nstd58 - Forsberg et al 2012 - dbVar Study

nstd58 (Forsberg et al. 2012)

Organism:: Human
Study Type:: Control Set
Submitter:: Chiara Rasi
Description:: Using age-stratified cohorts of monozygotic twins and singleborn subjects, we describe age-related accumulation of copy number variation (CNV) in the nuclear genomes in vivo. DNA from peripheral blood was run on Illumina genotyping arrays and the LogR Ratio and B-allele-frequency data were used to identify somatic copy number events. See Variant Summary counts for nstd58 in dbVar Variant Summary.
Publication(s):: Forsberg et al. 2012

Links

Source: NCBI

Detailed Information: Download 7 Variant Regions, Download 7 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	1	1	Remapped	NC_000001.11
NC_000004.12	Chr4	1	1	Remapped	NC_000004.12
NC_000005.10	Chr5	1	1	Remapped	NC_000005.10
NC_000008.11	Chr8	1	1	Remapped	NC_000008.11
NC_000010.11	Chr10	1	1	Remapped	NC_000010.11
NC_000020.11	Chr20	2	2	Remapped	NC_000020.11

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	1	1	Remapped	NC_000001.10
NC_000004.11	Chr4	1	1	Remapped	NC_000004.11
NC_000005.9	Chr5	1	1	Remapped	NC_000005.9
NC_000008.10	Chr8	1	1	Remapped	NC_000008.10
NC_000010.10	Chr10	1	1	Remapped	NC_000010.10
NC_000020.10	Chr20	2	2	Remapped	NC_000020.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	1	1	Submitted	NC_000001.9
NC_000004.10	Chr4	1	1	Submitted	NC_000004.10
NC_000005.8	Chr5	1	1	Submitted	NC_000005.8
NC_000008.9	Chr8	1	1	Submitted	NC_000008.9
NC_000010.9	Chr10	1	1	Submitted	NC_000010.9
NC_000020.9	Chr20	2	2	Submitted	NC_000020.9

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	1	1	0	0	0	0	1	1	0	0	0	0
NC_000004.10	Chr4	1	0	1	0	0	0	1	0	1	0	0	0
NC_000005.8	Chr5	1	0	1	0	0	0	1	0	1	0	0	0
NC_000008.9	Chr8	1	1	0	0	0	0	1	1	0	0	0	0
NC_000010.9	Chr10	1	0	1	0	0	0	1	0	1	0	0	0
NC_000020.9	Chr20	2	0	2	0	0	0	2	0	2	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	1	1	0	0	0	0	1	1	0	0	0	0
NC_000004.10	Chr4	1	0	1	0	0	0	1	0	1	0	0	0
NC_000005.8	Chr5	1	0	1	0	0	0	1	0	1	0	0	0
NC_000008.9	Chr8	1	1	0	0	0	0	1	1	0	0	0	0
NC_000010.9	Chr10	1	0	1	0	0	0	1	0	1	0	0	0
NC_000020.9	Chr20	2	0	2	0	0	0	2	0	2	0	0	0

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: SATSA
Description:: Monozygotic twins over the age of 60, from the Swedish Adoption Twin Study of Aging (SATSA)
Size:: 3
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Aging

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Subject Phenotype
TP30-1	whole blood	TP30-1	Aging
TP12-2	whole blood	TP12-2	Aging
TP25-2	whole blood	TP25-2	Aging

Sampleset ID:: 2
Name:: ULSAM
Description:: Uppsala Longitudinal Study of Adult Men, singleborn individuals, 88 years old.
Size:: 3
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Aging

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Subject Phenotype
102	whole blood	102	Aging
340	whole blood	340	Aging
697	whole blood	697	Aging

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Data	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Illumina Human1M-Duov3 DNA Analysis BeadChip (Human1M-Duov3_B), Illumina Human660W Quad v1, Illumina Human660W-Quad v1.0 BeadChip	GEO	3
2	Discovery	SNP array	SNP genotyping analysis	Illumina Human1M Duo v3, Illumina Human1M-Duov3 DNA Analysis BeadChip (Human1M-Duov3_B), Illumina Human660W-Quad v1.0 BeadChip	GEO	4

dbVar

Database of genomic structural variation

nstd58 (Forsberg et al. 2012)

Links

Detailed Information: Download 7 Variant Regions, Download 7 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: 2

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd58 (Forsberg et al. 2012)

Links

Detailed Information: Download 7 Variant Regions, Download 7 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: 2

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: