nstd104 - Dumanski et al 2014 - dbVar Study

nstd104 (Dumanski et al. 2014)

Organism:: Human
Study Type:: Control Set
Submitter:: Chiara Rasi
Description:: We analyzed the possible causes of loss of chromosome Y (LOY) in blood cells of adult men by studying 6014 men from three independent prospective cohorts: TwinGene (n=4373) in this study, and ULSAM (n=1153) and PIVUS (n=488), both in study nstd92. We demonstrated that smoking is associated with LOY in the three cohorts (odds ratios 2.4 –4.3), LOY being the most common acquired human mutation in the studied subjects. Our data also suggests that smoking has a transient and dose-dependent mutagenic effect on LOY-status. See Variant Summary counts for nstd104 in dbVar Variant Summary.
Publication(s):: Dumanski et al. 2014

Links

Source: NCBI

Detailed Information: Download 1 Variant Region, Download 328 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_000024.10	ChrY	1	328	Remapped	NC_000024.10

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000024.9	ChrY	1	328	Submitted	NC_000024.9

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_000024.9	ChrY	1	0	1	0	0	0	328	0	328	0	0	0

Samplesets

Number of Samplesets: 1

Name:: TwinGene with LOY
Sampleset Type:: Control
Description:: TwinGene men with loss of chromosome Y
Size:: 328
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Male

Samples for sampleset 1 (displaying 100 of the 328 samples)
Sample ID	Cell Type	Subject ID	Sex	Subject Age	Subject Phenotype
TG2961	whole blood	TG2961	Male	62 years	Not reported
TG1519	whole blood	TG1519	Male	73 years	Not reported
TG168	whole blood	TG168	Male	85 years	Not reported
TG1173	whole blood	TG1173	Male	82 years	Not reported
TG3117	whole blood	TG3117	Male	68 years	Not reported
TG1897	whole blood	TG1897	Male	63 years	Not reported
TG1743	whole blood	TG1743	Male	77 years	Not reported
TG1054	whole blood	TG1054	Male	70 years	Not reported
TG324	whole blood	TG324	Male	76 years	Not reported
TG2720	whole blood	TG2720	Male	65 years	Not reported
TG2016	whole blood	TG2016	Male	63 years	Not reported
TG2317	whole blood	TG2317	Male	74 years	Not reported
TG1892	whole blood	TG1892	Male	66 years	Not reported
TG1781	whole blood	TG1781	Male	80 years	Not reported
TG1707	whole blood	TG1707	Male	78 years	Not reported
TG1834	whole blood	TG1834	Male	71 years	Not reported
TG2356	whole blood	TG2356	Male	77 years	Not reported
TG135	whole blood	TG135	Male	71 years	Not reported
TG2840	whole blood	TG2840	Male	79 years	Not reported
TG2286	whole blood	TG2286	Male	74 years	Not reported
TG2854	whole blood	TG2854	Male	85 years	Not reported
TG2567	whole blood	TG2567	Male	76 years	Not reported
TG1968	whole blood	TG1968	Male	75 years	Not reported
TG1198	whole blood	TG1198	Male	65 years	Not reported
TG2742	whole blood	TG2742	Male	65 years	Not reported
TG2323	whole blood	TG2323	Male	69 years	Not reported
TG2500	whole blood	TG2500	Male	73 years	Not reported
TG240	whole blood	TG240	Male	81 years	Not reported
TG2289	whole blood	TG2289	Male	65 years	Not reported
TG3356	whole blood	TG3356	Male	67 years	Not reported
TG2772	whole blood	TG2772	Male	66 years	Not reported
TG256	whole blood	TG256	Male	62 years	Not reported
TG1905	whole blood	TG1905	Male	79 years	Not reported
TG245	whole blood	TG245	Male	76 years	Not reported
TG2971	whole blood	TG2971	Male	59 years	Not reported
TG3099	whole blood	TG3099	Male	76 years	Not reported
TG2443	whole blood	TG2443	Male	76 years	Not reported
TG1713	whole blood	TG1713	Male	67 years	Not reported
TG1341	whole blood	TG1341	Male	64 years	Not reported
TG2449	whole blood	TG2449	Male	65 years	Not reported
TG1005	whole blood	TG1005	Male	71 years	Not reported
TG1780	whole blood	TG1780	Male	80 years	Not reported
TG1583	whole blood	TG1583	Male	78 years	Not reported
TG3272	whole blood	TG3272	Male	84 years	Not reported
TG2536	whole blood	TG2536	Male	77 years	Not reported
TG211	whole blood	TG211	Male	74 years	Not reported
TG2380	whole blood	TG2380	Male	83 years	Not reported
TG1266	whole blood	TG1266	Male	75 years	Not reported
TG3147	whole blood	TG3147	Male	71 years	Not reported
TG1656	whole blood	TG1656	Male	79 years	Not reported
TG3232	whole blood	TG3232	Male	81 years	Not reported
TG3128	whole blood	TG3128	Male	70 years	Not reported
TG1269	whole blood	TG1269	Male	84 years	Not reported
TG1021	whole blood	TG1021	Male	63 years	Not reported
TG3260	whole blood	TG3260	Male	72 years	Not reported
TG323	whole blood	TG323	Male	76 years	Not reported
TG3060	whole blood	TG3060	Male	63 years	Not reported
TG2778	whole blood	TG2778	Male	77 years	Not reported
TG197	whole blood	TG197	Male	86 years	Not reported
TG1034	whole blood	TG1034	Male	83 years	Not reported
TG2211	whole blood	TG2211	Male	66 years	Not reported
TG1868	whole blood	TG1868	Male	70 years	Not reported
TG2693	whole blood	TG2693	Male	64 years	Not reported
TG2288	whole blood	TG2288	Male	62 years	Not reported
TG2588	whole blood	TG2588	Male	66 years	Not reported
TG1202	whole blood	TG1202	Male	74 years	Not reported
TG1917	whole blood	TG1917	Male	59 years	Not reported
TG2990	whole blood	TG2990	Male	85 years	Not reported
TG2950	whole blood	TG2950	Male	67 years	Not reported
TG1931	whole blood	TG1931	Male	60 years	Not reported
TG3344	whole blood	TG3344	Male	79 years	Not reported
TG1527	whole blood	TG1527	Male	66 years	Not reported
TG1287	whole blood	TG1287	Male	90 years	Not reported
TG2395	whole blood	TG2395	Male	83 years	Not reported
TG2377	whole blood	TG2377	Male	82 years	Not reported
TG3258	whole blood	TG3258	Male	75 years	Not reported
TG1061	whole blood	TG1061	Male	58 years	Not reported
TG1711	whole blood	TG1711	Male	60 years	Not reported
TG1555	whole blood	TG1555	Male	83 years	Not reported
TG146	whole blood	TG146	Male	76 years	Not reported
TG2518	whole blood	TG2518	Male	74 years	Not reported
TG2719	whole blood	TG2719	Male	61 years	Not reported
TG186	whole blood	TG186	Male	83 years	Not reported
TG2444	whole blood	TG2444	Male	76 years	Not reported
TG1425	whole blood	TG1425	Male	83 years	Not reported
TG1386	whole blood	TG1386	Male	63 years	Not reported
TG2381	whole blood	TG2381	Male	73 years	Not reported
TG106	whole blood	TG106	Male	75 years	Not reported
TG3085	whole blood	TG3085	Male	84 years	Not reported
TG3074	whole blood	TG3074	Male	86 years	Not reported
TG1443	whole blood	TG1443	Male	74 years	Not reported
TG1114	whole blood	TG1114	Male	64 years	Not reported
TG2066	whole blood	TG2066	Male	80 years	Not reported
TG1819	whole blood	TG1819	Male	65 years	Not reported
TG2044	whole blood	TG2044	Male	61 years	Not reported
TG3182	whole blood	TG3182	Male	61 years	Not reported
TG3375	whole blood	TG3375	Male	74 years	Not reported
TG3233	whole blood	TG3233	Male	80 years	Not reported
TG3155	whole blood	TG3155	Male	63 years	Not reported
TG143	whole blood	TG143	Male	78 years	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	HumanOmniExpress BeadChip	328

dbVar

Database of genomic structural variation

nstd104 (Dumanski et al. 2014)

Links

Detailed Information: Download 1 Variant Region, Download 328 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

nstd104 (Dumanski et al. 2014)

Links

Detailed Information: Download 1 Variant Region, Download 328 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: