Variant Details

Variant: esv2757365

Internal ID

9979442

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr10:6609029..6623387	hg38	UCSC Ensembl
Inner	chr10:6650991..6665349	hg19	UCSC Ensembl
Inner	chr10:6690997..6705355	hg18	UCSC Ensembl
Inner	chr10:6690997..6705355	hg17	UCSC Ensembl

Cytoband

10p14

Allele length

Assembly	Allele length
hg38	14359
hg19	14359
hg18	14359
hg17	14359

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2759730

Supporting Variants

essv19047, essv18572, essv21928, essv18912

Samples

NA12717, NA10851, NA12057, NA07034

Known Genes

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)

esv2757365

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	4
Observed Complex	0
Frequency	n/a