Variant Details

Variant: nsv433266

Internal ID

15031848

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr11:55600413..55676000	hg38	UCSC Ensembl
Inner	chr11:55367889..55443476	hg19	UCSC Ensembl
Inner	chr11:55124465..55200052	hg18	UCSC Ensembl
Inner	chr11:55124465..55200052	hg17	UCSC Ensembl

Cytoband

11q11

Allele length

Assembly	Allele length
hg38	75588
hg19	75588
hg18	75588
hg17	75588

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

dgv6n14

Supporting Variants

nssv463147

Samples

NA12878

Known Genes

OR4C11, OR4C6, OR4P4, OR4S2

Method

SNP array

Analysis

Large 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.

Platform

Illumina Human1Mv1 DNA Analysis BeadChip (Human1Mv1_C)

Comments

Reference

Cooper_et_al_2008

Pubmed ID

18776910

Accession Number(s)

nsv433266

Frequency

Sample Size	9
Observed Gain	0
Observed Loss	1
Observed Complex	0
Frequency	n/a