nstd218 - Wijesiriwardhana et al 2021 - dbVar Study

nstd218 (Wijesiriwardhana et al. 2021)

Organism:: Human
Study Type:: Case-Control
Submitter:: Prabhavi Wijesiriwardhana
Description:: In the current study we have evaluated the contribution of germline CNV to hereditary breast cancer risk in a cohort of Sri Lankan patients who do not harbor pathogenic variants in known breast cancer predisposing genes. The data analysis showed both rare and common CNVs might contribute to breast cancer predisposition. Some CNVs were found to be assoicaited with various metabolic pathways that involved in progression of various diseases such as cancer. See Variant Summary counts for nstd218 in dbVar Variant Summary.
Project:: PRJNA795679
Publication(s):: Wijesiriwardhana et al. 2021

Links

Source: NCBI

Detailed Information: Download 103 Variant Regions, Download 105 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p13 (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_000001.11	Chr1	9	9	Remapped	NC_000001.11
NC_000002.12	Chr2	8	8	Remapped	NC_000002.12
NC_000003.12	Chr3	3	3	Remapped	NC_000003.12
NC_000004.12	Chr4	5	5	Remapped	NC_000004.12
NC_000005.10	Chr5	2	2	Remapped	NC_000005.10
NC_000006.12	Chr6	9	9	Remapped	NC_000006.12
NC_000007.14	Chr7	6	6	Remapped	NC_000007.14
NC_000008.11	Chr8	5	5	Remapped	NC_000008.11
NC_000009.12	Chr9	1	1	Remapped	NC_000009.12
NC_000010.11	Chr10	6	6	Remapped	NC_000010.11
NC_000012.12	Chr12	4	4	Remapped	NC_000012.12
NC_000013.11	Chr13	1	1	Remapped	NC_000013.11
NC_000014.9	Chr14	13	13	Remapped	NC_000014.9
NC_000015.10	Chr15	8	9	Remapped	NC_000015.10
NC_000016.10	Chr16	5	5	Remapped	NC_000016.10
NC_000017.11	Chr17	3	3	Remapped	NC_000017.11
NC_000018.10	Chr18	2	2	Remapped	NC_000018.10
NC_000019.10	Chr19	1	1	Remapped	NC_000019.10
NC_000020.11	Chr20	2	2	Remapped	NC_000020.11
NC_000021.9	Chr21	1	1	Remapped	NC_000021.9
NC_000022.11	Chr22	7	7	Remapped	NC_000022.11
NW_018654707.1	Chr1\|NW_018654707.1	1	1	Remapped	NW_018654707.1
NT_187523.1	Chr2\|NT_187523.1	2	2	Remapped	NT_187523.1
NT_187647.1	Chr2\|NT_187647.1	2	2	Remapped	NT_187647.1
NT_187678.1	Chr3\|NT_187678.1	1	1	Remapped	NT_187678.1
NT_187688.1	Chr3\|NT_187688.1	1	1	Remapped	NT_187688.1
NT_187689.1	Chr3\|NT_187689.1	1	1	Remapped	NT_187689.1
NT_187690.1	Chr3\|NT_187690.1	1	1	Remapped	NT_187690.1
NT_187691.1	Chr3\|NT_187691.1	1	1	Remapped	NT_187691.1
NT_187532.1	Chr3\|NT_187532.1	1	1	Remapped	NT_187532.1
NT_187649.1	Chr3\|NT_187649.1	1	1	Remapped	NT_187649.1
NT_187651.1	Chr5\|NT_187651.1	1	1	Remapped	NT_187651.1
NW_003315917.2	Chr5\|NW_003315917.2	1	1	Remapped	NW_003315917.2
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1
NW_003315972.2	Chr22\|NW_003315972.2	1	1	Remapped	NW_003315972.2
NT_187600.1	Chr14\|NT_187600.1	3	3	Remapped	NT_187600.1
NT_187661.1	Chr17\|NT_187661.1	1	1	Remapped	NT_187661.1
NT_187614.1	Chr17\|NT_187614.1	1	1	Remapped	NT_187614.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	11	11	Submitted	NC_000001.10
NC_000002.11	Chr2	8	8	Submitted	NC_000002.11
NC_000003.11	Chr3	3	3	Submitted	NC_000003.11
NC_000004.11	Chr4	5	5	Submitted	NC_000004.11
NC_000005.9	Chr5	2	2	Submitted	NC_000005.9
NC_000006.11	Chr6	10	10	Submitted	NC_000006.11
NC_000007.13	Chr7	5	5	Submitted	NC_000007.13
NC_000008.10	Chr8	5	5	Submitted	NC_000008.10
NC_000009.11	Chr9	1	1	Submitted	NC_000009.11
NC_000010.10	Chr10	6	6	Submitted	NC_000010.10
NC_000012.11	Chr12	4	4	Submitted	NC_000012.11
NC_000013.10	Chr13	1	1	Submitted	NC_000013.10
NC_000014.8	Chr14	14	15	Submitted	NC_000014.8
NC_000015.9	Chr15	8	9	Submitted	NC_000015.9
NC_000016.9	Chr16	4	4	Submitted	NC_000016.9
NC_000017.10	Chr17	3	3	Submitted	NC_000017.10
NC_000018.9	Chr18	2	2	Submitted	NC_000018.9
NC_000019.9	Chr19	1	1	Submitted	NC_000019.9
NC_000020.10	Chr20	2	2	Submitted	NC_000020.10
NC_000021.8	Chr21	1	1	Submitted	NC_000021.8
NC_000022.10	Chr22	7	7	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_000001.10	Chr1	11	2	3	2	2	2	11	2	3	2	2	2
NC_000002.11	Chr2	8	2	1	3	0	2	8	2	1	3	0	2
NC_000003.11	Chr3	3	2	0	0	0	1	3	2	0	0	0	1
NC_000004.11	Chr4	5	5	0	0	0	0	5	5	0	0	0	0
NC_000005.9	Chr5	2	0	1	0	0	1	2	0	1	0	0	1
NC_000006.11	Chr6	10	9	0	0	1	0	10	9	0	0	1	0
NC_000007.13	Chr7	5	4	1	0	0	0	5	4	1	0	0	0
NC_000008.10	Chr8	5	5	0	0	0	0	5	5	0	0	0	0
NC_000009.11	Chr9	1	1	0	0	0	0	1	1	0	0	0	0
NC_000010.10	Chr10	6	0	0	6	0	0	6	0	0	6	0	0
NC_000012.11	Chr12	4	4	0	0	0	0	4	4	0	0	0	0
NC_000013.10	Chr13	1	1	0	0	0	0	1	1	0	0	0	0
NC_000014.8	Chr14	14	2	7	1	1	3	15	2	7	1	2	3
NC_000015.9	Chr15	8	3	3	2	0	0	9	3	3	3	0	0
NC_000016.9	Chr16	4	2	0	2	0	0	4	2	0	2	0	0
NC_000017.10	Chr17	3	1	0	0	0	2	3	1	0	0	0	2
NC_000018.9	Chr18	2	2	0	0	0	0	2	2	0	0	0	0
NC_000019.9	Chr19	1	0	1	0	0	0	1	0	1	0	0	0
NC_000020.10	Chr20	2	2	0	0	0	0	2	2	0	0	0	0
NC_000021.8	Chr21	1	1	0	0	0	0	1	1	0	0	0	0
NC_000022.10	Chr22	7	2	4	0	0	1	7	2	4	0	0	1

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: SL_BC_CNVs
Sampleset Type:: Case
Description:: CNVs identified in a cohort of Sri Lankan breast cancer patients awho do not harbor single nucleotide varaints in known breast cancer predisposing genes
Size:: 10
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Breast cancer
Sex:: Female

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
1	Peripheral leukocytes	CG 11	Female	Sri Lankan	19 years	breast cancer
2	Peripheral leukocytes	CG 23	Female	Sri Lankan	35 years	breast cancer
3	Peripheral leukocytes	CG 24	Female	Sri Lankan	48 years	breast cancer
4	Peripheral leukocytes	CG 27	Female	Sri Lankan	49 years	breast cancer
5	Peripheral leukocytes	CG 45	Female	Sri Lankan	42 years	breast cancer
6	Peripheral leukocytes	CG 51	Female	Sri Lankan	45 years	breast cancer
7	Peripheral leukocytes	CG 199	Female	Sri Lankan	51 years	breast cancer
8	Peripheral leukocytes	CG 235	Female	Sri Lankan	45 years	breast cancer
9	Peripheral leukocytes	CG 256	Female	Sri Lankan	41 years	breast cancer
10	Peripheral leukocytes	CG 272	Female	Sri Lankan	45 years	breast cancer

Sampleset ID:: 2
Name:: SL_BC_CNVs_control
Sampleset Type:: Control
Description:: control samples
Size:: 4
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Healthy
Sex:: Female

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
11	Peripheral leukocytes	CT 1	Female	Sri Lankan	36 years	healthy
12	Peripheral leukocytes	CT 2	Female	Sri Lankan	42 years	healthy
13	Peripheral leukocytes	CT 3	Female	Sri Lankan	45 years	healthy
14	Peripheral leukocytes	CT 4	Female	Sri Lankan	44 years	healthy

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Oligo aCGH	Probe signal intensity	SurePrint G3 Human CGH 4x180K Microarray	105

dbVar

Database of genomic structural variation

nstd218 (Wijesiriwardhana et al. 2021)

Links

Detailed Information: Download 103 Variant Regions, Download 105 Variant Calls, Download Both, FTP

Variant Summary

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

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd218 (Wijesiriwardhana et al. 2021)

Links

Detailed Information: Download 103 Variant Regions, Download 105 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: