nstd197 - Boujemaa et al 2021 - dbVar Study

nstd197 (Boujemaa et al. 2021)

Organism:: Human
Study Type:: Case-Set
Submitter:: Yosr HAMDI
Description:: In the current study we have evaluated the contribution of germline CNVs to hereditary breast cancer risk in Tunisian patients who were negative for pathogenic mutations in known breast cancer susceptibility genes. Overall, 483 CNVs have been identified and data analysis showed that both rare and common CNVs might contribute to breast cancer predisposition. Besides, some CNVs were found to be likely associated with disease prognosis and drug response. See Variant Summary counts for nstd197 in dbVar Variant Summary.
Project:: PRJNA674608
Publication(s):: Boujemaa et al. 2021

Links

Source: NCBI

Detailed Information: Download 280 Variant Regions, Download 483 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	27	48	Remapped	NC_000001.11
NC_000002.12	Chr2	17	25	Remapped	NC_000002.12
NC_000003.12	Chr3	13	13	Remapped	NC_000003.12
NC_000004.12	Chr4	7	10	Remapped	NC_000004.12
NC_000005.10	Chr5	11	25	Remapped	NC_000005.10
NC_000006.12	Chr6	13	30	Remapped	NC_000006.12
NC_000007.14	Chr7	18	32	Remapped	NC_000007.14
NC_000008.11	Chr8	4	6	Remapped	NC_000008.11
NC_000009.12	Chr9	7	11	Remapped	NC_000009.12
NC_000010.11	Chr10	14	32	Remapped	NC_000010.11
NC_000011.10	Chr11	14	18	Remapped	NC_000011.10
NC_000012.12	Chr12	9	12	Remapped	NC_000012.12
NC_000013.11	Chr13	2	2	Remapped	NC_000013.11
NC_000014.9	Chr14	16	37	Remapped	NC_000014.9
NC_000015.10	Chr15	16	22	Remapped	NC_000015.10
NC_000016.10	Chr16	18	25	Remapped	NC_000016.10
NC_000017.11	Chr17	16	26	Remapped	NC_000017.11
NC_000018.10	Chr18	1	2	Remapped	NC_000018.10
NC_000019.10	Chr19	29	44	Remapped	NC_000019.10
NC_000020.11	Chr20	5	7	Remapped	NC_000020.11
NC_000021.9	Chr21	2	3	Remapped	NC_000021.9
NC_000022.11	Chr22	13	23	Remapped	NC_000022.11
NW_012132915.1	Chr2\|NW_012132915.1	1	1	Remapped	NW_012132915.1
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
NW_016107298.1	Chr5\|NW_016107298.1	1	1	Remapped	NW_016107298.1
NT_187561.1	Chr7\|NT_187561.1	1	1	Remapped	NT_187561.1
NT_187570.1	Chr8\|NT_187570.1	1	1	Remapped	NT_187570.1
NW_018654717.1	Chr8\|NW_018654717.1	2	4	Remapped	NW_018654717.1
NT_187583.1	Chr11\|NT_187583.1	1	2	Remapped	NT_187583.1
NW_011332695.1	Chr11\|NW_011332695.1	1	2	Remapped	NW_011332695.1
NT_187658.1	Chr12\|NT_187658.1	2	2	Remapped	NT_187658.1
NW_003571050.1	Chr12\|NW_003571050.1	2	2	Remapped	NW_003571050.1
NW_018654722.1	Chr14\|NW_018654722.1	1	2	Remapped	NW_018654722.1
NT_187607.1	Chr16\|NT_187607.1	1	2	Remapped	NT_187607.1
NW_003315945.1	Chr16\|NW_003315945.1	1	1	Remapped	NW_003315945.1
NW_017852933.1	Chr16\|NW_017852933.1	2	2	Remapped	NW_017852933.1
NT_187663.1	Chr17\|NT_187663.1	1	2	Remapped	NT_187663.1
NW_003871093.1	Chr17\|NW_003871093.1	1	1	Remapped	NW_003871093.1
NW_017363819.1	Chr17\|NW_017363819.1	1	3	Remapped	NW_017363819.1
NW_003571061.2	Chr19\|NW_003571061.2	2	5	Remapped	NW_003571061.2
NW_003571060.1	Chr19\|NW_003571060.1	2	8	Remapped	NW_003571060.1
NW_003571055.2	Chr19\|NW_003571055.2	1	1	Remapped	NW_003571055.2
NW_003571054.1	Chr19\|NW_003571054.1	3	9	Remapped	NW_003571054.1
NT_187682.1	Chr22\|NT_187682.1	1	4	Remapped	NT_187682.1
NW_003315972.2	Chr22\|NW_003315972.2	1	1	Remapped	NW_003315972.2
NT_187562.1	Chr7\|NT_187562.1	1	1	Remapped	NT_187562.1
NT_187600.1	Chr14\|NT_187600.1	5	10	Remapped	NT_187600.1
NT_187661.1	Chr17\|NT_187661.1	2	6	Remapped	NT_187661.1
NT_187614.1	Chr17\|NT_187614.1	3	7	Remapped	NT_187614.1
NT_187693.1	Chr19\|NT_187693.1	4	21	Remapped	NT_187693.1
NW_009646206.1	Chr19\|NW_009646206.1	1	2	Remapped	NW_009646206.1
NT_187633.1	Chr22\|NT_187633.1	2	5	Remapped	NT_187633.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	27	48	Submitted	NC_000001.10
NC_000002.11	Chr2	17	25	Submitted	NC_000002.11
NC_000003.11	Chr3	13	13	Submitted	NC_000003.11
NC_000004.11	Chr4	7	10	Submitted	NC_000004.11
NC_000005.9	Chr5	11	25	Submitted	NC_000005.9
NC_000006.11	Chr6	13	30	Submitted	NC_000006.11
NC_000007.13	Chr7	18	32	Submitted	NC_000007.13
NC_000008.10	Chr8	4	6	Submitted	NC_000008.10
NC_000009.11	Chr9	7	11	Submitted	NC_000009.11
NC_000010.10	Chr10	14	32	Submitted	NC_000010.10
NC_000011.9	Chr11	14	18	Submitted	NC_000011.9
NC_000012.11	Chr12	9	12	Submitted	NC_000012.11
NC_000013.10	Chr13	2	2	Submitted	NC_000013.10
NC_000014.8	Chr14	17	38	Submitted	NC_000014.8
NC_000015.9	Chr15	16	22	Submitted	NC_000015.9
NC_000016.9	Chr16	18	25	Submitted	NC_000016.9
NC_000017.10	Chr17	17	31	Submitted	NC_000017.10
NC_000018.9	Chr18	2	4	Submitted	NC_000018.9
NC_000019.9	Chr19	32	59	Submitted	NC_000019.9
NC_000020.10	Chr20	5	7	Submitted	NC_000020.10
NC_000021.8	Chr21	2	3	Submitted	NC_000021.8
NC_000022.10	Chr22	15	30	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	27	26	1	0	0	0	48	47	1	0	0	0
NC_000002.11	Chr2	17	13	3	0	0	1	25	19	5	0	0	1
NC_000003.11	Chr3	13	11	1	0	0	1	13	11	1	0	0	1
NC_000004.11	Chr4	7	7	0	0	0	0	10	10	0	0	0	0
NC_000005.9	Chr5	11	9	0	0	0	2	25	23	0	0	0	2
NC_000006.11	Chr6	13	13	0	0	0	0	30	30	0	0	0	0
NC_000007.13	Chr7	18	15	1	0	0	2	32	29	1	0	0	2
NC_000008.10	Chr8	4	1	0	0	0	3	6	1	0	0	0	5
NC_000009.11	Chr9	7	7	0	0	0	0	11	11	0	0	0	0
NC_000010.10	Chr10	14	9	3	2	0	0	32	19	9	4	0	0
NC_000011.9	Chr11	14	13	0	0	0	1	18	16	0	0	0	2
NC_000012.11	Chr12	9	6	0	0	0	3	12	9	0	0	0	3
NC_000013.10	Chr13	2	2	0	0	0	0	2	2	0	0	0	0
NC_000014.8	Chr14	17	8	2	0	1	6	38	11	14	0	1	12
NC_000015.9	Chr15	16	16	0	0	0	0	22	22	0	0	0	0
NC_000016.9	Chr16	18	14	0	0	0	4	25	20	0	0	0	5
NC_000017.10	Chr17	17	12	0	0	0	5	31	21	0	0	0	10
NC_000018.9	Chr18	2	1	0	0	1	0	4	2	0	0	2	0
NC_000019.9	Chr19	32	29	0	0	0	3	59	50	0	0	0	9
NC_000020.10	Chr20	5	5	0	0	0	0	7	7	0	0	0	0
NC_000021.8	Chr21	2	2	0	0	0	0	3	3	0	0	0	0
NC_000022.10	Chr22	15	11	2	0	0	2	30	24	3	0	0	3

Samplesets

Number of Samplesets: 1

Name:: TUN_BC_CNVs
Description:: CNVs identified in Tunisian breast cancer patients who do not harbor point pathogenic mutations in known breast cancer susceptibility genes
Size:: 9
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Breast Cancer
Sex:: Female

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
BC39	Peripheral Leukocytes	BC39	Female	Tunisian	breast cancer
BC19	Peripheral Leukocytes	BC19	Female	Tunisian	breast cancer
BC47	Peripheral Leukocytes	BC47	Female	Tunisian	breast cancer
BC1-1	Peripheral Leukocytes	BC1-1	Female	Tunisian	breast cancer
BC37	Peripheral Leukocytes	BC37	Female	Tunisian	breast cancer
BC40	Peripheral Leukocytes	BC40	Female	Tunisian	breast cancer
BC52	Peripheral Leukocytes	BC52	Female	Tunisian	breast cancer
BC1-8	Peripheral Leukocytes	BC1-8	Female	Tunisian	breast cancer
BC22	Peripheral Leukocytes	BC22	Female	Tunisian	breast cancer

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Read depth	Illumina HiSeq2000 platform	483

dbVar

Database of genomic structural variation

nstd197 (Boujemaa et al. 2021)

Links

Detailed Information: Download 280 Variant Regions, Download 483 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: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd197 (Boujemaa et al. 2021)

Links

Detailed Information: Download 280 Variant Regions, Download 483 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p13 (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: