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Series GSE19048 Query DataSets for GSE19048
Status Public on Feb 18, 2010
Title Complete Genomes of a Hunter-Gatherer and a Bantu from Southern Africa
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts.
 
Overall design Copy number differences between NA18507 and KB1 were predicted from the depth of whole-genome shotgun sequence reads. These predictions were then validated using array-CGH using a a genome-wide design as well as a custom design targeted at specific regions of copy number difference
 
Contributor(s) Alkan C, Kidd JM, Eichler EE
Citation(s) 20164927
Submission date Nov 16, 2009
Last update date Mar 21, 2012
Contact name Jeffrey M Kidd
E-mail(s) kiddj@u.washington.edu
Phone 2066857336
Fax 2062215795
Organization name University of Washington
Department Department of Genome Sciences
Lab Eichler Lab
Street address 1705 NE Pacific St
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
 
Platforms (2)
GPL9681 Eichler-NimbleGen Human 135K Custom CNV array
GPL9684 Eichler-NimbleGen Human 2.1 HD2 CGH chip
Samples (3)
GSM471434 KB1 vs ABC8 (NA18507) on HD2
GSM471435 KB1_vs_ABC8 Targeted CGH
GSM471436 NA18507_vs KB1 array CGH
Relations
BioProject PRJNA120543

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE19048_KB1_gene_validation.2009_10_01.TableS14.txt.gz 8.8 Kb (ftp)(http) TXT
GSE19048_RAW.tar 238.3 Mb (http)(custom) TAR (of PAIR)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data included within Sample table
Processed data is available on Series record

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