Variant Details

Variant: esv15558

Internal ID

11032792

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr9:38815447..39397758	hg38	UCSC Ensembl
Inner	chr9:65467706..65918330	hg19	UCSC Ensembl
Inner	chr9:65207526..65658150	hg18	UCSC Ensembl

Cytoband

9q12

Allele length

Assembly	Allele length
hg38	582312
hg19	450625
hg18	450625

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

esv24325

Supporting Variants

essv81266, essv40642

Samples

NA12878, NA19114

Known Genes

FAM74A2, FAM74A4, SPATA31A5, SPATA31A7

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)

esv15558

Frequency

Sample Size	40
Observed Gain	2
Observed Loss	0
Observed Complex	0
Frequency	n/a