Variant Details

Variant: essv3847

Internal ID

9625359

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr6:160039050..160610686	hg38	UCSC Ensembl
Outer	chr6:160011299..160649838	hg38	UCSC Ensembl
Inner	chr6:160460082..161031718	hg19	UCSC Ensembl
Outer	chr6:160432331..161070870	hg19	UCSC Ensembl
Inner	chr6:160380072..160951708	hg18	UCSC Ensembl
Outer	chr6:160352321..160990860	hg18	UCSC Ensembl
Inner	chr6:160430493..161002129	hg17	UCSC Ensembl
Outer	chr6:160402742..161041281	hg17	UCSC Ensembl

Cytoband

6q25.3

Allele length

Assembly	Allele length
hg38	638540
hg19	638540
hg18	638540
hg17	638540

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757197

Supporting Variants

Samples

NA18953

Known Genes

IGF2R, LOC729603, LPA, LPAL2, SLC22A1, SLC22A2, SLC22A3

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)

essv3847

Frequency

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