A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2946



Internal ID28922
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr6:31228279..31322604hg19UCSC Ensembl
chr6:31336258..31430583hg18UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg19n/a
hg18n/a
Variant TypeCNV Duplication
Copy Number
Allele State
Allele Origin
Probe Count
Merged StatusS
Merged Variants
Supporting Variantsessv25387
SamplesYH
Known GenesHLA-B, HLA-C
MethodSequencing
AnalysisWe defined a read pair as a diagnostic paired-end (PE) if the two ends of a read pair 1) could both be aligned but 2) could not meet the pair-end insert size and/or orientation requirement. We grouped abnormally mapped paired-end reads with coordinate distances smaller than the maximum insert size on both ends into diagnostic PE clusters. In order to avoid misalignment, PE clusters with greater than 4 pairs were discarded. Common structural variations like deletions, translocations, duplications, inversions etc. were examined and summarized into alignment models. This paired-end method (PEM) is substantially biased to deletion events. In addition to searching for SVs using paired-end methods (PEM), we also identified copy number variations (CNV) based on read depth. By modeling sequencing depth distribution on different levels of GC content, we found 1701 CNV regions that had a lower copy number (1-47 kb in length, median at 1 kb) and 1299 that had a higher copy number (1-105 kb in length, median at 1 kb) than NCBI36. Approximately 82% of the CNV regions that had a lower copy number and 61% CNVs that had a higher copy number had more than a 50% overlap with the annotated repeats, which was not surprising. However, these regions may be somewhat inaccurate because sequencing depth can be affected by many factors, including GC content and alignment difficulties in repetitive region.
PlatformIllumina Genome Analyzer
Comments
ReferenceWang et al 2008
Pubmed ID18987735
Accession Number(s)esv2946
Frequency
Sample Size1
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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