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
Detailed Information: Download 5513 Variant Regions, Download 5513 Variant Calls, Download Both, FTP
Variant Summary
Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)
| 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 |
| 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
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 |