Variant Details

Variant: esv28218

Internal ID

11045451

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr3:189645419..189674054	hg38	UCSC Ensembl
Inner	chr3:189363208..189391843	hg19	UCSC Ensembl
Inner	chr3:190845902..190874537	hg18	UCSC Ensembl

Cytoband

3q28

Allele length

Assembly	Allele length
hg38	28636
hg19	28636
hg18	28636

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv11225, esv15928

Samples

NA18502, NA18508, NA11931, NA19190, NA18907, NA19114, NA19099, NA19225, NA19108, NA18505

Known Genes

TP63

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)

esv28218

Frequency

Sample Size	40
Observed Gain	1
Observed Loss	9
Observed Complex	0
Frequency	n/a