Variant Details

Variant: essv13220

Internal ID

9610582

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr7:62978903..63245808	hg38	UCSC Ensembl
Outer	chr7:62371529..63651887	hg38	UCSC Ensembl
Inner	chr7:62439281..62706186	hg19	UCSC Ensembl
Outer	chr7:61815780..63112265	hg19	UCSC Ensembl
Inner	chr7:62076716..62343621	hg18	UCSC Ensembl
Outer	chr7:61453215..62749700	hg18	UCSC Ensembl
Inner	chr7:61883431..62150336	hg17	UCSC Ensembl
Outer	chr7:61259930..62556415	hg17	UCSC Ensembl

Cytoband

7q11.21

Allele length

Assembly	Allele length
hg38	1280359
hg19	1296486
hg18	1296486
hg17	1296486

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2756802

Supporting Variants

Samples

NA19120

Known Genes

LOC100287704, LOC100287834, MIR4283-1, MIR4283-2, ZNF733P

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)

essv13220

Frequency

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