Variant Details

Variant: esv21244

Internal ID

11038478

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrX:154141623..154294064	hg38	UCSC Ensembl
Inner	chrX:153407097..153522418	hg19	UCSC Ensembl
Inner	chrX:153060291..153175612	hg18	UCSC Ensembl

Cytoband

Xq28

Allele length

Assembly	Allele length
hg38	152442
hg19	115322
hg18	115322

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv27518

Supporting Variants

essv34170, essv81942, essv53904, essv43307, essv61424, essv65021, essv37233, essv72061, essv56444, essv58105, essv38684, essv48453, essv67458, essv80808, essv41513, essv63632, essv50966

Samples

NA18502, NA11995, NA18508, NA11931, NA12828, NA07045, NA19114, NA11894, NA12239, NA19257, NA19225, NA18909, NA19108, NA19240, NA07037, NA18505, NA12776

Known Genes

OPN1LW, OPN1MW, OPN1MW2, TEX28

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)

esv21244

Frequency

Sample Size	40
Observed Gain	10
Observed Loss	7
Observed Complex	0
Frequency	n/a