Variant Details

Variant: essv5642

Internal ID

9964931

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr21:13319046..13425916	hg38	UCSC Ensembl
Outer	chr21:13318911..13535268	hg38	UCSC Ensembl
Inner	chr21:14691367..14798237	hg19	UCSC Ensembl
Outer	chr21:14691232..14907589	hg19	UCSC Ensembl
Inner	chr21:13613238..13720108	hg18	UCSC Ensembl
Outer	chr21:13613103..13829460	hg18	UCSC Ensembl
Inner	chr21:13613238..13720108	hg17	UCSC Ensembl
Outer	chr21:13613103..13829460	hg17	UCSC Ensembl

Cytoband

21q11.2

Allele length

Assembly	Allele length
hg38	216358
hg19	216358
hg18	216358
hg17	216358

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756746

Supporting Variants

Samples

NA18579

Known Genes

MIR3156-3

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)

essv5642

Frequency

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