Variant Details

Variant: essv16568

Internal ID

9614300

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr17:16814911..16820990	hg38	UCSC Ensembl
Outer	chr17:16814911..16830849	hg38	UCSC Ensembl
Inner	chr17:16718225..16724304	hg19	UCSC Ensembl
Outer	chr17:16718225..16734163	hg19	UCSC Ensembl
Inner	chr17:16658950..16665029	hg18	UCSC Ensembl
Outer	chr17:16658950..16674888	hg18	UCSC Ensembl
Inner	chr17:16658950..16665029	hg17	UCSC Ensembl
Outer	chr17:16658950..16674888	hg17	UCSC Ensembl

Cytoband

17p11.2

Allele length

Assembly	Allele length
hg38	15939
hg19	15939
hg18	15939
hg17	15939

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757653

Supporting Variants

Samples

NA19193

Known Genes

KRT16P2

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)

essv16568

Frequency

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