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Series GSE20275 Query DataSets for GSE20275
Status Public on Feb 12, 2013
Title Affymetrix SNP and CNV data for the HuRef individual
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. We applied a multi-step sequence and microarray-based analysis to identify numerous previously unknown SVs within the first genome sequence reported from an individual.
Overall design An Affymetrix SNP array experiment was performed according to the manufacturer's directions on DNA extracted from a lymphoblastoid cell line (HuRef).
Copy number analysis of Affymetrix 6.0 SNP arrays was performed for the HuRef sample. The HuRef sample was run in a batch of 50 control samples, which were used as baseline for calling CNVs.
Contributor(s) Pang AW
Citation(s) 20482838
Submission date Feb 10, 2010
Last update date Nov 27, 2018
Contact name Andy Pang
Organization name The Centre for Applied Genomics
Lab Stephen W. Scherer
Street address MaRS Centre - East Tower, 101 College Street, Room 14-701
City Toronto
State/province ON
ZIP/Postal code M5G 1L7
Country Canada
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (1)
GSM508411 HuRef lymphoblastoid cell line_Affymetrix
This SubSeries is part of SuperSeries:
GSE20290 Towards a comprehensive structural variation map of an individual human genome for personalized medicine
BioProject PRJNA189284

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
GSE20275_RAW.tar 41.4 Mb (http)(custom) TAR (of CEL, CHP, GFF)
Processed data included within Sample table
Processed data provided as supplementary file

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