Variant Details

Variant: nsv433438

Internal ID

15032020

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr16:21414023..21918356	hg38	UCSC Ensembl
Inner	chr16:21425344..21929677	hg19	UCSC Ensembl
Inner	chr16:21332845..21837178	hg18	UCSC Ensembl
Inner	chr16:21332845..21837178	hg17	UCSC Ensembl

Cytoband

16p12.1

Allele length

Assembly	Allele length
hg38	504334
hg19	504334
hg18	504334
hg17	504334

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv463319

Samples

NA18517

Known Genes

IGSF6, LOC100190986, LOC100271836, METTL9, NPIPB3, OTOA, RRN3P1, SLC7A5P2

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)

nsv433438

Frequency

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