Variant Details

Variant: essv19863

Internal ID

9617961

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:88108735..88144923	hg38	UCSC Ensembl
Outer	chr4:88037340..88208104	hg38	UCSC Ensembl
Inner	chr4:89029887..89066075	hg19	UCSC Ensembl
Outer	chr4:88958492..89129256	hg19	UCSC Ensembl
Inner	chr4:89248911..89285099	hg18	UCSC Ensembl
Outer	chr4:89177516..89348280	hg18	UCSC Ensembl
Inner	chr4:89387066..89423254	hg17	UCSC Ensembl
Outer	chr4:89315671..89486435	hg17	UCSC Ensembl

Cytoband

4q22.1

Allele length

Assembly	Allele length
hg38	170765
hg19	170765
hg18	170765
hg17	170765

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2757073

Supporting Variants

Samples

NA12234

Known Genes

ABCG2, PKD2

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)

essv19863

Frequency

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