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| 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
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| 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.
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| 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.
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| |
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| Contributor(s) |
Pang AW |
| Citation(s) |
20482838 |
| |
| Submission date |
Feb 10, 2010 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Andy Pang |
| E-mail(s) |
andypang@sickkids.ca
|
| 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 |
| |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (1) |
| GSM508411 |
HuRef lymphoblastoid cell line_Affymetrix |
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| This SubSeries is part of SuperSeries: |
| GSE20290 |
Towards a comprehensive structural variation map of an individual human genome for personalized medicine |
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| Relations |
| BioProject |
PRJNA189284 |
