Advances in integrative African genomics

被引:11
作者
Zhang, Chao [1 ]
Hansen, Matthew E. B. [1 ]
Tishkoff, Sarah A. [1 ,2 ]
机构
[1] Univ Penn, Perelman Sch Med, Dept Genet, Philadelphia, PA 19104 USA
[2] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA
关键词
SOUTHERN COMMUNITY COHORT; NATURAL-SELECTION; DNA METHYLATION; GUT MICROBIOME; DEMOGRAPHIC HISTORY; HUNTER-GATHERERS; WIDE ASSOCIATION; PLASMODIUM-FALCIPARUM; GENETIC ADAPTATION; SKIN PIGMENTATION;
D O I
10.1016/j.tig.2021.09.013
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
There has been a rapid increase in human genome sequencing in the past two decades, resulting in the identification of millions of previously unknown genetic variants. However, African populations are under-represented in sequencing efforts. Additional sequencing from diverse African populations and the construction of African-specific reference genomes is needed to better characterize the full spectrum of variation in humans. However, sequencing alone is insufficient to address the molecular and cellular mechanisms underlying variable phenotypes and disease risks. Determining functional consequences of genetic variation using multi-omics approaches is a fundamental post-genomic challenge. We discuss approaches to close the knowledge gaps about African genomic diversity and review advances in African integrative genomic studies and their implications for precision medicine.
引用
收藏
页码:152 / 168
页数:17
相关论文
共 171 条
  • [91] Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations
    Lorente-Galdos, Belen
    Lao, Oscar
    Serra-Vidal, Gerard
    Santpere, Gabriel
    Kuderna, Lukas F. K.
    Arauna, Lara R.
    Fadhlaoui-Zid, Karima
    Pimenoff, Ville N.
    Soodyall, Himla
    Zalloua, Pierre
    Marques-Bonet, Tomas
    Comas, David
    [J]. GENOME BIOLOGY, 2019, 20 (1)
  • [92] The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
    Mallick, Swapan
    Li, Heng
    Lipson, Mark
    Mathieson, Iain
    Gymrek, Melissa
    Racimo, Fernando
    Zhao, Mengyao
    Chennagiri, Niru
    Nordenfelt, Susanne
    Tandon, Arti
    Skoglund, Pontus
    Lazaridis, Iosif
    Sankararaman, Sriram
    Fu, Qiaomei
    Rohland, Nadin
    Renaud, Gabriel
    Erlich, Yaniv
    Willems, Thomas
    Gallo, Carla
    Spence, Jeffrey P.
    Song, Yun S.
    Poletti, Giovanni
    Balloux, Francois
    van Driem, George
    de Knijff, Peter
    Romero, Irene Gallego
    Jha, Aashish R.
    Behar, Doron M.
    Bravi, Claudio M.
    Capelli, Cristian
    Hervig, Tor
    Moreno-Estrada, Andres
    Posukh, Olga L.
    Balanovska, Elena
    Balanovsky, Oleg
    Karachanak-Yankova, Sena
    Sahakyan, Hovhannes
    Toncheva, Draga
    Yepiskoposyan, Levon
    Tyler-Smith, Chris
    Xue, Yali
    Abdullah, M. Syafiq
    Ruiz-Linares, Andres
    Beall, Cynthia M.
    Di Rienzo, Anna
    Jeong, Choongwon
    Starikovskaya, Elena B.
    Metspalu, Ene
    Parik, Juri
    Villems, Richard
    [J]. NATURE, 2016, 538 (7624) : 201 - +
  • [93] An Unexpectedly Complex Architecture for Skin Pigmentation in Africans
    Martin, Alicia R.
    Lin, Meng
    Granka, Julie M.
    Myrick, Justin W.
    Liu, Xiaomin
    Sockell, Alexandra
    Atkinson, Elizabeth G.
    Werely, Cedric J.
    Moller, Marlo
    Sandhu, Manjinder S.
    Kingsley, David M.
    Hoal, Eileen G.
    Liu, Xiao
    Daly, Mark J.
    Feldman, Marcus W.
    Gignoux, Christopher R.
    Bustamante, Carlos D.
    Henn, Brenna M.
    [J]. CELL, 2017, 171 (06) : 1340 - +
  • [94] Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations
    Martin, Alicia R.
    Gignoux, Christopher R.
    Walters, Raymond K.
    Wojcik, Genevieve L.
    Neale, Benjamin M.
    Gravel, Simon
    Daly, Mark J.
    Bustamante, Carlos D.
    Kenny, Eimear E.
    [J]. AMERICAN JOURNAL OF HUMAN GENETICS, 2017, 100 (04) : 635 - 649
  • [95] A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data
    Mather, Niklas
    Traves, Samuel M.
    Ho, Simon Y. W.
    [J]. ECOLOGY AND EVOLUTION, 2020, 10 (01): : 579 - 589
  • [96] The Ensembl Variant Effect Predictor
    McLaren, William
    Gil, Laurent
    Hunt, Sarah E.
    Riat, Harpreet Singh
    Ritchie, Graham R. S.
    Thormann, Anja
    Flicek, Paul
    Cunningham, Fiona
    [J]. GENOME BIOLOGY, 2016, 17
  • [97] Host Genetic Factors Associated with Vaginal Microbiome Composition in Kenyan Women
    Mehta, Supriya D.
    Nannini, Drew R.
    Otieno, Fredrick
    Green, Stefan J.
    Agingu, Walter
    Landay, Alan
    Zheng, Yinan
    Hou, Lifang
    [J]. MSYSTEMS, 2020, 5 (04)
  • [98] The GWAS Diversity Monitor tracks diversity by disease in real time
    Mills, Melinda C.
    Rahal, Charles
    [J]. NATURE GENETICS, 2020, 52 (03) : 242 - 243
  • [99] Different response to Plasmodium falciparum malaria in West African sympatric ethnic groups
    Modiano, D
    Petrarca, V
    Sirima, BS
    Nebie, I
    Diallo, D
    Esposito, F
    Coluzzi, M
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1996, 93 (23) : 13206 - 13211
  • [100] H3Africa: current perspectives
    Mulder, Nicola
    Abimiku, Alash'le
    Adebamowo, Sally N.
    de Vries, Jantina
    Matimba, Alice
    Olowoyo, Paul
    Ramsay, Michele
    Skelton, Michelle
    Stein, Dan J.
    [J]. PHARMACOGENOMICS & PERSONALIZED MEDICINE, 2018, 11 : 59 - 66