Variant Details

Variant: esv20331

Internal ID

11037565

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr4:98892383..98897090	hg38	UCSC Ensembl
Inner	chr4:99813534..99818241	hg19	UCSC Ensembl
Inner	chr4:100032557..100037264	hg18	UCSC Ensembl

Cytoband

4q23

Allele length

Assembly	Allele length
hg38	4708
hg19	4708
hg18	4708

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv27868

Supporting Variants

essv71822, essv79528, essv80308, essv74667, essv68432, essv53767, essv70924, essv50624, essv54450, essv55982, essv33212, essv37068, essv81718

Samples

NA11995, NA18508, NA12004, NA18916, NA19114, NA11894, NA19099, NA19225, NA18858, NA19147, NA18517, NA12749, NA12776

Known Genes

EIF4E

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)

esv20331

Frequency

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