Variant Details

Variant: essv4327

Internal ID

9625893

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr17:41510342..41609462	hg38	UCSC Ensembl
Outer	chr17:41496870..41740591	hg38	UCSC Ensembl
Inner	chr17:39666594..39765714	hg19	UCSC Ensembl
Outer	chr17:39653122..39896843	hg19	UCSC Ensembl
Inner	chr17:36920120..37019240	hg18	UCSC Ensembl
Outer	chr17:36906648..37150369	hg18	UCSC Ensembl
Inner	chr17:36920120..37019240	hg17	UCSC Ensembl
Outer	chr17:36906648..37150369	hg17	UCSC Ensembl

Cytoband

17q21.2

Allele length

Assembly	Allele length
hg38	243722
hg19	243722
hg18	243722
hg17	243722

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757658

Supporting Variants

Samples

NA18564

Known Genes

EIF1, GAST, HAP1, KRT13, KRT14, KRT15, KRT16, KRT17, KRT19, KRT42P, KRT9, LINC00974, MIR6510

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)

essv4327

Frequency

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