Variant Details

Variant: essv24452

Internal ID

9623061

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:31235010..31855355	hg38	UCSC Ensembl
Outer	chr1:31209533..32000730	hg38	UCSC Ensembl
Inner	chr1:31707857..32320956	hg19	UCSC Ensembl
Outer	chr1:31682380..32466331	hg19	UCSC Ensembl
Inner	chr1:31480444..32093543	hg18	UCSC Ensembl
Outer	chr1:31454967..32238918	hg18	UCSC Ensembl
Inner	chr1:31376950..31990049	hg17	UCSC Ensembl
Outer	chr1:31351473..32135424	hg17	UCSC Ensembl

Cytoband

1p35.1

Allele length

Assembly	Allele length
hg38	791198
hg19	783952
hg18	783952
hg17	783952

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756841

Supporting Variants

Samples

NA12865

Known Genes

BAI2, COL16A1, FABP3, HCRTR1, LOC149086, LOC284551, MIR4254, NKAIN1, PEF1, PTP4A2, SERINC2, SNRNP40, SPOCD1, TINAGL1, ZCCHC17

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)

essv24452

Frequency

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