Variant Details

Variant: esv2760023

Internal ID

9635482

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr15:31474097..32694378	hg38	UCSC Ensembl
Inner	chr15:31766300..32986579	hg19	UCSC Ensembl
Inner	chr15:29553592..30773871	hg18	UCSC Ensembl
Inner	chr15:29553592..30773871	hg17	UCSC Ensembl

Cytoband

15q13.3

Allele length

Assembly	Allele length
hg38	1220282
hg19	1220280
hg18	1220280
hg17	1220280

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv2757594, esv2758375

Samples

NA11830, NA18603, NA12801, NA18959, NA12865, NA18870, NA12155, NA12813, NA19127, NA19201, NA19119, NA19131, NA18960, NA11992, NA18582, NA19138, NA18611, NA12156, NA11994, NA19207, NA12815, NA18990, NA18973, NA19007, NA10831, NA19152, NA12878, NA19161, NA18515, NA18516, NA18871, NA18981, NA19208, NA19221, NA19202, NA19142, NA10830, NA19154, NA12264, NA19099, NA19101, NA18523, NA19132, NA10856, NA18593, NA18576, NA18542, NA11881, NA19140, NA10861, NA12763, NA07055, NA19223, NA19211, NA10860, NA19102, NA12875, NA19116, NA18872, NA18852, NA18623, NA12154, NA19153, NA18577

Known Genes

ARHGAP11A, CHRNA7, GOLGA8K, GOLGA8O, GOLGA8R, LOC100996255, OTUD7A, SCG5, ULK4P1, ULK4P2, ULK4P3, WHAMMP1

Method

BAC aCGH
SNP array

Analysis

Array images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
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)
Agilent

Comments

Reference

Redon_et_al_2006

Pubmed ID

17122850

Accession Number(s)

esv2760023

Frequency

Sample Size	270
Observed Gain	6
Observed Loss	61
Observed Complex	0
Frequency	n/a