nstd17 - Conrad et al 2005 - dbVar Study

nstd17 (Conrad et al. 2005)

Organism:: Human
Study Type:: Control Set
Submitter:: Donald Conrad
Description:: We report a new method that uses SNP genotype data from parent-offspring trios to identify polymorphic deletions. We applied this method to data from the International HapMap Project to produce the first high-resolution population surveys of deletion polymorphism. Approximately 100 of these deletions have been experimentally validated using comparative genome hybridization on tiling-resolution oligonucleotide microarrays. Our analysis identifies a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the families. See Variant Summary counts for nstd17 in dbVar Variant Summary.
Publication(s):: Conrad et al. 2005

Links

Source: NCBI

Detailed Information: Download 935 Variant Regions, Download 935 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	120	120	Remapped	NC_000001.11
NC_000002.12	Chr2	58	58	Remapped	NC_000002.12
NC_000003.12	Chr3	76	76	Remapped	NC_000003.12
NC_000004.12	Chr4	121	121	Remapped	NC_000004.12
NC_000005.10	Chr5	23	23	Remapped	NC_000005.10
NC_000006.12	Chr6	70	70	Remapped	NC_000006.12
NC_000007.14	Chr7	69	69	Remapped	NC_000007.14
NC_000008.11	Chr8	81	81	Remapped	NC_000008.11
NC_000009.12	Chr9	27	27	Remapped	NC_000009.12
NC_000010.11	Chr10	77	77	Remapped	NC_000010.11
NC_000011.10	Chr11	21	21	Remapped	NC_000011.10
NC_000012.12	Chr12	76	76	Remapped	NC_000012.12
NC_000013.11	Chr13	24	24	Remapped	NC_000013.11
NC_000014.9	Chr14	3	3	Remapped	NC_000014.9
NC_000015.10	Chr15	6	6	Remapped	NC_000015.10
NC_000016.10	Chr16	11	11	Remapped	NC_000016.10
NC_000017.11	Chr17	6	6	Remapped	NC_000017.11
NC_000018.10	Chr18	13	13	Remapped	NC_000018.10
NC_000019.10	Chr19	7	7	Remapped	NC_000019.10
NC_000020.11	Chr20	11	11	Remapped	NC_000020.11
NC_000021.9	Chr21	8	8	Remapped	NC_000021.9
NC_000022.11	Chr22	9	9	Remapped	NC_000022.11
NC_000023.11	ChrX	2	2	Remapped	NC_000023.11
NW_018654707.1	Chr1\|NW_018654707.1	8	8	Remapped	NW_018654707.1
NT_187678.1	Chr3\|NT_187678.1	1	1	Remapped	NT_187678.1
NT_187688.1	Chr3\|NT_187688.1	1	1	Remapped	NT_187688.1
NT_187689.1	Chr3\|NT_187689.1	1	1	Remapped	NT_187689.1
NT_187690.1	Chr3\|NT_187690.1	1	1	Remapped	NT_187690.1
NT_187691.1	Chr3\|NT_187691.1	1	1	Remapped	NT_187691.1
NT_187532.1	Chr3\|NT_187532.1	1	1	Remapped	NT_187532.1
NT_187539.1	Chr3\|NT_187539.1	2	2	Remapped	NT_187539.1
NT_187649.1	Chr3\|NT_187649.1	1	1	Remapped	NT_187649.1
NW_003871060.2	Chr3\|NW_003871060.2	1	1	Remapped	NW_003871060.2
NW_019805489.1	Chr3\|NW_019805489.1	1	1	Remapped	NW_019805489.1
NT_187544.1	Chr4\|NT_187544.1	1	1	Remapped	NT_187544.1
NT_187545.1	Chr4\|NT_187545.1	2	2	Remapped	NT_187545.1
NW_003315914.1	Chr4\|NW_003315914.1	1	1	Remapped	NW_003315914.1
NW_003315915.1	Chr4\|NW_003315915.1	6	6	Remapped	NW_003315915.1
NT_167246.2	Chr6\|NT_167246.2	16	16	Remapped	NT_167246.2
NT_167247.2	Chr6\|NT_167247.2	11	11	Remapped	NT_167247.2
NT_167248.2	Chr6\|NT_167248.2	17	17	Remapped	NT_167248.2
NT_167249.2	Chr6\|NT_167249.2	17	17	Remapped	NT_167249.2
NT_167245.2	Chr6\|NT_167245.2	15	15	Remapped	NT_167245.2
NT_113891.3	Chr6\|NT_113891.3	18	18	Remapped	NT_113891.3
NT_167244.2	Chr6\|NT_167244.2	11	11	Remapped	NT_167244.2
NW_018654713.1	Chr6\|NW_018654713.1	1	1	Remapped	NW_018654713.1
NW_018654714.1	Chr7\|NW_018654714.1	1	1	Remapped	NW_018654714.1
NT_187576.1	Chr8\|NT_187576.1	4	4	Remapped	NT_187576.1
NW_018654717.1	Chr8\|NW_018654717.1	6	6	Remapped	NW_018654717.1
NW_013171806.1	Chr10\|NW_013171806.1	5	5	Remapped	NW_013171806.1
NW_003315936.1	Chr11\|NW_003315936.1	1	1	Remapped	NW_003315936.1
NT_187658.1	Chr12\|NT_187658.1	4	4	Remapped	NT_187658.1
NW_003315940.1	Chr12\|NW_003315940.1	1	1	Remapped	NW_003315940.1
NW_011332696.1	Chr12\|NW_011332696.1	1	1	Remapped	NW_011332696.1
NW_019805499.1	Chr12\|NW_019805499.1	1	1	Remapped	NW_019805499.1
NT_187594.1	Chr13\|NT_187594.1	2	2	Remapped	NT_187594.1
NW_011332699.1	Chr13\|NW_011332699.1	1	1	Remapped	NW_011332699.1
NW_011332701.1	Chr15\|NW_011332701.1	1	1	Remapped	NW_011332701.1
NT_187665.1	Chr18\|NT_187665.1	1	1	Remapped	NT_187665.1
NW_003315958.1	Chr18\|NW_003315958.1	1	1	Remapped	NW_003315958.1
NT_187693.1	Chr19\|NT_187693.1	1	1	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	121	121	Remapped	NC_000001.10
NC_000002.11	Chr2	58	58	Remapped	NC_000002.11
NC_000003.11	Chr3	76	76	Remapped	NC_000003.11
NC_000004.11	Chr4	121	121	Remapped	NC_000004.11
NC_000005.9	Chr5	23	23	Remapped	NC_000005.9
NC_000006.11	Chr6	71	71	Remapped	NC_000006.11
NC_000007.13	Chr7	68	68	Remapped	NC_000007.13
NC_000008.10	Chr8	82	82	Remapped	NC_000008.10
NC_000009.11	Chr9	27	27	Remapped	NC_000009.11
NC_000010.10	Chr10	78	78	Remapped	NC_000010.10
NC_000011.9	Chr11	21	21	Remapped	NC_000011.9
NC_000012.11	Chr12	76	76	Remapped	NC_000012.11
NC_000013.10	Chr13	24	24	Remapped	NC_000013.10
NC_000014.8	Chr14	3	3	Remapped	NC_000014.8
NC_000015.9	Chr15	6	6	Remapped	NC_000015.9
NC_000016.9	Chr16	10	10	Remapped	NC_000016.9
NC_000017.10	Chr17	6	6	Remapped	NC_000017.10
NC_000018.9	Chr18	13	13	Remapped	NC_000018.9
NC_000019.9	Chr19	7	7	Remapped	NC_000019.9
NC_000020.10	Chr20	11	11	Remapped	NC_000020.10
NC_000021.8	Chr21	8	8	Remapped	NC_000021.8
NC_000022.10	Chr22	9	9	Remapped	NC_000022.10
NC_000023.10	ChrX	2	2	Remapped	NC_000023.10
NW_003871055.3	Chr1\|NW_003871055.3	11	11	Remapped	NW_003871055.3
NW_003871056.3	Chr1\|NW_003871056.3	1	1	Remapped	NW_003871056.3
NW_003871058.1	Chr3\|NW_003871058.1	1	1	Remapped	NW_003871058.1
NW_003871060.1	Chr3\|NW_003871060.1	1	1	Remapped	NW_003871060.1
NW_003315914.1	Chr4\|NW_003315914.1	1	1	Remapped	NW_003315914.1
NW_003315915.1	Chr4\|NW_003315915.1	6	6	Remapped	NW_003315915.1
NT_113891.2	Chr6\|NT_113891.2	18	18	Remapped	NT_113891.2
NT_167244.1	Chr6\|NT_167244.1	11	11	Remapped	NT_167244.1
NT_167245.1	Chr6\|NT_167245.1	16	16	Remapped	NT_167245.1
NT_167246.1	Chr6\|NT_167246.1	17	17	Remapped	NT_167246.1
NT_167247.1	Chr6\|NT_167247.1	11	11	Remapped	NT_167247.1
NT_167248.1	Chr6\|NT_167248.1	17	17	Remapped	NT_167248.1
NT_167249.1	Chr6\|NT_167249.1	18	18	Remapped	NT_167249.1
NW_003871063.1	Chr6\|NW_003871063.1	11	11	Remapped	NW_003871063.1
NW_003571042.1	Chr8\|NW_003571042.1	4	4	Remapped	NW_003571042.1
NW_003871068.1	Chr10\|NW_003871068.1	4	4	Remapped	NW_003871068.1
NW_003871070.1	Chr10\|NW_003871070.1	2	2	Remapped	NW_003871070.1
NW_003315936.1	Chr11\|NW_003315936.1	1	1	Remapped	NW_003315936.1
NW_003315940.1	Chr12\|NW_003315940.1	1	1	Remapped	NW_003315940.1
NW_004166864.2	Chr17\|NW_004166864.2	2	2	Remapped	NW_004166864.2
NW_003315958.1	Chr18\|NW_003315958.1	1	1	Remapped	NW_003315958.1
NW_003571053.2	Chr19\|NW_003571053.2	2	2	Remapped	NW_003571053.2
NW_004166865.1	Chr19\|NW_004166865.1	1	1	Remapped	NW_004166865.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.7	Chr1	121	121	Submitted	NC_000001.7
GPC_000000200.1	Chr2	58	58	Submitted	GPC_000000200.1
NC_000003.8	Chr3	76	76	Submitted	NC_000003.8
NC_000004.8	Chr4	130	130	Submitted	NC_000004.8
NC_000005.7	Chr5	23	23	Submitted	NC_000005.7
NC_000006.8	Chr6	72	72	Submitted	NC_000006.8
NC_000007.10	Chr7	68	68	Submitted	NC_000007.10
NC_000008.8	Chr8	85	85	Submitted	NC_000008.8
GPC_000000201.1	Chr9	27	27	Submitted	GPC_000000201.1
NC_000010.7	Chr10	78	78	Submitted	NC_000010.7
NC_000011.7	Chr11	21	21	Submitted	NC_000011.7
NC_000012.8	Chr12	76	76	Submitted	NC_000012.8
NC_000013.8	Chr13	24	24	Submitted	NC_000013.8
NC_000014.6	Chr14	3	3	Submitted	NC_000014.6
NC_000015.7	Chr15	6	6	Submitted	NC_000015.7
NC_000016.7	Chr16	10	10	Submitted	NC_000016.7
NC_000017.8	Chr17	6	6	Submitted	NC_000017.8
NC_000018.7	Chr18	13	13	Submitted	NC_000018.7
NC_000019.8	Chr19	8	8	Submitted	NC_000019.8
NC_000020.8	Chr20	11	11	Submitted	NC_000020.8
NC_000021.6	Chr21	8	8	Submitted	NC_000021.6
NC_000022.7	Chr22	9	9	Submitted	NC_000022.7
NC_000023.7	ChrX	2	2	Submitted	NC_000023.7

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	58	57	0	1	0	0	58	57	0	1	0	0
GPC_000000201.1	Chr9	27	27	0	0	0	0	27	27	0	0	0	0
NC_000001.7	Chr1	121	103	2	4	0	12	121	103	2	4	0	12
NC_000003.8	Chr3	76	73	1	0	0	2	76	73	1	0	0	2
NC_000004.8	Chr4	130	114	0	0	9	7	130	114	0	0	9	7
NC_000005.7	Chr5	23	23	0	0	0	0	23	23	0	0	0	0
NC_000006.8	Chr6	72	53	0	1	0	18	72	53	0	1	0	18
NC_000007.10	Chr7	68	67	0	1	0	0	68	67	0	1	0	0
NC_000008.8	Chr8	85	80	1	3	0	1	85	80	1	3	0	1
NC_000010.7	Chr10	78	72	0	0	0	6	78	72	0	0	0	6
NC_000011.7	Chr11	21	20	0	0	0	1	21	20	0	0	0	1
NC_000012.8	Chr12	76	75	0	0	0	1	76	75	0	0	0	1
NC_000013.8	Chr13	24	24	0	0	0	0	24	24	0	0	0	0
NC_000014.6	Chr14	3	3	0	0	0	0	3	3	0	0	0	0
NC_000015.7	Chr15	6	5	0	1	0	0	6	5	0	1	0	0
NC_000016.7	Chr16	10	10	0	0	0	0	10	10	0	0	0	0
NC_000017.8	Chr17	6	4	0	0	0	2	6	4	0	0	0	2
NC_000018.7	Chr18	13	12	0	0	0	1	13	12	0	0	0	1
NC_000019.8	Chr19	8	5	1	0	0	2	8	5	1	0	0	2
NC_000020.8	Chr20	11	10	1	0	0	0	11	10	1	0	0	0
NC_000021.6	Chr21	8	7	1	0	0	0	8	7	1	0	0	0
NC_000022.7	Chr22	9	9	0	0	0	0	9	9	0	0	0	0
NC_000023.7	ChrX	2	2	0	0	0	0	2	2	0	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
GPC_000000200.1	Chr2	58	54	3	1	0	0	58	54	3	1	0	0
GPC_000000201.1	Chr9	27	27	0	0	0	0	27	27	0	0	0	0
NC_000001.7	Chr1	121	95	13	3	1	9	121	95	13	3	1	9
NC_000003.8	Chr3	76	70	1	0	0	5	76	70	1	0	0	5
NC_000004.8	Chr4	130	111	0	0	9	10	130	111	0	0	9	10
NC_000005.7	Chr5	23	23	0	0	0	0	23	23	0	0	0	0
NC_000006.8	Chr6	72	52	0	1	0	19	72	52	0	1	0	19
NC_000007.10	Chr7	68	64	1	2	0	1	68	64	1	2	0	1
NC_000008.8	Chr8	85	76	1	2	0	6	85	76	1	2	0	6
NC_000010.7	Chr10	78	70	2	0	1	5	78	70	2	0	1	5
NC_000011.7	Chr11	21	18	2	0	0	1	21	18	2	0	0	1
NC_000012.8	Chr12	76	69	0	0	0	7	76	69	0	0	0	7
NC_000013.8	Chr13	24	22	0	0	0	2	24	22	0	0	0	2
NC_000014.6	Chr14	3	3	0	0	0	0	3	3	0	0	0	0
NC_000015.7	Chr15	6	5	0	0	0	1	6	5	0	0	0	1
NC_000016.7	Chr16	10	10	0	0	0	0	10	10	0	0	0	0
NC_000017.8	Chr17	6	6	0	0	0	0	6	6	0	0	0	0
NC_000018.7	Chr18	13	12	0	0	0	1	13	12	0	0	0	1
NC_000019.8	Chr19	8	6	2	0	0	0	8	6	2	0	0	0
NC_000020.8	Chr20	11	11	0	0	0	0	11	11	0	0	0	0
NC_000021.6	Chr21	8	7	0	0	0	1	8	7	0	0	0	1
NC_000022.7	Chr22	9	9	0	0	0	0	9	9	0	0	0	0
NC_000023.7	ChrX	2	2	0	0	0	0	2	2	0	0	0	0

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: 30 CEPH trios
Size:: 30
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA10860	B-Lymphocyte	NA10860	Male	UTAH/MORMON	50 Years	Not reported
NA10847	B-Lymphocyte	NA10847	Female	UTAH/MORMON	38 Years	Not reported
NA10839	B-Lymphocyte	NA10839	Female	UTAH/MORMON	55 Years	Not reported
NA07348	B-Lymphocyte	NA07348	Female	UTAH/MORMON	45 Years	Not reported
NA10851	B-Lymphocyte	NA10851	Male	UTAH/MORMON	52 Years	Not reported
NA12752	B-Lymphocyte	NA12752	Male	UTAH/MORMON		Not reported
NA12801	B-Lymphocyte	NA12801	Male	UTAH/MORMON		Not reported
NA07029	B-Lymphocyte	NA07029	Male	UTAH/MORMON	47 Years	Not reported
NA12865	B-Lymphocyte	NA12865	Female	UTAH/MORMON		Not reported
NA10863	B-Lymphocyte	NA10863	Female	UTAH/MORMON	43 Years	Not reported
NA10859	B-Lymphocyte	NA10859	Female	UTAH/MORMON	41 Years	Not reported
NA10855	B-Lymphocyte	NA10855	Female	UTAH/MORMON	37 Years	Not reported
NA10854	B-Lymphocyte	NA10854	Female	UTAH/MORMON	42 Years	Not reported
NA10838	B-Lymphocyte	NA10838	Male	UTAH/MORMON	60 Years	Not reported
NA06991	B-Lymphocyte	NA06991	Female	UTAH/MORMON	42 Years	Not reported
NA07019	B-Lymphocyte	NA07019	Female	UTAH/MORMON	45 Years	Not reported
NA12707	B-Lymphocyte	NA12707	Male	UTAH/MORMON		Not reported
NA10835	B-Lymphocyte	NA10835	Male	UTAH/MORMON	39 Years	Not reported
NA10857	B-Lymphocyte	NA10857	Male	UTAH/MORMON	47 Years	Not reported
NA12878	B-Lymphocyte	NA12878	Female	UTAH/MORMON		Not reported
NA12864	B-Lymphocyte	NA12864	Male	UTAH/MORMON		Not reported
NA10831	B-Lymphocyte	NA10831	Female	UTAH/MORMON	59 Years	Not reported
NA10830	B-Lymphocyte	NA10830	Male	UTAH/MORMON	66 Years	Not reported
NA10861	B-Lymphocyte	NA10861	Female	UTAH/MORMON	49 Years	Not reported
NA10846	B-Lymphocyte	NA10846	Male	UTAH/MORMON	43 Years	Not reported
NA10856	B-Lymphocyte	NA10856	Male	UTAH/MORMON	46 Years	Not reported
NA12802	B-Lymphocyte	NA12802	Female	UTAH/MORMON		Not reported
NA07048	B-Lymphocyte	NA07048	Male	UTAH/MORMON	43 Years	Not reported
NA12740	B-Lymphocyte	NA12740	Female	UTAH/MORMON		Not reported
NA12753	B-Lymphocyte	NA12753	Female	UTAH/MORMON		Not reported

Sampleset ID:: 2
Name:: 30 Yoruba trios
Size:: 30
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
NA19132	B-Lymphocyte	NA19132	Female	YORUBA	Not reported
NA19221	B-Lymphocyte	NA19221	Female	YORUBA	Not reported
NA18500	B-Lymphocyte	NA18500	Male	YORUBA	Not reported
NA19120	B-Lymphocyte	NA19120	Male	YORUBA	Not reported
NA19103	B-Lymphocyte	NA19103	Male	YORUBA	Not reported
NA19161	B-Lymphocyte	NA19161	Male	YORUBA	Not reported
NA19211	B-Lymphocyte	NA19211	Male	YORUBA	Not reported
NA18872	B-Lymphocyte	NA18872	Male	YORUBA	Not reported
NA18854	B-Lymphocyte	NA18854	Male	YORUBA	Not reported
NA19208	B-Lymphocyte	NA19208	Male	YORUBA	Not reported
NA19145	B-Lymphocyte	NA19145	Male	YORUBA	Not reported
NA19142	B-Lymphocyte	NA19142	Male	YORUBA	Not reported
NA18863	B-Lymphocyte	NA18863	Male	YORUBA	Not reported
NA19202	B-Lymphocyte	NA19202	Female	YORUBA	Not reported
NA19194	B-Lymphocyte	NA19194	Male	YORUBA	Not reported
NA19094	B-Lymphocyte	NA19094	Female	YORUBA	Not reported
NA18503	B-Lymphocyte	NA18503	Male	YORUBA	Not reported
NA19205	B-Lymphocyte	NA19205	Male	YORUBA	Not reported
NA19154	B-Lymphocyte	NA19154	Male	YORUBA	Not reported
NA19139	B-Lymphocyte	NA19139	Male	YORUBA	Not reported
NA18914	B-Lymphocyte	NA18914	Male	YORUBA	Not reported
NA19173	B-Lymphocyte	NA19173	Male	YORUBA	Not reported
NA19129	B-Lymphocyte	NA19129	Female	YORUBA	Not reported
NA18506	B-Lymphocyte	NA18506	Male	YORUBA	Not reported
NA18521	B-Lymphocyte	NA18521	Male	YORUBA	Not reported
NA19100	B-Lymphocyte	NA19100	Female	YORUBA	Not reported
NA18860	B-Lymphocyte	NA18860	Male	YORUBA	Not reported
NA18857	B-Lymphocyte	NA18857	Male	YORUBA	Not reported
NA19240	B-Lymphocyte	NA19240	Female	YORUBA	Not reported
NA18515	B-Lymphocyte	NA18515	Male	YORUBA	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Data	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis		ftp://ftp.hapmap.org/hapmap/genotypes/2005-06_16c.1_phaseI/full/redundant-unfiltered/	935
2	Validation	Oligo aCGH	Probe signal intensity	Sanger (Hurles) - Homo sapiens - 385K feature custom tiling path array - v1.0	GEO	80

Validations

Experiment ID	Method	Analysis	Platform	Data	Number of Variant Calls Validated
2	Oligo aCGH	Probe signal intensity	Sanger (Hurles) - Homo sapiens - 385K feature custom tiling path array - v1.0	GEO	80

dbVar

Database of genomic structural variation

nstd17 (Conrad et al. 2005)

Links

Detailed Information: Download 935 Variant Regions, Download 935 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: 2

Experimental Details

Validations

Variant Summary for:

Remapping summary: