nstd192 - Smajlagić et al 2020 - dbVar Study

nstd192 (Smajlagić et al. 2020)

Organism:: Human
Study Type:: Collection
Submitter:: Stefan Johansson
Description:: The study performs array-based CNV calling in 12252 mother-father-child trios from the Norwegian Mother, Father and Child Cohort Study (MoBa) and analyse the inheritance pattern of 26 common and recurrent CNVs associated with neurodevelopmental disorders. See Variant Summary counts for nstd192 in dbVar Variant Summary.
Publication(s):: Smajlagic et al. 2020

Links

Source: NCBI

Detailed Information: Download 35 Variant Regions, Download 59 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	2	2	Remapped	NC_000001.11
NC_000003.12	Chr3	1	1	Remapped	NC_000003.12
NC_000015.10	Chr15	8	14	Remapped	NC_000015.10
NC_000016.10	Chr16	9	22	Remapped	NC_000016.10
NC_000017.11	Chr17	3	4	Remapped	NC_000017.11
NC_000022.11	Chr22	6	7	Remapped	NC_000022.11
NT_187660.1	Chr15\|NT_187660.1	1	2	Remapped	NT_187660.1
NW_011332701.1	Chr15\|NW_011332701.1	2	3	Remapped	NW_011332701.1
NT_187614.1	Chr17\|NT_187614.1	4	5	Remapped	NT_187614.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	7	10	Submitted	NC_000001.10
NC_000003.11	Chr3	1	1	Submitted	NC_000003.11
NC_000015.9	Chr15	8	14	Submitted	NC_000015.9
NC_000016.9	Chr16	9	22	Submitted	NC_000016.9
NC_000017.10	Chr17	4	5	Submitted	NC_000017.10
NC_000022.10	Chr22	6	7	Submitted	NC_000022.10

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	7	0	0	2	5	0	10	0	0	2	8	0
NC_000003.11	Chr3	1	1	0	0	0	0	1	1	0	0	0	0
NC_000015.9	Chr15	8	5	0	1	0	2	14	10	0	1	0	3
NC_000016.9	Chr16	9	9	0	0	0	0	22	22	0	0	0	0
NC_000017.10	Chr17	4	0	1	0	0	3	5	0	1	0	0	4
NC_000022.10	Chr22	6	0	0	6	0	0	7	0	0	7	0	0

Samplesets

Number of Samplesets: 1

Size:: 59
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Ethnicity	Subject Phenotype
mb1:o29	mb1:o29	Norwegian ancestry	Not reported
mb1:o7	mb1:o7	Norwegian ancestry	Not reported
mb1:o45	mb1:o45	Norwegian ancestry	Not reported
mb1:o22	mb1:o22	Norwegian ancestry	Not reported
mb1:o2	mb1:o2	Norwegian ancestry	Not reported
mb1:o55	mb1:o55	Norwegian ancestry	Not reported
mb1:o38	mb1:o38	Norwegian ancestry	Not reported
mb1:o39	mb1:o39	Norwegian ancestry	Not reported
mb2:o21	mb2:o21	Norwegian ancestry	Not reported
mb1:o33	mb1:o33	Norwegian ancestry	Not reported
mb1:o19	mb1:o19	Norwegian ancestry	Not reported
mb2:o39	mb2:o39	Norwegian ancestry	Not reported
mb2:o22	mb2:o22	Norwegian ancestry	Not reported
mb1:o44	mb1:o44	Norwegian ancestry	Not reported
mb1:o46	mb1:o46	Norwegian ancestry	Not reported
mb1:o51	mb1:o51	Norwegian ancestry	Not reported
mb2:o20	mb2:o20	Norwegian ancestry	Not reported
mb2:o4	mb2:o4	Norwegian ancestry	Not reported
mb1:o53	mb1:o53	Norwegian ancestry	Not reported
mb1:o1	mb1:o1	Norwegian ancestry	Not reported
mb1:o23	mb1:o23	Norwegian ancestry	Not reported
mb1:o4	mb1:o4	Norwegian ancestry	Not reported
mb1:o13	mb1:o13	Norwegian ancestry	Not reported
mb2:o42	mb2:o42	Norwegian ancestry	Not reported
mb1:o32	mb1:o32	Norwegian ancestry	Not reported
mb2:o35	mb2:o35	Norwegian ancestry	Not reported
mb1:o26	mb1:o26	Norwegian ancestry	Not reported
mb1:o30	mb1:o30	Norwegian ancestry	Not reported
mb1:o21	mb1:o21	Norwegian ancestry	Not reported
mb1:o40	mb1:o40	Norwegian ancestry	Not reported
mb1:o52	mb1:o52	Norwegian ancestry	Not reported
mb1:o3	mb1:o3	Norwegian ancestry	Not reported
mb1:o49	mb1:o49	Norwegian ancestry	Not reported
mb2:o1	mb2:o1	Norwegian ancestry	Not reported
mb2:o5	mb2:o5	Norwegian ancestry	Not reported
mb2:o2	mb2:o2	Norwegian ancestry	Not reported
mb1:o57	mb1:o57	Norwegian ancestry	Not reported
mb1:o24	mb1:o24	Norwegian ancestry	Not reported
mb1:o36	mb1:o36	Norwegian ancestry	Not reported
mb1:o25	mb1:o25	Norwegian ancestry	Not reported
mb1:o5	mb1:o5	Norwegian ancestry	Not reported
mb1:o8	mb1:o8	Norwegian ancestry	Not reported
mb1:o31	mb1:o31	Norwegian ancestry	Not reported
mb1:o34	mb1:o34	Norwegian ancestry	Not reported
mb1:o47	mb1:o47	Norwegian ancestry	Not reported
mb1:o56	mb1:o56	Norwegian ancestry	Not reported
mb2:o14	mb2:o14	Norwegian ancestry	Not reported
mb1:o28	mb1:o28	Norwegian ancestry	Not reported
mb1:o35	mb1:o35	Norwegian ancestry	Not reported
mb1:o58	mb1:o58	Norwegian ancestry	Not reported
mb2:o6	mb2:o6	Norwegian ancestry	Not reported
mb1:o20	mb1:o20	Norwegian ancestry	Not reported
mb1:o37	mb1:o37	Norwegian ancestry	Not reported
mb1:o54	mb1:o54	Norwegian ancestry	Not reported
mb1:o50	mb1:o50	Norwegian ancestry	Not reported
mb2:o3	mb2:o3	Norwegian ancestry	Not reported
mb1:o6	mb1:o6	Norwegian ancestry	Not reported
mb2:o9	mb2:o9	Norwegian ancestry	Not reported
mb1:o14	mb1:o14	Norwegian ancestry	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Illumina HumanCoreExome-12 v.1.1 <!>Illumina HumanCoreExome-24 v.1.0 <!>llumina Global Screening Array v.1.0.	59

dbVar

Database of genomic structural variation

nstd192 (Smajlagić et al. 2020)

Links

Detailed Information: Download 35 Variant Regions, Download 59 Variant Calls, Download Both, FTP

Variant Summary

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

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

nstd192 (Smajlagić et al. 2020)

Links

Detailed Information: Download 35 Variant Regions, Download 59 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

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: