nstd127 - Dumanski et al 2016 - dbVar Study

nstd127 (Dumanski et al. 2016)

Organism:: Human
Study Type:: Somatic
Submitter:: Chiara Rasi
Description:: Men have a shorter life expectancy compared with women but the underlying factor(s) are not clear. Late-onset, sporadic Alzheimer’s disease (AD) is a common and lethal neurodegenerative disorder and many germline inherited variants have been found to influence the risk of developing AD. Our previous results show that a fundamentally different genetic variant, i.e. lifetime-acquired loss of chromosome Y (LOY) in blood cells, is associated with all-cause mortality, an increased risk of non-hematological tumors and that LOY could be induced by tobacco smoking. We tested here a hypothesis whether men with LOY are more susceptible to AD and show that LOY is associated with AD in three independent studies of different types. In a case-control study, males with AD diagnosis had higher degree of LOY mosaicism (adjusted odds ratio=2.80, p=0.0184, AD events=606). Furthermore, in two prospective studies men with LOY at blood sampling had greater risk for incident AD diagnosis during follow-up time (hazard ratio HR=6.80, 95% confidence interval (95% CI)=2.16-21.43, AD events=140, p=0.0011). Thus, LOY in blood is associated with risks of both AD and cancer, suggesting a role of LOY in blood cells on disease processes in other tissues, possibly via defective immunosurveillance. As a male-specific risk factor, LOY might explain why males on average live shorter lives than females. See Variant Summary counts for nstd127 in dbVar Variant Summary.
Publication(s):: Dumanski et al. 2016

Links

Source: NCBI

Detailed Information: Download 1 Variant Region, Download 248 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_000024.10	ChrY	1	248	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	248	Remapped	NC_000024.9

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000024.8	ChrY	1	248	Submitted	NC_000024.8

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_000024.8	ChrY	1	0	1	0	0	0	248	0	248	0	0	0

	Variant Region remap status		Variant Call remap status
NC_000024.8	ChrY	1	0	1	0	0	0	248	0	248	0	0	0

Samplesets

Number of Samplesets: 1

Name:: Adult men from the EADI cohort affected by somatic loss of chromosome Y
Description:: 248 subjects belonging to the European Alzheimer's Disease Initiative (EADI) scored with loss of chromosome Y. The EADI cohort id described in PubMed ID 24162737.
Size:: 248
Organisms:: Homo sapiens
Sampleset Phenotype(s):: Some of these men are affected by Alzheimer's
Sex:: Male

Samples for sampleset 1 (displaying 100 of the 248 samples)
Sample ID	Cell Type	Subject ID	Sex	Subject Age	Subject Phenotype
B007Q3K	DNA extracted from whole blood	B007Q3K	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PJ7	DNA extracted from whole blood	B007PJ7	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008P3O	DNA extracted from whole blood	B008P3O	Male	65 years	Some of these men are affected by Alzheimer's
B007PSR	DNA extracted from whole blood	B007PSR	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PUD	DNA extracted from whole blood	B008PUD	Male	65 years	Some of these men are affected by Alzheimer's
B007PPH	DNA extracted from whole blood	B007PPH	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PE3	DNA extracted from whole blood	B008PE3	Male	65 years	Some of these men are affected by Alzheimer's
B007PO4	DNA extracted from whole blood	B007PO4	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PXB	DNA extracted from whole blood	B007PXB	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008POO	DNA extracted from whole blood	B008POO	Male	65 years	Some of these men are affected by Alzheimer's
B007PS0	DNA extracted from whole blood	B007PS0	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PQ8	DNA extracted from whole blood	B007PQ8	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PXD	DNA extracted from whole blood	B007PXD	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PKE	DNA extracted from whole blood	B007PKE	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PQZ	DNA extracted from whole blood	B008PQZ	Male	65 years	Some of these men are affected by Alzheimer's
B008P29	DNA extracted from whole blood	B008P29	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q1C	DNA extracted from whole blood	B007Q1C	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007POY	DNA extracted from whole blood	B007POY	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008Q2S	DNA extracted from whole blood	B008Q2S	Male	65 years	Some of these men are affected by Alzheimer's
B008PNW	DNA extracted from whole blood	B008PNW	Male	65 years	Some of these men are affected by Alzheimer's
B007PTE	DNA extracted from whole blood	B007PTE	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008Q3F	DNA extracted from whole blood	B008Q3F	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084GH	DNA extracted from whole blood	B0084GH	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PLH	DNA extracted from whole blood	B007PLH	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008P5I	DNA extracted from whole blood	B008P5I	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PQC	DNA extracted from whole blood	B008PQC	Male	65 years	Some of these men are affected by Alzheimer's
B007PJS	DNA extracted from whole blood	B007PJS	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084H4	DNA extracted from whole blood	B0084H4	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084E5	DNA extracted from whole blood	B0084E5	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B00847I	DNA extracted from whole blood	B00847I	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q9K	DNA extracted from whole blood	B007Q9K	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PL1	DNA extracted from whole blood	B007PL1	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PXQ	DNA extracted from whole blood	B008PXQ	Male	65 years	Some of these men are affected by Alzheimer's
B007QAC	DNA extracted from whole blood	B007QAC	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PUU	DNA extracted from whole blood	B007PUU	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084J1	DNA extracted from whole blood	B0084J1	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B00847F	DNA extracted from whole blood	B00847F	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PR0	DNA extracted from whole blood	B007PR0	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PQQ	DNA extracted from whole blood	B008PQQ	Male	65 years	Some of these men are affected by Alzheimer's
B007PT5	DNA extracted from whole blood	B007PT5	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B00849F	DNA extracted from whole blood	B00849F	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PX3	DNA extracted from whole blood	B007PX3	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PCT	DNA extracted from whole blood	B008PCT	Male	65 years	Some of these men are affected by Alzheimer's
B007Q3Z	DNA extracted from whole blood	B007Q3Z	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PQG	DNA extracted from whole blood	B008PQG	Male	65 years	Some of these men are affected by Alzheimer's
B008PQ5	DNA extracted from whole blood	B008PQ5	Male	65 years	Some of these men are affected by Alzheimer's
B007Q6Z	DNA extracted from whole blood	B007Q6Z	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q2D	DNA extracted from whole blood	B007Q2D	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PXX	DNA extracted from whole blood	B008PXX	Male	65 years	Some of these men are affected by Alzheimer's
B007QAG	DNA extracted from whole blood	B007QAG	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PSG	DNA extracted from whole blood	B008PSG	Male	65 years	Some of these men are affected by Alzheimer's
B0084GL	DNA extracted from whole blood	B0084GL	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q9E	DNA extracted from whole blood	B007Q9E	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084EZ	DNA extracted from whole blood	B0084EZ	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q2U	DNA extracted from whole blood	B007Q2U	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008P68	DNA extracted from whole blood	B008P68	Male	65 years	Some of these men are affected by Alzheimer's
B00847O	DNA extracted from whole blood	B00847O	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PFH	DNA extracted from whole blood	B008PFH	Male	65 years	Some of these men are affected by Alzheimer's
B007PSM	DNA extracted from whole blood	B007PSM	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008Q02	DNA extracted from whole blood	B008Q02	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008Q0D	DNA extracted from whole blood	B008Q0D	Male	65 years	Some of these men are affected by Alzheimer's
B007Q82	DNA extracted from whole blood	B007Q82	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q55	DNA extracted from whole blood	B007Q55	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q72	DNA extracted from whole blood	B007Q72	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q08	DNA extracted from whole blood	B007Q08	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B00849Q	DNA extracted from whole blood	B00849Q	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PP0	DNA extracted from whole blood	B008PP0	Male	65 years	Some of these men are affected by Alzheimer's
B007PWF	DNA extracted from whole blood	B007PWF	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q6E	DNA extracted from whole blood	B007Q6E	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PM6	DNA extracted from whole blood	B008PM6	Male	65 years	Some of these men are affected by Alzheimer's
B007PUO	DNA extracted from whole blood	B007PUO	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q9J	DNA extracted from whole blood	B007Q9J	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PPN	DNA extracted from whole blood	B008PPN	Male	65 years	Some of these men are affected by Alzheimer's
B007PWZ	DNA extracted from whole blood	B007PWZ	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PM3	DNA extracted from whole blood	B008PM3	Male	65 years	Some of these men are affected by Alzheimer's
B007PNP	DNA extracted from whole blood	B007PNP	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PIV	DNA extracted from whole blood	B007PIV	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084BD	DNA extracted from whole blood	B0084BD	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008PS2	DNA extracted from whole blood	B008PS2	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PKW	DNA extracted from whole blood	B007PKW	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008Q0W	DNA extracted from whole blood	B008Q0W	Male	65 years	Some of these men are affected by Alzheimer's
B007PXS	DNA extracted from whole blood	B007PXS	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084A9	DNA extracted from whole blood	B0084A9	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q1O	DNA extracted from whole blood	B007Q1O	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q3S	DNA extracted from whole blood	B007Q3S	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q4P	DNA extracted from whole blood	B007Q4P	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008P9E	DNA extracted from whole blood	B008P9E	Male	65 years	Some of these men are affected by Alzheimer's
B008P39	DNA extracted from whole blood	B008P39	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PIW	DNA extracted from whole blood	B007PIW	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084H8	DNA extracted from whole blood	B0084H8	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B0084FB	DNA extracted from whole blood	B0084FB	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PJF	DNA extracted from whole blood	B007PJF	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q1V	DNA extracted from whole blood	B007Q1V	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008Q1U	DNA extracted from whole blood	B008Q1U	Male	65 years	Some of these men are affected by Alzheimer's
B008P36	DNA extracted from whole blood	B008P36	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PUS	DNA extracted from whole blood	B007PUS	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007PT3	DNA extracted from whole blood	B007PT3	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B008P4S	DNA extracted from whole blood	B008P4S	Male	65 years	Some of these men are affected by Alzheimer's
B008P3G	DNA extracted from whole blood	B008P3G	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's
B007Q40	DNA extracted from whole blood	B007Q40	Male	65 years	Alzheimer disease Some of these men are affected by Alzheimer's

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	Illumina Human610-Quad v1.0 BeadChip	248

dbVar

Database of genomic structural variation

nstd127 (Dumanski et al. 2016)

Links

Detailed Information: Download 1 Variant Region, Download 248 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: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd127 (Dumanski et al. 2016)

Links

Detailed Information: Download 1 Variant Region, Download 248 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: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: