nstd85 - vanSilfhout et al 2013 - dbVar Study

nstd85 (vanSilfhout et al. 2013)

Organism:: Human
Study Type:: Case-Control
Submitter:: Jayne Hehir-Kwa
Description:: The study consists of a cohort of 5,531 consecutive patients with intellectual disability who were screened for CNVs using the Affymetrix 250K NspI single-nucleotide polymorphism (SNP) array platform, between 2006 and 2011. See Variant Summary counts for nstd85 in dbVar Variant Summary.
Publication(s):: Vulto-van Silfhout et al. 2013

Links

Source: NCBI

Detailed Information: Download 1416 Variant Regions, Download 1663 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: NCBI35 (hg17)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	87	108	Remapped	NC_000001.11
NC_000002.12	Chr2	106	115	Remapped	NC_000002.12
NC_000003.12	Chr3	91	92	Remapped	NC_000003.12
NC_000004.12	Chr4	76	78	Remapped	NC_000004.12
NC_000005.10	Chr5	67	74	Remapped	NC_000005.10
NC_000006.12	Chr6	60	62	Remapped	NC_000006.12
NC_000007.14	Chr7	80	99	Remapped	NC_000007.14
NC_000008.11	Chr8	61	66	Remapped	NC_000008.11
NC_000009.12	Chr9	65	70	Remapped	NC_000009.12
NC_000010.11	Chr10	63	65	Remapped	NC_000010.11
NC_000011.10	Chr11	56	59	Remapped	NC_000011.10
NC_000012.12	Chr12	55	55	Remapped	NC_000012.12
NC_000013.11	Chr13	40	42	Remapped	NC_000013.11
NC_000014.9	Chr14	30	32	Remapped	NC_000014.9
NC_000015.10	Chr15	62	97	Remapped	NC_000015.10
NC_000016.10	Chr16	72	94	Remapped	NC_000016.10
NC_000017.11	Chr17	55	73	Remapped	NC_000017.11
NC_000018.10	Chr18	45	50	Remapped	NC_000018.10
NC_000019.10	Chr19	14	14	Remapped	NC_000019.10
NC_000020.11	Chr20	36	38	Remapped	NC_000020.11
NC_000021.9	Chr21	23	24	Remapped	NC_000021.9
NC_000022.11	Chr22	62	102	Remapped	NC_000022.11
NC_000023.11	ChrX	107	151	Remapped	NC_000023.11
NT_187519.1	Chr1\|NT_187519.1	1	1	Remapped	NT_187519.1
NW_014040927.1	Chr1\|NW_014040927.1	1	1	Remapped	NW_014040927.1
NW_003315915.1	Chr4\|NW_003315915.1	1	1	Remapped	NW_003315915.1
NW_016107297.1	Chr5\|NW_016107297.1	1	1	Remapped	NW_016107297.1
NW_016107298.1	Chr5\|NW_016107298.1	1	1	Remapped	NW_016107298.1
NT_187565.1	Chr8\|NT_187565.1	1	1	Remapped	NT_187565.1
NT_187576.1	Chr8\|NT_187576.1	1	1	Remapped	NT_187576.1
NW_018654717.1	Chr8\|NW_018654717.1	6	6	Remapped	NW_018654717.1
NT_187578.1	Chr9\|NT_187578.1	1	1	Remapped	NT_187578.1
NW_003315930.1	Chr9\|NW_003315930.1	1	2	Remapped	NW_003315930.1
NW_003871074.1	Chr11\|NW_003871074.1	1	1	Remapped	NW_003871074.1
NW_011332696.1	Chr12\|NW_011332696.1	1	1	Remapped	NW_011332696.1
NW_018654718.1	Chr12\|NW_018654718.1	2	2	Remapped	NW_018654718.1
NT_187600.1	Chr14\|NT_187600.1	2	2	Remapped	NT_187600.1
NT_187660.1	Chr15\|NT_187660.1	5	27	Remapped	NT_187660.1
NW_011332701.1	Chr15\|NW_011332701.1	5	27	Remapped	NW_011332701.1
NT_187607.1	Chr16\|NT_187607.1	13	29	Remapped	NT_187607.1
NW_013171813.1	Chr16\|NW_013171813.1	1	1	Remapped	NW_013171813.1
NW_017852933.1	Chr16\|NW_017852933.1	1	1	Remapped	NW_017852933.1
NT_187663.1	Chr17\|NT_187663.1	5	7	Remapped	NT_187663.1
NT_167251.2	Chr17\|NT_167251.2	4	6	Remapped	NT_167251.2
NT_187612.1	Chr17\|NT_187612.1	1	2	Remapped	NT_187612.1
NT_187613.1	Chr17\|NT_187613.1	4	4	Remapped	NT_187613.1
NT_187614.1	Chr17\|NT_187614.1	4	11	Remapped	NT_187614.1
NW_003315952.3	Chr17\|NW_003315952.3	1	1	Remapped	NW_003315952.3
NW_017363817.1	Chr17\|NW_017363817.1	1	1	Remapped	NW_017363817.1
NW_003315960.1	Chr18\|NW_003315960.1	1	2	Remapped	NW_003315960.1
NT_187693.1	Chr19\|NT_187693.1	1	1	Remapped	NT_187693.1
NW_003571061.2	Chr19\|NW_003571061.2	1	1	Remapped	NW_003571061.2
NW_003571057.2	Chr19\|NW_003571057.2	1	1	Remapped	NW_003571057.2
NW_003571058.2	Chr19\|NW_003571058.2	1	1	Remapped	NW_003571058.2
NW_003571059.2	Chr19\|NW_003571059.2	1	1	Remapped	NW_003571059.2
NW_003571060.1	Chr19\|NW_003571060.1	1	1	Remapped	NW_003571060.1
NW_003571056.2	Chr19\|NW_003571056.2	1	1	Remapped	NW_003571056.2
NW_003571055.2	Chr19\|NW_003571055.2	1	1	Remapped	NW_003571055.2
NW_003571054.1	Chr19\|NW_003571054.1	1	1	Remapped	NW_003571054.1
NT_187624.1	Chr20\|NT_187624.1	1	1	Remapped	NT_187624.1
NT_187667.1	ChrX\|NT_187667.1	1	3	Remapped	NT_187667.1
NT_187634.1	ChrX\|NT_187634.1	1	3	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	90	111	Remapped	NC_000001.10
NC_000002.11	Chr2	106	115	Remapped	NC_000002.11
NC_000003.11	Chr3	91	92	Remapped	NC_000003.11
NC_000004.11	Chr4	76	78	Remapped	NC_000004.11
NC_000005.9	Chr5	67	74	Remapped	NC_000005.9
NC_000006.11	Chr6	60	62	Remapped	NC_000006.11
NC_000007.13	Chr7	80	99	Remapped	NC_000007.13
NC_000008.10	Chr8	61	66	Remapped	NC_000008.10
NC_000009.11	Chr9	65	70	Remapped	NC_000009.11
NC_000010.10	Chr10	63	65	Remapped	NC_000010.10
NC_000011.9	Chr11	56	59	Remapped	NC_000011.9
NC_000012.11	Chr12	55	55	Remapped	NC_000012.11
NC_000013.10	Chr13	40	42	Remapped	NC_000013.10
NC_000014.8	Chr14	30	32	Remapped	NC_000014.8
NC_000015.9	Chr15	62	97	Remapped	NC_000015.9
NC_000016.9	Chr16	72	94	Remapped	NC_000016.9
NC_000017.10	Chr17	55	73	Remapped	NC_000017.10
NC_000018.9	Chr18	45	50	Remapped	NC_000018.9
NC_000019.9	Chr19	14	14	Remapped	NC_000019.9
NC_000020.10	Chr20	36	38	Remapped	NC_000020.10
NC_000021.8	Chr21	23	24	Remapped	NC_000021.8
NC_000022.10	Chr22	62	102	Remapped	NC_000022.10
NC_000023.10	ChrX	107	151	Remapped	NC_000023.10
NW_003871055.3	Chr1\|NW_003871055.3	9	25	Remapped	NW_003871055.3
NW_003315915.1	Chr4\|NW_003315915.1	1	1	Remapped	NW_003315915.1
NW_003871064.1	Chr7\|NW_003871064.1	6	21	Remapped	NW_003871064.1
NW_003571042.1	Chr8\|NW_003571042.1	1	1	Remapped	NW_003571042.1
NW_003315930.1	Chr9\|NW_003315930.1	1	2	Remapped	NW_003315930.1
NW_003871071.1	Chr10\|NW_003871071.1	1	1	Remapped	NW_003871071.1
NW_003871074.1	Chr11\|NW_003871074.1	1	1	Remapped	NW_003871074.1
NW_004070871.1	Chr11\|NW_004070871.1	1	1	Remapped	NW_004070871.1
NW_004166863.1	Chr14\|NW_004166863.1	1	1	Remapped	NW_004166863.1
NT_167251.1	Chr17\|NT_167251.1	4	6	Remapped	NT_167251.1
NW_004070872.2	Chr17\|NW_004070872.2	1	1	Remapped	NW_004070872.2
NW_003315960.1	Chr18\|NW_003315960.1	1	2	Remapped	NW_003315960.1
NW_004504304.1	Chr20\|NW_004504304.1	1	1	Remapped	NW_004504304.1
NW_003871103.3	ChrX\|NW_003871103.3	3	3	Remapped	NW_003871103.3
NW_004070877.1	ChrX\|NW_004070877.1	1	1	Remapped	NW_004070877.1
NW_004070888.1	ChrX\|NW_004070888.1	1	1	Remapped	NW_004070888.1
NW_004070890.2	ChrX\|NW_004070890.2	5	6	Remapped	NW_004070890.2

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.8	Chr1	90	111	Submitted	NC_000001.8
NC_000002.9	Chr2	106	115	Submitted	NC_000002.9
NC_000003.9	Chr3	91	92	Submitted	NC_000003.9
NC_000004.9	Chr4	76	78	Submitted	NC_000004.9
NC_000005.8	Chr5	67	74	Submitted	NC_000005.8
NC_000006.9	Chr6	60	62	Submitted	NC_000006.9
NC_000007.11	Chr7	80	99	Submitted	NC_000007.11
NC_000008.9	Chr8	61	66	Submitted	NC_000008.9
NC_000009.9	Chr9	65	70	Submitted	NC_000009.9
NC_000010.8	Chr10	63	65	Submitted	NC_000010.8
NC_000011.8	Chr11	56	59	Submitted	NC_000011.8
NC_000012.9	Chr12	55	55	Submitted	NC_000012.9
NC_000013.9	Chr13	40	42	Submitted	NC_000013.9
NC_000014.7	Chr14	30	32	Submitted	NC_000014.7
NC_000015.8	Chr15	62	97	Submitted	NC_000015.8
NC_000016.8	Chr16	72	94	Submitted	NC_000016.8
NC_000017.9	Chr17	55	73	Submitted	NC_000017.9
NC_000018.8	Chr18	45	50	Submitted	NC_000018.8
NC_000019.8	Chr19	14	14	Submitted	NC_000019.8
NC_000020.9	Chr20	36	38	Submitted	NC_000020.9
NC_000021.7	Chr21	23	24	Submitted	NC_000021.7
NC_000022.8	Chr22	62	102	Submitted	NC_000022.8
NC_000023.8	ChrX	107	151	Submitted	NC_000023.8

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_000001.8	Chr1	90	58	19	4	0	9	111	62	20	4	0	25
NC_000002.9	Chr2	106	85	20	1	0	0	115	94	20	1	0	0
NC_000003.9	Chr3	91	82	6	3	0	0	92	83	6	3	0	0
NC_000004.9	Chr4	76	51	16	8	0	1	78	53	16	8	0	1
NC_000005.8	Chr5	67	61	6	0	0	0	74	68	6	0	0	0
NC_000006.9	Chr6	60	50	10	0	0	0	62	52	10	0	0	0
NC_000007.11	Chr7	80	61	12	1	0	6	99	65	12	1	0	21
NC_000008.9	Chr8	61	40	18	2	0	1	66	43	20	2	0	1
NC_000009.9	Chr9	65	59	2	3	0	1	70	63	2	3	0	2
NC_000010.8	Chr10	63	48	11	3	0	1	65	49	12	3	0	1
NC_000011.8	Chr11	56	51	3	0	0	2	59	54	3	0	0	2
NC_000012.9	Chr12	55	46	7	2	0	0	55	46	7	2	0	0
NC_000013.9	Chr13	40	36	4	0	0	0	42	38	4	0	0	0
NC_000014.7	Chr14	30	25	4	0	0	1	32	27	4	0	0	1
NC_000015.8	Chr15	62	37	23	2	0	0	97	63	32	2	0	0
NC_000016.8	Chr16	72	67	4	1	0	0	94	89	4	1	0	0
NC_000017.9	Chr17	55	33	11	6	0	5	73	42	18	6	0	7
NC_000018.8	Chr18	45	30	14	0	0	1	50	34	14	0	0	2
NC_000019.8	Chr19	14	11	1	2	0	0	14	11	1	2	0	0
NC_000020.9	Chr20	36	32	2	1	0	1	38	34	2	1	0	1
NC_000021.7	Chr21	23	17	5	1	0	0	24	17	6	1	0	0
NC_000022.8	Chr22	62	40	22	0	0	0	102	52	50	0	0	0
NC_000023.8	ChrX	107	41	49	7	0	10	151	45	86	9	0	11

			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_000001.8	Chr1	90	54	25	6	3	2	111	62	26	18	3	2
NC_000002.9	Chr2	106	79	24	3	0	0	115	88	24	3	0	0
NC_000003.9	Chr3	91	73	16	2	0	0	92	73	17	2	0	0
NC_000004.9	Chr4	76	55	15	5	0	1	78	57	15	5	0	1
NC_000005.8	Chr5	67	55	10	0	0	2	74	61	11	0	0	2
NC_000006.9	Chr6	60	42	16	2	0	0	62	43	16	3	0	0
NC_000007.11	Chr7	80	59	19	2	0	0	99	63	34	2	0	0
NC_000008.9	Chr8	61	35	18	0	0	8	66	38	20	0	0	8
NC_000009.9	Chr9	65	58	2	3	0	2	70	62	2	3	0	3
NC_000010.8	Chr10	63	46	14	3	0	0	65	47	15	3	0	0
NC_000011.8	Chr11	56	45	10	0	0	1	59	48	10	0	0	1
NC_000012.9	Chr12	55	42	8	2	0	3	55	42	8	2	0	3
NC_000013.9	Chr13	40	35	4	1	0	0	42	37	4	1	0	0
NC_000014.7	Chr14	30	23	5	0	0	2	32	25	5	0	0	2
NC_000015.8	Chr15	62	33	16	8	0	5	97	37	22	11	0	27
NC_000016.8	Chr16	72	48	9	0	0	15	94	53	10	0	0	31
NC_000017.9	Chr17	55	22	17	0	0	16	73	23	24	0	0	26
NC_000018.8	Chr18	45	30	14	0	0	1	50	34	14	0	0	2
NC_000019.8	Chr19	14	10	3	0	0	1	14	10	3	0	0	1
NC_000020.9	Chr20	36	24	9	2	0	1	38	26	9	2	0	1
NC_000021.7	Chr21	23	15	5	3	0	0	24	15	5	4	0	0
NC_000022.8	Chr22	62	13	38	11	0	0	102	15	49	38	0	0
NC_000023.8	ChrX	107	46	55	5	0	1	151	61	82	5	0	3

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: ID Patients
Sampleset Type:: Case
Description:: Patients with Intellectual Disability
Size:: 5,531 (sample data not available)
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Cognitive impairment

Sampleset ID:: 2
Name:: Combined Male and Female Control Pools
Sampleset Type:: Control
Description:: pool of 10 healthy males and 10 healthy females
Size:: 20 (sample data not available)
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Affymetrix 250k NspI array	1,663

dbVar

Database of genomic structural variation

nstd85 (vanSilfhout et al. 2013)

Links

Detailed Information: Download 1416 Variant Regions, Download 1663 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI35 (hg17)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd85 (vanSilfhout et al. 2013)

Links

Detailed Information: Download 1416 Variant Regions, Download 1663 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI35 (hg17)

Remapping summary: NCBI35->GRCh37.p13NCBI35->GRCh38.p12

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: