nstd202 - Ghazali et al 2021 - dbVar Study

nstd202 (Ghazali et al. 2021)

Organism:: Human
Study Type:: Somatic
Submitter:: Norliana Ghazali
Description:: This study identified the genetic aberration involved in both NSCL/P and hypodontia pathogenesis. There were a significant gain and loss, of both SKI and FHIT copy number in NSCL/P with hypodontia compared to the non-cleft group (p<0.05). The results supported that CNVs significantly furnish to the development of NSCL/P with hypodontia. See Variant Summary counts for nstd202 in dbVar Variant Summary.
Publication(s):: Ghazali et al. 2021

Links

Source: NCBI

Detailed Information: Download 2 Variant Regions, Download 2 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Submitted: GRCh38 (hg38)
Remapped: GRCh37.p13 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000003.12	Chr3	2	2	Submitted	NC_000003.12

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000003.11	Chr3	2	2	Remapped	NC_000003.11
NW_003871058.1	Chr3\|NW_003871058.1	1	1	Remapped	NW_003871058.1

Remapping summary:

			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_000003.12	Chr3	2	1	0	0	0	1	2	1	0	0	0	1

Samplesets

Number of Samplesets: 1

Name:: NSCL/P with hypodontia
Sampleset Type:: Case
Size:: 2
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Not reported
Sex:: Male

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
CLP-400014	Saliva	CLP-400014	Male	Malay	10 years	not reported
CLP-4000136	Saliva	CLP-4000136	Male	Malay	10 years	not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	Probe signal intensity	Cytoscan 750K Array (CNV-targeted Array)	2

dbVar

Database of genomic structural variation

nstd202 (Ghazali et al. 2021)

Links

Detailed Information: Download 2 Variant Regions, Download 2 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Submitted: GRCh38 (hg38)
Remapped: GRCh37.p13 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd202 (Ghazali et al. 2021)

Links

Detailed Information: Download 2 Variant Regions, Download 2 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38 (hg38)GRCh37.p13 (hg19)

Remapping summary: GRCh38->GRCh37.p13

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: