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Series GSE85428 Query DataSets for GSE85428
Status Public on Aug 11, 2016
Title Affymetrix SNP array data for family UNK-129-KW with multiple patients suffering from a lethal form of a primary immunodeficiency.
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Linkage analysis and Copy Number Variation were performed on DNA isolated from the peripheral blood of the 2 affected male patients, their unaffected parents, and their unaffected 4 male siblings, according to the manufacturer's description. This allowed to narrow down the region of homozygosity specifice to the patients. This approach, in combination with Whole Exome sequencing performed on DNA isolated from the 2 affected patients and their mother, allowed to identify a homozygous missense mutation in the base excision repair enzyme NEIL3 that reduced its enzymatic activity, and a homozygous duplication of exons 48-53 of the LPS Responsive Beige-Like Anchor Protein LRBA that abolished protein expression.
 
Overall design Homozygozity mapping was performed with the Affymetrix genome-wide human single nucleotide polymorphism (SNP) array 6.0, and analyzed with Birdsuite version 1.4 and PLINK version 1.07.
 
Contributor(s) Massaad MJ, Geha RS, Schmitz K, Kyriacos M, Chou J, Ohsumi TK
Citation(s) 27760045
Submission date Aug 10, 2016
Last update date Nov 27, 2018
Contact name Michel Massaad
E-mail(s) MICHEL.MASSAAD@CHILDRENS.HARVARD.EDU
Phone 6178207634
Organization name Boston Children's Hospital
Department Mdicine/Immunology
Lab Raif Geha
Street address One Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (8)
GSM2266796 Peripheral blood mononuclear cell gDNA [UNK-129F-KW]
GSM2266797 Peripheral blood mononuclear cell gDNA [UNK-129M-KW]
GSM2266798 Peripheral blood mononuclear cell gDNA [UNK-129-KW]
Relations
BioProject PRJNA338443

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
GSE85428_ALL.CNVs.Catalogue_._Small_Projects._Cat_P10.Good.W_CNV-A_X__3Soft.xlsx.gz 106.0 Kb (ftp)(http) XLSX
GSE85428_RAW.tar 238.0 Mb (http)(custom) TAR (of CEL)
Processed data are available on Series record

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