nstd185 - Puig et al 2020 - dbVar Study

nstd185 (Puig et al. 2020)

Organism:: Human
Study Type:: Collection
Submitter:: Mario Cáceres
Description:: The presence of large repeats at the breakpoints hinders the analysis of many structural variants. This is especially problematic for inversions, in which typically there is no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays for 20 inversions ranging in size from 3.1 to 742 kb and flanked by inverted repeats up to 134-kb long. We validated 13 inversions predicted by genome-wide techniques and generated experimental population genotyping data across 95 individuals for 18 of them. Most inversions are widespread and recurrent. Thanks to this method complex genomic variants can be screened quickly in a large number of samples for the first time. See Variant Summary counts for nstd185 in dbVar Variant Summary.
Project:: PRJNA601674
Publication(s):: Puig et al. 2020

Links

Source: NCBI

Detailed Information: Download 19 Variant Regions, Download 19 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Submitted: GRCh38.p13 (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_000001.11	Chr1	1	1	Submitted	NC_000001.11
NC_000002.12	Chr2	1	1	Submitted	NC_000002.12
NC_000006.12	Chr6	1	1	Submitted	NC_000006.12
NC_000007.14	Chr7	1	1	Submitted	NC_000007.14
NC_000008.11	Chr8	1	1	Submitted	NC_000008.11
NC_000016.10	Chr16	3	3	Submitted	NC_000016.10
NC_000017.11	Chr17	1	1	Submitted	NC_000017.11
NC_000020.11	Chr20	1	1	Submitted	NC_000020.11
NC_000023.11	ChrX	8	8	Submitted	NC_000023.11
NC_000024.10	ChrY	1	1	Submitted	NC_000024.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	1	1	Remapped	NC_000001.10
NC_000002.11	Chr2	1	1	Remapped	NC_000002.11
NC_000006.11	Chr6	1	1	Remapped	NC_000006.11
NC_000007.13	Chr7	1	1	Remapped	NC_000007.13
NC_000008.10	Chr8	1	1	Remapped	NC_000008.10
NC_000016.9	Chr16	3	3	Remapped	NC_000016.9
NC_000017.10	Chr17	1	1	Remapped	NC_000017.10
NC_000020.10	Chr20	1	1	Remapped	NC_000020.10
NC_000023.10	ChrX	8	8	Remapped	NC_000023.10
NC_000024.9	ChrY	1	1	Remapped	NC_000024.9
NW_003871055.3	Chr1\|NW_003871055.3	1	1	Remapped	NW_003871055.3
NW_003871103.3	ChrX\|NW_003871103.3	3	3	Remapped	NW_003871103.3
NW_004070877.1	ChrX\|NW_004070877.1	2	2	Remapped	NW_004070877.1
NW_004070885.1	ChrX\|NW_004070885.1	1	1	Remapped	NW_004070885.1
NW_004070890.2	ChrX\|NW_004070890.2	1	1	Remapped	NW_004070890.2

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_000001.11	Chr1	1	0	0	0	0	1	1	0	0	0	0	1
NC_000002.12	Chr2	1	1	0	0	0	0	1	1	0	0	0	0
NC_000006.12	Chr6	1	1	0	0	0	0	1	1	0	0	0	0
NC_000007.14	Chr7	1	1	0	0	0	0	1	1	0	0	0	0
NC_000008.11	Chr8	1	0	0	1	0	0	1	0	0	1	0	0
NC_000016.10	Chr16	3	3	0	0	0	0	3	3	0	0	0	0
NC_000017.11	Chr17	1	1	0	0	0	0	1	1	0	0	0	0
NC_000020.11	Chr20	1	1	0	0	0	0	1	1	0	0	0	0
NC_000023.11	ChrX	8	1	0	0	0	7	8	1	0	0	0	7
NC_000024.10	ChrY	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 1

Size:: 95
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
SAMN11392436	Epstein-Barr virus transformed B-Lymphocyte	GM12044	Female	CEU	70 Years	Not reported
SAMN11392645	Epstein-Barr virus transformed B-Lymphocyte	GM19150	Male	YRI		Not reported
SAMN11392485	Epstein-Barr virus transformed B-Lymphocyte	GM18505	Female	YRI		Not reported
SAMN11392430	Epstein-Barr virus transformed B-Lymphocyte	GM11995	Female	CEU	84 Years	Not reported
SAMN11392566	Epstein-Barr virus transformed B-Lymphocyte	GM18947	Female	JPT		Not reported
SAMN11392655	Epstein-Barr virus transformed B-Lymphocyte	GM19189	Male	YRI		Not reported
SAMN11392487	Epstein-Barr virus transformed B-Lymphocyte	GM18507	Male	YRI		Not reported
SAMN11392521	Epstein-Barr virus transformed B-Lymphocyte	GM18582	Female	CHB		Not reported
SAMN11392419	Epstein-Barr virus transformed B-Lymphocyte	GM11829	Male	CEU	72 Years	Not reported
SAMN11392467	Epstein-Barr virus transformed B-Lymphocyte	GM12814	Male	CEU		Not reported
SAMN11392442	Epstein-Barr virus transformed B-Lymphocyte	GM12154	Male	CEU	92 Years	Not reported
SAMN11392429	Epstein-Barr virus transformed B-Lymphocyte	GM11994	Male	CEU	80 Years	Not reported
SAMN11392532	Epstein-Barr virus transformed B-Lymphocyte	GM18621	Male	CHB		Not reported
SAMN11392444	Epstein-Barr virus transformed B-Lymphocyte	GM12156	Female	CEU	81 Years	Not reported
SAMN11392627	Epstein-Barr virus transformed B-Lymphocyte	GM19119	Male	YRI		Not reported
SAMN11392626	Epstein-Barr virus transformed B-Lymphocyte	GM19118	Female	YRI		Not reported
SAMN11392479	Epstein-Barr virus transformed B-Lymphocyte	GM18498	Male	YRI		Not reported
SAMN11392472	Epstein-Barr virus transformed B-Lymphocyte	GM12873	Female	CEU		Not reported
SAMN11392491	Epstein-Barr virus transformed B-Lymphocyte	GM18517	Female	YRI		Not reported
SAMN11392468	Epstein-Barr virus transformed B-Lymphocyte	GM12815	Female	CEU		Not reported
SAMN11392420	Epstein-Barr virus transformed B-Lymphocyte	GM11830	Female	CEU	63 Years	Not reported
SAMN11392421	Epstein-Barr virus transformed B-Lymphocyte	GM11831	Male	CEU	73 Years	Not reported
SAMN11392582	Epstein-Barr virus transformed B-Lymphocyte	GM18970	Male	JPT		Not reported
SAMN11392525	Epstein-Barr virus transformed B-Lymphocyte	GM18603	Male	CHB		Not reported
SAMN11392632	Epstein-Barr virus transformed B-Lymphocyte	GM19130	Male	YRI		Not reported
SAMN11392652	Epstein-Barr virus transformed B-Lymphocyte	GM19171	Male	YRI		Not reported
SAMN11392592	Epstein-Barr virus transformed B-Lymphocyte	GM18987	Female	JPT		Not reported
SAMN11392475	Epstein-Barr virus transformed B-Lymphocyte	GM12878	Female	CEU		Not reported
SAMN11392665	Epstein-Barr virus transformed B-Lymphocyte	GM19206	Female	YRI		Not reported
SAMN11392650	Epstein-Barr virus transformed B-Lymphocyte	GM19160	Male	YRI		Not reported
SAMN11392435	Epstein-Barr virus transformed B-Lymphocyte	GM12043	Male	CEU	74 Years	Not reported
SAMN11392593	Epstein-Barr virus transformed B-Lymphocyte	GM18990	Male	JPT		Not reported
SAMN11392666	Epstein-Barr virus transformed B-Lymphocyte	GM19207	Male	YRI		Not reported
SAMN11392425	Epstein-Barr virus transformed B-Lymphocyte	GM11881	Male	CEU	62 Years	Not reported
SAMN00000467	Epstein-Barr virus transformed B-Lymphocyte	GM18647	Male	CHB		Not reported
SAMN11392453	Epstein-Barr virus transformed B-Lymphocyte	GM12717	Female	CEU		Not reported
SAMN11392432	Epstein-Barr virus transformed B-Lymphocyte	GM12004	Female	CEU	92 Years	Not reported
SAMN00000452	Epstein-Barr virus transformed B-Lymphocyte	GM18628	Female	CHB		Not reported
SAMN11392602	Epstein-Barr virus transformed B-Lymphocyte	GM19003	Female	JPT		Not reported
SAMN11392455	Epstein-Barr virus transformed B-Lymphocyte	GM12750	Male	CEU		Not reported
SAMN11392646	Epstein-Barr virus transformed B-Lymphocyte	GM19152	Female	YRI		Not reported
SAMN11392539	Epstein-Barr virus transformed B-Lymphocyte	GM18636	Male	CHB		Not reported
SAMN11392663	Epstein-Barr virus transformed B-Lymphocyte	GM19204	Female	YRI		Not reported
SAMN11392505	Epstein-Barr virus transformed B-Lymphocyte	GM18550	Female	CHB		Not reported
SAMN11392597	Epstein-Barr virus transformed B-Lymphocyte	GM18995	Male	JPT		Not reported
SAMN11392618	Epstein-Barr virus transformed B-Lymphocyte	GM19098	Male	YRI		Not reported
SAMN11392571	Epstein-Barr virus transformed B-Lymphocyte	GM18953	Male	JPT		Not reported
SAMN11392500	Epstein-Barr virus transformed B-Lymphocyte	GM18537	Female	CHB		Not reported
SAMN11392585	Epstein-Barr virus transformed B-Lymphocyte	GM18973	Female	JPT		Not reported
SAMN11392668	Epstein-Barr virus transformed B-Lymphocyte	GM19209	Female	YRI		Not reported
SAMN00000494	Epstein-Barr virus transformed B-Lymphocyte	GM18977	Male	JPT		Not reported
SAMN11392562	Epstein-Barr virus transformed B-Lymphocyte	GM18942	Female	JPT		Not reported
SAMN11392554	Epstein-Barr virus transformed B-Lymphocyte	GM18870	Female	YRI		Not reported
SAMN11392443	Epstein-Barr virus transformed B-Lymphocyte	GM12155	Male	CEU	86 Years	Not reported
SAMN11392553	Epstein-Barr virus transformed B-Lymphocyte	GM18867	Female	YRI		Not reported
SAMN11392461	Epstein-Barr virus transformed B-Lymphocyte	GM12762	Male	CEU		Not reported
SAMN11392473	Epstein-Barr virus transformed B-Lymphocyte	GM12874	Male	CEU		Not reported
SAMN11392433	Epstein-Barr virus transformed B-Lymphocyte	GM12005	Male	CEU	77 Years	Not reported
SAMN11392631	Epstein-Barr virus transformed B-Lymphocyte	GM19129	Female	YRI		Not reported
SAMN11392445	Epstein-Barr virus transformed B-Lymphocyte	GM12234	Female	CEU	74 Years	Not reported
SAMN11392619	Epstein-Barr virus transformed B-Lymphocyte	GM19099	Female	YRI		Not reported
SAMN11392497	Epstein-Barr virus transformed B-Lymphocyte	GM18526	Female	CHB		Not reported
SAMN11392624	Epstein-Barr virus transformed B-Lymphocyte	GM19108	Female	YRI		Not reported
SAMN11392465	Epstein-Barr virus transformed B-Lymphocyte	GM12812	Male	CEU		Not reported
SAMN11392460	Epstein-Barr virus transformed B-Lymphocyte	GM12761	Female	CEU		Not reported
SAMN11392507	Epstein-Barr virus transformed B-Lymphocyte	GM18555	Female	CHB		Not reported
SAMN11392557	Epstein-Barr virus transformed B-Lymphocyte	GM18910	Male	YRI		Not reported
SAMN11392565	Epstein-Barr virus transformed B-Lymphocyte	GM18945	Male	JPT		Not reported
SAMN11392439	Epstein-Barr virus transformed B-Lymphocyte	GM12144	Male	CEU	71 Years	Not reported
SAMN11392422	Epstein-Barr virus transformed B-Lymphocyte	GM11832	Female	CEU	58 Years	Not reported
SAMN00000917	Epstein-Barr virus transformed B-Lymphocyte	GM18527	Female	CHB		Not reported
SAMN11392644	Epstein-Barr virus transformed B-Lymphocyte	GM19146	Male	YRI		Not reported
SAMN11392577	Epstein-Barr virus transformed B-Lymphocyte	GM18965	Male	JPT		Not reported
SAMN11392572	Epstein-Barr virus transformed B-Lymphocyte	GM18956	Female	JPT		Not reported
SAMN11392482	Epstein-Barr virus transformed B-Lymphocyte	GM18502	Female	YRI		Not reported
SAMN11392424	Epstein-Barr virus transformed B-Lymphocyte	GM11840	Female	CEU	67 Years	Not reported
SAMN11392639	Epstein-Barr virus transformed B-Lymphocyte	GM19141	Male	YRI		Not reported
SAMN11392471	Epstein-Barr virus transformed B-Lymphocyte	GM12872	Male	CEU		Not reported
SAMN11392570	Epstein-Barr virus transformed B-Lymphocyte	GM18952	Male	JPT		Not reported
SAMN11392677	Epstein-Barr virus transformed B-Lymphocyte	GM19240	Female	YRI		Not reported
SAMN11392671	Epstein-Barr virus transformed B-Lymphocyte	GM19213	Male	YRI		Not reported
SAMN11392466	Epstein-Barr virus transformed B-Lymphocyte	GM12813	Female	CEU		Not reported
SAMN11392511	Epstein-Barr virus transformed B-Lymphocyte	GM18563	Male	CHB		Not reported
SAMN11392510	Epstein-Barr virus transformed B-Lymphocyte	GM18562	Male	CHB		Not reported
SAMN11392615	Epstein-Barr virus transformed B-Lymphocyte	GM19092	Male	YRI		Not reported
SAMN11392459	Epstein-Barr virus transformed B-Lymphocyte	GM12760	Male	CEU		Not reported
SAMN11392488	Epstein-Barr virus transformed B-Lymphocyte	GM18508	Female	YRI		Not reported
SAMN11392533	Epstein-Barr virus transformed B-Lymphocyte	GM18622	Male	CHB		Not reported
SAMN11392492	Epstein-Barr virus transformed B-Lymphocyte	GM18519	Male	YRI		Not reported
SAMN11392622	Epstein-Barr virus transformed B-Lymphocyte	GM19102	Female	YRI		Not reported
SAMN00000513	Epstein-Barr virus transformed B-Lymphocyte	GM19010	Female	JPT		Not reported
SAMN11392462	Epstein-Barr virus transformed B-Lymphocyte	GM12763	Female	CEU		Not reported
SAMN11392536	Epstein-Barr virus transformed B-Lymphocyte	GM18632	Male	CHB		Not reported
SAMN11392569	Epstein-Barr virus transformed B-Lymphocyte	GM18951	Female	JPT		Not reported
SAMN00000434	Epstein-Barr virus transformed B-Lymphocyte	GM18606	Male	CHB		Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Data	Number of Variant Calls
1	Discovery	ddPCR	Other	http://invfestdb.uab.cat/	19

dbVar

Database of genomic structural variation

nstd185 (Puig et al. 2020)

Links

Detailed Information: Download 19 Variant Regions, Download 19 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Submitted: GRCh38.p13 (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

nstd185 (Puig et al. 2020)

Links

Detailed Information: Download 19 Variant Regions, Download 19 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p13 (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: