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Series GSE65726 Query DataSets for GSE65726
Status Public on Feb 01, 2016
Title Complete Haplotype Phasing of the MHC and KIR Loci with Targeted HaploSeq
Organism Homo sapiens
Experiment type Other
Summary Rapid advances in biochemical technologies have enabled several strategies for typing candidate HLA alleles, but linking them into a single MHC haplotype structure remains challenging. Here we have developed a multi-loci haplotype phasing technique and demonstrate its utility towards phasing of MHC and KIR loci in human samples. We accurately (~99%) reconstruct the complete haplotypes for over 90% of sequence variants spanning the 4-megabase region of these two loci. By haplotyping a majority of coding and non-coding alleles at the MHC and KIR loci in a single assay, this method has the potential to assist transplantation matching and facilitate investigation of the genetic basis of human immunity and disease.
Overall design Complete haplotype phasing of 2 loci (MHC and KIR) in 1 human cell line.
Contributor(s) Selvaraj S, Schmitt A, Ren B
Citation(s) 26541200
Submission date Feb 06, 2015
Last update date May 15, 2019
Contact name Anthony D Schmitt
Phone 6178429022
Organization name UC San Diego
Department Cellular and Molecular Medicine
Lab Dr. Bing Ren
Street address 9500 GILMAN DR., BLDG. CMME RM 2071
City La Jolla
State/province California
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (2)
GSM1603856 GM12878 Rep1
GSM1603857 GM12878 Rep2
BioProject PRJNA274802
SRA SRP053311

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

Supplementary file Size Download File type/resource
GSE65726_GM12878_KIR_TargHS.vcf.gz 4.0 Kb (ftp)(http) VCF
GSE65726_GM12878_MHC_TargHS.vcf.gz 65.2 Kb (ftp)(http) VCF
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Raw data are available in SRA
Processed data are available on Series record

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