A curated catalogue of human genomic structural variation




Variant Details

Variant: esv3753



Internal ID28556
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr14:88889923..88890365hg19UCSC Ensembl
chr14:87959676..87960118hg18UCSC Ensembl
Cytoband14q31.3
Allele length
AssemblyAllele length
hg19n/a
hg18n/a
Variant TypeCNV Deletion
Copy Number
Allele State
Allele Origin
Probe Count
Merged StatusS
Merged Variants
Supporting Variantsessv26194
SamplesYH
Known GenesSPATA7
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)esv3753
Frequency
Sample Size1
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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