Variant Details

Variant: essv13379

Internal ID

9610757

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrX:48027602..48111343	hg38	UCSC Ensembl
Outer	chrX:48011876..48209787	hg38	UCSC Ensembl
Inner	chrX:47886996..47970727	hg19	UCSC Ensembl
Outer	chrX:47871270..48069222	hg19	UCSC Ensembl
Inner	chrX:47771940..47855671	hg18	UCSC Ensembl
Outer	chrX:47756214..47954166	hg18	UCSC Ensembl
Inner	chrX:47643250..47726981	hg17	UCSC Ensembl
Outer	chrX:47627524..47825476	hg17	UCSC Ensembl

Cytoband

Xp11.23

Allele length

Assembly	Allele length
hg38	197912
hg19	197953
hg18	197953
hg17	197953

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756771

Supporting Variants

Samples

NA19159

Known Genes

SPACA5, SPACA5B, SSX5, SSX6, ZNF630

Method

SNP array

Analysis

The algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.

Platform

Affymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)

Comments

Reference

Redon_et_al_2006

Pubmed ID

17122850

Accession Number(s)

essv13379

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	1
Observed Complex	0
Frequency	n/a