Variant Details

Variant: essv12022

Internal ID

9609251

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:148827663..148926242	hg38	UCSC Ensembl
Outer	chr1:145891159..148926786	hg38	UCSC Ensembl
Inner	chr1:144958247..145056717	hg19	UCSC Ensembl
Outer	chr1:144957703..145543917	hg19	UCSC Ensembl
Inner	chr1:143669604..143768074	hg18	UCSC Ensembl
Outer	chr1:143669060..144255274	hg18	UCSC Ensembl
Inner	chr1:142447291..142545761	hg17	UCSC Ensembl
Outer	chr1:142446747..143032961	hg17	UCSC Ensembl

Cytoband

1q21.1

Allele length

Assembly	Allele length
hg38	3035628
hg19	586215
hg18	586215
hg17	586215

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756861

Supporting Variants

Samples

NA19141

Known Genes

ANKRD34A, GNRHR2, HFE2, ITGA10, LIX1L, LOC100288142, LOC101929780, NBPF10, NBPF12, NBPF9, NOTCH2NL, PDE4DIP, PEX11B, POLR3GL, RBM8A, SEC22B, TXNIP

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)

essv12022

Frequency

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