estd176 - Banerjee et al 2011 - dbVar Study

estd176 (Banerjee et al. 2011)

Organism:: Human
Study Type:: Control Set
Submitter:: Samprit Banerjee
Description:: We propose a three step computational framework (Identification of germline Changes in Copy Number or IgC2N) to discover and genotype germline CNVs. First, we detect candidate CNV loci by combining information across multiple samples without imposing restrictions to the number of coverage markers or to the variant size. Secondly, we fine tune the detection of rare variants and infer the putative copy number classes for each locus. Last, for each variant we combine the relative distance between consecutive copy number classes with genetic information in a novel attempt to estimate the reference model bias. This computational approach is applied to genome-wide data from 1250 HapMap individuals. See Variant Summary counts for estd176 in dbVar Variant Summary.
Publication(s):: Banerjee et al. 2011

Links

Source: NCBI

Detailed Information: Download 734 Variant Regions, Download 1081 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	61	86	Remapped	NC_000001.11
NC_000002.12	Chr2	55	79	Remapped	NC_000002.12
NC_000003.12	Chr3	48	76	Remapped	NC_000003.12
NC_000004.12	Chr4	74	114	Remapped	NC_000004.12
NC_000005.10	Chr5	47	63	Remapped	NC_000005.10
NC_000006.12	Chr6	47	67	Remapped	NC_000006.12
NC_000007.14	Chr7	45	65	Remapped	NC_000007.14
NC_000008.11	Chr8	40	60	Remapped	NC_000008.11
NC_000009.12	Chr9	23	37	Remapped	NC_000009.12
NC_000010.11	Chr10	35	55	Remapped	NC_000010.11
NC_000011.10	Chr11	37	56	Remapped	NC_000011.10
NC_000012.12	Chr12	37	58	Remapped	NC_000012.12
NC_000013.11	Chr13	21	31	Remapped	NC_000013.11
NC_000014.9	Chr14	20	28	Remapped	NC_000014.9
NC_000015.10	Chr15	26	34	Remapped	NC_000015.10
NC_000016.10	Chr16	30	45	Remapped	NC_000016.10
NC_000017.11	Chr17	17	26	Remapped	NC_000017.11
NC_000018.10	Chr18	26	36	Remapped	NC_000018.10
NC_000019.10	Chr19	12	19	Remapped	NC_000019.10
NC_000020.11	Chr20	14	20	Remapped	NC_000020.11
NC_000021.9	Chr21	10	15	Remapped	NC_000021.9
NC_000022.11	Chr22	9	11	Remapped	NC_000022.11
NT_187519.1	Chr1\|NT_187519.1	2	2	Remapped	NT_187519.1
NW_011332687.1	Chr1\|NW_011332687.1	1	2	Remapped	NW_011332687.1
NT_187522.1	Chr2\|NT_187522.1	1	2	Remapped	NT_187522.1
NW_019805489.1	Chr3\|NW_019805489.1	1	2	Remapped	NW_019805489.1
NW_003315914.1	Chr4\|NW_003315914.1	1	1	Remapped	NW_003315914.1
NW_013171801.1	Chr4\|NW_013171801.1	1	1	Remapped	NW_013171801.1
NT_187549.1	Chr5\|NT_187549.1	1	1	Remapped	NT_187549.1
NT_167246.2	Chr6\|NT_167246.2	1	1	Remapped	NT_167246.2
NT_187655.1	Chr8\|NT_187655.1	2	3	Remapped	NT_187655.1
NW_018654717.1	Chr8\|NW_018654717.1	5	7	Remapped	NW_018654717.1
NW_013171807.1	Chr10\|NW_013171807.1	1	2	Remapped	NW_013171807.1
NW_003315938.1	Chr12\|NW_003315938.1	1	2	Remapped	NW_003315938.1
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1
NT_167251.2	Chr17\|NT_167251.2	1	1	Remapped	NT_167251.2
NW_019805502.1	Chr18\|NW_019805502.1	1	2	Remapped	NW_019805502.1
NW_003315962.1	Chr19\|NW_003315962.1	1	1	Remapped	NW_003315962.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	61	86	Remapped	NC_000001.10
NC_000002.11	Chr2	55	79	Remapped	NC_000002.11
NC_000003.11	Chr3	48	76	Remapped	NC_000003.11
NC_000004.11	Chr4	74	114	Remapped	NC_000004.11
NC_000005.9	Chr5	47	63	Remapped	NC_000005.9
NC_000006.11	Chr6	47	67	Remapped	NC_000006.11
NC_000007.13	Chr7	45	65	Remapped	NC_000007.13
NC_000008.10	Chr8	40	60	Remapped	NC_000008.10
NC_000009.11	Chr9	23	37	Remapped	NC_000009.11
NC_000010.10	Chr10	35	55	Remapped	NC_000010.10
NC_000011.9	Chr11	37	56	Remapped	NC_000011.9
NC_000012.11	Chr12	37	58	Remapped	NC_000012.11
NC_000013.10	Chr13	21	31	Remapped	NC_000013.10
NC_000014.8	Chr14	20	28	Remapped	NC_000014.8
NC_000015.9	Chr15	26	34	Remapped	NC_000015.9
NC_000016.9	Chr16	30	45	Remapped	NC_000016.9
NC_000017.10	Chr17	17	26	Remapped	NC_000017.10
NC_000018.9	Chr18	26	36	Remapped	NC_000018.9
NC_000019.9	Chr19	12	19	Remapped	NC_000019.9
NC_000020.10	Chr20	14	20	Remapped	NC_000020.10
NC_000021.8	Chr21	10	15	Remapped	NC_000021.8
NC_000022.10	Chr22	9	11	Remapped	NC_000022.10
NW_003871055.3	Chr1\|NW_003871055.3	1	1	Remapped	NW_003871055.3
NW_003315914.1	Chr4\|NW_003315914.1	1	1	Remapped	NW_003315914.1
NT_167246.1	Chr6\|NT_167246.1	1	1	Remapped	NT_167246.1
NW_003315933.1	Chr10\|NW_003315933.1	1	2	Remapped	NW_003315933.1
NW_003315938.1	Chr12\|NW_003315938.1	1	2	Remapped	NW_003315938.1
NT_167251.1	Chr17\|NT_167251.1	1	1	Remapped	NT_167251.1
NW_003871088.1	Chr17\|NW_003871088.1	1	2	Remapped	NW_003871088.1
NW_003315962.1	Chr19\|NW_003315962.1	1	1	Remapped	NW_003315962.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	61	86	Submitted	NC_000001.9
NC_000002.10	Chr2	55	79	Submitted	NC_000002.10
NC_000003.10	Chr3	48	76	Submitted	NC_000003.10
NC_000004.10	Chr4	74	114	Submitted	NC_000004.10
NC_000005.8	Chr5	47	63	Submitted	NC_000005.8
NC_000006.10	Chr6	47	67	Submitted	NC_000006.10
NC_000007.12	Chr7	45	65	Submitted	NC_000007.12
NC_000008.9	Chr8	40	60	Submitted	NC_000008.9
NC_000009.10	Chr9	23	37	Submitted	NC_000009.10
NC_000010.9	Chr10	35	55	Submitted	NC_000010.9
NC_000011.8	Chr11	37	56	Submitted	NC_000011.8
NC_000012.10	Chr12	37	58	Submitted	NC_000012.10
NC_000013.9	Chr13	21	31	Submitted	NC_000013.9
NC_000014.7	Chr14	20	28	Submitted	NC_000014.7
NC_000015.8	Chr15	26	34	Submitted	NC_000015.8
NC_000016.8	Chr16	30	45	Submitted	NC_000016.8
NC_000017.9	Chr17	17	26	Submitted	NC_000017.9
NC_000018.8	Chr18	26	36	Submitted	NC_000018.8
NC_000019.8	Chr19	12	19	Submitted	NC_000019.8
NC_000020.9	Chr20	14	20	Submitted	NC_000020.9
NC_000021.7	Chr21	10	15	Submitted	NC_000021.7
NC_000022.9	Chr22	9	11	Submitted	NC_000022.9

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	61	60	0	0	0	1	86	85	0	0	0	1
NC_000002.10	Chr2	55	54	1	0	0	0	79	77	2	0	0	0
NC_000003.10	Chr3	48	48	0	0	0	0	76	76	0	0	0	0
NC_000004.10	Chr4	74	72	1	0	0	1	114	111	2	0	0	1
NC_000005.8	Chr5	47	47	0	0	0	0	63	63	0	0	0	0
NC_000006.10	Chr6	47	45	0	1	0	1	67	64	0	2	0	1
NC_000007.12	Chr7	45	45	0	0	0	0	65	65	0	0	0	0
NC_000008.9	Chr8	40	40	0	0	0	0	60	60	0	0	0	0
NC_000009.10	Chr9	23	23	0	0	0	0	37	37	0	0	0	0
NC_000010.9	Chr10	35	34	0	0	0	1	55	53	0	0	0	2
NC_000011.8	Chr11	37	37	0	0	0	0	56	56	0	0	0	0
NC_000012.10	Chr12	37	35	1	0	0	1	58	55	1	0	0	2
NC_000013.9	Chr13	21	21	0	0	0	0	31	31	0	0	0	0
NC_000014.7	Chr14	20	20	0	0	0	0	28	28	0	0	0	0
NC_000015.8	Chr15	26	26	0	0	0	0	34	34	0	0	0	0
NC_000016.8	Chr16	30	30	0	0	0	0	45	45	0	0	0	0
NC_000017.9	Chr17	17	15	0	0	0	2	26	23	0	0	0	3
NC_000018.8	Chr18	26	26	0	0	0	0	36	36	0	0	0	0
NC_000019.8	Chr19	12	11	0	0	0	1	19	18	0	0	0	1
NC_000020.9	Chr20	14	14	0	0	0	0	20	20	0	0	0	0
NC_000021.7	Chr21	10	10	0	0	0	0	15	15	0	0	0	0
NC_000022.9	Chr22	9	9	0	0	0	0	11	11	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
NC_000001.9	Chr1	61	58	0	0	0	3	86	82	0	0	0	4
NC_000002.10	Chr2	55	54	0	0	0	1	79	77	0	0	0	2
NC_000003.10	Chr3	48	47	0	0	0	1	76	74	0	0	0	2
NC_000004.10	Chr4	74	71	1	0	0	2	114	110	2	0	0	2
NC_000005.8	Chr5	47	46	0	0	0	1	63	62	0	0	0	1
NC_000006.10	Chr6	47	45	0	1	0	1	67	64	0	2	0	1
NC_000007.12	Chr7	45	45	0	0	0	0	65	65	0	0	0	0
NC_000008.9	Chr8	40	33	0	0	0	7	60	50	0	0	0	10
NC_000009.10	Chr9	23	23	0	0	0	0	37	37	0	0	0	0
NC_000010.9	Chr10	35	34	0	0	0	1	55	53	0	0	0	2
NC_000011.8	Chr11	37	37	0	0	0	0	56	56	0	0	0	0
NC_000012.10	Chr12	37	35	1	0	0	1	58	55	1	0	0	2
NC_000013.9	Chr13	21	21	0	0	0	0	31	31	0	0	0	0
NC_000014.7	Chr14	20	20	0	0	0	0	28	28	0	0	0	0
NC_000015.8	Chr15	26	26	0	0	0	0	34	34	0	0	0	0
NC_000016.8	Chr16	30	29	1	0	0	0	45	43	2	0	0	0
NC_000017.9	Chr17	17	16	0	0	0	1	26	25	0	0	0	1
NC_000018.8	Chr18	26	24	1	0	0	1	36	32	2	0	0	2
NC_000019.8	Chr19	12	11	0	0	0	1	19	18	0	0	0	1
NC_000020.9	Chr20	14	14	0	0	0	0	20	20	0	0	0	0
NC_000021.7	Chr21	10	10	0	0	0	0	15	15	0	0	0	0
NC_000022.9	Chr22	9	9	0	0	0	0	11	11	0	0	0	0

Samplesets

Number of Samplesets: 1

Name:: HapMap
Description:: HapMap cell lines from HapMap Consortium phase 2 & 3
Size:: 1,250
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1 (displaying 100 of the 1250 samples)
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA10836	Published sequence	NA10836	Female	Caucasian	44 Years	Not reported
NA07348	Published sequence	NA07348	Female	Caucasian	45 Years	Not reported
NA11993	Published sequence	NA11993	Female	Caucasian	80 Years	Not reported
NA10843	Published sequence	NA10843	Female	Caucasian	49 Years	Not reported
NA12154	Published sequence	NA12154	Male	Caucasian	92 Years	Not reported
NA12057	Published sequence	NA12057	Female	Caucasian	75 Years	Not reported
NA10857	Published sequence	NA10857	Male	Caucasian	47 Years	Not reported
NA11839	Published sequence	NA11839	Male	Caucasian	67 Years	Not reported
NA12156	Published sequence	NA12156	Female	Caucasian	81 Years	Not reported
NA11881	Published sequence	NA11881	Male	Caucasian	62 Years	Not reported
NA11831	Published sequence	NA11831	Male	Caucasian	73 Years	Not reported
NA10830	Published sequence	NA10830	Male	Caucasian	66 Years	Not reported
NA06993	Published sequence	NA06993	Male	Caucasian	74 Years	Not reported
NA07014	Published sequence	NA07014	Female	Caucasian	39 Years	Not reported
NA10856	Published sequence	NA10856	Male	Caucasian	46 Years	Not reported
NA10840	Published sequence	NA10840	Female	Caucasian	42 Years	Not reported
NA07048	Published sequence	NA07048	Male	Caucasian	43 Years	Not reported
NA12056	Published sequence	NA12056	Male	Caucasian	79 Years	Not reported
NA12236	Published sequence	NA12236	Female	Caucasian	86 Years	Not reported
NA10845	Published sequence	NA10845	Male	Caucasian	49 Years	Not reported
NA12155	Published sequence	NA12155	Male	Caucasian	86 Years	Not reported
NA06995	Published sequence	NA06995	Male	Caucasian	45 Years	Not reported
NA12146	Published sequence	NA12146	Male	Caucasian	61 Years	Not reported
NA11917	Published sequence	NA11917	Male	Caucasian	66 Years	Not reported
NA11920	Published sequence	NA11920	Female	Caucasian	66 Years	Not reported
NA12249	Published sequence	NA12249	Female	Caucasian	77 Years	Not reported
NA11830	Published sequence	NA11830	Female	Caucasian	63 Years	Not reported
NA10837	Published sequence	NA10837	Male	Caucasian	43 Years	Not reported
NA10859	Published sequence	NA10859	Female	Caucasian	41 Years	Not reported
NA10838	Published sequence	NA10838	Male	Caucasian	60 Years	Not reported
NA06991	Published sequence	NA06991	Female	Caucasian	42 Years	Not reported
NA11843	Published sequence	NA11843	Male	Caucasian	77 Years	Not reported
NA11995	Published sequence	NA11995	Female	Caucasian	84 Years	Not reported
NA06989	Published sequence	NA06989	Female	Caucasian	62 Years	Not reported
NA11931	Published sequence	NA11931	Female	Caucasian	78 Years	Not reported
NA10831	Published sequence	NA10831	Female	Caucasian	59 Years	Not reported
NA11894	Published sequence	NA11894	Female	Caucasian	69 Years	Not reported
NA11829	Published sequence	NA11829	Male	Caucasian	72 Years	Not reported
NA11992	Published sequence	NA11992	Male	Caucasian	86 Years	Not reported
NA10850	Published sequence	NA10850	Female	Caucasian	48 Years	Not reported
NA12043	Published sequence	NA12043	Male	Caucasian	74 Years	Not reported
NA12003	Published sequence	NA12003	Male	Caucasian	97 Years	Not reported
NA07022	Published sequence	NA07022	Male	Caucasian	63 Years	Not reported
NA06997	Published sequence	NA06997	Female	Caucasian	40 Years	Not reported
NA06984	Published sequence	NA06984	Male	Caucasian	63 Years	Not reported
NA10860	Published sequence	NA10860	Male	Caucasian	50 Years	Not reported
NA06985	Published sequence	NA06985	Female	Caucasian	69 Years	Not reported
NA12044	Published sequence	NA12044	Female	Caucasian	70 Years	Not reported
NA10852	Published sequence	NA10852	Female	Caucasian	48 Years	Not reported
NA12264	Published sequence	NA12264	Male	Caucasian	72 Years	Not reported
NA12234	Published sequence	NA12234	Female	Caucasian	74 Years	Not reported
NA12145	Published sequence	NA12145	Female	Caucasian	70 Years	Not reported
NA10851	Published sequence	NA10851	Male	Caucasian	52 Years	Not reported
NA12004	Published sequence	NA12004	Female	Caucasian	92 Years	Not reported
NA07029	Published sequence	NA07029	Male	Caucasian	47 Years	Not reported
NA07347	Published sequence	NA07347	Male	Caucasian	86 Years	Not reported
NA07357	Published sequence	NA07357	Male	Caucasian	69 Years	Not reported
NA07045	Published sequence	NA07045	Female	Caucasian	67 Years	Not reported
NA06994	Published sequence	NA06994	Male	Caucasian	68 Years	Not reported
NA07349	Published sequence	NA07349	Male	Caucasian	49 Years	Not reported
NA11891	Published sequence	NA11891	Male	Caucasian	76 Years	Not reported
NA11930	Published sequence	NA11930	Male	Caucasian		Not reported
NA11919	Published sequence	NA11919	Male	Caucasian	67 Years	Not reported
NA11840	Published sequence	NA11840	Female	Caucasian	67 Years	Not reported
NA07051	Published sequence	NA07051	Male	Caucasian	67 Years	Not reported
NA10864	Published sequence	NA10864	Female	Caucasian	40 Years	Not reported
NA11892	Published sequence	NA11892	Female	Caucasian	73 Years	Not reported
NA07034	Published sequence	NA07034	Male	Caucasian	71 Years	Not reported
NA11918	Published sequence	NA11918	Female	Caucasian	64 Years	Not reported
NA12248	Published sequence	NA12248	Male	Caucasian	89 Years	Not reported
NA11994	Published sequence	NA11994	Male	Caucasian	80 Years	Not reported
NA07031	Published sequence	NA07031	Female	Caucasian	63 Years	Not reported
NA12005	Published sequence	NA12005	Male	Caucasian	77 Years	Not reported
NA11893	Published sequence	NA11893	Male	Caucasian	71 Years	Not reported
NA07345	Published sequence	NA07345	Female	Caucasian	69 Years	Not reported
NA06986	Published sequence	NA06986	Male	Caucasian	74 Years	Not reported
NA10853	Published sequence	NA10853	Male	Caucasian	45 Years	Not reported
NA10839	Published sequence	NA10839	Female	Caucasian	55 Years	Not reported
NA10847	Published sequence	NA10847	Female	Caucasian	38 Years	Not reported
NA12058	Published sequence	NA12058	Female	Caucasian	81 Years	Not reported
NA12006	Published sequence	NA12006	Female	Caucasian	75 Years	Not reported
NA12144	Published sequence	NA12144	Male	Caucasian	71 Years	Not reported
NA10865	Published sequence	NA10865	Male	Caucasian	42 Years	Not reported
NA12045	Published sequence	NA12045	Male	Caucasian	74 Years	Not reported
NA07055	Published sequence	NA07055	Female	Caucasian	70 Years	Not reported
NA10855	Published sequence	NA10855	Female	Caucasian	37 Years	Not reported
NA10863	Published sequence	NA10863	Female	Caucasian	43 Years	Not reported
NA07435	Published sequence	NA07435	Male	Caucasian	77 Years	Not reported
NA10854	Published sequence	NA10854	Female	Caucasian	42 Years	Not reported
NA11882	Published sequence	NA11882	Female	Caucasian	61 Years	Not reported
NA07346	Published sequence	NA07346	Female	Caucasian	85 Years	Not reported
NA07019	Published sequence	NA07019	Female	Caucasian	45 Years	Not reported
NA10835	Published sequence	NA10835	Male	Caucasian	39 Years	Not reported
NA07037	Published sequence	NA07037	Female	Caucasian	65 Years	Not reported
NA07056	Published sequence	NA07056	Female	Caucasian	65 Years	Not reported
NA10846	Published sequence	NA10846	Male	Caucasian	43 Years	Not reported
NA10861	Published sequence	NA10861	Female	Caucasian	49 Years	Not reported
NA07000	Published sequence	NA07000	Female	Caucasian	66 Years	Not reported
NA12239	Published sequence	NA12239	Female	Caucasian	61 Years	Not reported
NA11832	Published sequence	NA11832	Female	Caucasian	58 Years	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	Other	Affymetrix SNP 6.0	1,081

dbVar

Database of genomic structural variation

estd176 (Banerjee et al. 2011)

Links

Detailed Information: Download 734 Variant Regions, Download 1081 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

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

estd176 (Banerjee et al. 2011)

Links

Detailed Information: Download 734 Variant Regions, Download 1081 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

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: