Variant Details

Variant: esv2756880

Internal ID

9632339

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:196740093..197096944	hg38	UCSC Ensembl
Inner	chr1:196709223..197066074	hg19	UCSC Ensembl
Inner	chr1:194975846..195332697	hg18	UCSC Ensembl
Inner	chr1:193440880..193797731	hg17	UCSC Ensembl

Cytoband

1q31.3

Allele length

Assembly	Allele length
hg38	356852
hg19	356852
hg18	356852
hg17	356852

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2758990

Supporting Variants

essv12109, essv25131, essv8002, essv13991, essv19727, essv12059, essv10514, essv12879, essv25182, essv15157, essv24614, essv18518, essv16577, essv11072, essv15974, essv13314, essv14815, essv23762, essv14957, essv16182, essv6527, essv12896, essv25164, essv2931, essv8031, essv13235, essv8557, essv17396, essv8588, essv14227, essv3443, essv17360, essv13407, essv5655, essv18545, essv752, essv22279, essv11332, essv11293, essv14254, essv21109, essv6214, essv14667, essv19871, essv8977, essv20529, essv9847, essv12084, essv9517, essv12151, essv14840, essv8897, essv9542, essv13259

Samples

NA18502, NA18861, NA18855, NA18507, NA19145, NA19098, NA18870, NA18526, NA18563, NA19171, NA19201, NA10854, NA19119, NA19131, NA12762, NA19138, NA19130, NA18611, NA19238, NA11994, NA19128, NA11993, NA19007, NA19210, NA18956, NA18871, NA18503, NA11839, NA19221, NA19142, NA11840, NA19099, NA19132, NA10856, NA19003, NA12716, NA11881, NA18517, NA18863, NA10859, NA18913, NA19100, NA19144, NA19193, NA12763, NA19143, NA19173, NA18521, NA18506, NA12875, NA18872, NA18505, NA19139, NA18522

Known Genes

ASPM, CFH, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, F13B

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)

esv2756880

Frequency

Sample Size	270
Observed Gain	10
Observed Loss	44
Observed Complex	0
Frequency	n/a