nstd81 - Low et al 2016 - dbVar Study

Organism:: Human
Study Type:: Case-Control
Submitter:: Joyce Low
Description:: Nasopharyngeal carcinoma (NPC), is a malignant tumour arising from the epithelial lining of the nasopharynx. While a number of studies on single nucleotide polymorphisms (SNPs) associated to susceptibility to NPC had previously been carried out, studies on CNV had not been prevalent even though the functional effects of these structural variants in pathogenesis can be significant. Hence, by genotyping more than 700,000 SNPs using Illumina® Human OmniExpress SNP-based microarrays, this study aims to discover associations between copy number variants (CNVs) in the genomes of our Malaysian Chinese study population with the susceptibility to NPC. See Variant Summary counts for nstd81 in dbVar Variant Summary.
Publication(s):: Low et al. 2016

Source: NCBI

Variant Summary

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000011.10	Chr11	1	2	Remapped	NC_000011.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000011.9	Chr11	1	2	Remapped	NC_000011.9

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000011.8	Chr11	1	2	Submitted	NC_000011.8

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000011.8	Chr11	1	1	0	0	0	0	2	2	0	0	0	0

	Variant Region remap status		Variant Call remap status
NC_000011.8	Chr11	1	1	0	0	0	0	2	2	0	0	0	0

Sampleset ID:: 1
Name:: Case
Sampleset Type:: Case
Size:: 140
Organisms:: Homo sapiens
Sampleset Phenotype(s):: NASOPHARYNGEAL CARCINOMA
NASOPHARYNGEAL CARCINOMA, SUSCEPTIBILITY TO, 2; NPCA2
Sex:: Male

Samples for sampleset 1 (displaying 100 of the 140 samples)
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
1_2E04	Peripheral leukocyte	1_2E04	Male	Malaysian Chinese	60 years	NASOPHARYNGEAL CARCINOMA NASOPHARYNGEAL CARCINOMA, SUSCEPTIBILITY TO, 2; NPCA2
1_2C07	Peripheral leukocyte	1_2C07	Male	Malaysian Chinese	54 years	NASOPHARYNGEAL CARCINOMA NASOPHARYNGEAL CARCINOMA, SUSCEPTIBILITY TO, 2; NPCA2

Experiment ID	Type	Method	Analysis	Platforms	Site	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Illumina Human OmniExpress	The Institutes of Physical and Chemical Research (RIKEN), University of Malaya	2
2	Validation	qPCR	Probe signal intensity	ABI QuantStudio	University of Malaya	2

Experiment ID	Method	Analysis	Platform	Number of Variant Calls Validated
2	qPCR	Probe signal intensity	ABI QuantStudio	2