Variant Details

Variant: essv3514

Internal ID

9624990

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr19:43055178..43177075	hg38	UCSC Ensembl
Outer	chr19:43055178..43207440	hg38	UCSC Ensembl
Inner	chr19:43559330..43681227	hg19	UCSC Ensembl
Outer	chr19:43559330..43711592	hg19	UCSC Ensembl
Inner	chr19:48251170..48373067	hg18	UCSC Ensembl
Outer	chr19:48251170..48403432	hg18	UCSC Ensembl
Inner	chr19:48251170..48373067	hg17	UCSC Ensembl
Outer	chr19:48251170..48403432	hg17	UCSC Ensembl

Cytoband

19q13.31

Allele length

Assembly	Allele length
hg38	152263
hg19	152263
hg18	152263
hg17	152263

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757697

Supporting Variants

Samples

NA18999

Known Genes

PSG2, PSG4, PSG5

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)

essv3514

Frequency

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