Variant Details

Variant: essv8492

Internal ID

9630520

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:16632967..16696908	hg38	UCSC Ensembl
Outer	chr1:16593976..16908148	hg38	UCSC Ensembl
Inner	chr1:16959462..17023403	hg19	UCSC Ensembl
Outer	chr1:16920471..17234643	hg19	UCSC Ensembl
Inner	chr1:16832049..16895990	hg18	UCSC Ensembl
Outer	chr1:16793058..17107230	hg18	UCSC Ensembl
Inner	chr1:16704768..16768709	hg17	UCSC Ensembl
Outer	chr1:16665777..16979949	hg17	UCSC Ensembl

Cytoband

1p36.13

Allele length

Assembly	Allele length
hg38	314173
hg19	314173
hg18	314173
hg17	314173

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756838

Supporting Variants

Samples

NA18854

Known Genes

CROCCP2, ESPNP, LOC729574, MIR3675, MST1L, MST1P2, NBPF1

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)

essv8492

Frequency

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