Variant Details

Variant: esv25064

Internal ID

11042297

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr10:87893078..87893955	hg38	UCSC Ensembl
Inner	chr10:89652835..89653712	hg19	UCSC Ensembl
Inner	chr10:89642815..89643692	hg18	UCSC Ensembl

Cytoband

10q23.31

Allele length

Assembly	Allele length
hg38	878
hg19	878
hg18	878

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv13725

Samples

NA18502, NA11995, NA18508, NA11931, NA12004, NA19190, NA18916, NA12287, NA12828, NA18907, NA19114, NA11894, NA12239, NA15510, NA19099, NA19225, NA06985, NA18523, NA18909, NA19108, NA19147, NA18517, NA19240, NA07037, NA12749, NA18505, NA19129, NA12006

Known Genes

PTEN

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)

esv25064

Frequency

Sample Size	40
Observed Gain	28
Observed Loss	0
Observed Complex	0
Frequency	n/a