Variant Details

Variant: essv2754

Internal ID

9624145

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr5:179323255..179481731	hg38	UCSC Ensembl
Outer	chr5:179293967..179534709	hg38	UCSC Ensembl
Inner	chr5:178750256..178908732	hg19	UCSC Ensembl
Outer	chr5:178720968..178961710	hg19	UCSC Ensembl
Inner	chr5:178682862..178841338	hg18	UCSC Ensembl
Outer	chr5:178653574..178894316	hg18	UCSC Ensembl
Inner	chr5:178682862..178841338	hg17	UCSC Ensembl
Outer	chr5:178653574..178894316	hg17	UCSC Ensembl

Cytoband

5q35.3

Allele length

Assembly	Allele length
hg38	240743
hg19	240743
hg18	240743
hg17	240743

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757148

Supporting Variants

Samples

NA19000

Known Genes

ADAMTS2

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)

essv2754

Frequency

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