Variant Details

Variant: nssv463075

Internal ID

15031568

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:248581469..248652258	hg38	UCSC Ensembl
Inner	chr1:248744770..248815559	hg19	UCSC Ensembl
Inner	chr1:246811393..246882182	hg18	UCSC Ensembl
Inner	chr1:245070811..245141600	hg17	UCSC Ensembl

Cytoband

1q44

Allele length

Assembly	Allele length
hg38	70790
hg19	70790
hg18	70790
hg17	70790

Variant Type

CNV loss

Copy Number

Allele State

Hemizygous

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

nsv433194

Supporting Variants

Samples

NA18517

Known Genes

OR2T10, OR2T11, OR2T27, OR2T35

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)

nssv463075

Frequency

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