Variant Details

Variant: essv20533

Internal ID

9618707

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr22:25268441..25522707	hg38	UCSC Ensembl
Outer	chr22:25212195..25529111	hg38	UCSC Ensembl
Inner	chr22:25664408..25918674	hg19	UCSC Ensembl
Outer	chr22:25608162..25925078	hg19	UCSC Ensembl
Inner	chr22:23994408..24248674	hg18	UCSC Ensembl
Outer	chr22:23938162..24255078	hg18	UCSC Ensembl
Inner	chr22:23988962..24243228	hg17	UCSC Ensembl
Outer	chr22:23932716..24249632	hg17	UCSC Ensembl

Cytoband

22q11.23

Allele length

Assembly	Allele length
hg38	316917
hg19	316917
hg18	316917
hg17	316917

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756760

Supporting Variants

Samples

NA11995

Known Genes

CRYBB2, CRYBB2P1, IGLL3P, LRP5L, MIR6817

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)

essv20533

Frequency

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