Variant Details

Variant: esv29822

Internal ID

11047055

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:101038965..101040048	hg38	UCSC Ensembl
Inner	chr4:101960122..101961205	hg19	UCSC Ensembl
Inner	chr4:102179145..102180228	hg18	UCSC Ensembl

Cytoband

4q23

Allele length

Assembly	Allele length
hg38	1084
hg19	1084
hg18	1084

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv13497, esv20737

Samples

NA12489, NA18861, NA18523, NA19114, NA18511, NA11931, NA12776, NA19108, NA15510, NA12287, NA19147, NA18508, NA12004, NA11894, NA11995, NA19190, NA07045, NA19129, NA06985, NA18502, NA18907, NA18909, NA12749, NA19099, NA19225, NA11993

Known Genes

PPP3CA

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)

esv29822

Frequency

Sample Size	40
Observed Gain	24
Observed Loss	2
Observed Complex	0
Frequency	n/a