Variant Details

Variant: nsv471696

Internal ID

15561210

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr17:13571274..13750252	hg38	UCSC Ensembl
Inner	chr17:13474591..13653569	hg19	UCSC Ensembl
Inner	chr17:13415316..13594294	hg18	UCSC Ensembl
Inner	chr17:13675157..13854135	hg16	UCSC Ensembl

Cytoband

17p12

Allele length

Assembly	Allele length
hg38	178979
hg19	178979
hg18	178979
hg16	178979

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv549982, nssv549985, nssv549987, nssv549980, nssv549986, nssv549983, nssv549990, nssv549979, nssv549988, nssv549989, nssv549984, nssv549981

Samples

P86GA, NA16689, NA17059, NA10473, NA17015, NA15733, NA15726, NA15731, NA17052, JK1688B, NA16688, NA11323

Known Genes

HS3ST3A1

Method

BAC aCGH

Analysis

Array image analysis and normalization were performed using UCSF Spot and Sproc software (Jain et al. 2002). BACs for which only one of the triplicates printed on the array yielded data, or for which the standard deviation of log2 ratio for the triplicates was 10.2, were removed from final analysis. Furthermore, we discarded BACs that failed to yield data in <20% of cases. For each hybridization experiment, we established a threshold log2 ratio of 2 SDs from the mean of all autosomal clones, and BACs that exceeded this threshold in both independent dye-swap experiments were classified as variant.

Platform

GPL4010

Comments

Reference

Sharp_et_al_2005

Pubmed ID

15918152

Accession Number(s)

nsv471696

Frequency

Sample Size	48
Observed Gain	10
Observed Loss	2
Observed Complex	0
Frequency	n/a