Variant Details

Variant: esv25172

Internal ID

11042405

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr1:109644224..109716486	hg38	UCSC Ensembl
Inner	chr1:110186846..110259108	hg19	UCSC Ensembl
Inner	chr1:109988369..110060631	hg18	UCSC Ensembl

Cytoband

1p13.3

Allele length

Assembly	Allele length
hg38	72263
hg19	72263
hg18	72263

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv10506, esv13941, esv14035, esv19304, esv15769, esv16117

Samples

NA18861, NA07037, NA19114, NA11931, NA18517, NA19257, NA19108, NA18505, NA12044, NA12287, NA19147, NA12414, NA18508, NA12004, NA11894, NA11995, NA18916, NA12006, NA07045, NA12239, NA19129, NA06985, NA18502, NA18858, NA18907, NA18909, NA12749, NA19099, NA12878, NA19225, NA19240

Known Genes

GSTM1, GSTM2, GSTM4, GSTM5

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)

esv25172

Frequency

Sample Size	40
Observed Gain	28
Observed Loss	10
Observed Complex	0
Frequency	n/a