RT Journal Article
SR Electronic
T1 Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.05.19.444732
DO 10.1101/2021.05.19.444732
A1 Elizabeth G. Atkinson
A1 Shareefa Dalvie
A1 Yakov Pichkar
A1 Allan Kalungi
A1 Lerato Majara
A1 Anne Stevenson
A1 Tamrat Abebe
A1 Dickens Akena
A1 Melkam Alemayehu
A1 Fred K. Ashaba
A1 Lukoye Atwoli
A1 Mark Baker
A1 Lori B. Chibnik
A1 Nicole Creanza
A1 Mark J. Daly
A1 Abebaw Fekadu
A1 Bizu Gelaye
A1 Stella Gichuru
A1 Wilfred E. Injera
A1 Roxanne James
A1 Symon M. Kariuki
A1 Gabriel Kigen
A1 Nastassja Koen
A1 Karestan C. Koenen
A1 Zan Koenig
A1 Edith Kwobah
A1 Joseph Kyebuzibwa
A1 Henry Musinguzi
A1 Rehema M. Mwema
A1 Benjamin M. Neale
A1 Carter P. Newman
A1 Charles R.J.C. Newton
A1 Linnet Ongeri
A1 Sohini Ramachandran
A1 Raj Ramesar
A1 Welelta Shiferaw
A1 Dan J. Stein
A1 Rocky E. Stroud
A1 Solomon Teferra
A1 Zukiswa Zingela
A1 Alicia R. Martin
A1 NeuroGAP-Psychosis Study Team
YR 2021
UL http://biorxiv.org/content/early/2021/10/21/2021.05.19.444732.abstract
AB African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multigenerational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We further find significantly higher language transmission rates for matrilineal groups as compared to patrilineal. We highlight both the diversity of variation within the African continent, as well as how within-Africa variation can be informative for broader variant interpretation; many variants appearing rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity within Africa.Competing Interest StatementA.R.M. has consulted for 23andMe and Illumina and received speaker fees from Genentech, Pfizer, and Illumina. B.M.N. is a member of the Deep Genomics Scientific Advisory Board. He also serves as a consultant for the Camp4 Therapeutics Corporation, Takeda Pharmaceutical and Biogen. M.J.D. is a founder of Maze Therapeutics. The remaining authors declare no competing interests.