nstd14 - Cooper et al 2008 - dbVar Study

nstd14 (Cooper et al. 2008)

Organism:: Human
Study Type:: Control Set
Submitter:: Evan Eichler
Description:: Using independent, sequence based CNV maps, we find that commonly used SNP platforms have limited or no probe coverage for a large fraction of CNVs. Despite this, in 9 samples we inferred 368 CNVs using Illumina SNP genotyping data and experimentally validated over two-thirds of these. See Variant Summary counts for nstd14 in dbVar Variant Summary.
Publication(s):: Cooper et al. 2008

Links

Source: NCBI

Detailed Information: Download 368 Variant Regions, Download 368 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	31	31	Remapped	NC_000001.11
NC_000002.12	Chr2	31	31	Remapped	NC_000002.12
NC_000003.12	Chr3	21	21	Remapped	NC_000003.12
NC_000004.12	Chr4	20	20	Remapped	NC_000004.12
NC_000005.10	Chr5	24	24	Remapped	NC_000005.10
NC_000006.12	Chr6	10	10	Remapped	NC_000006.12
NC_000007.14	Chr7	17	17	Remapped	NC_000007.14
NC_000008.11	Chr8	27	27	Remapped	NC_000008.11
NC_000009.12	Chr9	21	21	Remapped	NC_000009.12
NC_000010.11	Chr10	13	13	Remapped	NC_000010.11
NC_000011.10	Chr11	15	15	Remapped	NC_000011.10
NC_000012.12	Chr12	5	5	Remapped	NC_000012.12
NC_000013.11	Chr13	10	10	Remapped	NC_000013.11
NC_000014.9	Chr14	11	11	Remapped	NC_000014.9
NC_000015.10	Chr15	23	23	Remapped	NC_000015.10
NC_000016.10	Chr16	21	21	Remapped	NC_000016.10
NC_000017.11	Chr17	13	13	Remapped	NC_000017.11
NC_000018.10	Chr18	6	6	Remapped	NC_000018.10
NC_000019.10	Chr19	10	10	Remapped	NC_000019.10
NC_000020.11	Chr20	3	3	Remapped	NC_000020.11
NC_000021.9	Chr21	3	3	Remapped	NC_000021.9
NC_000022.11	Chr22	17	17	Remapped	NC_000022.11
NC_000023.11	ChrX	8	8	Remapped	NC_000023.11
NT_187519.1	Chr1\|NT_187519.1	1	1	Remapped	NT_187519.1
NW_012132914.1	Chr1\|NW_012132914.1	1	1	Remapped	NW_012132914.1
NW_017852928.1	Chr1\|NW_017852928.1	1	1	Remapped	NW_017852928.1
NT_187539.1	Chr3\|NT_187539.1	1	1	Remapped	NT_187539.1
NW_003315915.1	Chr4\|NW_003315915.1	1	1	Remapped	NW_003315915.1
NT_187651.1	Chr5\|NT_187651.1	1	1	Remapped	NT_187651.1
NW_003315917.2	Chr5\|NW_003315917.2	2	2	Remapped	NW_003315917.2
NW_016107298.1	Chr5\|NW_016107298.1	1	1	Remapped	NW_016107298.1
NT_167246.2	Chr6\|NT_167246.2	1	1	Remapped	NT_167246.2
NT_167247.2	Chr6\|NT_167247.2	2	2	Remapped	NT_167247.2
NT_167248.2	Chr6\|NT_167248.2	2	2	Remapped	NT_167248.2
NT_167249.2	Chr6\|NT_167249.2	2	2	Remapped	NT_167249.2
NT_167245.2	Chr6\|NT_167245.2	2	2	Remapped	NT_167245.2
NT_113891.3	Chr6\|NT_113891.3	2	2	Remapped	NT_113891.3
NT_167244.2	Chr6\|NT_167244.2	1	1	Remapped	NT_167244.2
NT_187558.1	Chr7\|NT_187558.1	1	1	Remapped	NT_187558.1
NT_187562.1	Chr7\|NT_187562.1	2	2	Remapped	NT_187562.1
NT_187653.1	Chr7\|NT_187653.1	1	1	Remapped	NT_187653.1
NT_187570.1	Chr8\|NT_187570.1	3	3	Remapped	NT_187570.1
NT_187576.1	Chr8\|NT_187576.1	3	3	Remapped	NT_187576.1
NW_017852932.1	Chr8\|NW_017852932.1	1	1	Remapped	NW_017852932.1
NW_018654717.1	Chr8\|NW_018654717.1	1	1	Remapped	NW_018654717.1
NW_009646201.1	Chr9\|NW_009646201.1	1	1	Remapped	NW_009646201.1
NT_187579.1	Chr10\|NT_187579.1	1	1	Remapped	NT_187579.1
NW_013171806.1	Chr10\|NW_013171806.1	1	1	Remapped	NW_013171806.1
NW_019805495.1	Chr11\|NW_019805495.1	1	1	Remapped	NW_019805495.1
NT_187600.1	Chr14\|NT_187600.1	4	4	Remapped	NT_187600.1
NT_187660.1	Chr15\|NT_187660.1	1	1	Remapped	NT_187660.1
NT_187382.1	Chr15\|NT_187382.1	1	1	Remapped	NT_187382.1
NT_187602.1	Chr15\|NT_187602.1	1	1	Remapped	NT_187602.1
NT_187603.1	Chr15\|NT_187603.1	1	1	Remapped	NT_187603.1
NW_003315943.1	Chr15\|NW_003315943.1	1	1	Remapped	NW_003315943.1
NW_011332701.1	Chr15\|NW_011332701.1	4	4	Remapped	NW_011332701.1
NW_017852933.1	Chr16\|NW_017852933.1	2	2	Remapped	NW_017852933.1
NT_187661.1	Chr17\|NT_187661.1	1	1	Remapped	NT_187661.1
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1
NT_187614.1	Chr17\|NT_187614.1	3	3	Remapped	NT_187614.1
NT_187693.1	Chr19\|NT_187693.1	2	2	Remapped	NT_187693.1
NW_003571060.1	Chr19\|NW_003571060.1	2	2	Remapped	NW_003571060.1
NW_003571054.1	Chr19\|NW_003571054.1	2	2	Remapped	NW_003571054.1
NT_187629.1	Chr22\|NT_187629.1	4	4	Remapped	NT_187629.1
NT_187633.1	Chr22\|NT_187633.1	2	2	Remapped	NT_187633.1
NW_003315972.2	Chr22\|NW_003315972.2	1	1	Remapped	NW_003315972.2

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	32	32	Remapped	NC_000001.10
NC_000002.11	Chr2	31	31	Remapped	NC_000002.11
NC_000003.11	Chr3	21	21	Remapped	NC_000003.11
NC_000004.11	Chr4	20	20	Remapped	NC_000004.11
NC_000005.9	Chr5	24	24	Remapped	NC_000005.9
NC_000006.11	Chr6	10	10	Remapped	NC_000006.11
NC_000007.13	Chr7	17	17	Remapped	NC_000007.13
NC_000008.10	Chr8	28	28	Remapped	NC_000008.10
NC_000009.11	Chr9	21	21	Remapped	NC_000009.11
NC_000010.10	Chr10	13	13	Remapped	NC_000010.10
NC_000011.9	Chr11	15	15	Remapped	NC_000011.9
NC_000012.11	Chr12	5	5	Remapped	NC_000012.11
NC_000013.10	Chr13	10	10	Remapped	NC_000013.10
NC_000014.8	Chr14	11	11	Remapped	NC_000014.8
NC_000015.9	Chr15	22	22	Remapped	NC_000015.9
NC_000016.9	Chr16	21	21	Remapped	NC_000016.9
NC_000017.10	Chr17	15	15	Remapped	NC_000017.10
NC_000018.9	Chr18	6	6	Remapped	NC_000018.9
NC_000019.9	Chr19	10	10	Remapped	NC_000019.9
NC_000020.10	Chr20	3	3	Remapped	NC_000020.10
NC_000021.8	Chr21	3	3	Remapped	NC_000021.8
NC_000022.10	Chr22	18	18	Remapped	NC_000022.10
NC_000023.10	ChrX	8	8	Remapped	NC_000023.10
NW_003315903.1	Chr1\|NW_003315903.1	1	1	Remapped	NW_003315903.1
NW_003871055.3	Chr1\|NW_003871055.3	1	1	Remapped	NW_003871055.3
NW_003315915.1	Chr4\|NW_003315915.1	1	1	Remapped	NW_003315915.1
NW_003315917.2	Chr5\|NW_003315917.2	4	4	Remapped	NW_003315917.2
NT_113891.2	Chr6\|NT_113891.2	2	2	Remapped	NT_113891.2
NT_167244.1	Chr6\|NT_167244.1	1	1	Remapped	NT_167244.1
NT_167245.1	Chr6\|NT_167245.1	2	2	Remapped	NT_167245.1
NT_167246.1	Chr6\|NT_167246.1	1	1	Remapped	NT_167246.1
NT_167247.1	Chr6\|NT_167247.1	2	2	Remapped	NT_167247.1
NT_167248.1	Chr6\|NT_167248.1	2	2	Remapped	NT_167248.1
NT_167249.1	Chr6\|NT_167249.1	2	2	Remapped	NT_167249.1
NW_003871063.1	Chr6\|NW_003871063.1	1	1	Remapped	NW_003871063.1
NW_003571040.1	Chr7\|NW_003571040.1	2	2	Remapped	NW_003571040.1
NW_003571042.1	Chr8\|NW_003571042.1	3	3	Remapped	NW_003571042.1
NW_003315925.1	Chr9\|NW_003315925.1	1	1	Remapped	NW_003315925.1
NW_003871068.1	Chr10\|NW_003871068.1	1	1	Remapped	NW_003871068.1
NW_003571045.1	Chr11\|NW_003571045.1	1	1	Remapped	NW_003571045.1
NW_004166863.1	Chr14\|NW_004166863.1	3	3	Remapped	NW_004166863.1
NW_003315949.1	Chr17\|NW_003315949.1	1	1	Remapped	NW_003315949.1
NW_003871086.1	Chr17\|NW_003871086.1	1	1	Remapped	NW_003871086.1
NW_003571053.2	Chr19\|NW_003571053.2	3	3	Remapped	NW_003571053.2
NW_003315972.1	Chr22\|NW_003315972.1	1	1	Remapped	NW_003315972.1
NW_004070880.2	ChrX\|NW_004070880.2	3	3	Remapped	NW_004070880.2

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.8	Chr1	32	32	Submitted	NC_000001.8
NC_000002.9	Chr2	31	31	Submitted	NC_000002.9
NC_000003.9	Chr3	21	21	Submitted	NC_000003.9
NC_000004.9	Chr4	20	20	Submitted	NC_000004.9
NC_000005.8	Chr5	24	24	Submitted	NC_000005.8
NC_000006.9	Chr6	10	10	Submitted	NC_000006.9
NC_000007.11	Chr7	17	17	Submitted	NC_000007.11
NC_000008.9	Chr8	30	30	Submitted	NC_000008.9
NC_000009.9	Chr9	21	21	Submitted	NC_000009.9
NC_000010.8	Chr10	13	13	Submitted	NC_000010.8
NC_000011.8	Chr11	15	15	Submitted	NC_000011.8
NC_000012.9	Chr12	5	5	Submitted	NC_000012.9
NC_000013.9	Chr13	10	10	Submitted	NC_000013.9
NC_000014.7	Chr14	11	11	Submitted	NC_000014.7
NC_000015.8	Chr15	24	24	Submitted	NC_000015.8
NC_000016.8	Chr16	21	21	Submitted	NC_000016.8
NC_000017.9	Chr17	15	15	Submitted	NC_000017.9
NC_000018.8	Chr18	6	6	Submitted	NC_000018.8
NC_000019.8	Chr19	10	10	Submitted	NC_000019.8
NC_000020.9	Chr20	3	3	Submitted	NC_000020.9
NC_000021.7	Chr21	3	3	Submitted	NC_000021.7
NC_000022.8	Chr22	18	18	Submitted	NC_000022.8
NC_000023.8	ChrX	8	8	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	32	28	1	1	0	2	32	28	1	1	0	2
NC_000002.9	Chr2	31	31	0	0	0	0	31	31	0	0	0	0
NC_000003.9	Chr3	21	21	0	0	0	0	21	21	0	0	0	0
NC_000004.9	Chr4	20	19	0	0	0	1	20	19	0	0	0	1
NC_000005.8	Chr5	24	19	0	1	0	4	24	19	0	1	0	4
NC_000006.9	Chr6	10	8	0	0	0	2	10	8	0	0	0	2
NC_000007.11	Chr7	17	14	1	0	0	2	17	14	1	0	0	2
NC_000008.9	Chr8	30	29	0	0	0	1	30	29	0	0	0	1
NC_000009.9	Chr9	21	20	0	0	0	1	21	20	0	0	0	1
NC_000010.8	Chr10	13	12	0	0	0	1	13	12	0	0	0	1
NC_000011.8	Chr11	15	14	0	0	0	1	15	14	0	0	0	1
NC_000012.9	Chr12	5	5	0	0	0	0	5	5	0	0	0	0
NC_000013.9	Chr13	10	10	0	0	0	0	10	10	0	0	0	0
NC_000014.7	Chr14	11	7	1	0	0	3	11	7	1	0	0	3
NC_000015.8	Chr15	24	20	2	0	2	0	24	20	2	0	2	0
NC_000016.8	Chr16	21	21	0	0	0	0	21	21	0	0	0	0
NC_000017.9	Chr17	15	6	7	0	0	2	15	6	7	0	0	2
NC_000018.8	Chr18	6	6	0	0	0	0	6	6	0	0	0	0
NC_000019.8	Chr19	10	7	0	0	0	3	10	7	0	0	0	3
NC_000020.9	Chr20	3	3	0	0	0	0	3	3	0	0	0	0
NC_000021.7	Chr21	3	3	0	0	0	0	3	3	0	0	0	0
NC_000022.8	Chr22	18	17	0	0	0	1	18	17	0	0	0	1
NC_000023.8	ChrX	8	4	0	1	0	3	8	4	0	1	0	3

			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	32	23	4	1	1	3	32	23	4	1	1	3
NC_000002.9	Chr2	31	28	3	0	0	0	31	28	3	0	0	0
NC_000003.9	Chr3	21	20	0	0	0	1	21	20	0	0	0	1
NC_000004.9	Chr4	20	18	1	0	0	1	20	18	1	0	0	1
NC_000005.8	Chr5	24	20	0	1	0	3	24	20	0	1	0	3
NC_000006.9	Chr6	10	8	0	0	0	2	10	8	0	0	0	2
NC_000007.11	Chr7	17	12	2	0	0	3	17	12	2	0	0	3
NC_000008.9	Chr8	30	25	0	0	0	5	30	25	0	0	0	5
NC_000009.9	Chr9	21	18	1	1	0	1	21	18	1	1	0	1
NC_000010.8	Chr10	13	11	0	0	0	2	13	11	0	0	0	2
NC_000011.8	Chr11	15	13	1	0	0	1	15	13	1	0	0	1
NC_000012.9	Chr12	5	5	0	0	0	0	5	5	0	0	0	0
NC_000013.9	Chr13	10	10	0	0	0	0	10	10	0	0	0	0
NC_000014.7	Chr14	11	5	1	1	0	4	11	5	1	1	0	4
NC_000015.8	Chr15	24	16	1	1	0	6	24	16	1	1	0	6
NC_000016.8	Chr16	21	17	0	2	0	2	21	17	0	2	0	2
NC_000017.9	Chr17	15	7	6	0	0	2	15	7	6	0	0	2
NC_000018.8	Chr18	6	6	0	0	0	0	6	6	0	0	0	0
NC_000019.8	Chr19	10	8	0	0	0	2	10	8	0	0	0	2
NC_000020.9	Chr20	3	3	0	0	0	0	3	3	0	0	0	0
NC_000021.7	Chr21	3	3	0	0	0	0	3	3	0	0	0	0
NC_000022.8	Chr22	18	5	7	0	0	6	18	5	7	0	0	6
NC_000023.8	ChrX	8	4	3	1	0	0	8	4	3	1	0	0

Samplesets

Number of Samplesets: 1

Size:: 9
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA12156	B-Lymphocyte	NA12156	Female	UTAH/MORMON	81 Years	Not reported
NA18507	B-Lymphocyte	NA18507	Male	YORUBA		Not reported
NA12878	B-Lymphocyte	NA12878	Female	UTAH/MORMON		Not reported
NA19129	B-Lymphocyte	NA19129	Female	YORUBA		Not reported
NA18956	B-Lymphocyte	NA18956	Female	JAPANESE		Not reported
NA15510	B-Lymphocyte	NA15510	Female			Not reported
NA18517	B-Lymphocyte	NA18517	Female	YORUBA		Not reported
NA19240	B-Lymphocyte	NA19240	Female	YORUBA		Not reported
NA18555	B-Lymphocyte	NA18555	Female	HAN CHINESE		Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Data	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Illumina Human1Mv1 DNA Analysis BeadChip (Human1Mv1_C)	GEO	368

dbVar

Database of genomic structural variation

nstd14 (Cooper et al. 2008)

Links

Detailed Information: Download 368 Variant Regions, Download 368 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: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd14 (Cooper et al. 2008)

Links

Detailed Information: Download 368 Variant Regions, Download 368 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: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: