ABI Linkage Panels: allele frequencies in global population samples

Population samples :

Ten population samples were typed:

• The Biaka (BIA) Pygmies from the Central African Republic
• The Mbuti (MBU) Pygmies from NW Zaire
• A sample of unrelated Danish (DAN) blood donors
• The Druze (DRU), a Moslem community from Northern Israel
• A sample of Han Chinese (CHI) living in the San Francisco Bay Area and New Haven
• A sample of native Japanese (JPN) from the Osaka area, or visitors to Stanford or Yale
• The Yakut (YAK) from Siberia
• The Nasioi (NAS) from Bougainville, Melanesia
• The Mayan (MAY) from Yucatan, Mexico
• The Rondonian Surui (SUR) from the SW Amazon, Brazil

Click here to see a genetic tree drawn from these data
 

Typing procedures :
Amplification  products were run in an ABI 373 DNA sequencer following manufacturer's protocols modified only by increasing gel concentration to 8% acrylamide. Alleles were called using Genotyper and rounding the decimal part of allele sizes. For every marker, we provide the genotype obtained in this study of CEPH individual 884-15, as well as, in parentheses, the deviation in basepairs from the genotype of the same individual as given in ABI reference documentation.
 

Statistics :
Allele frequencies were estimated by simple allele counting. Standard errors of the allele frequencies are not provided, but they can be easily computed as the square root of p(1-p)/2N, where p is the relative allele frequency, and 2N is number of chromosomes typed. Expected heterozygosity, calculated as one minus the sum of the squared allele frequencies, is given for every marker and population.
 

Data organization :
The data files are organized by panels: the allele frequencies for all the loci in a panel are contained in a single file, which can be easily downloaded by using the "Save as" command, "Text" option in most browsers. Beware that attempting to print the frequency table for one locus directly from Netscape will result in the entire panel (10-15 loci) being printed. We recommend copying and pasting the desired table to a word processing program. Allele frequencies for a particular marker can be accessed through the lists given by panel or by chromosome.

Search:

• Chromosomes 5 and 6 (Panels 8, 9, and 10)
• Chromosomes 7 and 8 (Panel 11)  [Panel 12 not available yet]
• Chromosomes 9, 10, and 11 (Panels 13, 14, 15, and 16)

 F. Calafell, A. Shuster, W.C. Speed, J.R. Kidd, and K.K. Kidd (1998)  Short tandem repeat polymorphisms in humans. European Journal of Human Genetics 6:38-49.

 F. Calafell,  A. Shuster,  W.C. Speed,  J.R. Kidd,  F.L. Black, and K.K. Kidd (1999)  Genealogy reconstruction from short tandem repeat genotypes in an Amazonian population. American Journal of Physical Anthropology 108:137-146.

 Note: Calafell et al. (1998) and (1999) were based on 45 of the 51 STRPs in ABI Panels 13, 14, 15, and 16 that cover chromosomes 9, 10, and 11. The six STRPs from those panels that were not included in those two publications include: D9S167, D9S158, D10S561, D10S201, D10S190, and D11S901.
 

For any questions or comments, please contact Francesc Calafell.