Variant Details

Variant: esv2759855

Internal ID

9982000

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr11:96979526..97321796	hg38	UCSC Ensembl
Inner	chr11:96850526..97192796	hg19	UCSC Ensembl
Inner	chr11:96355736..96698006	hg18	UCSC Ensembl
Inner	chr11:96355736..96698006	hg17	UCSC Ensembl

Cytoband

11q21

Allele length

Assembly	Allele length
hg38	342271
hg19	342271
hg18	342271
hg17	342271

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2758283, esv2758284, esv2757467

Samples

NA06993, NA18912

Known Genes

Method

BAC aCGH
SNP array

Analysis

Array images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
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)
Agilent

Comments

Reference

Redon_et_al_2006

Pubmed ID

17122850

Accession Number(s)

esv2759855

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	2
Observed Complex	0
Frequency	n/a