nstd75 - ClinGen Prenatal - dbVar Study

nstd75 (ClinGen Prenatal)

Organism:: Human
Study Type:: Case-Set
Submitter:: NICHD Prenatal Array Study (R01 HD055651)
Submitter URL:: http://www.clinicalgenome.org
Description:: Prenatal Dataset, ClinGen. This study contains the microarray data from a large, prospective study of prenatal diagnostic samples to assess, in blinded fashion, the ability of microarray analysis to diagnose common chromosome abnormalities and to gauge the extent of additional information provided by microarray analysis as compared with standard karyotyping. See Variant Summary counts for nstd75 in dbVar Variant Summary.
Project:: PRJNA42509
Publication(s):: Wapner et al. 2012
dbGaP:: Subjects in this study are not consented to be included in a public DNA archive. To gain access to subject level data, see dbGaP.
dbGaP Release Date:: 2012-11-01
Last updated:: 2014-10-06

Links

Source: NCBI

Detailed Information: Download 927 Variant Regions, Download 2419 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
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	29	48	Remapped	NC_000001.11
NC_000002.12	Chr2	70	110	Remapped	NC_000002.12
NC_000003.12	Chr3	14	14	Remapped	NC_000003.12
NC_000004.12	Chr4	10	10	Remapped	NC_000004.12
NC_000005.10	Chr5	14	22	Remapped	NC_000005.10
NC_000006.12	Chr6	45	356	Remapped	NC_000006.12
NC_000007.14	Chr7	15	15	Remapped	NC_000007.14
NC_000008.11	Chr8	35	293	Remapped	NC_000008.11
NC_000009.12	Chr9	17	17	Remapped	NC_000009.12
NC_000010.11	Chr10	81	262	Remapped	NC_000010.11
NC_000011.10	Chr11	12	19	Remapped	NC_000011.10
NC_000012.12	Chr12	10	10	Remapped	NC_000012.12
NC_000013.11	Chr13	15	45	Remapped	NC_000013.11
NC_000014.9	Chr14	54	79	Remapped	NC_000014.9
NC_000015.10	Chr15	171	315	Remapped	NC_000015.10
NC_000016.10	Chr16	121	301	Remapped	NC_000016.10
NC_000017.11	Chr17	13	14	Remapped	NC_000017.11
NC_000018.10	Chr18	19	101	Remapped	NC_000018.10
NC_000019.10	Chr19	3	3	Remapped	NC_000019.10
NC_000020.11	Chr20	4	5	Remapped	NC_000020.11
NC_000021.9	Chr21	56	195	Remapped	NC_000021.9
NC_000022.11	Chr22	30	45	Remapped	NC_000022.11
NC_000023.11	ChrX	74	116	Remapped	NC_000023.11
NC_000024.10	ChrY	24	28	Remapped	NC_000024.10
NW_012132915.1	Chr2\|NW_012132915.1	6	6	Remapped	NW_012132915.1
NT_187651.1	Chr5\|NT_187651.1	1	1	Remapped	NT_187651.1
NW_018654717.1	Chr8\|NW_018654717.1	1	1	Remapped	NW_018654717.1
NT_187579.1	Chr10\|NT_187579.1	1	1	Remapped	NT_187579.1
NW_003571049.1	Chr12\|NW_003571049.1	1	1	Remapped	NW_003571049.1
NT_187600.1	Chr14\|NT_187600.1	14	19	Remapped	NT_187600.1
NT_187660.1	Chr15\|NT_187660.1	10	12	Remapped	NT_187660.1
NT_187603.1	Chr15\|NT_187603.1	7	10	Remapped	NT_187603.1
NW_011332701.1	Chr15\|NW_011332701.1	15	19	Remapped	NW_011332701.1
NT_187607.1	Chr16\|NT_187607.1	8	11	Remapped	NT_187607.1
NW_017852933.1	Chr16\|NW_017852933.1	1	1	Remapped	NW_017852933.1
NT_187614.1	Chr17\|NT_187614.1	6	6	Remapped	NT_187614.1
NW_015148969.1	Chr22\|NW_015148969.1	1	1	Remapped	NW_015148969.1
NT_187667.1	ChrX\|NT_187667.1	6	6	Remapped	NT_187667.1
NT_187634.1	ChrX\|NT_187634.1	6	6	Remapped	NT_187634.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	37	63	Remapped	NC_000001.10
NC_000002.11	Chr2	61	97	Remapped	NC_000002.11
NC_000003.11	Chr3	14	14	Remapped	NC_000003.11
NC_000004.11	Chr4	10	10	Remapped	NC_000004.11
NC_000005.9	Chr5	14	22	Remapped	NC_000005.9
NC_000006.11	Chr6	45	356	Remapped	NC_000006.11
NC_000007.13	Chr7	11	11	Remapped	NC_000007.13
NC_000008.10	Chr8	35	293	Remapped	NC_000008.10
NC_000009.11	Chr9	27	31	Remapped	NC_000009.11
NC_000010.10	Chr10	81	262	Remapped	NC_000010.10
NC_000011.9	Chr11	12	19	Remapped	NC_000011.9
NC_000012.11	Chr12	9	9	Remapped	NC_000012.11
NC_000013.10	Chr13	15	45	Remapped	NC_000013.10
NC_000014.8	Chr14	54	79	Remapped	NC_000014.8
NC_000015.9	Chr15	171	315	Remapped	NC_000015.9
NC_000016.9	Chr16	117	297	Remapped	NC_000016.9
NC_000017.10	Chr17	13	14	Remapped	NC_000017.10
NC_000018.9	Chr18	19	101	Remapped	NC_000018.9
NC_000019.9	Chr19	3	3	Remapped	NC_000019.9
NC_000020.10	Chr20	1	1	Remapped	NC_000020.10
NC_000021.8	Chr21	56	195	Remapped	NC_000021.8
NC_000022.10	Chr22	23	37	Remapped	NC_000022.10
NC_000023.10	ChrX	74	116	Remapped	NC_000023.10
NC_000024.9	ChrY	24	28	Remapped	NC_000024.9
NW_003871055.3	Chr1\|NW_003871055.3	96	126	Remapped	NW_003871055.3
NW_004775427.1	Chr4\|NW_004775427.1	1	1	Remapped	NW_004775427.1
NW_003871064.1	Chr7\|NW_003871064.1	1	1	Remapped	NW_003871064.1
NW_003871068.1	Chr10\|NW_003871068.1	34	126	Remapped	NW_003871068.1
NW_003571048.1	Chr12\|NW_003571048.1	1	1	Remapped	NW_003571048.1
NW_004166863.1	Chr14\|NW_004166863.1	7	7	Remapped	NW_004166863.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	37	63	Submitted	NC_000001.9
NC_000002.10	Chr2	61	97	Submitted	NC_000002.10
NC_000003.10	Chr3	14	14	Submitted	NC_000003.10
NC_000004.10	Chr4	10	10	Submitted	NC_000004.10
NC_000005.8	Chr5	14	22	Submitted	NC_000005.8
NC_000006.10	Chr6	45	356	Submitted	NC_000006.10
NC_000007.12	Chr7	11	11	Submitted	NC_000007.12
NC_000008.9	Chr8	35	293	Submitted	NC_000008.9
NC_000009.10	Chr9	27	31	Submitted	NC_000009.10
NC_000010.9	Chr10	81	262	Submitted	NC_000010.9
NC_000011.8	Chr11	12	19	Submitted	NC_000011.8
NC_000012.10	Chr12	10	10	Submitted	NC_000012.10
NC_000013.9	Chr13	15	45	Submitted	NC_000013.9
NC_000014.7	Chr14	54	79	Submitted	NC_000014.7
NC_000015.8	Chr15	171	315	Submitted	NC_000015.8
NC_000016.8	Chr16	117	297	Submitted	NC_000016.8
NC_000017.9	Chr17	13	14	Submitted	NC_000017.9
NC_000018.8	Chr18	19	101	Submitted	NC_000018.8
NC_000019.8	Chr19	3	3	Submitted	NC_000019.8
NC_000020.9	Chr20	1	1	Submitted	NC_000020.9
NC_000021.7	Chr21	56	195	Submitted	NC_000021.7
NC_000022.9	Chr22	23	37	Submitted	NC_000022.9
NC_000023.9	ChrX	74	116	Submitted	NC_000023.9
NC_000024.8	ChrY	24	28	Submitted	NC_000024.8

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_000001.9	Chr1	37	17	5	3	0	12	63	33	5	4	0	21
NC_000002.10	Chr2	61	21	2	33	0	5	97	52	2	38	0	5
NC_000003.10	Chr3	14	13	0	1	0	0	14	13	0	1	0	0
NC_000004.10	Chr4	10	7	2	0	0	1	10	7	2	0	0	1
NC_000005.8	Chr5	14	14	0	0	0	0	22	22	0	0	0	0
NC_000006.10	Chr6	45	41	4	0	0	0	356	352	4	0	0	0
NC_000007.12	Chr7	11	7	3	0	0	1	11	7	3	0	0	1
NC_000008.9	Chr8	35	9	10	16	0	0	293	13	28	252	0	0
NC_000009.10	Chr9	27	13	5	9	0	0	31	13	5	13	0	0
NC_000010.9	Chr10	81	37	6	4	0	34	262	125	6	5	0	126
NC_000011.8	Chr11	12	11	1	0	0	0	19	18	1	0	0	0
NC_000012.10	Chr12	10	7	2	1	0	0	10	7	2	1	0	0
NC_000013.9	Chr13	15	6	9	0	0	0	45	7	38	0	0	0
NC_000014.7	Chr14	54	22	23	2	0	7	79	30	40	2	0	7
NC_000015.8	Chr15	171	16	17	138	0	0	315	18	26	271	0	0
NC_000016.8	Chr16	117	36	2	0	0	79	297	195	2	0	0	100
NC_000017.9	Chr17	13	6	5	2	0	0	14	7	5	2	0	0
NC_000018.8	Chr18	19	7	12	0	0	0	101	7	94	0	0	0
NC_000019.8	Chr19	3	2	1	0	0	0	3	2	1	0	0	0
NC_000020.9	Chr20	1	0	1	0	0	0	1	0	1	0	0	0
NC_000021.7	Chr21	56	3	53	0	0	0	195	3	192	0	0	0
NC_000022.9	Chr22	23	10	13	0	0	0	37	20	17	0	0	0
NC_000023.9	ChrX	74	29	41	4	0	0	116	40	72	4	0	0
NC_000024.8	ChrY	24	17	2	5	0	0	28	18	5	5	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	37	10	3	16	4	4	63	10	3	35	11	4
NC_000002.10	Chr2	61	14	5	36	0	6	97	45	5	41	0	6
NC_000003.10	Chr3	14	11	2	1	0	0	14	11	2	1	0	0
NC_000004.10	Chr4	10	7	2	1	0	0	10	7	2	1	0	0
NC_000005.8	Chr5	14	13	0	0	0	1	22	21	0	0	0	1
NC_000006.10	Chr6	45	40	5	0	0	0	356	351	5	0	0	0
NC_000007.12	Chr7	11	7	4	0	0	0	11	7	4	0	0	0
NC_000008.9	Chr8	35	8	10	16	0	1	293	12	28	252	0	1
NC_000009.10	Chr9	27	12	5	3	0	7	31	12	5	6	0	8
NC_000010.9	Chr10	81	34	9	37	0	1	262	122	10	129	0	1
NC_000011.8	Chr11	12	9	3	0	0	0	19	16	3	0	0	0
NC_000012.10	Chr12	10	8	1	0	0	1	10	8	1	0	0	1
NC_000013.9	Chr13	15	6	9	0	0	0	45	7	38	0	0	0
NC_000014.7	Chr14	54	2	9	29	0	14	79	2	10	48	0	19
NC_000015.8	Chr15	171	5	8	138	0	20	315	5	12	271	0	27
NC_000016.8	Chr16	117	27	3	78	0	9	297	183	3	99	0	12
NC_000017.9	Chr17	13	3	4	0	0	6	14	4	4	0	0	6
NC_000018.8	Chr18	19	7	0	12	0	0	101	7	0	94	0	0
NC_000019.8	Chr19	3	1	1	1	0	0	3	1	1	1	0	0
NC_000020.9	Chr20	1	0	1	0	0	0	1	0	1	0	0	0
NC_000021.7	Chr21	56	3	37	16	0	0	195	3	163	29	0	0
NC_000022.9	Chr22	23	5	7	10	0	1	37	6	16	14	0	1
NC_000023.9	ChrX	74	32	34	2	0	6	116	45	63	2	0	6
NC_000024.8	ChrY	24	17	7	0	0	0	28	18	10	0	0	0

Samplesets

Number of Samplesets: 1

Name:: Research Cytogenomic Testing (Prenatal)
Sampleset Type:: Case
Description:: Patients recruited for research-based prenatal cytogenomic testing.
Size:: 2,387
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Indications for prenatal diagnosis were advanced maternal age (46.6%)

Experimental Details

Experiment ID	Type	Method	Analysis	Data	Number of Variant Calls
1	Discovery	Oligo aCGH	Probe signal intensity	dbGaP	2,419
2	Validation	FISH	Manual observation	dbGaP	120
3	Validation	Karyotyping	Manual observation	dbGaP	424
4	Validation	PCR	Manual observation	dbGaP	1

Validations

Experiment ID	Method	Analysis	Data	Number of Variant Calls Validated
2	FISH	Manual observation	dbGaP	120
3	Karyotyping	Manual observation	dbGaP	424
4	PCR	Manual observation	dbGaP	1

dbVar

Database of genomic structural variation

nstd75 (ClinGen Prenatal)

Links

Detailed Information: Download 927 Variant Regions, Download 2419 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: NCBI36->GRCh37.p13NCBI36->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

Variant Summary for:

Remapping summary: