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13Th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Joint Report

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13Th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Joint Report 87604$$187 P187 30-05-06 13:24:33 PDF GL 87604 C3 JR187 S. J. Mack 13th International Histocompatibility Y. Tsai Workshop Anthropology/Human A. Sanchez-Mazas H. A. Erlich, Genetic Diversity Joint Report Editors Chapter 3: Anthropology/human genetic diversity population reports Editors’ addresses Steven J. Mack1,2, Yingssu Tsai3, Alicia Sanchez-Mazas4, Each participating laboratory has prepared a report describing Henry A. Erlich1,2 the origins and historical, ethnographic and demographic in- 1 Children’s Hospital Oakland Research formation for each population sample, along with relevant Institute, Oakland, CA; 2Roche Molecular Systems, Alameda, CA; 3University of results of previous genetic studies and summaries of the California, Berkeley, CA; 4Laboratory of IHWG Biostatistic Core’s analyses. Anthropology, Genetics, and Peopling History, These reports are organized by the geographic region in Department of Antropology and Ecology, University of Geneva, Switzerland the sections that follow. In some cases, population samples from different regions are described in the same report, and Acknowledgements these instances are noted in the table for each region. When This work was supported by the Swiss SNF grant .3100-49771.96 to A.S.-M. there is a discrepancy between the name of the population described in a report and the name used for the population sample in the analyses, the population sample name is pro- vided in parentheses. The allele, genotype, haplotype data and analyses for each sampled population can be found in appendices C, Tables 1 and 2 respectively, posted at the IHWG website under the Anthropology component (http://www.ihwg.org/com- ponents/diversr.htm), and in the eBook edition of HLA 2004 to be published by PubMed (http://www.ncbi.nlm.- nih.gov/entrez/query.fcgi?dbΩBooks). Sub Saharan Africa Population: Kenyan from Kenya Authors: Ma Luo1, Joanne Embree1, Suzie Ramdahin1, Jecko- niah Ndinya-Achola2, Simon Njenga2, Job B. Bwayo2, Kristine Jacobson3, Luvinia Kwan3, Marlis Schroeder3, Sha Pan1, Marc Jevan Narayansingh1, Shehzad Iqbal1, Robert C. Brunham1,4 and Francis A. Plummer1,2,5 Authors’ addresses: 1Department Of Medical Microbiology, University Of HLA 2004: Manitoba, 730 William Avenue, Winnipeg, Manitoba Canada. 2Department Immunobiology of the Human MHC. 3 Proceedings of the 13th International Of Medical Microbiology, University Of Nairobi, Nairobi, Kenya. HLA Lab, Histocompatibility Workshop and Congress Cancer Care Manitoba, Winnipeg, Canada. 4University Of British Columbia 1 Mack et al ¡ 13th IHWS Anthropology/Human Genetic Diversity Joint Report – Chapter 3: Population Reports Centre Of Disease Control, Vancouver, Bc, Canada. 5National Microbiology Kenyan women who were enrolled in a study of mother-to- Laboratory, Winnipeg, Manitoba, Canada. child HIV transmission as a control population at the onset of the current HIV epidemic, when prevalence rates were ap- As the ‘‘cradle of humanity’’, Kenya’s diverse population is the proximately 2%. The women were enrolled in the study when result of early settlements and migrations. The oldest human they gave birth in the hospital of Nairobi. They originate from remains, predating tool-use, have been found in the Lake Vic- different areas of Kenya and represent diverse ethnic origins, toria Highlands and Rift Valley regions of Kenya. Three major therefore, this population is a representative of the larger Ken- historical migrations into Kenya, along with the fusion of yan population. A high-resolution sequence-based method immigrants with early Kenyan hunters and gatherers, resulted using a taxonomy-based sequence analysis (TBSA) to assign in three major linguistic groups – Bantus, Nilotes and Cus- alleles (7–8) was used to type HLA class I (A, B and C) and hites – and the formation of more than 70 ethnic groups. class II (DPA, DPB1, DQA1, and DQB1) loci. The quality of The Bantu people migrated into east Africa through several the typing was controlled using the IHWG QC samples. The routes; those who settled on the hilltops behind the coastline population genetic analysis was carried out by the IHWG Bi- formed the Mijikenda. Those who settled around Lake Victo- ostatistic Core. ria and Mt. Elgon became the ancestors of the Abaluhyia, Of seven HLA loci examined, the overall distributions of Abagusii and Abakuria. In the central regions, they became genotypes at the HLA-A, B, C, DPA1, DPB1, and DQB1 loci the Taveta, the Dawida and the Akamba people, while in the do not deviate significantly from expected Hardy-Weinberg Kenya highlands they became the Agikuyu, Aembu, Chuka, proportions, whereas the distributions of genotypes at the Tharaka, and the Ameru. The Cushitic migrations brought HLA-DQA1 locus deviate significantly from what would be Somali people to the northeastern part of Kenya, in the area expected (p-valueΩ0.0145). An excess of homozygous geno- located between the Juba and the Tana rivers. The eastern types observed for the DPB1 locus (p-valueΩ0.0122) could Cushites are reprsented by Yaaku, who live near Doldol, be due to population admixture, as most of the DPB1 homo- northwest of Mount Kenya. Migration also brought Orma, zygotes observed are originally from regions inhabited by dif- Boranna and Rendille into northern Kenya from southern ferent tribes. Ethiopia. The Nilotic migrations brought three groups of Ni- Ewens-Watterson analysis of Homozygosity indicated that lotic tribes into Kenya. The riverlake Nilotes are made up of while the values of homozygosity at HLA-A, B, C, DQB1 and the Luo, who settled around Lake Victoria. The plains Nilotes DPA1 loci are lower than the expected neutral values, they do are made up of the Teso, Turkana, Maasai, Njemps and Samb- not deviate significantly from the expected neutral values. A uru. The highland Nilotes are made up of the Omotik, Kalen- slightly higher than expected homozygosity value was ob- jin-Pokot, Marakwet, Elgeyo, Tugen, Nandi and Terik. Since served at DPB1 locus. Ewens-Watterson analysis showed that 600 AD, Arabs, Europeans and Asians have settled in the the heterozygosity at DQA1 locus is significantly higher (p coastal area. Today these groups make up the smallest percen- valueΩ0.0250) than the expected neutral value, and is consis- tage of the population and are scattered all over Kenya (1–6). tent with the action of balancing selection in this population The origins and great diversity of the Kenyan population are at this locus. These data suggest that, in the face of an ex- of great interest for anthopological studies. tremely diverse ethnic composition, the Kenyan population is We studied the HLA allelic diversity of a group of unrelated overall under balancing selection. References 1.Wills AJ. The Story Of Africa From The Ear- 5. Were GS. Western Kenya Historical Texts: 7. Luo M, Blanchard J, Pan Y, Brunham K, liest Times. London, University Of London Bbaluyia, Teso, And Elgon Kalenjin. Nairo- Brunham RC. 1999 High-Resolution Se- Press. 1968–69. bi, East African Literature Bureau. 1967. quence Typing Of HLA-DQA1 and DQB1 2.Kenya, An Official Handbook. Published For 6. Luo M, Embree J, Ramdahin S, Jeckoniah Exon 2 DNA with Taxonomy-Based Sequence The Government Of The Republic Of Ke- Ndinya-Achola, Simon Njenga, Job B. Bwayo, Analysis (TBSA) Allele Assignment. Tissue An- nya. East African Pub. House 1973. Pan S, Mao X, Cheang M, Stuart T, Brunham tigens 54, 69–82. 3.Kenya. An Official Handbook. [Nairobi, Ke- RC, And Plummer F. 2002 HLA-A and HLA- nya: Ministry Of Information And Broadcast- B in Kenya, Africa: Allele Frequencies and ing, 1989. Identification of HLA-B*1567 and HLA- 4.Sharman M 1972 Africa Through The Ages; B*4426. Tissue Antigens 59, 370–380. Anillustrated History. [2nd Edition, Lon- don] Evens Brothers. 1972. 2 HLA 2004: Immunobiology of the Human MHC Mack et al ¡ 13th IHWS Anthropology/Human Genetic Diversity Joint Report – Chapter 3: Population Reports A*2301, A*6601, and A*2902 are frequent in both groups. Population: Luo and Nandi from Kenya The A*0202, A*0205, A*3402, A*3001, and A*3002 alleles Authors: A. M. Moormann1,K.Cao2,3, C. Masaberg2,3, are present with relatively high frequencies in one population O. P. Sumba4, D. Koech5,J.Ng2,3, R. J. Hartzman2, J. Kazura1, (e.g. A*0202, A*0205, and A*3402 in the Nandi, and A*3001 M. A. Ferna´ndez-Vin˜a2,3 and A*3002 in the Luo) but have low frequencies in the other. Authors’ addresses: 1The Center for Global Health and Diseases at Case For HLA-B the most common alleles are B*5801, B*5802, Western Reserve University, Cleveland Ohio, USA, 2C.W. Bill Young/DoD B*1503, B*5301, B*4201, B*4501, and B*1801 with fre- Marrow Donor Program, Naval Medical Research Center, Bethesda MD, USA, quencies ranging from 0.1245 to 0.0434. The B*1402, 3The Department of Oncology, Georgetown University, Washington DC, USA, B*2703, B*5703, and B*8101 alleles have high frequencies in 4The Center for Vector Biology and Control Research, KERMI, Kisumu, Ke- one group but low frequencies in the other (B*2703 and nya, 5Kenya Medical Research Institute, Nairobi, Kenya B*5703 are high in the Nandi, and B*1402 and B*8101 are high in the Luo). For HLA-C, the most frequent alleles in both Kenya is home to many different populations that speak more populations are Cw*0602, Cw*0701, Cw*0401, Cw*1701, than 60 languages. Two homogeneous populations of Luo Cw*0202, and Cw*0704, with frequencies ranging from (NΩ265) and Nandi (NΩ241) from Kenya were studied. The 0.2167 to 0.0509. Cw*0702 and Cw*0802 are present in the Luo were from Kanyawegi, (0.11 degrees south latitude, Luo with higher frequencies, whereas Cw*1402 and Cw*1602 34.63 degrees east longitude) which is located in the lowland have higher frequencies in the Nandi.
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