nstd79 - Dittwald et al 2013 - dbVar Study

nstd79 (Dittwald et al. 2013)

Organism:: Human
Study Type:: Case-Set
Submitter:: Pawel Stankiewicz
Description:: Here, we constructed bioinformatically a new genome-wide map of the DP-LCR-flanked regions in human genome build hg19 using a concept of LCR clusters. We then queried and cross referenced our database of 25,144 high-resolution genomic analyses performed on patients referred for Chromosomal Microarray Analysis (CMA). This approach enabled us to determine the relative frequencies in this clinical population of known recurrent genomic disorders, and also quantitate genomic architectural features genome-wide that are associated with individual locus events, to gain insights into the parameters rendering genomic instability. See Variant Summary counts for nstd79 in dbVar Variant Summary.
Publication(s):: Dittwald et al. 2013

Links

Source: NCBI

Detailed Information: Download 64 Variant Regions, Download 2213 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted; Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

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	97	Remapped	NC_000001.11
NC_000002.12	Chr2	8	401	Remapped	NC_000002.12
NC_000003.12	Chr3	1	29	Remapped	NC_000003.12
NC_000005.10	Chr5	1	6	Remapped	NC_000005.10
NC_000007.14	Chr7	4	80	Remapped	NC_000007.14
NC_000008.11	Chr8	1	16	Remapped	NC_000008.11
NC_000010.11	Chr10	3	18	Remapped	NC_000010.11
NC_000013.11	Chr13	2	11	Remapped	NC_000013.11
NC_000015.10	Chr15	14	619	Remapped	NC_000015.10
NC_000016.10	Chr16	6	339	Remapped	NC_000016.10
NC_000017.11	Chr17	10	119	Remapped	NC_000017.11
NC_000022.11	Chr22	8	292	Remapped	NC_000022.11
NC_000023.11	ChrX	4	152	Remapped	NC_000023.11
NW_018654717.1	Chr8\|NW_018654717.1	0	6	Remapped	NW_018654717.1
NT_187660.1	Chr15\|NT_187660.1	1	162	Remapped	NT_187660.1
NT_187603.1	Chr15\|NT_187603.1	0	31	Remapped	NT_187603.1
NW_011332701.1	Chr15\|NW_011332701.1	2	209	Remapped	NW_011332701.1
NT_187607.1	Chr16\|NT_187607.1	1	41	Remapped	NT_187607.1
NW_017852933.1	Chr16\|NW_017852933.1	0	4	Remapped	NW_017852933.1
NT_187663.1	Chr17\|NT_187663.1	0	1	Remapped	NT_187663.1
NT_187614.1	Chr17\|NT_187614.1	1	40	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	2	25	Submitted	NC_000001.10
NC_000002.11	Chr2	8	82	Submitted	NC_000002.11
NC_000003.11	Chr3	1	5	Submitted	NC_000003.11
NC_000005.9	Chr5	1	1	Submitted	NC_000005.9
NC_000007.13	Chr7	3	21	Submitted	NC_000007.13
NC_000008.10	Chr8	1	3	Submitted	NC_000008.10
NC_000010.10	Chr10	3	3	Submitted	NC_000010.10
NC_000013.10	Chr13	2	3	Submitted	NC_000013.10
NC_000015.9	Chr15	14	143	Submitted	NC_000015.9
NC_000016.9	Chr16	6	62	Submitted	NC_000016.9
NC_000017.10	Chr17	11	31	Submitted	NC_000017.10
NC_000022.10	Chr22	8	66	Submitted	NC_000022.10
NC_000023.10	ChrX	4	41	Submitted	NC_000023.10
NC_000001.10	Chr1	0	94	Remapped	NC_000001.10
NC_000002.11	Chr2	0	319	Remapped	NC_000002.11
NC_000003.11	Chr3	0	24	Remapped	NC_000003.11
NC_000005.9	Chr5	0	5	Remapped	NC_000005.9
NC_000007.13	Chr7	0	55	Remapped	NC_000007.13
NC_000008.10	Chr8	0	13	Remapped	NC_000008.10
NC_000010.10	Chr10	0	15	Remapped	NC_000010.10
NC_000013.10	Chr13	0	8	Remapped	NC_000013.10
NC_000015.9	Chr15	0	476	Remapped	NC_000015.9
NC_000016.9	Chr16	0	277	Remapped	NC_000016.9
NC_000017.10	Chr17	0	94	Remapped	NC_000017.10
NC_000022.10	Chr22	0	226	Remapped	NC_000022.10
NC_000023.10	ChrX	0	111	Remapped	NC_000023.10
NW_003871055.3	Chr1\|NW_003871055.3	0	1	Remapped	NW_003871055.3
NW_003871064.1	Chr7\|NW_003871064.1	0	54	Remapped	NW_003871064.1
NW_003871068.1	Chr10\|NW_003871068.1	0	2	Remapped	NW_003871068.1
NW_003871103.3	ChrX\|NW_003871103.3	0	24	Remapped	NW_003871103.3

Sequence ID	Chr	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	99	Submitted	NC_000001.9
NC_000002.10	Chr2	319	Submitted	NC_000002.10
NC_000003.10	Chr3	24	Submitted	NC_000003.10
NC_000005.8	Chr5	5	Submitted	NC_000005.8
NC_000007.12	Chr7	58	Submitted	NC_000007.12
NC_000008.9	Chr8	13	Submitted	NC_000008.9
NC_000010.9	Chr10	15	Submitted	NC_000010.9
NC_000013.9	Chr13	8	Submitted	NC_000013.9
NC_000015.8	Chr15	478	Submitted	NC_000015.8
NC_000016.8	Chr16	277	Submitted	NC_000016.8
NC_000017.9	Chr17	94	Submitted	NC_000017.9
NC_000022.9	Chr22	226	Submitted	NC_000022.9
NC_000023.9	ChrX	111	Submitted	NC_000023.9

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	2	0	0	0	1	1	25	0	1	1	23	0
NC_000002.11	Chr2	8	6	1	1	0	0	82	79	1	2	0	0
NC_000003.11	Chr3	1	1	0	0	0	0	5	5	0	0	0	0
NC_000005.9	Chr5	1	1	0	0	0	0	1	1	0	0	0	0
NC_000007.13	Chr7	3	1	0	2	0	0	21	0	20	1	0	0
NC_000008.10	Chr8	1	1	0	0	0	0	3	2	0	0	0	1
NC_000010.10	Chr10	3	2	0	1	0	0	3	1	0	2	0	0
NC_000013.10	Chr13	2	2	0	0	0	0	3	3	0	0	0	0
NC_000015.9	Chr15	14	5	4	3	0	2	143	23	39	21	0	60
NC_000016.9	Chr16	6	5	0	0	0	1	62	54	0	0	0	8
NC_000017.10	Chr17	11	10	1	0	0	0	31	19	6	0	0	6
NC_000022.10	Chr22	8	1	5	2	0	0	66	2	32	32	0	0
NC_000023.10	ChrX	4	0	4	0	0	0	41	0	41	0	0	0

			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_000001.9	Chr1	0	0	0	0	0	0	99	1	0	92	5	1
NC_000002.10	Chr2	0	0	0	0	0	0	319	38	10	271	0	0
NC_000003.10	Chr3	0	0	0	0	0	0	24	7	17	0	0	0
NC_000005.8	Chr5	0	0	0	0	0	0	5	5	0	0	0	0
NC_000007.12	Chr7	0	0	0	0	0	0	58	1	3	3	0	51
NC_000008.9	Chr8	0	0	0	0	0	0	13	0	13	0	0	0
NC_000010.9	Chr10	0	0	0	0	0	0	15	10	3	0	0	2
NC_000013.9	Chr13	0	0	0	0	0	0	8	8	0	0	0	0
NC_000015.8	Chr15	0	0	0	0	0	0	478	219	155	102	2	0
NC_000016.8	Chr16	0	0	0	0	0	0	277	277	0	0	0	0
NC_000017.9	Chr17	0	0	0	0	0	0	94	26	40	28	0	0
NC_000022.9	Chr22	0	0	0	0	0	0	226	41	185	0	0	0
NC_000023.9	ChrX	0	0	0	0	0	0	111	0	87	0	0	24

			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_000001.9	Chr1	0	0	0	0	0	0	99	0	11	85	3	0
NC_000002.10	Chr2	0	0	0	0	0	0	319	37	11	271	0	0
NC_000003.10	Chr3	0	0	0	0	0	0	24	7	17	0	0	0
NC_000005.8	Chr5	0	0	0	0	0	0	5	5	0	0	0	0
NC_000007.12	Chr7	0	0	0	0	0	0	58	1	42	13	0	2
NC_000008.9	Chr8	0	0	0	0	0	0	13	0	8	0	0	5
NC_000010.9	Chr10	0	0	0	0	0	0	15	9	3	3	0	0
NC_000013.9	Chr13	0	0	0	0	0	0	8	8	0	0	0	0
NC_000015.8	Chr15	0	0	0	0	0	0	478	88	136	93	2	159
NC_000016.8	Chr16	0	0	0	0	0	0	277	227	13	0	0	37
NC_000017.9	Chr17	0	0	0	0	0	0	94	25	40	0	0	29
NC_000022.9	Chr22	0	0	0	0	0	0	226	6	34	186	0	0
NC_000023.9	ChrX	0	0	0	0	0	0	111	87	24	0	0	0

Samplesets

Number of Samplesets: 1

Size:: 2,137
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1 (displaying 100 of the 2137 samples)
Sample ID	Subject ID	Sex	Subject Phenotype
1	1	Female	Not reported
10	10	Female	Not reported
100	100	Female	Not reported
101	101	Male	Not reported
102	102	Female	Not reported
103	103	Male	Not reported
104	104	Female	Not reported
105	105	Male	Not reported
106	106	Female	Not reported
107	107	Female	Not reported
108	108	Male	Not reported
1000	1000	Male	Not reported
1001	1001	Female	Not reported
1002	1002	Female	Not reported
1003	1003	Male	Not reported
1004	1004	Male	Not reported
1005	1005	Male	Not reported
1006	1006	Male	Not reported
1007	1007	Female	Not reported
1008	1008	Female	Not reported
1009	1009	Female	Not reported
1010	1010	Male	Not reported
1011	1011	Male	Not reported
1012	1012	Female	Not reported
1013	1013	Male	Not reported
1014	1014	Male	Not reported
1015	1015	Male	Not reported
1016	1016	Female	Not reported
1017	1017	Male	Not reported
1018	1018	Male	Not reported
1019	1019	Male	Not reported
1020	1020	Male	Not reported
1021	1021	Female	Not reported
1022	1022	Male	Not reported
1023	1023	Male	Not reported
1024	1024	Male	Not reported
1025	1025	Female	Not reported
1026	1026	Female	Not reported
1027	1027	Male	Not reported
1028	1028	Female	Not reported
1029	1029	Male	Not reported
1030	1030	Male	Not reported
1031	1031	Female	Not reported
1032	1032	Female	Not reported
1033	1033	Female	Not reported
1034	1034	Male	Not reported
1035	1035	Male	Not reported
1036	1036	Female	Not reported
1037	1037	Female	Not reported
1038	1038	Female	Not reported
1039	1039	Male	Not reported
1040	1040	Female	Not reported
1041	1041	Female	Not reported
1042	1042	Male	Not reported
1043	1043	Male	Not reported
1044	1044	Female	Not reported
1045	1045	Male	Not reported
1046	1046	Female	Not reported
1047	1047	Female	Not reported
1048	1048	Male	Not reported
1049	1049	Male	Not reported
1050	1050	Female	Not reported
1051	1051	Male	Not reported
1052	1052	Female	Not reported
1053	1053	Male	Not reported
1054	1054	Male	Not reported
1055	1055	Female	Not reported
1056	1056	Male	Not reported
1057	1057	Male	Not reported
1058	1058	Male	Not reported
1059	1059	Male	Not reported
1060	1060	Female	Not reported
1061	1061	Female	Not reported
1062	1062	Female	Not reported
1063	1063	Female	Not reported
1064	1064	Male	Not reported
1065	1065	Male	Not reported
1066	1066	Male	Not reported
1067	1067	Male	Not reported
1068	1068	Male	Not reported
1069	1069	Male	Not reported
1070	1070	Male	Not reported
1071	1071	Female	Not reported
1072	1072	Female	Not reported
1073	1073	Female	Not reported
1074	1074	Male	Not reported
1075	1075	Female	Not reported
1076	1076	Female	Not reported
1077	1077	Male	Not reported
1078	1078	Female	Not reported
1079	1079	Male	Not reported
1080	1080	Male	Not reported
1081	1081	Male	Not reported
1082	1082	Male	Not reported
1083	1083	Male	Not reported
1084	1084	Female	Not reported
1085	1085	Male	Not reported
1086	1086	Male	Not reported
1087	1087	Male	Not reported
1088	1088	Female	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Oligo aCGH	Probe signal intensity	2,213

dbVar

Database of genomic structural variation

nstd79 (Dittwald et al. 2013)

Links

Detailed Information: Download 64 Variant Regions, Download 2213 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted; Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

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

nstd79 (Dittwald et al. 2013)

Links

Detailed Information: Download 64 Variant Regions, Download 2213 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI36 (hg18)

Remapping summary: GRCh37->GRCh38.p12NCBI36->GRCh37.p13NCBI36->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: