nstd230 - Sugimoto et al 2023 - dbVar Study

nstd230 (Sugimoto et al. 2023)

Organism:: Human
Study Type:: Case-Set
Submitter:: Hiroki Kurahashi
Description:: We analyzed the breakpoint location of three-way or more complex constitutional translocations using genomic and epigenomic analyses. This breakpoint distribution corresponded specifically to the ATAC-seq read data peak of mature sperm and not to other chromatin markers or tissues. We propose that the DNA breaks in constitutional complex chromosomal rearrangements might develop at an accessible region of densely packaged chromatin during post-meiotic spermiogenesis. See Variant Summary counts for nstd230 in dbVar Variant Summary.

Links

Source: NCBI

Detailed Information: Download 14 Variant Regions, Download 184 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (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	3	13	Remapped	NC_000001.11
NC_000002.12	Chr2	3	28	Remapped	NC_000002.12
NC_000003.12	Chr3	4	50	Remapped	NC_000003.12
NC_000004.12	Chr4	2	6	Remapped	NC_000004.12
NC_000005.10	Chr5	3	5	Remapped	NC_000005.10
NC_000006.12	Chr6	4	39	Remapped	NC_000006.12
NC_000007.14	Chr7	2	4	Remapped	NC_000007.14
NC_000008.11	Chr8	2	24	Remapped	NC_000008.11
NC_000009.12	Chr9	4	11	Remapped	NC_000009.12
NC_000010.11	Chr10	3	9	Remapped	NC_000010.11
NC_000011.10	Chr11	3	12	Remapped	NC_000011.10
NC_000012.12	Chr12	3	21	Remapped	NC_000012.12
NC_000013.11	Chr13	2	23	Remapped	NC_000013.11
NC_000014.9	Chr14	1	2	Remapped	NC_000014.9
NC_000015.10	Chr15	1	2	Remapped	NC_000015.10
NC_000016.10	Chr16	1	2	Remapped	NC_000016.10
NC_000018.10	Chr18	4	13	Remapped	NC_000018.10
NC_000020.11	Chr20	1	4	Remapped	NC_000020.11
NC_000021.9	Chr21	1	2	Remapped	NC_000021.9
NW_018654711.1	Chr3\|NW_018654711.1	1	2	Remapped	NW_018654711.1
NT_187541.1	Chr4\|NT_187541.1	1	2	Remapped	NT_187541.1
NT_187578.1	Chr9\|NT_187578.1	1	2	Remapped	NT_187578.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	3	13	Submitted	NC_000001.10
NC_000002.11	Chr2	3	28	Submitted	NC_000002.11
NC_000003.11	Chr3	4	50	Submitted	NC_000003.11
NC_000004.11	Chr4	2	6	Submitted	NC_000004.11
NC_000005.9	Chr5	3	5	Submitted	NC_000005.9
NC_000006.11	Chr6	4	39	Submitted	NC_000006.11
NC_000007.13	Chr7	2	4	Submitted	NC_000007.13
NC_000008.10	Chr8	2	24	Submitted	NC_000008.10
NC_000009.11	Chr9	4	11	Submitted	NC_000009.11
NC_000010.10	Chr10	3	9	Submitted	NC_000010.10
NC_000011.9	Chr11	3	12	Submitted	NC_000011.9
NC_000012.11	Chr12	3	21	Submitted	NC_000012.11
NC_000013.10	Chr13	2	23	Submitted	NC_000013.10
NC_000014.8	Chr14	1	2	Submitted	NC_000014.8
NC_000015.9	Chr15	1	2	Submitted	NC_000015.9
NC_000016.9	Chr16	1	2	Submitted	NC_000016.9
NC_000018.9	Chr18	4	13	Submitted	NC_000018.9
NC_000020.10	Chr20	1	4	Submitted	NC_000020.10
NC_000021.8	Chr21	1	2	Submitted	NC_000021.8

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	3	0	0	0	0	28	13	0	0	0	0	28
NC_000002.11	Chr2	3	0	0	0	0	88	28	0	0	0	0	88
NC_000003.11	Chr3	4	0	0	0	0	156	50	0	0	0	0	156
NC_000004.11	Chr4	2	0	0	0	0	16	6	0	0	0	0	16
NC_000005.9	Chr5	3	0	0	0	0	16	5	0	0	0	0	16
NC_000006.11	Chr6	4	0	0	0	0	108	39	0	0	0	0	108
NC_000007.13	Chr7	2	0	0	0	0	8	4	0	0	0	0	8
NC_000008.10	Chr8	2	0	0	0	0	64	24	0	0	0	0	64
NC_000009.11	Chr9	4	0	0	0	0	24	11	0	0	0	0	24
NC_000010.10	Chr10	3	0	0	0	0	20	9	0	0	0	0	20
NC_000011.9	Chr11	3	0	0	0	0	24	12	0	0	0	0	24
NC_000012.11	Chr12	3	0	0	0	0	60	21	0	0	0	0	60
NC_000013.10	Chr13	2	0	0	0	0	64	23	0	0	0	0	64
NC_000014.8	Chr14	1	0	0	0	0	4	2	0	0	0	0	4
NC_000015.9	Chr15	1	0	0	0	0	4	2	0	0	0	0	4
NC_000016.9	Chr16	1	0	0	0	0	4	2	0	0	0	0	4
NC_000018.9	Chr18	4	0	0	0	0	36	13	0	0	0	0	36
NC_000020.10	Chr20	1	0	0	0	0	8	4	0	0	0	0	8
NC_000021.8	Chr21	1	0	0	0	0	4	2	0	0	0	0	4

Samplesets

Number of Samplesets: 1

Size:: 14
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Subject Phenotype
FHU15-167	FHU15-167	Not reported
FHU19-192	FHU19-192	Not reported
FHU17-282	FHU17-282	Not reported
FHU19-162	FHU19-162	Not reported
FHU15-080	FHU15-080	Not reported
FHU17-112	FHU17-112	Not reported
FHU18-163	FHU18-163	Not reported
FHU18-275	FHU18-275	Not reported
FHU15-147	FHU15-147	Not reported
FHU20-098	FHU20-098	Not reported
FHU17-359	FHU17-359	Not reported
FHU15-170	FHU15-170	Not reported
FHU15-242	FHU15-242	Not reported
FHU14-134	FHU14-134	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Sequence alignment	184

dbVar

Database of genomic structural variation

nstd230 (Sugimoto et al. 2023)

Links

Detailed Information: Download 14 Variant Regions, Download 184 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (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

nstd230 (Sugimoto et al. 2023)

Links

Detailed Information: Download 14 Variant Regions, Download 184 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (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: