Variant Details

Variant: esv28756

Internal ID

11045989

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr21:10324359..10814516	hg38	UCSC Ensembl
Inner	chr21:10697941..11188098	hg19	UCSC Ensembl
Inner	chr21:9719812..10209969	hg18	UCSC Ensembl

Cytoband

21p11.1

Allele length

Assembly	Allele length
hg38	490158
hg19	490158
hg18	490158

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv15016, esv18137, esv10775, esv18932, esv10739, esv10299, esv13930, esv11634, esv18399, esv13330, esv14720, esv14620, esv10837

Samples

NA18502, NA11995, NA18861, NA18508, NA12414, NA11931, NA12004, NA19190, NA18916, NA12287, NA12044, NA12828, NA11993, NA12489, NA12878, NA18907, NA07045, NA19114, NA11894, NA12239, NA15510, NA19099, NA19257, NA19225, NA06985, NA18523, NA18858, NA18909, NA19108, NA19147, NA18517, NA19240, NA07037, NA12749, NA18505, NA19129, NA18511, NA12776

Known Genes

BAGE, BAGE2, BAGE3, BAGE4, BAGE5, TPTE

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)

esv28756

Frequency

Sample Size	40
Observed Gain	30
Observed Loss	27
Observed Complex	0
Frequency	n/a