nstd205 - Kwong et al 2021 - dbVar Study

nstd205 (Kwong et al. 2021)

Organism:: Human
Study Type:: Case-Set
Submitter:: Chun Hang Au
Description:: Copy number variants (CNV) of breast and/or ovarian cancer susceptibility genes are a known class of clinically significant variants. CNV detection resolution by routine gene panel NGS is often limited to individual exon level without exact CNV breakpoint and direction. In this study, we mapped exact CNV breakpoints by PCR-free long-read Nanopore sequencing for better interpretation of its pathogenicity. See Variant Summary counts for nstd205 in dbVar Variant Summary.
Project:: PRJNA700481

Links

Source: NCBI

Detailed Information: Download 16 Variant Regions, Download 16 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

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

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000013.11	Chr13	3	3	Remapped	NC_000013.11
NC_000016.10	Chr16	2	2	Remapped	NC_000016.10
NC_000017.11	Chr17	10	10	Remapped	NC_000017.11
NC_000022.11	Chr22	1	1	Remapped	NC_000022.11

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000013.10	Chr13	3	3	Submitted	NC_000013.10
NC_000016.9	Chr16	2	2	Submitted	NC_000016.9
NC_000017.10	Chr17	10	10	Submitted	NC_000017.10
NC_000022.10	Chr22	1	1	Submitted	NC_000022.10

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_000013.10	Chr13	3	3	0	0	0	0	3	3	0	0	0	0
NC_000016.9	Chr16	2	2	0	0	0	0	2	2	0	0	0	0
NC_000017.10	Chr17	10	9	1	0	0	0	10	9	1	0	0	0
NC_000022.10	Chr22	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 1

Size:: 16
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Subject Phenotype
1	1	Not reported
2	2	Not reported
3	3	Not reported
4	4	Not reported
5	5	Not reported
6	6	Not reported
7	7	Not reported
8	8	Not reported
9	9	Not reported
10	10	Not reported
11	11	Not reported
12	12	Not reported
13	13	Not reported
14	14	Not reported
15	15	Not reported
16	16	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Split read mapping	16

dbVar

Database of genomic structural variation

nstd205 (Kwong et al. 2021)

Links

Detailed Information: Download 16 Variant Regions, Download 16 Variant Calls, Download Both, FTP

Variant Summary

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

nstd205 (Kwong et al. 2021)

Links

Detailed Information: Download 16 Variant Regions, Download 16 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: