Variant Details

Variant: esv2758935

Internal ID

9634394

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:53022892..53066445	hg38	UCSC Ensembl
Inner	chr1:53488564..53532117	hg19	UCSC Ensembl
Inner	chr1:53261152..53304705	hg18	UCSC Ensembl
Inner	chr1:53200585..53244138	hg17	UCSC Ensembl

Cytoband

1p32.3

Allele length

Assembly	Allele length
hg38	43554
hg19	43554
hg18	43554
hg17	43554

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2756843

Samples

NA19128, NA18853

Known Genes

PODN, SCP2

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)

esv2758935

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	2
Observed Complex	0
Frequency	n/a