The African Genome Variation Project shapes medical genetics in Africa

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2014-12-11 02:16Z by Steven

The African Genome Variation Project shapes medical genetics in Africa

Nature: International Weekly Journal of Science
Published online: 2014-12-03
15 pages
DOI: 10.1038/nature13997

Deepti Gurdasani
Wellcome Trust Sanger Institute
Genome Campus
Hinxton, Cambridge, United Kingdom

et. al.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

Read the entire article here.

Tags: , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,

Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy

Posted in Africa, Anthropology, Articles, History, Media Archive, United Kingdom on 2010-10-15 18:50Z by Steven

Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy

European Journal of Human Genetics
Volume 15 (2007)
pages 288–293
DOI: 10.1038/sj.ejhg.5201771

Turi E. King
University of Leicester

Emma J. Parkin
University of Leicester

Geoff Swinfield
Geoff Swinfield Genealogical Services, Mottingham, London

Fulvio Cruciani
Università degli Studi di Roma ‘La Sapienza’

Rosaria Scozzari
Università degli Studi di Roma ‘La Sapienza’

Alexandra Rosa
Università degli Studi di Roma ‘La Sapienza’

Si-Keun Lim
Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Yali Xue
Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Chris Tyler-Smith
Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Mark A. Jobling
University of Leicester

The presence of Africans in Britain has been recorded since Roman times, but has left no apparent genetic trace among modern inhabitants. Y chromosomes belonging to the deepest-rooting clade of the Y phylogeny, haplogroup (hg) A, are regarded as African-specific, and no examples have been reported from Britain or elsewhere in Western Europe. We describe the presence of an hgA1 chromosome in an indigenous British male; comparison with African examples suggests a Western African origin. Seven out of 18 men carrying the same rare east-Yorkshire surname as the original male also carry hgA1 chromosomes, and documentary research resolves them into two genealogies with most-recent-common-ancestors living in Yorkshire in the late 18th century. Analysis using 77 Y-short tandem repeats (STRs) is consistent with coalescence a few generations earlier. Our findings represent the first genetic evidence of Africans among ‘indigenous’ British, and emphasize the complexity of human migration history as well as the pitfalls of assigning geographical origin from Y-chromosomal haplotypes.

Introduction

The population of the UK today is culturally diverse, with 8% of its 54 million inhabitants belonging to ethnic minorities, and over one million classifying themselves as ‘Black or Black British’ in the 2001 census. These people owe their origins to immigration from the Caribbean and Africa beginning in the mid-20th century; before this time, the population has been seen as typically Western European, and its history has been interpreted in terms of more local immigration, including that of the Saxons, Vikings and Normans. However, in reality, Britain has a long history of contact with Africa (reviewed by Fryer). Africans were first recorded in the north 1800 years ago, as Roman soldiers defending Hadrian’s wall –‘a division of Moors’. Some historians suggest that Vikings brought captured North Africans to Britain in the 9th century. After a hiatus of several hundred years, the influence of the Atlantic slave trade began to be felt, with the first group of West Africans being brought to Britain in 1555. African domestic servants, musicians, entertainers and slaves then became common in the Tudor period, prompting an unsuccessful attempt by Elizabeth I to expel them in 1601. By the last third of the 18th century, there were an estimated 10,000 black people in Britain, mostly concentrated in cities such as London.

Has this presence left a genetic trace among people regarded as ‘indigenous’ British? In principle, Y-chromosomal haplotyping offers a means to detect long-established African lineages. Haplotypes of the non-recombining region of the Y, defined by slowly mutating binary markers such as SNPs, can be arranged into a unique phylogeny.  These binary haplotypes, known as haplogroups (hg), show a high degree of geographical differentiation, reflecting the powerful influence of genetic drift on this chromosome. Some clades of the phylogeny are so specific to particular continents or regions that they have been used to assign population-of-origin to individual DNA samples, and in quantifying the origins of the components of admixed populations using simple allele-counting methods.

Studies of British genetic diversity, generally sampling on the criterion of two generations of residence, have found no evidence of African Y-chromosomal lineages, suggesting that they either never became assimilated into the general population or have been lost by drift. However, here, we describe a globally rare and archetypically African sublineage in Britain and show that it has been resident there for at least 250 years, representing the first genetic trace of an appreciable African presence that has existed for several centuries…

Read the entire article here.

Tags: , , , , , , , , , , , , , , , ,