Variant Details

Variant: esv27976

Internal ID

11045209

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:115592696..116135006	hg38	UCSC Ensembl
Inner	chr1:116135317..116677627	hg19	UCSC Ensembl
Inner	chr1:115936840..116479150	hg18	UCSC Ensembl

Cytoband

1p13.1

Allele length

Assembly	Allele length
hg38	542311
hg19	542311
hg18	542311

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv15965, esv12135, esv10537

Samples

NA18861, NA18508, NA11931, NA12004, NA12287, NA12044, NA12828, NA12878, NA18907, NA19114, NA12239, NA15510, NA19099, NA18523, NA18858, NA19108, NA18517, NA12749, NA12006

Known Genes

CASQ2, MAB21L3, NHLH2, SLC22A15, VANGL1

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)

esv27976

Frequency

Sample Size	40
Observed Gain	0
Observed Loss	19
Observed Complex	0
Frequency	n/a