Variant Details

Variant: esv2757689

Internal ID

9633148

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr19:20388716..20591541	hg38	UCSC Ensembl
Inner	chr19:20499525..20774347	hg19	UCSC Ensembl
Inner	chr19:20360525..20566187	hg18	UCSC Ensembl
Inner	chr19:20360525..20566187	hg17	UCSC Ensembl

Cytoband

19p12

Allele length

Assembly	Allele length
hg38	202826
hg19	274823
hg18	205663
hg17	205663

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv2758749

Supporting Variants

essv13985, essv17992, essv1653, essv3490, essv8899, essv3663, essv1330, essv5885, essv2729, essv18786, essv3911, essv6102, essv5857, essv2958, essv2918, essv7470, essv14675, essv758, essv7254, essv21924, essv22018, essv12103, essv13284, essv12048, essv24344, essv20704, essv8547, essv4341, essv710, essv6059, essv632, essv3594, essv7988, essv7435, essv9863

Samples

NA18998, NA19145, NA18999, NA18603, NA19098, NA18633, NA18969, NA19171, NA18940, NA19201, NA12802, NA18635, NA12891, NA18960, NA18582, NA12005, NA12815, NA10839, NA18973, NA19007, NA18991, NA18503, NA19221, NA18573, NA18555, NA18576, NA19003, NA18961, NA12057, NA19144, NA19173, NA19116, NA18972, NA18622, NA18965

Known Genes

MIR1270-1, MIR1270-2, ZNF737, ZNF826P

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)

esv2757689

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	35
Observed Complex	0
Frequency	n/a