Variant Details

Variant: essv7904

Internal ID

9629867

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr2:131197674..131338866	hg38	UCSC Ensembl
Outer	chr2:131197674..131340569	hg38	UCSC Ensembl
Inner	chr2:131955247..132096439	hg19	UCSC Ensembl
Outer	chr2:131955247..132098142	hg19	UCSC Ensembl
Inner	chr2:131671717..131812909	hg18	UCSC Ensembl
Outer	chr2:131671717..131814612	hg18	UCSC Ensembl
Inner	chr2:131788979..131930171	hg17	UCSC Ensembl
Outer	chr2:131788979..131931874	hg17	UCSC Ensembl

Cytoband

2q21.1

Allele length

Assembly	Allele length
hg38	142896
hg19	142896
hg18	142896
hg17	142896

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756946

Supporting Variants

Samples

NA19239

Known Genes

LOC440910, POTEE

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)

essv7904

Frequency

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