Variant Details

Variant: esv22725

Internal ID

11039958

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr16:88831204..88832084	hg38	UCSC Ensembl
Inner	chr16:88897612..88898492	hg19	UCSC Ensembl
Inner	chr16:87425113..87425993	hg18	UCSC Ensembl

Cytoband

16q24.3

Allele length

Assembly	Allele length
hg38	881
hg19	881
hg18	881

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv15404

Samples

NA12489, NA18861, NA07037, NA18523, NA19114, NA18511, NA11931, NA18517, NA12776, NA19257, NA19108, NA18505, NA12044, NA12287, NA19147, NA18508, NA11995, NA18916, NA19190, NA07045, NA12239, NA18502, NA18858, NA18907, NA18909, NA12749, NA12156, NA19099, NA19225, NA19240

Known Genes

GALNS

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)

esv22725

Frequency

Sample Size	40
Observed Gain	0
Observed Loss	30
Observed Complex	0
Frequency	n/a