DNA was extracted from blood using DNeasy Blood and Tissue Kit (Qiagen Inc., Valencia, CA). Genome-wide SNP screening on the two affected individuals from Family 1 was performed using Affymetrix 6.0 SNP Array (Affymetrix, USA). SNP genotyping data was used to perform homozygosity and copy number analyses. Homozygosity mapping was performed as previously described35 (link). CNV analysis was performed using four algorithms in parallel (Birdsuite, PennCNV, Nexus and Affymetrix Genotyping Console), requiring a minimum of 10 probes and the concordance of at least two algorithms for specificity. To distinguish rare from common variation, results were matched against a catalog of reference CNVs generated via the same pipeline, using 1251 samples from the HapMap project (11 subpopulations, public release #3). For additional stringency, CNVs were further matched with CNVs present in the Database of Genomic Variants (DGV) as well as an internal database of CNVs from over 12000 unrelated research samples (including >1000 from the Middle East with a variety of neurodevelopmental conditions, and >105 healthy Saudi individuals).
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Genome-wide SNP Screening for Rare CNVs
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Corresponding Organization :
Other organizations : Boston Children's Hospital, Howard Hughes Medical Institute, Texas Scottish Rite Hospital for Children, King Faisal Specialist Hospital & Research Centre, King Saud University, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Allen Institute, Allen Institute for Brain Science, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, University of California, San Francisco, Harvard University, Johns Hopkins University
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Variable analysis
independent variables
- DNA extraction method (DNeasy Blood and Tissue Kit)
- Genome-wide SNP screening (Affymetrix 6.0 SNP Array)
- Homozygosity mapping analysis
- Copy number variation (CNV) analysis using four algorithms (Birdsuite, PennCNV, Nexus and Affymetrix Genotyping Console)
- SNP genotyping data
- Homozygosity regions
- Copy number variations
- Minimum of 10 probes for CNV analysis
- Concordance of at least two algorithms for CNV analysis
- Matching CNVs against a catalog of reference CNVs from the HapMap project and the Database of Genomic Variants (DGV)
- Matching CNVs against an internal database of CNVs from over 12000 unrelated research samples
- Not explicitly mentioned
- Not explicitly mentioned
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