Variant Details

Variant: esv2759660

Internal ID

9635119

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr9:5288908..5454512	hg38	UCSC Ensembl
Inner	chr9:5288908..5454512	hg19	UCSC Ensembl
Inner	chr9:5278908..5444512	hg18	UCSC Ensembl
Inner	chr9:5278908..5444512	hg17	UCSC Ensembl

Cytoband

9p24.1

Allele length

Assembly	Allele length
hg38	165605
hg19	165605
hg18	165605
hg17	165605

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2758177, esv2757305, esv2757306

Samples

NA19141, NA12717, NA19128, NA12707

Known Genes

CD274, PLGRKT, RLN1, RLN2

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)

esv2759660

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	4
Observed Complex	0
Frequency	n/a