ALFRED: allele frequency database

The ALlele FREquency Database
ALFRED is a resource of gene frequency data on human populations
supported by the Yale Center for Medical Informatics.

00ALFRED detailed record information

Population Information

Name	ALFRED UID	Primary Language	Language Family
San	PO000073K		KHOISAN

Synonyms:
Geographic Location¹: 15S, 13E; 26S, 26E

Sites typed for this population: View List
Population Samples: See Sample Information
External Resources: Art & Life in Africa: San Record
References: See references
Population Description: The term "San" is a label that encompasses varied groups of hunter-gathers living in the Kalahari Desert of Namibia, Botswana, and the adjoining area of Angola. Currently, there are over 95,000 people defined as San "Bushmen" in southern Africa. The San groups speak many dialects of Khoisan languages. There are three main groups that are included: The Central San also known as "Khwe" (Gwikwe, Hiechware, Hukwe, Naron, Tannekwe, Tserekwe...); the Northern San also known as "Ju" (Vasekele, Auen, Heikum, Kung...); and the Southern San who are also called "Kwi" (Nusan, Xam...).

Historically, there was no power hierarchy in the various groups. Every member of society shared resources and responsibilities equally. Currently, leadership amongst the San groups is reserved for the individual who has lived amongst the group for a considerable amount of time and who has the desirable leadership qualities. The political structure is organized through kinship relations.
References:

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: San

Sample UID: SA000117J

Sample Description:San

Number of Chromosomes: 30

Relation to Other Samples:

References:
- Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, Carpenter KD, Soodyall H, Jenkins T, Rogers AR. "Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data.". Am. J. Hum. Genet. 57:523-538. (1995) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: San

Sample UID: SA000073K

Sample Description:San

Number of Chromosomes: 92

Relation to Other Samples:

References:
- Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, Kidd JR, Pakstis AJ, Jenkins T, Kidd KK. "A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations". Am. J. Hum. Genet. 62:1389-402. (1998) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: San

Sample UID: SA000074L

Sample Description:San (DM)

Number of Chromosomes: 138

Relation to Other Samples:

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: San

Sample UID: SA000485R

Sample Description:This sample was collected from San from northwest Namibia.

Number of Chromosomes: 30

Relation to Other Samples:

References:
- Hollox EJ, Poulter M, Wang Y, Krause A, Swallow DM. "Common polymorphism in a highly variable region upstream of the human lactase gene affects DNA-protein interactions". Eur J Hum Genet 7:791-800. (1999) Online citation.

- Hollox EJ, Poulter M, Zvarik M, Ferak V, Krause A, Jenkins T, Saha N, Kozlov AI, Swallow DM. "Lactase Haplotype Diversity in the Old World ". Am. J. Hum. Genet. 68:160-172. (2001) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: San, HGDP-CEPH

Sample UID: SA001469U

Sample Description:This sample from Namibia is part of the Human Genome Diversity Cell Line Panel collected by the Human Genome Diversity Project (HGDP) and the Foundation Jean Dausset (CEPH). This sample consists of unrelated individuals and was collected with proper informed consent.

Note: In many publications subset H952 of the HGDP panel (with first and second degree relatives excluded from the original set) was typed and for this population that decreases the sample size from 7 to 6 individuals.

Number of Chromosomes: 14

Relation to Other Samples:

References:
- Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. "Genetic structure of human populations". Science 298:2381-2385. (2002) Online citation.

- Rosenberg NA. "Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.". Ann Hum Genet. 70:841-847. (2006) Online citation.

Sample Information:

Graph estimated heterozygosities for various sites

Sample Name: San

Sample UID: SA003179U

Sample Description:This sample consists of San individuals. The study was carried out according to the Declaration of Helsinki (2000)of the World Medical Association. Informed consent was obtained from all individuals. Ethnicity was assigned based on the submission that parents and grandparents of the volunteers were of the same self-identified ethnic group. The DNA of these samples are stored in the AiBST Biobank of African Populations.

Number of Chromosomes: 80

Relation to Other Samples:

References:
- Matimba A, Del-Favero J, Van Broeckhoven C, Masimirembwa C "Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects". Hum Genomics. 3:169-90. (2009) Online citation.

¹Geographic Coordinates represent two opposite corners of a rectangle encompassing the area where the population lives.This data is preliminary and changing.

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© 2019 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan