Variant Details

Variant: esv2758901

Internal ID

9634360

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrX:152745001..152849208	hg38	UCSC Ensembl
Inner	chrX:151902054..152017752	hg19	UCSC Ensembl
Inner	chrX:151652710..151768408	hg18	UCSC Ensembl
Inner	chrX:151572622..151688320	hg17	UCSC Ensembl

Cytoband

Xq28

Allele length

Assembly	Allele length
hg38	104208
hg19	115699
hg18	115699
hg17	115699

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2756794

Samples

NA18523

Known Genes

CETN2, CSAG1, CSAG2, CSAG3, CSAG4, MAGEA12, MAGEA2, MAGEA2B, MAGEA3, NSDHL

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)

esv2758901

Frequency

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