Variant Details

Variant: esv29345

Internal ID

11046578

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr5:42628146..42631168	hg38	UCSC Ensembl
Inner	chr5:42628248..42631270	hg19	UCSC Ensembl
Inner	chr5:42664005..42667027	hg18	UCSC Ensembl

Cytoband

5p12

Allele length

Assembly	Allele length
hg38	3023
hg19	3023
hg18	3023

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv18870, esv14363

Samples

NA12489, NA18523, NA19114, NA18517, NA19257, NA19108, NA12044, NA19147, NA12414, NA18508, NA12004, NA18916, NA19190, NA07045, NA12239, NA18907, NA18909, NA12749, NA19099, NA19225, NA19240

Known Genes

GHR

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)

esv29345

Frequency

Sample Size	40
Observed Gain	0
Observed Loss	21
Observed Complex	0
Frequency	n/a