Variant Details

Variant: essv11467

Internal ID

9608633

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:16596753..16601278	hg38	UCSC Ensembl
Outer	chr1:16596753..16604511	hg38	UCSC Ensembl
Inner	chr1:16923248..16927773	hg19	UCSC Ensembl
Outer	chr1:16923248..16931006	hg19	UCSC Ensembl
Inner	chr1:16795835..16800360	hg18	UCSC Ensembl
Outer	chr1:16795835..16803593	hg18	UCSC Ensembl
Inner	chr1:16668554..16673079	hg17	UCSC Ensembl
Outer	chr1:16668554..16676312	hg17	UCSC Ensembl

Cytoband

1p36.13

Allele length

Assembly	Allele length
hg38	7759
hg19	7759
hg18	7759
hg17	7759

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756838

Supporting Variants

Samples

NA18856

Known Genes

NBPF1

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)

essv11467

Frequency

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