a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.

Published
2023
Full Text
View/download PDF

9. Additional file 1 of The genetic and evolutionary basis of gene expression variation in East Africans

Author

Kelly, Derek E., Ramdas, Shweta, Ma, Rong, Rawlings-Goss, Renata A., Grant, Gregory R., Ranciaro, Alessia, Hirbo, Jibril B., Beggs, William, Yeager, Meredith, Chanock, Stephen, Nyambo, Thomas B., Omar, Sabah A., Woldemeskel, Dawit, Belay, Gurja, Li, Hongzhe, Brown, Christopher D., and Tishkoff, Sarah A.

Abstract

Additional file 1: Fig S1. Principal Component Analysis of East African and 1000 Genome Project. Fig S2. ADMIXTURE analysis across K values 2-12. Fig S3. Genomic context of tQTLs. Fig S4. π1 of eQTL p-values of SNP-gene pairs ascertained as sQTLs. Fig S5. π1 between sQTLs and eQTLs across gene length deciles. Fig S6. π1 value of ascertained eQTLs and sQTLs in GTEx. Fig S7. Mapping statistics from STAR. Fig S8. Frequency and LD differences between African samples and 1000 Genomes EURpopulations. Fig S9. tQTL effect size vs MAF. Fig S10. Fraction of FST outliers among eQTLs and sQTLs compared with matched background. Fig S11. Population-specific FST outliers. Fig. S12. Global frequencies of SNPs associated with pigmentation variation and TMEM216 expression and splicing. Fig S13. Colocalization of Mursi PBS and d-statistics with TMEM216 eQTLs. Fig S14. Colocalization of Mursi PBS and d-statistics with pigmentation GWAS. Fig S15. eQTL associations for TMEM216 across populations. Fig S16. ‘LocusCompare’ plots of African pigmentation GWAS and GTEx v8 eQTLs. Fig S17. ‘LocusCompare’ plots of African pigmentation GWAS and GTEx v8 sQTLs.

Published
2023
Full Text
View/download PDF

10. Additional file 3 of The genetic and evolutionary basis of gene expression variation in East Africans

Author

Kelly, Derek E., Ramdas, Shweta, Ma, Rong, Rawlings-Goss, Renata A., Grant, Gregory R., Ranciaro, Alessia, Hirbo, Jibril B., Beggs, William, Yeager, Meredith, Chanock, Stephen, Nyambo, Thomas B., Omar, Sabah A., Woldemeskel, Dawit, Belay, Gurja, Li, Hongzhe, Brown, Christopher D., and Tishkoff, Sarah A.

Abstract

Additional file 3. Reviewhistory.

Published
2023
Full Text
View/download PDF

11. Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

Author

Wang, Ying, primary, Namba, Shinichi, additional, Lopera, Esteban, additional, Kerminen, Sini, additional, Tsuo, Kristin, additional, Läll, Kristi, additional, Kanai, Masahiro, additional, Zhou, Wei, additional, Wu, Kuan-Han, additional, Favé, Marie-Julie, additional, Bhatta, Laxmi, additional, Awadalla, Philip, additional, Brumpton, Ben, additional, Deelen, Patrick, additional, Hveem, Kristian, additional, Lo Faro, Valeria, additional, Mägi, Reedik, additional, Murakami, Yoshinori, additional, Sanna, Serena, additional, Smoller, Jordan W., additional, Uzunovic, Jasmina, additional, Wolford, Brooke N., additional, Willer, Cristen, additional, Gamazon, Eric R., additional, Cox, Nancy J., additional, Surakka, Ida, additional, Okada, Yukinori, additional, Martin, Alicia R., additional, Hirbo, Jibril, additional, Wu, Kuan-Han H., additional, Rasheed, Humaira, additional, Hirbo, Jibril B., additional, Wang, Ying, additional, Bhattacharya, Arjun, additional, Zhao, Huiling, additional, Lopera-Maya, Esteban A., additional, Chapman, Sinéad B., additional, Karjalainen, Juha, additional, Kurki, Mitja, additional, Mutaamba, Maasha, additional, Partanen, Juulia J., additional, Brumpton, Ben M., additional, Chavan, Sameer, additional, Chen, Tzu-Ting, additional, Daya, Michelle, additional, Ding, Yi, additional, Feng, Yen-Chen A., additional, Gignoux, Christopher R., additional, Graham, Sarah E., additional, Hornsby, Whitney E., additional, Ingold, Nathan, additional, Johnson, Ruth, additional, Laisk, Triin, additional, Lin, Kuang, additional, Lv, Jun, additional, Millwood, Iona Y., additional, Palta, Priit, additional, Pandit, Anita, additional, Preuss, Michael H., additional, Thorsteinsdottir, Unnur, additional, Zawistowski, Matthew, additional, Zhong, Xue, additional, Campbell, Archie, additional, Crooks, Kristy, additional, de Bock, Geertruida H., additional, Douville, Nicholas J., additional, Finer, Sarah, additional, Fritsche, Lars G., additional, Griffiths, Christopher J., additional, Guo, Yu, additional, Hunt, Karen A., additional, Konuma, Takahiro, additional, Marioni, Riccardo E., additional, Nomdo, Jansonius, additional, Patil, Snehal, additional, Rafaels, Nicholas, additional, Richmond, Anne, additional, Shortt, Jonathan A., additional, Straub, Peter, additional, Tao, Ran, additional, Vanderwerff, Brett, additional, Barnes, Kathleen C., additional, Boezen, Marike, additional, Chen, Zhengming, additional, Chen, Chia-Yen, additional, Cho, Judy, additional, Smith, George Davey, additional, Finucane, Hilary K., additional, Franke, Lude, additional, Ganna, Andrea, additional, Gaunt, Tom R., additional, Ge, Tian, additional, Huang, Hailiang, additional, Huffman, Jennifer, additional, Koskela, Jukka T., additional, Lajonchere, Clara, additional, Law, Matthew H., additional, Li, Liming, additional, Lindgren, Cecilia M., additional, Loos, Ruth J.F., additional, MacGregor, Stuart, additional, Matsuda, Koichi, additional, Olsen, Catherine M., additional, Porteous, David J., additional, Shavit, Jordan A., additional, Snieder, Harold, additional, Trembath, Richard C., additional, Vonk, Judith M., additional, Whiteman, David, additional, Wicks, Stephen J., additional, Wijmenga, Cisca, additional, Wright, John, additional, Zheng, Jie, additional, Zhou, Xiang, additional, Boehnke, Michael, additional, Geschwind, Daniel H., additional, Hayward, Caroline, additional, Kenny, Eimear E., additional, Lin, Yen-Feng, additional, Martin, Hilary C., additional, Medland, Sarah E., additional, Palotie, Aarno V., additional, Pasaniuc, Bogdan, additional, Stefansson, Kari, additional, van Heel, David A., additional, Walters, Robin G., additional, Zöllner, Sebastian, additional, Willer, Cristen J., additional, Daly, Mark J., additional, and Neale, Benjamin M., additional

Published
2023
Full Text
View/download PDF

14. Best practices for multi-ancestry, meta-analytic transcriptome-wide association studies: Lessons from the Global Biobank Meta-analysis Initiative

Author

Bhattacharya, Arjun, Hirbo, Jibril B, Zhou, Dan, Zhou, Wei, Zheng, Jie, Kanai, Masahiro, Global Biobank Meta-Analysis Initiative, Pasaniuc, Bogdan, Gamazon, Eric R, Cox, Nancy J, Bhattacharya, Arjun [0000-0003-1196-4385], Gamazon, Eric R [0000-0003-4204-8734], and Apollo - University of Cambridge Repository

Subjects
Global Biobank Meta-analysis Initiative
Abstract

The Global Biobank Meta-analysis Initiative (GBMI), through its diversity, provides a valuable opportunity to study population-wide and ancestry-specific genetic associations. However, with multiple ascertainment strategies and multi-ancestry study populations across biobanks, GBMI presents unique challenges in implementing statistical genetics methods. Transcriptome-wide association studies (TWASs) boost detection power for and provide biological context to genetic associations by integrating genetic variant-to-trait associations from genome-wide association studies (GWASs) with predictive models of gene expression. TWASs present unique challenges beyond GWASs, especially in a multi-biobank, meta-analytic setting. Here, we present the GBMI TWAS pipeline, outlining practical considerations for ancestry and tissue specificity, meta-analytic strategies, and open challenges at every step of the framework. We advise conducting ancestry-stratified TWASs using ancestry-specific expression models and meta-analyzing results using inverse-variance weighting, showing the least test statistic inflation. Our work provides a foundation for adding transcriptomic context to biobank-linked GWASs, allowing for ancestry-aware discovery to accelerate genomic medicine.

Published
2022
Full Text
View/download PDF

17. The Genetic Structure and History of Africans and African Americans

Author

Tishkoff, Sarah A., Reed, Floyd A., Friedlaender, Françoise R., Ehret, Christopher, Ranciaro, Alessia, Froment, Alain, Hirbo, Jibril B., Awomoyi, Agnes A., Bodo, Jean-Marie, Doumbo, Ogobara, Ibrahim, Muntaser, Juma, Abdalla T., Kotze, Maritha J., Lema, Godfrey, Moore, Jason H., Mortensen, Holly, Nyambo, Thomas B., Omar, Sabah A., Powell, Kweli, Pretorius, Gideon S., Smith, Michael W., Thera, Mahamadou A., Wambebe, Charles, Weber, James L., and Williams, Scott M.

Published
2009
Full Text
View/download PDF

18. Global Biobank Meta-analysis Initiative:Powering genetic discovery across human disease

Author

Zhou, Wei, Kanai, Masahiro, Wu, Kuan Han H., Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B., Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N., Lo Faro, Valeria, Lopera-Maya, Esteban A., Läll, Kristi, Favé, Marie Julie, Partanen, Juulia J., Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M., Chavan, Sameer, Chen, Tzu Ting, Daya, Michelle, Ding, Yi, Feng, Yen Chen A., Guare, Lindsay A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Ismail, Said I., Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H., Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, Loos, Ruth J.F., Zhou, Wei, Kanai, Masahiro, Wu, Kuan Han H., Rasheed, Humaira, Tsuo, Kristin, Hirbo, Jibril B., Wang, Ying, Bhattacharya, Arjun, Zhao, Huiling, Namba, Shinichi, Surakka, Ida, Wolford, Brooke N., Lo Faro, Valeria, Lopera-Maya, Esteban A., Läll, Kristi, Favé, Marie Julie, Partanen, Juulia J., Chapman, Sinéad B., Karjalainen, Juha, Kurki, Mitja, Maasha, Mutaamba, Brumpton, Ben M., Chavan, Sameer, Chen, Tzu Ting, Daya, Michelle, Ding, Yi, Feng, Yen Chen A., Guare, Lindsay A., Gignoux, Christopher R., Graham, Sarah E., Hornsby, Whitney E., Ingold, Nathan, Ismail, Said I., Johnson, Ruth, Laisk, Triin, Lin, Kuang, Lv, Jun, Millwood, Iona Y., Moreno-Grau, Sonia, Nam, Kisung, Palta, Priit, Pandit, Anita, Preuss, Michael H., Saad, Chadi, Setia-Verma, Shefali, Thorsteinsdottir, Unnur, Uzunovic, Jasmina, Verma, Anurag, Zawistowski, Matthew, and Loos, Ruth J.F.

Abstract

Biobanks facilitate genome-wide association studies (GWASs), which have mapped genomic loci across a range of human diseases and traits. However, most biobanks are primarily composed of individuals of European ancestry. We introduce the Global Biobank Meta-analysis Initiative (GBMI)—a collaborative network of 23 biobanks from 4 continents representing more than 2.2 million consented individuals with genetic data linked to electronic health records. GBMI meta-analyzes summary statistics from GWASs generated using harmonized genotypes and phenotypes from member biobanks for 14 exemplar diseases and endpoints. This strategy validates that GWASs conducted in diverse biobanks can be integrated despite heterogeneity in case definitions, recruitment strategies, and baseline characteristics. This collaborative effort improves GWAS power for diseases, benefits understudied diseases, and improves risk prediction while also enabling the nomination of disease genes and drug candidates by incorporating gene and protein expression data and providing insight into the underlying biology of human diseases and traits.

Published
2022

20. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics

Author

International IPF Genetics Consortium, Global Biobank Meta-Analysis Initiative (GBMI), Partanen, Juulia J., Häppölä, Paavo, Zhou, Wei, Lehisto, Arto A., Ainola, Mari, Sutinen, Eva, Allen, Richard J., Stockwell, Amy D., Leavy, Olivia C., Oldham, Justin M., Guillen-Guio, Beatriz, Cox, Nancy J., Hirbo, Jibril B., Schwartz, David A., Fingerlin, Tasha E., Flores, Carlos, Noth, Imre, Yaspan, Brian L., Jenkins, R. Gisli, Wain, Louise V., Ripatti, Samuli, Pirinen, Matti, Laitinen, Tarja, Kaarteenaho, Riitta, Myllärniemi, Marjukka, Daly, Mark J., Koskela, Jukka T., Tampere University, Department of General Administration, Complex Disease Genetics, Institute for Molecular Medicine Finland, University of Helsinki, Helsinki Institute of Life Science HiLIFE, Genomics of Neurological and Neuropsychiatric Disorders, CAMM - Research Program for Clinical and Molecular Metabolism, INDIVIDRUG - Individualized Drug Therapy, HUS Heart and Lung Center, Keuhkosairauksien yksikkö, CAN-PRO - Translational Cancer Medicine Program, Centre of Excellence in Complex Disease Genetics, Department of Public Health, Samuli Olli Ripatti / Principal Investigator, Faculty Common Matters (Faculty of Social Sciences), Faculty of Medicine, Department of Mathematics and Statistics, Helsinki Institute for Information Technology, Statistical and population genetics, Department of Medicine, Clinicum, and Helsinki University Hospital Area

Subjects
ancestry, 1184 Genetics, developmental biology, physiology, COVID-19, cross-population analysis, 3121 Internal medicine, idiopathic pulmonary fibrosis, Biochemistry, Genetics and Molecular Biology (miscellaneous), MUC5B, meta-analysis, fine-mapping, Global Biobank Meta-Analysis Initiative, 3121 General medicine, internal medicine and other clinical medicine, Genetics, GWAS
Abstract

Publisher Copyright: © 2022 The Author(s) The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor—the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus MUC5B.

Published
2022

21. The Genetic and Evolutionary Basis of Gene Expression Variation in East Africans

Author

Kelly, Derek E., primary, Ramdas, Shweta, additional, Ma, Rong, additional, Rawlings-Goss, Renata A., additional, Grant, Gregory R., additional, Ranciaro, Alessia, additional, Hirbo, Jibril B., additional, Beggs, William, additional, Yeager, Meredith, additional, Chanock, Stephen, additional, Nyambo, Thomas B., additional, Omar, Sabah A, additional, Meskel, Dawit Wolde, additional, Belay, Gurja, additional, Li, Hongzhe, additional, Brown, Christopher D., additional, and Tishkoff, Sarah A., additional

Published
2022
Full Text
View/download PDF

23. Analysis of Genetically Determined Gene Expression Suggests Role of Inflammatory Processes in Exfoliation Syndrome

Author

Hirbo, Jibril B., primary, Pasutto, Francesca, additional, Gamazon, Eric R., additional, Evans, Patrick, additional, Pawar, Priyanka, additional, Berner, Daniel, additional, Sealock, Julia, additional, Tao, Ran, additional, Straub, Peter S., additional, Konkashbaev, Anuar I., additional, Breyer, Max, additional, Schlötzer-Schrehardt, Ursula, additional, Reis, André, additional, Brantley, Milam A., additional, Khor, Chiea C., additional, Joos, Karen M., additional, and Cox, Nancy J., additional

Published
2020
Full Text
View/download PDF

24. Convergent adaptation of human lactase persistence in Africa and Europe

Author

Tishkoff, Sarah A, primary, Reed, Floyd A, additional, Ranciaro, Alessia, additional, Voight, Benjamin F, additional, Babbitt, Courtney C, additional, Silverman, Jesse S, additional, Powell, Kweli, additional, Mortensen, Holly M, additional, Hirbo, Jibril B, additional, Osman, Maha, additional, Ibrahim, Muntaser, additional, Omar, Sabah A, additional, Lema, Godfrey, additional, Nyambo, Thomas B, additional, Ghori, Jilur, additional, Bumpstead, Suzannah, additional, Pritchard, Jonathan K, additional, Wray, Gregory A, additional, and Deloukas, Panos, additional

Published
2006
Full Text
View/download PDF

25. Convergent adaptation of human lactase persistence in Africa and Europe.

Author

Tishkoff, Sarah A., Reed, Floyd A., Ranciaro, Alessia, Voight, Benjamin F., Babbitt, Courtney C., Silverman, Jesse S., Powell, Kweli, Mortensen, Holly M., Hirbo, Jibril B., Osman, Maha, Ibrahim, Muntaser, Omar, Sabah A., Lema, Godfrey, Nyambo, Thomas B., Ghori, Jilur, Bumpstead, Suzannah, Pritchard, Jonathan K., Wray, Gregory A., and Deloukas, Panos

Subjects
LACTASE persistence, MILK consumption, LACTOSE intolerance, NUCLEOTIDE sequence, EUROPEANS, AFRICANS, HEALTH
Abstract

A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past ∼7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits—animal domestication and adult milk consumption. [ABSTRACT FROM AUTHOR]

Published
2007
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results