Variant Details

Variant: essv17988

Internal ID

9615877

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:161545047..161660441	hg38	UCSC Ensembl
Outer	chr1:161527427..161668740	hg38	UCSC Ensembl
Inner	chr1:161514837..161630231	hg19	UCSC Ensembl
Outer	chr1:161497217..161638530	hg19	UCSC Ensembl
Inner	chr1:159781461..159896855	hg18	UCSC Ensembl
Outer	chr1:159763841..159905154	hg18	UCSC Ensembl
Inner	chr1:158327892..158361898	hg17	UCSC Ensembl
Outer	chr1:158310272..158370202	hg17	UCSC Ensembl

Cytoband

1q23.3

Allele length

Assembly	Allele length
hg38	141314
hg19	141314
hg18	141314
hg17	59931

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756866

Supporting Variants

Samples

NA12005

Known Genes

FCGR2B, FCGR2C, FCGR3A, FCGR3B, HSPA7

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)

essv17988

Frequency

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