estd218 - Simpson et al 2015 - dbVar Study

estd218 (Simpson et al. 2015)

Organism:: Human
Study Type:: Case-Set
Submitter:: Dianne Newbury
Description:: An exploratory genome-wide copy number variant (CNV) study was performed in 127 independent cases with specific language impairment (SLI) and their first-degree relatives (385 individuals). See Variant Summary counts for estd218 in dbVar Variant Summary.
Publication(s):: Simpson et al. 2015

Links

Source: NCBI

Detailed Information: Download 5513 Variant Regions, Download 5513 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

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

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	366	366	Remapped	NC_000001.11
NC_000002.12	Chr2	529	529	Remapped	NC_000002.12
NC_000003.12	Chr3	520	520	Remapped	NC_000003.12
NC_000004.12	Chr4	222	222	Remapped	NC_000004.12
NC_000005.10	Chr5	367	367	Remapped	NC_000005.10
NC_000006.12	Chr6	437	437	Remapped	NC_000006.12
NC_000007.14	Chr7	328	328	Remapped	NC_000007.14
NC_000008.11	Chr8	347	347	Remapped	NC_000008.11
NC_000009.12	Chr9	173	173	Remapped	NC_000009.12
NC_000010.11	Chr10	271	271	Remapped	NC_000010.11
NC_000011.10	Chr11	367	367	Remapped	NC_000011.10
NC_000012.12	Chr12	286	286	Remapped	NC_000012.12
NC_000013.11	Chr13	122	122	Remapped	NC_000013.11
NC_000014.9	Chr14	132	132	Remapped	NC_000014.9
NC_000015.10	Chr15	200	200	Remapped	NC_000015.10
NC_000016.10	Chr16	103	103	Remapped	NC_000016.10
NC_000017.11	Chr17	158	158	Remapped	NC_000017.11
NC_000018.10	Chr18	121	121	Remapped	NC_000018.10
NC_000019.10	Chr19	250	250	Remapped	NC_000019.10
NC_000020.11	Chr20	58	58	Remapped	NC_000020.11
NC_000021.9	Chr21	32	32	Remapped	NC_000021.9
NC_000022.11	Chr22	58	58	Remapped	NC_000022.11
NC_000023.11	ChrX	65	65	Remapped	NC_000023.11
NT_187515.1	Chr1\|NT_187515.1	1	1	Remapped	NT_187515.1
NT_187516.1	Chr1\|NT_187516.1	1	1	Remapped	NT_187516.1
NW_003315907.2	Chr1\|NW_003315907.2	4	4	Remapped	NW_003315907.2
NW_011332688.1	Chr1\|NW_011332688.1	3	3	Remapped	NW_011332688.1
NW_012132914.1	Chr1\|NW_012132914.1	19	19	Remapped	NW_012132914.1
NW_014040927.1	Chr1\|NW_014040927.1	1	1	Remapped	NW_014040927.1
NT_187523.1	Chr2\|NT_187523.1	40	40	Remapped	NT_187523.1
NT_187647.1	Chr2\|NT_187647.1	40	40	Remapped	NT_187647.1
NT_187689.1	Chr3\|NT_187689.1	2	2	Remapped	NT_187689.1
NT_187532.1	Chr3\|NT_187532.1	2	2	Remapped	NT_187532.1
NW_018654711.1	Chr3\|NW_018654711.1	2	2	Remapped	NW_018654711.1
NW_019805488.1	Chr3\|NW_019805488.1	11	11	Remapped	NW_019805488.1
NT_187540.1	Chr4\|NT_187540.1	1	1	Remapped	NT_187540.1
NW_013171799.1	Chr4\|NW_013171799.1	1	1	Remapped	NW_013171799.1
NT_187546.1	Chr5\|NT_187546.1	2	2	Remapped	NT_187546.1
NT_187651.1	Chr5\|NT_187651.1	8	8	Remapped	NT_187651.1
NT_187652.1	Chr5\|NT_187652.1	2	2	Remapped	NT_187652.1
NW_003315917.2	Chr5\|NW_003315917.2	8	8	Remapped	NW_003315917.2
NW_003315920.1	Chr5\|NW_003315920.1	2	2	Remapped	NW_003315920.1
NT_187556.1	Chr6\|NT_187556.1	2	2	Remapped	NT_187556.1
NW_012132918.1	Chr6\|NW_012132918.1	4	4	Remapped	NW_012132918.1
NT_187558.1	Chr7\|NT_187558.1	22	22	Remapped	NT_187558.1
NT_187561.1	Chr7\|NT_187561.1	1	1	Remapped	NT_187561.1
NT_187562.1	Chr7\|NT_187562.1	25	25	Remapped	NT_187562.1
NT_187653.1	Chr7\|NT_187653.1	22	22	Remapped	NT_187653.1
NW_018654714.1	Chr7\|NW_018654714.1	3	3	Remapped	NW_018654714.1
NW_019805493.1	Chr7\|NW_019805493.1	1	1	Remapped	NW_019805493.1
NT_187571.1	Chr8\|NT_187571.1	1	1	Remapped	NT_187571.1
NT_187576.1	Chr8\|NT_187576.1	18	18	Remapped	NT_187576.1
NW_018654716.1	Chr8\|NW_018654716.1	2	2	Remapped	NW_018654716.1
NW_018654717.1	Chr8\|NW_018654717.1	13	13	Remapped	NW_018654717.1
NW_003315934.1	Chr10\|NW_003315934.1	3	3	Remapped	NW_003315934.1
NW_019805495.1	Chr11\|NW_019805495.1	9	9	Remapped	NW_019805495.1
NT_187587.1	Chr12\|NT_187587.1	45	45	Remapped	NT_187587.1
NW_018654718.1	Chr12\|NW_018654718.1	12	12	Remapped	NW_018654718.1
NT_187592.1	Chr13\|NT_187592.1	1	1	Remapped	NT_187592.1
NT_187594.1	Chr13\|NT_187594.1	1	1	Remapped	NT_187594.1
NT_187600.1	Chr14\|NT_187600.1	6	6	Remapped	NT_187600.1
NW_018654722.1	Chr14\|NW_018654722.1	4	4	Remapped	NW_018654722.1
NT_187660.1	Chr15\|NT_187660.1	13	13	Remapped	NT_187660.1
NT_187605.1	Chr15\|NT_187605.1	3	3	Remapped	NT_187605.1
NW_011332701.1	Chr15\|NW_011332701.1	13	13	Remapped	NW_011332701.1
NT_187607.1	Chr16\|NT_187607.1	4	4	Remapped	NT_187607.1
NW_017852933.1	Chr16\|NW_017852933.1	4	4	Remapped	NW_017852933.1
NT_187661.1	Chr17\|NT_187661.1	58	58	Remapped	NT_187661.1
NT_187663.1	Chr17\|NT_187663.1	29	29	Remapped	NT_187663.1
NT_187612.1	Chr17\|NT_187612.1	1	1	Remapped	NT_187612.1
NT_187614.1	Chr17\|NT_187614.1	58	58	Remapped	NT_187614.1
NW_003315957.1	Chr18\|NW_003315957.1	1	1	Remapped	NW_003315957.1
NW_003315960.1	Chr18\|NW_003315960.1	1	1	Remapped	NW_003315960.1
NW_019805503.1	Chr18\|NW_019805503.1	2	2	Remapped	NW_019805503.1
NT_187693.1	Chr19\|NT_187693.1	18	18	Remapped	NT_187693.1
NW_003571061.2	Chr19\|NW_003571061.2	3	3	Remapped	NW_003571061.2
NW_003571060.1	Chr19\|NW_003571060.1	16	16	Remapped	NW_003571060.1
NW_003571055.2	Chr19\|NW_003571055.2	2	2	Remapped	NW_003571055.2
NT_187620.1	Chr19\|NT_187620.1	1	1	Remapped	NT_187620.1
NW_003315962.1	Chr19\|NW_003315962.1	9	9	Remapped	NW_003315962.1
NW_003571054.1	Chr19\|NW_003571054.1	18	18	Remapped	NW_003571054.1
NW_003315968.2	Chr21\|NW_003315968.2	7	7	Remapped	NW_003315968.2
NW_003315970.2	Chr21\|NW_003315970.2	1	1	Remapped	NW_003315970.2

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	366	366	Submitted	NC_000001.10
NC_000002.11	Chr2	529	529	Submitted	NC_000002.11
NC_000003.11	Chr3	520	520	Submitted	NC_000003.11
NC_000004.11	Chr4	222	222	Submitted	NC_000004.11
NC_000005.9	Chr5	367	367	Submitted	NC_000005.9
NC_000006.11	Chr6	437	437	Submitted	NC_000006.11
NC_000007.13	Chr7	328	328	Submitted	NC_000007.13
NC_000008.10	Chr8	347	347	Submitted	NC_000008.10
NC_000009.11	Chr9	173	173	Submitted	NC_000009.11
NC_000010.10	Chr10	272	272	Submitted	NC_000010.10
NC_000011.9	Chr11	367	367	Submitted	NC_000011.9
NC_000012.11	Chr12	286	286	Submitted	NC_000012.11
NC_000013.10	Chr13	122	122	Submitted	NC_000013.10
NC_000014.8	Chr14	132	132	Submitted	NC_000014.8
NC_000015.9	Chr15	200	200	Submitted	NC_000015.9
NC_000016.9	Chr16	103	103	Submitted	NC_000016.9
NC_000017.10	Chr17	158	158	Submitted	NC_000017.10
NC_000018.9	Chr18	121	121	Submitted	NC_000018.9
NC_000019.9	Chr19	250	250	Submitted	NC_000019.9
NC_000020.10	Chr20	58	58	Submitted	NC_000020.10
NC_000021.8	Chr21	32	32	Submitted	NC_000021.8
NC_000022.10	Chr22	58	58	Submitted	NC_000022.10
NC_000023.10	ChrX	65	65	Submitted	NC_000023.10

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_000001.10	Chr1	366	219	109	9	0	29	366	219	109	9	0	29
NC_000002.11	Chr2	529	417	69	3	0	40	529	417	69	3	0	40
NC_000003.11	Chr3	520	501	4	0	0	15	520	501	4	0	0	15
NC_000004.11	Chr4	222	213	7	0	0	2	222	213	7	0	0	2
NC_000005.9	Chr5	367	349	6	0	0	12	367	349	6	0	0	12
NC_000006.11	Chr6	437	429	2	0	0	6	437	429	2	0	0	6
NC_000007.13	Chr7	328	260	14	2	0	52	328	260	14	2	0	52
NC_000008.10	Chr8	347	310	1	2	0	34	347	310	1	2	0	34
NC_000009.11	Chr9	173	172	1	0	0	0	173	172	1	0	0	0
NC_000010.10	Chr10	272	260	4	4	1	3	272	260	4	4	1	3
NC_000011.9	Chr11	367	355	3	0	0	9	367	355	3	0	0	9
NC_000012.11	Chr12	286	229	0	0	0	57	286	229	0	0	0	57
NC_000013.10	Chr13	122	117	0	3	0	2	122	117	0	3	0	2
NC_000014.8	Chr14	132	115	4	3	0	10	132	115	4	3	0	10
NC_000015.9	Chr15	200	175	8	1	0	16	200	175	8	1	0	16
NC_000016.9	Chr16	103	94	0	1	0	8	103	94	0	1	0	8
NC_000017.10	Chr17	158	57	9	4	0	88	158	57	9	4	0	88
NC_000018.9	Chr18	121	116	1	0	0	4	121	116	1	0	0	4
NC_000019.9	Chr19	250	218	3	1	0	28	250	218	3	1	0	28
NC_000020.10	Chr20	58	55	3	0	0	0	58	55	3	0	0	0
NC_000021.8	Chr21	32	23	1	0	0	8	32	23	1	0	0	8
NC_000022.10	Chr22	58	51	6	1	0	0	58	51	6	1	0	0
NC_000023.10	ChrX	65	48	14	3	0	0	65	48	14	3	0	0

Samplesets

Number of Samplesets: 1

Sampleset Type:: Case
Description:: 127 indepenedent cases affected by SLI and their first degree relatives (sibs and parents)
Size:: 512
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Specific language impairment 1

Samples for sampleset 1 (displaying 100 of the 512 samples)
Sample ID	Subject ID	Ethnicity	Subject Phenotype
SLI_105_3	SLI_105_3	British	Specific language impairment 1
SLI_113_2	SLI_113_2	British	Specific language impairment 1
SLI_115_4	SLI_115_4	British	Specific language impairment 1
SLI_121_2	SLI_121_2	British	Specific language impairment 1
SLI_100_2	SLI_100_2	British	Specific language impairment 1
SLI_115_5	SLI_115_5	British	Specific language impairment 1
SLI_104_1	SLI_104_1	British	Specific language impairment 1
SLI_10_2	SLI_10_2	British	Specific language impairment 1
SLI_112_1	SLI_112_1	British	Specific language impairment 1
SLI_117_2	SLI_117_2	British	Specific language impairment 1
SLI_114_1	SLI_114_1	British	Specific language impairment 1
SLI_10_5	SLI_10_5	British	Specific language impairment 1
SLI_109_2	SLI_109_2	British	Specific language impairment 1
SLI_117_5	SLI_117_5	British	Specific language impairment 1
SLI_116_3	SLI_116_3	British	Specific language impairment 1
SLI_115_2	SLI_115_2	British	Specific language impairment 1
SLI_113_1	SLI_113_1	British	Specific language impairment 1
SLI_121_1	SLI_121_1	British	Specific language impairment 1
SLI_102_4	SLI_102_4	British	Specific language impairment 1
SLI_106_3	SLI_106_3	British	Specific language impairment 1
SLI_117_1	SLI_117_1	British	Specific language impairment 1
SLI_120_2	SLI_120_2	British	Specific language impairment 1
SLI_119_3	SLI_119_3	British	Specific language impairment 1
SLI_116_1	SLI_116_1	British	Specific language impairment 1
SLI_10_1	SLI_10_1	British	Specific language impairment 1
SLI_101_1	SLI_101_1	British	Specific language impairment 1
SLI_100_3	SLI_100_3	British	Specific language impairment 1
SLI_102_5	SLI_102_5	British	Specific language impairment 1
SLI_105_2	SLI_105_2	British	Specific language impairment 1
SLI_103_2	SLI_103_2	British	Specific language impairment 1
SLI_101_2	SLI_101_2	British	Specific language impairment 1
SLI_120_1	SLI_120_1	British	Specific language impairment 1
SLI_102_1	SLI_102_1	British	Specific language impairment 1
SLI_11_2	SLI_11_2	British	Specific language impairment 1
SLI_119_2	SLI_119_2	British	Specific language impairment 1
SLI_108_4	SLI_108_4	British	Specific language impairment 1
SLI_120_4	SLI_120_4	British	Specific language impairment 1
SLI_107_4	SLI_107_4	British	Specific language impairment 1
SLI_114_2	SLI_114_2	British	Specific language impairment 1
SLI_112_3	SLI_112_3	British	Specific language impairment 1
SLI_113_3	SLI_113_3	British	Specific language impairment 1
SLI_106_2	SLI_106_2	British	Specific language impairment 1
SLI_101_4	SLI_101_4	British	Specific language impairment 1
SLI_108_5	SLI_108_5	British	Specific language impairment 1
SLI_117_4	SLI_117_4	British	Specific language impairment 1
SLI_109_3	SLI_109_3	British	Specific language impairment 1
SLI_124_1	SLI_124_1	British	Specific language impairment 1
SLI_11_1	SLI_11_1	British	Specific language impairment 1
SLI_108_2	SLI_108_2	British	Specific language impairment 1
SLI_120_3	SLI_120_3	British	Specific language impairment 1
SLI_119_4	SLI_119_4	British	Specific language impairment 1
SLI_117_3	SLI_117_3	British	Specific language impairment 1
SLI_102_2	SLI_102_2	British	Specific language impairment 1
SLI_103_1	SLI_103_1	British	Specific language impairment 1
SLI_112_4	SLI_112_4	British	Specific language impairment 1
SLI_122_1	SLI_122_1	British	Specific language impairment 1
SLI_116_2	SLI_116_2	British	Specific language impairment 1
SLI_10_4	SLI_10_4	British	Specific language impairment 1
SLI_110_2	SLI_110_2	British	Specific language impairment 1
SLI_118_1	SLI_118_1	British	Specific language impairment 1
SLI_123_2	SLI_123_2	British	Specific language impairment 1
SLI_122_3	SLI_122_3	British	Specific language impairment 1
SLI_107_3	SLI_107_3	British	Specific language impairment 1
SLI_106_1	SLI_106_1	British	Specific language impairment 1
SLI_103_5	SLI_103_5	British	Specific language impairment 1
SLI_107_1	SLI_107_1	British	Specific language impairment 1
SLI_108_1	SLI_108_1	British	Specific language impairment 1
SLI_111_5	SLI_111_5	British	Specific language impairment 1
SLI_115_3	SLI_115_3	British	Specific language impairment 1
SLI_114_3	SLI_114_3	British	Specific language impairment 1
SLI_104_2	SLI_104_2	British	Specific language impairment 1
SLI_123_1	SLI_123_1	British	Specific language impairment 1
SLI_119_1	SLI_119_1	British	Specific language impairment 1
SLI_111_4	SLI_111_4	British	Specific language impairment 1
SLI_104_3	SLI_104_3	British	Specific language impairment 1
SLI_100_1	SLI_100_1	British	Specific language impairment 1
SLI_115_1	SLI_115_1	British	Specific language impairment 1
SLI_124_2	SLI_124_2	British	Specific language impairment 1
SLI_111_2	SLI_111_2	British	Specific language impairment 1
SLI_114_4	SLI_114_4	British	Specific language impairment 1
SLI_105_4	SLI_105_4	British	Specific language impairment 1
SLI_103_4	SLI_103_4	British	Specific language impairment 1
SLI_111_1	SLI_111_1	British	Specific language impairment 1
SLI_11_3	SLI_11_3	British	Specific language impairment 1
SLI_108_3	SLI_108_3	British	Specific language impairment 1
SLI_111_3	SLI_111_3	British	Specific language impairment 1
SLI_109_1	SLI_109_1	British	Specific language impairment 1
SLI_122_2	SLI_122_2	British	Specific language impairment 1
SLI_112_2	SLI_112_2	British	Specific language impairment 1
SLI_11_4	SLI_11_4	British	Specific language impairment 1
SLI_105_1	SLI_105_1	British	Specific language impairment 1
SLI_110_1	SLI_110_1	British	Specific language impairment 1
SLI_107_2	SLI_107_2	British	Specific language impairment 1
SLI_123_3	SLI_123_3	British	Specific language impairment 1
SLI_102_3	SLI_102_3	British	Specific language impairment 1
SLI_120_5	SLI_120_5	British	Specific language impairment 1
SLI_105_5	SLI_105_5	British	Specific language impairment 1
SLI_101_3	SLI_101_3	British	Specific language impairment 1
SLI_10_3	SLI_10_3	British	Specific language impairment 1
SLI_103_3	SLI_103_3	British	Specific language impairment 1

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	Probe signal intensity	Illumina HumanOmniExpress-12v1 Beadchip	5,513
2	Validation	qPCR	Probe signal intensity	Unspecified	39

Validations

Experiment ID	Method	Analysis	Platform	Number of Variant Calls Validated
2	qPCR	Probe signal intensity	Unspecified	39

dbVar

Database of genomic structural variation

estd218 (Simpson et al. 2015)

Links

Detailed Information: Download 5513 Variant Regions, Download 5513 Variant Calls, Download Both, FTP

Variant Summary

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

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

Variant Summary for:

Remapping summary: