Variant Details

Variant: essv1292

Internal ID

9610247

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr11:5864481..5912814	hg38	UCSC Ensembl
Outer	chr11:5846931..5986383	hg38	UCSC Ensembl
Inner	chr11:5885711..5934044	hg19	UCSC Ensembl
Outer	chr11:5868161..6007613	hg19	UCSC Ensembl
Inner	chr11:5842287..5890620	hg18	UCSC Ensembl
Outer	chr11:5824737..5964189	hg18	UCSC Ensembl
Inner	chr11:5842287..5890620	hg17	UCSC Ensembl
Outer	chr11:5824737..5964189	hg17	UCSC Ensembl

Cytoband

11p15.4

Allele length

Assembly	Allele length
hg38	139453
hg19	139453
hg18	139453
hg17	139453

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757422

Supporting Variants

Samples

NA18980

Known Genes

OR52E4, OR52E8, OR52L1, OR56A3, OR56A5

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)

essv1292

Frequency

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