Variant Details

Variant: essv2400

Internal ID

9971027

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr7:153826260..153963508	hg38	UCSC Ensembl
Outer	chr7:153756791..154114753	hg38	UCSC Ensembl
Inner	chr7:153523345..153660593	hg19	UCSC Ensembl
Outer	chr7:153453876..153811838	hg19	UCSC Ensembl
Inner	chr7:153154278..153291526	hg18	UCSC Ensembl
Outer	chr7:153084809..153442771	hg18	UCSC Ensembl
Inner	chr7:152960993..153098241	hg17	UCSC Ensembl
Outer	chr7:152891524..153249486	hg17	UCSC Ensembl

Cytoband

7q36.2

Allele length

Assembly	Allele length
hg38	357963
hg19	357963
hg18	357963
hg17	357963

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756806

Supporting Variants

Samples

NA18976

Known Genes

DPP6

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)

essv2400

Frequency

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