Variant Details

Variant: essv3443

Internal ID

9624911

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:196832482..196917640	hg38	UCSC Ensembl
Outer	chr1:196740093..196947229	hg38	UCSC Ensembl
Inner	chr1:196801612..196886770	hg19	UCSC Ensembl
Outer	chr1:196709223..196916359	hg19	UCSC Ensembl
Inner	chr1:195068235..195153393	hg18	UCSC Ensembl
Outer	chr1:194975846..195182982	hg18	UCSC Ensembl
Inner	chr1:193533269..193618427	hg17	UCSC Ensembl
Outer	chr1:193440880..193648016	hg17	UCSC Ensembl

Cytoband

1q31.3

Allele length

Assembly	Allele length
hg38	207137
hg19	207137
hg18	207137
hg17	207137

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756880

Supporting Variants

Samples

NA18956

Known Genes

CFH, CFHR1, CFHR2, CFHR3, CFHR4

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)

essv3443

Frequency

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