Variant Details

Variant: essv8684

Internal ID

9630733

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrX:135623557..135737637	hg38	UCSC Ensembl
Outer	chrX:135623557..135831108	hg38	UCSC Ensembl
Inner	chrX:134757482..134906068	hg19	UCSC Ensembl
Outer	chrX:134757482..134948034	hg19	UCSC Ensembl
Inner	chrX:134585148..134733734	hg18	UCSC Ensembl
Outer	chrX:134585148..134775700	hg18	UCSC Ensembl
Inner	chrX:134483002..134631588	hg17	UCSC Ensembl
Outer	chrX:134483002..134673554	hg17	UCSC Ensembl

Cytoband

Xq26.3

Allele length

Assembly	Allele length
hg38	207552
hg19	190553
hg18	190553
hg17	190553

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756777

Supporting Variants

Samples

NA18912

Known Genes

CT45A1, CT45A2, CT45A3, CT45A4, CT45A5

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)

essv8684

Frequency

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