A curated catalogue of human genomic structural variation




Variant Details

Variant: dgv6n14



Internal ID20131395
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
chr11:55600413..55685447hg38UCSC Ensembl
chr11:55367889..55452923hg19UCSC Ensembl
chr11:55124465..55209499hg18UCSC Ensembl
chr11:55124465..55209499hg17UCSC Ensembl
Cytoband11q11
Allele length
AssemblyAllele length
hg3885035
hg1985035
hg1885035
hg1785035
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnsv433266, nsv433517, nsv433267, nsv433516, nsv433268
SamplesNA15510, NA18956, NA19129, NA12878, NA18555
Known GenesOR4C11, OR4C6, OR4P4, OR4S2
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)dgv6n14
Frequency
Sample Size9
Observed Gain0
Observed Loss5
Observed Complex0
Frequencyn/a


Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer