Variant Details

Variant: essv13400

Internal ID

9610782

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr2:87146998..87672331	hg38	UCSC Ensembl
Outer	chr2:86900319..87689337	hg38	UCSC Ensembl
Inner	chr2:87374121..87971850	hg19	UCSC Ensembl
Outer	chr2:87127442..87988856	hg19	UCSC Ensembl
Inner	chr2:87227632..87752965	hg18	UCSC Ensembl
Outer	chr2:86980953..87769971	hg18	UCSC Ensembl
Inner	chr2:87285779..87811112	hg17	UCSC Ensembl
Outer	chr2:87039100..87828118	hg17	UCSC Ensembl

Cytoband

2p11.2

Allele length

Assembly	Allele length
hg38	789019
hg19	861415
hg18	789019
hg17	789019

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756936

Supporting Variants

Samples

NA18872

Known Genes

LINC00152, LOC285074, MIR4435-1, MIR4435-2, MIR4771-1, MIR4771-2, PLGLB1, PLGLB2, RGPD1, RGPD2

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)

essv13400

Frequency

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