Variant Details

Variant: essv1665

Internal ID

9971680

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrX:6564051..6909654	hg38	UCSC Ensembl
Outer	chrX:6521421..6918342	hg38	UCSC Ensembl
Inner	chrX:6482092..6827695	hg19	UCSC Ensembl
Outer	chrX:6439462..6836383	hg19	UCSC Ensembl
Inner	chrX:6492092..6837695	hg18	UCSC Ensembl
Outer	chrX:6449462..6846383	hg18	UCSC Ensembl
Inner	chrX:6341828..6687431	hg17	UCSC Ensembl
Outer	chrX:6299198..6696119	hg17	UCSC Ensembl

Cytoband

Xp22.31

Allele length

Assembly	Allele length
hg38	396922
hg19	396922
hg18	396922
hg17	396922

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756769

Supporting Variants

Samples

NA18992

Known Genes

VCX3A

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)

essv1665

Frequency

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