nstd32 - Sharp et al 2005 - dbVar Study

nstd32 (Sharp et al. 2005)

Organism:: Human
Study Type:: Control Set
Submitter:: Evan Eichler
Description:: On the basis of the duplication architecture of the human genome, we defined a set of 130 potential rearrangement hotspots and constructed a targeted bacterial artificial chromosome (BAC) microarray (with 2,194 BACs) to assess copy-number variation in these regions by array comparative genomic hybridization. Using our segmental duplication BAC microarray, we screened a panel of 47 normal individuals, who represented populations from four continents, and we identified 119 regions of copy-number polymorphism (CNP), 73 of which were previously unreported. See Variant Summary counts for nstd32 in dbVar Variant Summary.
Publication(s):: Sharp et al. 2005

Links

Source: NCBI

Detailed Information: Download 119 Variant Regions, Download 2378 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: NCBI34 (hg16)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	11	140	Remapped	NC_000001.11
NC_000002.12	Chr2	4	9	Remapped	NC_000002.12
NC_000003.12	Chr3	2	39	Remapped	NC_000003.12
NC_000004.12	Chr4	4	75	Remapped	NC_000004.12
NC_000005.10	Chr5	6	122	Remapped	NC_000005.10
NC_000006.12	Chr6	3	26	Remapped	NC_000006.12
NC_000007.14	Chr7	10	104	Remapped	NC_000007.14
NC_000008.11	Chr8	4	182	Remapped	NC_000008.11
NC_000009.12	Chr9	7	370	Remapped	NC_000009.12
NC_000010.11	Chr10	4	11	Remapped	NC_000010.11
NC_000011.10	Chr11	2	8	Remapped	NC_000011.10
NC_000012.12	Chr12	1	1	Remapped	NC_000012.12
NC_000014.9	Chr14	2	182	Remapped	NC_000014.9
NC_000015.10	Chr15	13	203	Remapped	NC_000015.10
NC_000016.10	Chr16	4	71	Remapped	NC_000016.10
NC_000017.11	Chr17	7	209	Remapped	NC_000017.11
NC_000019.10	Chr19	1	24	Remapped	NC_000019.10
NC_000021.9	Chr21	3	63	Remapped	NC_000021.9
NC_000022.11	Chr22	7	173	Remapped	NC_000022.11
NC_000023.11	ChrX	8	183	Remapped	NC_000023.11
NC_000024.10	ChrY	6	35	Remapped	NC_000024.10
NT_187523.1	Chr2\|NT_187523.1	1	3	Remapped	NT_187523.1
NT_187647.1	Chr2\|NT_187647.1	1	3	Remapped	NT_187647.1
NT_187678.1	Chr3\|NT_187678.1	0	11	Remapped	NT_187678.1
NT_187688.1	Chr3\|NT_187688.1	0	11	Remapped	NT_187688.1
NT_187689.1	Chr3\|NT_187689.1	0	11	Remapped	NT_187689.1
NT_187690.1	Chr3\|NT_187690.1	0	11	Remapped	NT_187690.1
NT_187691.1	Chr3\|NT_187691.1	0	11	Remapped	NT_187691.1
NT_187532.1	Chr3\|NT_187532.1	0	11	Remapped	NT_187532.1
NT_187649.1	Chr3\|NT_187649.1	0	11	Remapped	NT_187649.1
NW_018654711.1	Chr3\|NW_018654711.1	1	13	Remapped	NW_018654711.1
NW_003315917.2	Chr5\|NW_003315917.2	1	32	Remapped	NW_003315917.2
NW_018654714.1	Chr7\|NW_018654714.1	1	13	Remapped	NW_018654714.1
NT_187570.1	Chr8\|NT_187570.1	0	42	Remapped	NT_187570.1
NT_187576.1	Chr8\|NT_187576.1	1	14	Remapped	NT_187576.1
NW_018654717.1	Chr8\|NW_018654717.1	1	7	Remapped	NW_018654717.1
NT_113796.3	Chr14\|NT_113796.3	1	2	Remapped	NT_113796.3
NT_187600.1	Chr14\|NT_187600.1	1	171	Remapped	NT_187600.1
NT_187660.1	Chr15\|NT_187660.1	2	41	Remapped	NT_187660.1
NT_187606.1	Chr15\|NT_187606.1	1	4	Remapped	NT_187606.1
NW_003315943.1	Chr15\|NW_003315943.1	1	8	Remapped	NW_003315943.1
NW_003315944.2	Chr15\|NW_003315944.2	1	1	Remapped	NW_003315944.2
NW_011332701.1	Chr15\|NW_011332701.1	1	33	Remapped	NW_011332701.1
NT_187383.1	Chr16\|NT_187383.1	1	6	Remapped	NT_187383.1
NT_187663.1	Chr17\|NT_187663.1	0	34	Remapped	NT_187663.1
NT_187614.1	Chr17\|NT_187614.1	1	30	Remapped	NT_187614.1
NT_187693.1	Chr19\|NT_187693.1	1	11	Remapped	NT_187693.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	11	138	Remapped	NC_000001.10
NC_000002.11	Chr2	4	9	Remapped	NC_000002.11
NC_000003.11	Chr3	2	39	Remapped	NC_000003.11
NC_000004.11	Chr4	4	75	Remapped	NC_000004.11
NC_000005.9	Chr5	6	122	Remapped	NC_000005.9
NC_000006.11	Chr6	3	26	Remapped	NC_000006.11
NC_000007.13	Chr7	10	104	Remapped	NC_000007.13
NC_000008.10	Chr8	4	183	Remapped	NC_000008.10
NC_000009.11	Chr9	6	379	Remapped	NC_000009.11
NC_000010.10	Chr10	5	31	Remapped	NC_000010.10
NC_000011.9	Chr11	2	8	Remapped	NC_000011.9
NC_000012.11	Chr12	1	1	Remapped	NC_000012.11
NC_000014.8	Chr14	2	182	Remapped	NC_000014.8
NC_000015.9	Chr15	14	186	Remapped	NC_000015.9
NC_000016.9	Chr16	5	77	Remapped	NC_000016.9
NC_000017.10	Chr17	7	209	Remapped	NC_000017.10
NC_000019.9	Chr19	1	24	Remapped	NC_000019.9
NC_000021.8	Chr21	2	25	Remapped	NC_000021.8
NC_000022.10	Chr22	7	173	Remapped	NC_000022.10
NC_000023.10	ChrX	8	183	Remapped	NC_000023.10
NC_000024.9	ChrY	6	35	Remapped	NC_000024.9
NW_003871055.3	Chr1\|NW_003871055.3	1	4	Remapped	NW_003871055.3
NW_003871056.3	Chr1\|NW_003871056.3	1	4	Remapped	NW_003871056.3
NW_003871057.1	Chr1\|NW_003871057.1	1	4	Remapped	NW_003871057.1
NW_003315917.2	Chr5\|NW_003315917.2	1	32	Remapped	NW_003315917.2
NW_004775428.1	Chr5\|NW_004775428.1	1	10	Remapped	NW_004775428.1
NW_003571039.1	Chr7\|NW_003571039.1	1	14	Remapped	NW_003571039.1
NW_004775430.1	Chr7\|NW_004775430.1	1	7	Remapped	NW_004775430.1
NW_003571042.1	Chr8\|NW_003571042.1	1	14	Remapped	NW_003571042.1
NW_003871068.1	Chr10\|NW_003871068.1	1	2	Remapped	NW_003871068.1
NW_004166863.1	Chr14\|NW_004166863.1	0	131	Remapped	NW_004166863.1
NW_003315944.1	Chr15\|NW_003315944.1	1	1	Remapped	NW_003315944.1
NW_003315949.1	Chr17\|NW_003315949.1	1	30	Remapped	NW_003315949.1
NW_003871086.1	Chr17\|NW_003871086.1	0	42	Remapped	NW_003871086.1
NW_003871094.1	Chr19\|NW_003871094.1	1	24	Remapped	NW_003871094.1
NW_004166865.1	Chr19\|NW_004166865.1	1	11	Remapped	NW_004166865.1
NW_004070877.1	ChrX\|NW_004070877.1	1	1	Remapped	NW_004070877.1
NW_004070880.2	ChrX\|NW_004070880.2	2	75	Remapped	NW_004070880.2
NW_004070888.1	ChrX\|NW_004070888.1	1	28	Remapped	NW_004070888.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.7	Chr1	13	186	Submitted	NC_000001.7
GPC_000000200.1	Chr2	4	9	Submitted	GPC_000000200.1
NC_000003.8	Chr3	2	39	Submitted	NC_000003.8
NC_000004.8	Chr4	4	75	Submitted	NC_000004.8
NC_000005.7	Chr5	7	154	Submitted	NC_000005.7
NC_000006.8	Chr6	3	26	Submitted	NC_000006.8
NC_000007.10	Chr7	10	104	Submitted	NC_000007.10
NC_000008.8	Chr8	4	183	Submitted	NC_000008.8
GPC_000000201.1	Chr9	10	430	Submitted	GPC_000000201.1
NC_000010.7	Chr10	5	31	Submitted	NC_000010.7
NC_000011.7	Chr11	2	8	Submitted	NC_000011.7
NC_000012.8	Chr12	1	1	Submitted	NC_000012.8
NC_000014.6	Chr14	2	182	Submitted	NC_000014.6
NC_000015.7	Chr15	14	207	Submitted	NC_000015.7
NC_000016.7	Chr16	5	77	Submitted	NC_000016.7
NC_000017.8	Chr17	8	215	Submitted	NC_000017.8
NC_000019.8	Chr19	2	35	Submitted	NC_000019.8
NC_000021.6	Chr21	2	25	Submitted	NC_000021.6
NC_000022.7	Chr22	7	173	Submitted	NC_000022.7
NC_000023.7	ChrX	8	183	Submitted	NC_000023.7
NC_000024.6	ChrY	6	35	Submitted	NC_000024.6

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
GPC_000000200.1	Chr2	4	3	0	1	0	0	9	6	0	3	0	0
GPC_000000201.1	Chr9	10	3	0	3	4	0	430	168	102	109	51	0
NC_000001.7	Chr1	13	8	0	3	1	1	186	105	0	33	44	4
NC_000003.8	Chr3	2	1	1	0	0	0	39	28	11	0	0	0
NC_000004.8	Chr4	4	3	0	1	0	0	75	53	0	22	0	0
NC_000005.7	Chr5	7	5	1	0	0	1	154	137	7	0	0	10
NC_000006.8	Chr6	3	2	0	1	0	0	26	19	0	7	0	0
NC_000007.10	Chr7	10	6	2	0	0	2	104	50	33	0	0	21
NC_000008.8	Chr8	4	2	0	1	0	1	183	156	0	13	0	14
NC_000010.7	Chr10	5	3	0	1	0	1	31	9	0	20	0	2
NC_000011.7	Chr11	2	2	0	0	0	0	8	8	0	0	0	0
NC_000012.8	Chr12	1	1	0	0	0	0	1	1	0	0	0	0
NC_000014.6	Chr14	2	1	0	1	0	0	182	51	0	0	0	131
NC_000015.7	Chr15	14	9	1	3	0	1	207	122	36	27	21	1
NC_000016.7	Chr16	5	3	1	0	0	1	77	54	17	0	0	6
NC_000017.8	Chr17	8	4	2	0	1	1	215	38	18	81	6	72
NC_000019.8	Chr19	2	0	1	0	0	1	35	0	11	0	0	24
NC_000021.6	Chr21	2	2	0	0	0	0	25	25	0	0	0	0
NC_000022.7	Chr22	7	6	0	1	0	0	173	158	0	15	0	0
NC_000023.7	ChrX	8	2	0	2	0	4	183	39	0	40	0	104
NC_000024.6	ChrY	6	3	1	2	0	0	35	14	7	14	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
GPC_000000200.1	Chr2	4	2	1	0	0	1	9	5	1	0	0	3
GPC_000000201.1	Chr9	10	2	1	5	2	0	430	152	140	116	22	0
NC_000001.7	Chr1	13	7	1	4	1	0	186	103	2	37	44	0
NC_000003.8	Chr3	2	0	1	0	0	1	39	15	0	0	0	24
NC_000004.8	Chr4	4	3	0	1	0	0	75	34	19	22	0	0
NC_000005.7	Chr5	7	4	3	0	0	0	154	116	38	0	0	0
NC_000006.8	Chr6	3	2	0	1	0	0	26	19	0	7	0	0
NC_000007.10	Chr7	10	6	3	0	0	1	104	44	47	0	0	13
NC_000008.8	Chr8	4	1	0	1	0	2	183	108	0	13	0	62
NC_000010.7	Chr10	5	4	0	0	1	0	31	11	0	0	20	0
NC_000011.7	Chr11	2	2	0	0	0	0	8	8	0	0	0	0
NC_000012.8	Chr12	1	1	0	0	0	0	1	1	0	0	0	0
NC_000014.6	Chr14	2	0	1	0	0	1	182	0	11	0	0	171
NC_000015.7	Chr15	14	6	3	2	0	3	207	80	53	32	0	42
NC_000016.7	Chr16	5	4	1	0	0	0	77	60	17	0	0	0
NC_000017.8	Chr17	8	4	2	0	1	1	215	80	18	47	6	64
NC_000019.8	Chr19	2	1	1	0	0	0	35	11	24	0	0	0
NC_000021.6	Chr21	2	2	0	0	0	0	25	25	0	0	0	0
NC_000022.7	Chr22	7	5	1	1	0	0	173	117	56	0	0	0
NC_000023.7	ChrX	8	3	4	1	0	0	183	40	108	35	0	0
NC_000024.6	ChrY	6	3	1	2	0	0	35	14	7	14	0	0

Samplesets

Number of Samplesets: 1

Description:: 47 normal individuals representing seven ethnicities from Asia, Europe, sub-Saharan Africa and South America.
Size:: 47
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
GM17052	B-Lymphocyte	GM17052	Female	Japanese	Not reported
GM10496A	B-Lymphocyte	GM10496	Female	Mbuti	Not reported
GM17058	B-Lymphocyte	GM17058	Female	Japanese	Not reported
GM15731	B-Lymphocyte	GM15731	Female	Czech	Not reported
GM10471	B-Lymphocyte	GM10471	Female	Biaka	Not reported
GM15730	B-Lymphocyte	GM15730	Female	Czech	Not reported
GM10469A	B-Lymphocyte	GM10469	Male	Biaka	Not reported
GM17014A	B-Lymphocyte	GM17014	Male	Chinese	Not reported
GM17059A	B-Lymphocyte	GM17059	Female	Japanese	Not reported
JK1058B	B-Lymphocyte	JK1058B		Mbuti	Not reported
GM11776	B-Lymphocyte	GM11776	Male	Amerindian	Not reported
GM11323	B-Lymphocyte	GM11323	Female	Chinese	Not reported
GM10979	B-Lymphocyte	GM10979	Female	Amerindian	Not reported
GM10473A	B-Lymphocyte	GM10473	Female	Biaka	Not reported
JK1688B	B-Lymphocyte	JK1688B		Biaka	Not reported
GM10969	B-Lymphocyte	GM10969	Male	Amerindian	Not reported
GM10492A	B-Lymphocyte	GM10492	Male	Mbuti	Not reported
GM10970	B-Lymphocyte	GM10970	Male	Amerindian	Not reported
GM15724	B-Lymphocyte	GM15724	Male	Czech	Not reported
GM15725	B-Lymphocyte	GM15725	Male	Czech	Not reported
GM10967	B-Lymphocyte	GM10967	Female	Amerindian	Not reported
GM16689	B-Lymphocyte	GM16689	Male	Chinese	Not reported
GM10494A	B-Lymphocyte	GM10494	Male	Mbuti	Not reported
GM10470A	B-Lymphocyte	GM10470	Male	Biaka	Not reported
GM11523	B-Lymphocyte	GM11523	Female	Druze	Not reported
GM17017	B-Lymphocyte	GM17017	Male	Chinese	Not reported
JK1051A	B-Lymphocyte	JK1051A		Mbuti	Not reported
GM15727	B-Lymphocyte	GM15727	Male	Czech	Not reported
GM17016	B-Lymphocyte	GM17016	Male	Chinese	Not reported
GM15729	B-Lymphocyte	GM15729	Female	Czech	Not reported
GM10971	B-Lymphocyte	GM10971	Male	Amerindian	Not reported
GM15732	B-Lymphocyte	GM15732	Female	Czech	Not reported
JK776	B-Lymphocyte	JK776		Biaka	Not reported
GM15728	B-Lymphocyte	GM15728	Male	Czech	Not reported
GM15733	B-Lymphocyte	GM15733	Female	Czech	Not reported
GM17015	B-Lymphocyte	GM17015	Male	Chinese	Not reported
GM10976	B-Lymphocyte	GM10976	Male	Amerindian	Not reported
GM15726	B-Lymphocyte	GM15726	Male	Czech	Not reported
GM16688	B-Lymphocyte	GM16688	Female	Chinese	Not reported
P86GA	B-Lymphocyte	P86GA		Mbuti	Not reported
GM17020A	B-Lymphocyte	GM17020	Male	Chinese	Not reported
GM17051	B-Lymphocyte	GM17051	Female	Japanese	Not reported
GM10495B	B-Lymphocyte	GM10495	Male	Mbuti	Not reported
GM11521	B-Lymphocyte	GM11521	Female	Druze	Not reported
JK1061	B-Lymphocyte	JK1061		Mbuti	Not reported
GM10472A	B-Lymphocyte	GM10472	Female	Biaka	Not reported
GM10493	B-Lymphocyte	GM10493	Female	Mbuti	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	BAC aCGH	Probe signal intensity	GPL4010	2,378
2	Validation	FISH	Manual observation		110

Validations

Experiment ID	Method	Analysis	Number of Variant Calls Validated
2	FISH	Manual observation	110

dbVar

Database of genomic structural variation

nstd32 (Sharp et al. 2005)

Links

Detailed Information: Download 119 Variant Regions, Download 2378 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI34 (hg16)

Remapping summary: NCBI34->GRCh37.p13NCBI34->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

Variant Summary for:

Remapping summary: