A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433450



Internal ID15032058
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr17:46489976..46572568hg38UCSC Ensembl
Innerchr17:44567342..44649934hg19UCSC Ensembl
Innerchr17:41922658..42005250hg18UCSC Ensembl
Innerchr17:41922658..42005250hg17UCSC Ensembl
Cytoband17q21.31
Allele length
AssemblyAllele length
hg3882593
hg1982593
hg1882593
hg1782593
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463331
SamplesNA12878
Known GenesARL17A, ARL17B, LRRC37A2
MethodSNP array
AnalysisLarge CNV discovery was accomplished by using HMMSeg, considering both the `LogR ratio' and `B-allele frequency' data for each sample simultaneously. We used a four-state model, one each for null (homozygous deletion), hemizygous deletion, diploid and amplification. Initial segmentation results were merged and filtered, requiring all variants to be larger than 1 kb in length and to span at least 10 probes for amplifications or hemizygous deletions, or 3 probes for homozygous deletions. We then used a combination of paired-end sequence maps, oligo array-CGH, and variant resequencing (described in Kidd et al. 2008) to support the calls.
PlatformIllumina Human1Mv1 DNA Analysis BeadChip (Human1Mv1_C)
Comments
ReferenceCooper_et_al_2008
Pubmed ID18776910
Accession Number(s)nsv433450
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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