Variant Details

Variant: esv2756825

Internal ID

9632284

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr19:15669231..15740451	hg38	UCSC Ensembl
Inner	chr19:15780041..15851261	hg19	UCSC Ensembl
Inner	chr19:15641041..15712261	hg18	UCSC Ensembl
Inner	chr19:15641041..15712261	hg17	UCSC Ensembl

Cytoband

19p13.12

Allele length

Assembly	Allele length
hg38	71221
hg19	71221
hg18	71221
hg17	71221

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2758747

Supporting Variants

essv10716, essv12112, essv16591, essv8909, essv10195, essv8517, essv15937, essv8496, essv9298, essv8967, essv12027, essv13115, essv16185, essv9265, essv12142

Samples

NA18508, NA19171, NA18860, NA19137, NA18859, NA18515, NA18516, NA18523, NA19173, NA18506, NA18854, NA19116, NA18852, NA18505, NA19139

Known Genes

CYP4F12, OR10H2

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)

esv2756825

Frequency

Sample Size	270
Observed Gain	14
Observed Loss	1
Observed Complex	0
Frequency	n/a