Variant Details

Variant: essv13411

Internal ID

9610794

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr2:107924531..108488738	hg38	UCSC Ensembl
Outer	chr2:107894222..108491067	hg38	UCSC Ensembl
Inner	chr2:108540987..109105194	hg19	UCSC Ensembl
Outer	chr2:108510678..109107523	hg19	UCSC Ensembl
Inner	chr2:107907419..108471626	hg18	UCSC Ensembl
Outer	chr2:107877110..108473955	hg18	UCSC Ensembl
Inner	chr2:107999505..108563712	hg17	UCSC Ensembl
Outer	chr2:107969196..108566041	hg17	UCSC Ensembl

Cytoband

2q12.3

Allele length

Assembly	Allele length
hg38	596846
hg19	596846
hg18	596846
hg17	596846

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756940

Supporting Variants

Samples

NA18872

Known Genes

GCC2, SLC5A7, SULT1C2, SULT1C2P1, SULT1C3, SULT1C4

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)

essv13411

Frequency

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