Variant Details

Variant: nsv433448

Internal ID

15032056

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr17:36110820..36215910	hg38	UCSC Ensembl
Inner	chr17:34438213..34543364	hg19	UCSC Ensembl
Inner	chr17:31462326..31567477	hg18	UCSC Ensembl
Inner	chr17:31462326..31567477	hg17	UCSC Ensembl

Cytoband

17q12

Allele length

Assembly	Allele length
hg38	105091
hg19	105152
hg18	105152
hg17	105152

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv463329

Samples

NA18517

Known Genes

CCL3L1, CCL3L3, CCL4L1, CCL4L2, TBC1D3B

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)

nsv433448

Frequency

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