Variant Details

Variant: esv25715

Internal ID

11042948

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr13:114198348..114344365	hg38	UCSC Ensembl
Inner	chr13:114963823..115109840	hg19	UCSC Ensembl
Inner	chr13:113981925..114127942	hg18	UCSC Ensembl

Cytoband

13q34

Allele length

Assembly	Allele length
hg38	146018
hg19	146018
hg18	146018

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv14379, esv10621, esv19157, esv18856, esv10503

Samples

NA18861, NA19190, NA12287, NA12156, NA12044, NA12828, NA11993, NA12489, NA19114, NA06985, NA19108, NA12749, NA19129

Known Genes

CDC16, CHAMP1, UPF3A

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)

esv25715

Frequency

Sample Size	40
Observed Gain	1
Observed Loss	13
Observed Complex	0
Frequency	n/a