Variant Details

Variant: esv17617

Internal ID

11034851

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:248574714..248632217	hg38	UCSC Ensembl
Inner	chr1:248738015..248795518	hg19	UCSC Ensembl
Inner	chr1:246804638..246862141	hg18	UCSC Ensembl

Cytoband

1q44

Allele length

Assembly	Allele length
hg38	57504
hg19	57504
hg18	57504

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv27363

Supporting Variants

essv77951, essv37930, essv80389, essv45428, essv40962, essv55715, essv59924, essv63894, essv50351, essv43473, essv41505, essv53929, essv65156

Samples

NA11995, NA18508, NA12878, NA07045, NA19099, NA19257, NA06985, NA18523, NA18909, NA18517, NA19240, NA18505, NA19129

Known Genes

OR2T10, OR2T11, OR2T34

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)

esv17617

Frequency

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