A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv16n14



Internal ID20131405
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr17:46572568..46712660hg38UCSC Ensembl
chr17:44649934..44790026hg19UCSC Ensembl
chr17:42005250..42145209hg18UCSC Ensembl
chr17:42005250..42145209hg17UCSC Ensembl
Cytoband17q21.31
Allele length
AssemblyAllele length
hg38140093
hg19140093
hg18139960
hg17139960
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433312, nsv433311, nsv433309
SamplesNA18517, NA18507, NA12878
Known GenesARL17A, ARL17B, NSF, NSFP1
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)dgv16n14
Frequency
Sample Size9
Observed Gain0
Observed Loss3
Observed Complex0
Frequencyn/a


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