Variant Details

Variant: esv13959

Internal ID

11031193

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr11:55597201..55685585	hg38	UCSC Ensembl
Inner	chr11:55364677..55453061	hg19	UCSC Ensembl
Inner	chr11:55121253..55209637	hg18	UCSC Ensembl

Cytoband

11q11

Allele length

Assembly	Allele length
hg38	88385
hg19	88385
hg18	88385

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv22842

Supporting Variants

essv63398, essv76147, essv67446, essv45815, essv38044, essv46742, essv35474, essv78159, essv36763, essv70322, essv34036, essv52649, essv39995, essv76795, essv56095, essv61649

Samples

NA18502, NA18861, NA12414, NA18916, NA12828, NA12878, NA18907, NA11894, NA12239, NA15510, NA19257, NA06985, NA19129, NA12006, NA18511, NA12776

Known Genes

OR4C11, OR4C6, OR4P4, OR4S2

Method

Oligo aCGH

Analysis

Segment log2 ratios from each sample. This was done running the GADA algorithm (Pique-Regi et al., 2008) using the options "-M 10 -T 10 -a 2.5". Filter non-CNV segments using intensity thresholds. Merge remaining CNV "calls" within each sample. Adjacent calls of the same direction (gain or loss) are merged if both: the distance between calls is less than 10kb, and the distance between calls is less than 10% of the size of the largest of the two calls.

Platform

Sanger H. Sapiens 42mCGH Array 5781_53 726K v1

Comments

Reference

Conrad_et_al_2009

Pubmed ID

19812545

Accession Number(s)

esv13959

Frequency

Sample Size	40
Observed Gain	0
Observed Loss	16
Observed Complex	0
Frequency	n/a