Variant Details

Variant: nsv433267

Internal ID

15031849

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr11:55600413..55685447	hg38	UCSC Ensembl
Inner	chr11:55367889..55452923	hg19	UCSC Ensembl
Inner	chr11:55124465..55209499	hg18	UCSC Ensembl
Inner	chr11:55124465..55209499	hg17	UCSC Ensembl

Cytoband

11q11

Allele length

Assembly	Allele length
hg38	85035
hg19	85035
hg18	85035
hg17	85035

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

dgv6n14

Supporting Variants

nssv463148

Samples

NA18555

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)

nsv433267

Frequency

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