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Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations.

ABSTRACT: BACKGROUND:The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to resolve 61 Y chromosome haplogroups, mainly within haplogroups A, B and E, found in Africa. RESULTS:Seven multiplex assays, which incorporated 60 Y chromosome markers, were developed. These resolved Y chromosomes to 61 terminal branches of the major African haplogroups A, B and E, while also including a few Eurasian haplogroups found occasionally in African males. Following its validation, the assays were used to screen 683 individuals from Southern Africa, including south eastern Bantu speakers (BAN), Khoe-San (KS) and South African Whites (SAW). Of the 61 haplogroups that the assays collectively resolved, 26 were found in the 683 samples. While haplogroup sharing was common between the BAN and KS, the frequencies of these haplogroups varied appreciably. Both groups showed low levels of assimilation of Eurasian haplogroups and only two individuals in the SAW clearly had Y chromosomes of African ancestry. CONCLUSIONS:The use of these single base extension assays in screening increased haplogroup resolution and sampling throughput, while saving time and DNA. Their use, together with the screening of short tandem repeat markers would considerably improve resolution, thus refining the geographic ancestry of individuals.

SUBMITTER: Naidoo T

PROVIDER: S-EPMC2988483 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature

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Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations.

Naidoo Thijessen T Schlebusch Carina M CM Makkan Heeran H Patel Pareen P Mahabeer Rajeshree R Erasmus Johannes C JC Soodyall Himla H

Investigative genetics 20100901 1

<h4>Background</h4>The ability of the Y chromosome to retain a record of its evolution has seen it become an essential tool of molecular anthropology. In the last few years, however, it has also found use in forensic genetics, providing information on the geographic origin of individuals. This has been aided by the development of efficient screening methods and an increased knowledge of geographic distribution. In this study, we describe the development of single base extension assays used to re ...[more]

PMID: 21092339

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Project description:Introduction: Investigating variation in genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterized in European and Asian populations, but data from African populations are under-studied—which has implications for drug safety and effective use in Africa. Results: We identified significant ADME gene variation in African populations using data from 458 high-coverage whole genome sequences, 412 of which are novel, and from previously available African sequences from the 1,000 Genomes Project. ADME variation was not uniform across African populations, particularly within high impact coding variation. Copy number variation was detected in 116 ADME genes, with equal ratios of duplications/deletions. We identified 930 potential high impact coding variants, of which most are discrete to a single African population cluster. Large frequency differences (i.e., >10%) were seen in common high impact variants between clusters. Several novel variants are predicted to have a significant impact on protein structure, but additional functional work is needed to confirm the outcome of these for PGx use. Most variants of known clinical outcome are rare in Africa compared to European populations, potentially reflecting a clinical PGx research bias to European populations. Discussion: The genetic diversity of ADME genes across sub-Saharan African populations is large. The Southern African population cluster is most distinct from that of far West Africa. PGx strategies based on European variants will be of limited use in African populations. Although established variants are important, PGx must take into account the full range of African variation. This work urges further characterization of variants in African populations including in vitro and in silico studies, and to consider the unique African ADME landscape when developing precision medicine guidelines and tools for African populations.

Project description:BackgroundSub-Saharan Africa suffers a disproportionate share of the world's burden of disease while having some of the world's greatest health care workforce shortages. Doctors are an important component of any high functioning health care system. However, efforts to strengthen the doctor workforce in the region have been limited by a small number of medical schools with limited enrolments, international migration of graduates, poor geographic distribution of doctors, and insufficient data on medical schools. The goal of the Sub-Saharan African Medical Schools Study (SAMSS) is to increase the level of understanding and expand the baseline data on medical schools in the region.MethodsThe SAMSS survey is a descriptive survey study of Sub-Saharan African medical schools. The survey instrument included quantitative and qualitative questions focused on institutional characteristics, student profiles, curricula, post-graduate medical education, teaching staff, resources, barriers to capacity expansion, educational innovations, and external relationships with government and non-governmental organizations. Surveys were sent via e-mail to medical school deans or officials designated by the dean. Analysis is both descriptive and multivariable.ResultsSurveys were distributed to 146 medical schools in 40 of 48 Sub-Saharan African countries. One hundred and five responses were received (72% response rate). An additional 23 schools were identified after the close of the survey period. Fifty-eight respondents have been founded since 1990, including 22 private schools. Enrolments for medical schools range from 2 to 1800 and graduates range from 4 to 384. Seventy-three percent of respondents (n = 64) increased first year enrolments in the past five years. On average, 26% of respondents' graduates were reported to migrate out of the country within five years of graduation (n = 68). The most significant reported barriers to increasing the number of graduates, and improving quality, related to infrastructure and faculty limitations, respectively. Significant correlations were seen between schools implementing increased faculty salaries and bonuses, and lower percentage loss of faculty over the previous five years (P = 0.018); strengthened institutional research tools (P = 0.00015) and funded faculty research time (P = 0.045) and greater faculty involvement in research; and country compulsory service requirements (P = 0.039), a moderate number (1-5) of post-graduate medical education programs (P = 0.016) and francophone schools (P = 0.016) and greater rural general practice after graduation.ConclusionsThe results of the SAMSS survey increases the level of data and understanding of medical schools in Sub-Saharan Africa. This data serves as a baseline for future research, policies and investment in the health care workforce in the region which will be necessary for improving health.

Dataset Information

Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations.

Publications

Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations.

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