Variant Details

Variant: esv2759337

Internal ID

9634796

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr5:32011912..32203394	hg38	UCSC Ensembl
Inner	chr5:32012018..32203500	hg19	UCSC Ensembl
Inner	chr5:32047775..32239257	hg18	UCSC Ensembl
Inner	chr5:32047775..32239257	hg17	UCSC Ensembl

Cytoband

5p13.3

Allele length

Assembly	Allele length
hg38	191483
hg19	191483
hg18	191483
hg17	191483

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2757992, esv2757112

Samples

NA12248, NA18959, NA18951, NA12264, NA18632

Known Genes

GOLPH3, PDZD2

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)

esv2759337

Frequency

Sample Size	270
Observed Gain	5
Observed Loss	0
Observed Complex	0
Frequency	n/a