Resources...

So you've read the paper, are excited by the results, and now you want to explore some of your own questions in our data sets or using our software. On this page you can download data sets and software generated by our lab, as well as find links to resources provided by other groups that we have found to be pretty useful. Can't find what you are after? E-mail Trevor Pemberton and he'll do his best to point you in the right direction.

Data Sets

Variation at 138 orthologous human-chimpanzee microsatellites

Microsatellite variation in 267 worldwide human populations

  • TJ Pemberton, M DeGiorgio, NA Rosenberg (2013) "Population structure in a comprehensive genomic data set on human microsatellite variation." G3:Genes|Genomes|Genetics 3(5):pp.903-919

    [ PubMed ] [ Journal ] [ PDF ] [ Supplemental Data PDF ] [ Cited By ]

  • Supplementary File S1 from the above paper, which contains two genotype data sets: (1) 645 microsatellite loci in 5,795 individuals from 267 worldwide human populations, and (2) 246 microsatellite loci in 5,795 individuals from 267 worldwide human populations together with 84 chimpanzees.

    Supplementary File S1. [Updated 24 March 2016 to include sex assignments for all individuals]

    Please note that, under the terms of the IRB approval provided by the Papua New Guinea (PNG) Medical Research Advisory Committee in Port Moresby, the Pacific Islander data included in the above dataset can only be used in accordance with the following conditions:

    1. Individual anonymity must be maintained.

    2. The data or samples must not be used in for-profit research.

    3. There should be no stigmatization of individuals or groups within these data.

    4. Copies of any resulting manuscripts should be forwarded to the PNG Medical Research Advisory Committee immediately upon publication. Please email a PDF of the manuscript to the Director of the Institute of Medical Research, Dr. William Pomat, requesting that he forward it to the PNG Medical Research Advisory Committee.

    Any individuals who wish to use these data for activites that would violate any of the above conditions must remove the Pacific Islander data prior to conducting their analyses. Please see the "pembertonEtAl2013.subsets.txt" file included in Supplementary File S1 for the list of samples that should be removed.

    Should you have any questions or concerns, please contact Dr. Trevor Pemberton.

Genome-wide homozygosity in 64 worldwide human populations

  • TJ Pemberton, D Absher, MW Feldman, RM Myers, NA Rosenberg, JZ Li (2012) "Genomic patterns of homozygosity in worldwide human populations." American Journal of Human Genetics 91(2):pp.275-292

    [ PubMed ] [ Journal ] [ PDF ] [ Supplemental Data PDF ] [ Cited By ]

  • Supplementary Tables S2-S5 from the above paper, which contain genome-wide homozygosity frequencies given separately for each of seven geographic regions (Africa, Middle East, Europe, Central/South Asia, East Asia, Oceania, and the Americas) as well as across all individuals in the data set.

    Supplementary Table S2. Class A ROH frequencies at each SNP in the data set.

    Supplementary Table S3. Class B ROH frequencies at each SNP in the data set.

    Supplementary Table S4. Class C ROH frequencies at each SNP in the data set.

    Supplementary Table S5. ROH frequencies at each SNP in the data set calculated over all three size classes.

    Provided below is a file listing all ROH detected across all individuals in the 64 worldwide populations - 53 HGDP-CEPH populations and 11 HapMap Phase III populations - grouped by their length classification, as described in the above paper.

    List of all ROH detected. [UCSC Genome Browser BED format]

    Provided below are genome-wide homozygosity frequencies given separately for each of 64 worldwide populations - 53 HGDP-CEPH populations and 11 HapMap Phase III populations - and for each of seven geographic regions (Africa, Middle East, Europe, Central/South Asia, East Asia, Oceania, and the Americas), as well as across all individuals in the data set, as described in the above paper.

    Genomic homozygosity frequency data separately in each population. [UCSC Genome Browser format]

    Genomic homozygosity frequency data separately in each geographic region. [UCSC Genome Browser format]

    Use this form to search the database of ROH segments identified in the above paper for those present in either a genomic or a gene region of your choosing. By default ROH identified in all 1,839 individuals will be displayed; however, you can choose to instead display only those ROH in individuals from a specific population or geographic region. The results will open in a new window/tab.

    Specify genome region:
    Chromosome:
    Start:
    Stop:
    Or
    Specify gene:
    Gene:
    Padding (+/-):

    Filter by population or geographic region:
    Population:
    Geographic region:
    Filter by ROH class:
    ROH class:
    Filter by Sex:
    Sex:

Microsatellite and mtDNA HVS1 variation in Asian Indians

2,810 single-nucleotide polymorphisms in 1,107 individuals from 63 human populations

Standardized subsets of the HapMap Phase III individuals controlling for relatedness

Sequence properties of 627 human microsatellites

Gene expression during enamel/root formation in the developing mouse tooth

Software

GARLIC