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Article ; Online: Extreme downregulation of chromosome Y and Alzheimer's disease in men.

Caceres, Alejandro / Jene, Aina / Esko, Tonu / Perez-Jurado, Luis A / Gonzalez, Juan R

2020 Volume 90, Page(s) 150.e1–150.e4

Abstract: Research has revealed scarcely any biological factors of Alzheimer's disease (AD) that are specific to men. Here, we found that the extreme downregulation of chromosome Y (EDY) increases the age-related risk of AD in men. We considered that EDY was a ... ...

Abstract	Research has revealed scarcely any biological factors of Alzheimer's disease (AD) that are specific to men. Here, we found that the extreme downregulation of chromosome Y (EDY) increases the age-related risk of AD in men. We considered that EDY was a possible male-specific pathway toward AD because EDY is the most likely consequence of the mosaic loss of chromosome Y, which has been recently associated with AD. We studied EDY in the undiseased brain of 371 individuals and observed that it co-occurred across multiple brain regions (p < 10
MeSH term(s)	Aging/genetics ; Alzheimer Disease/genetics ; Alzheimer Disease/metabolism ; Amyloid beta-Peptides/metabolism ; Brain/metabolism ; Chromosomes, Human, Y/genetics ; Chromosomes, Human, Y/metabolism ; Down-Regulation/genetics ; Female ; Genetic Predisposition to Disease/genetics ; Humans ; Male ; Mosaicism ; Sex Characteristics
Chemical Substances	Amyloid beta-Peptides
Language	English
Publishing date	2020-02-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2020.02.003
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Article ; Online: Extreme Downregulation of Chromosome Y and Cancer Risk in Men.

Cáceres, Alejandro / Jene, Aina / Esko, Tonu / Pérez-Jurado, Luis A / González, Juan R

Journal of the National Cancer Institute

2020 Volume 112, Issue 9, Page(s) 913–920

Abstract: Background: Understanding the biological differences between sexes in cancer is essential for personalized treatment and prevention. We hypothesized that the extreme downregulation of chromosome Y gene expression (EDY) is a signature of cancer risk in ... ...

Abstract	Background: Understanding the biological differences between sexes in cancer is essential for personalized treatment and prevention. We hypothesized that the extreme downregulation of chromosome Y gene expression (EDY) is a signature of cancer risk in men and the functional mediator of the reported association between the mosaic loss of chromosome Y (LOY) and cancer. Methods: We advanced a method to measure EDY from transcriptomic data. We studied EDY across 47 nondiseased tissues from the Genotype Tissue-Expression Project (n = 371) and its association with cancer status across 12 cancer studies from The Cancer Genome Atlas (n = 1774) and seven other studies (n = 7562). Associations of EDY with cancer status and presence of loss-off function mutations in chromosome X were tested with logistic regression models, and a Fisher's test was used to assess genome-wide association of EDY with the proportion of copy number gains. All statistical tests were two-sided. Results: EDY was likely to occur in multiple nondiseased tissues (P < .001) and was statistically significantly associated with the EGFR tyrosine kinase inhibitor resistance pathway (false discovery rate = 0.028). EDY strongly associated with cancer risk in men (odds ratio [OR] = 3.66, 95% confidence interval [CI] = 1.58 to 8.46, P = .002), adjusted by LOY and age, and its variability was largely explained by several genes of the nonrecombinant region whose chromosome X homologs showed loss-of-function mutations that co-occurred with EDY during cancer (OR = 2.82, 95% CI = 1.32 to 6.01, P = .007). EDY associated with a high proportion of EGFR amplifications (OR = 5.64, 95% CI = 3.70 to 8.59, false discovery rate < 0.001) and EGFR overexpression along with SRY hypomethylation and nonrecombinant region hypermethylation, indicating alternative causes of EDY in cancer other than LOY. EDY associations were independently validated for different cancers and exposure to smoking, and its status was accurately predicted from individual methylation patterns. Conclusions: EDY is a male-specific signature of cancer susceptibility that supports the escape from X-inactivation tumor suppressor hypothesis for genes that protect women compared with men from cancer risk.
MeSH term(s)	Case-Control Studies ; Chromosomes, Human, Y/genetics ; DNA Methylation/physiology ; Down-Regulation/genetics ; Female ; Gene Expression Regulation ; Genes, Tumor Suppressor ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Male ; Neoplasms/epidemiology ; Neoplasms/genetics ; Polymorphism, Single Nucleotide ; Risk Factors ; Sex Characteristics ; Transcriptome
Language	English
Publishing date	2020-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2992-0
ISSN	1460-2105 ; 0027-8874 ; 0198-0157
ISSN (online)	1460-2105
ISSN	0027-8874 ; 0198-0157
DOI	10.1093/jnci/djz232
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Article ; Online: A quality control portal for sequencing data deposited at the European genome-phenome archive.

Fernández-Orth, Dietmar / Rueda, Manuel / Singh, Babita / Moldes, Mauricio / Jene, Aina / Ferri, Marta / Vasallo, Claudia / Fromont, Lauren A / Navarro, Arcadi / Rambla, Jordi

Briefings in bioinformatics

2022 Volume 23, Issue 3

Abstract: Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability of the stored data, as of now, ...

Abstract	Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability of the stored data, as of now, data submitters are not mandated to perform any quality control (QC) before uploading their data and associated metadata information. Here, we present a new File QC Portal developed at EGA, along with QC reports performed and created for 1 694 442 files [Fastq, sequence alignment map (SAM)/binary alignment map (BAM)/CRAM and variant call format (VCF)] submitted at EGA. QC reports allow anonymous EGA users to view summary-level information regarding the files within a specific dataset, such as quality of reads, alignment quality, number and type of variants and other features. Researchers benefit from being able to assess the quality of data prior to the data access decision and thereby, increasing the reusability of data (https://ega-archive.org/blog/data-upcycling-powered-by-ega/).
MeSH term(s)	Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Metadata ; Quality Control ; Software
Language	English
Publishing date	2022-05-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbac136
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Article ; Online: The European Genome-phenome Archive in 2021.

Freeberg, Mallory Ann / Fromont, Lauren A / D'Altri, Teresa / Romero, Anna Foix / Ciges, Jorge Izquierdo / Jene, Aina / Kerry, Giselle / Moldes, Mauricio / Ariosa, Roberto / Bahena, Silvia / Barrowdale, Daniel / Barbero, Marcos Casado / Fernandez-Orth, Dietmar / Garcia-Linares, Carles / Garcia-Rios, Emilio / Haziza, Frédéric / Juhasz, Bela / Llobet, Oscar Martinez / Milla, Gemma /

Mohan, Anand / Rueda, Manuel / Sankar, Aravind / Shaju, Dona / Shimpi, Ashutosh / Singh, Babita / Thomas, Coline / de la Torre, Sabela / Uyan, Umuthan / Vasallo, Claudia / Flicek, Paul / Guigo, Roderic / Navarro, Arcadi / Parkinson, Helen / Keane, Thomas / Rambla, Jordi

Nucleic acids research

2021 Volume 50, Issue D1, Page(s) D980–D987

Abstract: The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is ... ...

Abstract	The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource.
MeSH term(s)	Confidentiality/legislation & jurisprudence ; Datasets as Topic ; Genome, Human ; Genotype ; History, 20th Century ; History, 21st Century ; Humans ; Information Dissemination/ethics ; Information Dissemination/methods ; Metadata/ethics ; Metadata/statistics & numerical data ; Phenomics/history ; Phenomics/organization & administration ; Phenotype ; Translational Research, Biomedical/methods
Language	English
Publishing date	2021-11-17
Publishing country	England
Document type	Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab1059
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Article ; Online: The Data Use Ontology to streamline responsible access to human biomedical datasets.

Lawson, Jonathan / Cabili, Moran N / Kerry, Giselle / Boughtwood, Tiffany / Thorogood, Adrian / Alper, Pinar / Bowers, Sarion R / Boyles, Rebecca R / Brookes, Anthony J / Brush, Matthew / Burdett, Tony / Clissold, Hayley / Donnelly, Stacey / Dyke, Stephanie O M / Freeberg, Mallory A / Haendel, Melissa A / Hata, Chihiro / Holub, Petr / Jeanson, Francis /

Jene, Aina / Kawashima, Minae / Kawashima, Shuichi / Konopko, Melissa / Kyomugisha, Irene / Li, Haoyuan / Linden, Mikael / Rodriguez, Laura Lyman / Morita, Mizuki / Mulder, Nicola / Muller, Jean / Nagaie, Satoshi / Nasir, Jamal / Ogishima, Soichi / Ota Wang, Vivian / Paglione, Laura D / Pandya, Ravi N / Parkinson, Helen / Philippakis, Anthony A / Prasser, Fabian / Rambla, Jordi / Reinold, Kathy / Rushton, Gregory A / Saltzman, Andrea / Saunders, Gary / Sofia, Heidi J / Spalding, John D / Swertz, Morris A / Tulchinsky, Ilia / van Enckevort, Esther J / Varma, Susheel / Voisin, Craig / Yamamoto, Natsuko / Yamasaki, Chisato / Zass, Lyndon / Guidry Auvil, Jaime M / Nyrönen, Tommi H / Courtot, Mélanie

Cell genomics

2021 Volume 1, Issue 2, Page(s) None

Abstract: Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and ... ...

Abstract	Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.
Language	English
Publishing date	2021-11-10
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2021.100028
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Article ; Online: GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Rehm, Heidi L / Page, Angela J H / Smith, Lindsay / Adams, Jeremy B / Alterovitz, Gil / Babb, Lawrence J / Barkley, Maxmillian P / Baudis, Michael / Beauvais, Michael J S / Beck, Tim / Beckmann, Jacques S / Beltran, Sergi / Bernick, David / Bernier, Alexander / Bonfield, James K / Boughtwood, Tiffany F / Bourque, Guillaume / Bowers, Sarion R / Brookes, Anthony J /

Brudno, Michael / Brush, Matthew H / Bujold, David / Burdett, Tony / Buske, Orion J / Cabili, Moran N / Cameron, Daniel L / Carroll, Robert J / Casas-Silva, Esmeralda / Chakravarty, Debyani / Chaudhari, Bimal P / Chen, Shu Hui / Cherry, J Michael / Chung, Justina / Cline, Melissa / Clissold, Hayley L / Cook-Deegan, Robert M / Courtot, Mélanie / Cunningham, Fiona / Cupak, Miro / Davies, Robert M / Denisko, Danielle / Doerr, Megan J / Dolman, Lena I / Dove, Edward S / Dursi, L Jonathan / Dyke, Stephanie O M / Eddy, James A / Eilbeck, Karen / Ellrott, Kyle P / Fairley, Susan / Fakhro, Khalid A / Firth, Helen V / Fitzsimons, Michael S / Fiume, Marc / Flicek, Paul / Fore, Ian M / Freeberg, Mallory A / Freimuth, Robert R / Fromont, Lauren A / Fuerth, Jonathan / Gaff, Clara L / Gan, Weiniu / Ghanaim, Elena M / Glazer, David / Green, Robert C / Griffith, Malachi / Griffith, Obi L / Grossman, Robert L / Groza, Tudor / Auvil, Jaime M Guidry / Guigó, Roderic / Gupta, Dipayan / Haendel, Melissa A / Hamosh, Ada / Hansen, David P / Hart, Reece K / Hartley, Dean Mitchell / Haussler, David / Hendricks-Sturrup, Rachele M / Ho, Calvin W L / Hobb, Ashley E / Hoffman, Michael M / Hofmann, Oliver M / Holub, Petr / Hsu, Jacob Shujui / Hubaux, Jean-Pierre / Hunt, Sarah E / Husami, Ammar / Jacobsen, Julius O / Jamuar, Saumya S / Janes, Elizabeth L / Jeanson, Francis / Jené, Aina / Johns, Amber L / Joly, Yann / Jones, Steven J M / Kanitz, Alexander / Kato, Kazuto / Keane, Thomas M / Kekesi-Lafrance, Kristina / Kelleher, Jerome / Kerry, Giselle / Khor, Seik-Soon / Knoppers, Bartha M / Konopko, Melissa A / Kosaki, Kenjiro / Kuba, Martin / Lawson, Jonathan / Leinonen, Rasko / Li, Stephanie / Lin, Michael F / Linden, Mikael / Liu, Xianglin / Udara Liyanage, Isuru / Lopez, Javier / Lucassen, Anneke M / Lukowski, Michael / Mann, Alice L / Marshall, John / Mattioni, Michele / Metke-Jimenez, Alejandro / Middleton, Anna / Milne, Richard J / Molnár-Gábor, Fruzsina / Mulder, Nicola / Munoz-Torres, Monica C / Nag, Rishi / Nakagawa, Hidewaki / Nasir, Jamal / Navarro, Arcadi / Nelson, Tristan H / Niewielska, Ania / Nisselle, Amy / Niu, Jeffrey / Nyrönen, Tommi H / O'Connor, Brian D / Oesterle, Sabine / Ogishima, Soichi / Wang, Vivian Ota / Paglione, Laura A D / Palumbo, Emilio / Parkinson, Helen E / Philippakis, Anthony A / Pizarro, Angel D / Prlic, Andreas / Rambla, Jordi / Rendon, Augusto / Rider, Renee A / Robinson, Peter N / Rodarmer, Kurt W / Rodriguez, Laura Lyman / Rubin, Alan F / Rueda, Manuel / Rushton, Gregory A / Ryan, Rosalyn S / Saunders, Gary I / Schuilenburg, Helen / Schwede, Torsten / Scollen, Serena / Senf, Alexander / Sheffield, Nathan C / Skantharajah, Neerjah / Smith, Albert V / Sofia, Heidi J / Spalding, Dylan / Spurdle, Amanda B / Stark, Zornitza / Stein, Lincoln D / Suematsu, Makoto / Tan, Patrick / Tedds, Jonathan A / Thomson, Alastair A / Thorogood, Adrian / Tickle, Timothy L / Tokunaga, Katsushi / Törnroos, Juha / Torrents, David / Upchurch, Sean / Valencia, Alfonso / Guimera, Roman Valls / Vamathevan, Jessica / Varma, Susheel / Vears, Danya F / Viner, Coby / Voisin, Craig / Wagner, Alex H / Wallace, Susan E / Walsh, Brian P / Williams, Marc S / Winkler, Eva C / Wold, Barbara J / Wood, Grant M / Woolley, J Patrick / Yamasaki, Chisato / Yates, Andrew D / Yung, Christina K / Zass, Lyndon J / Zaytseva, Ksenia / Zhang, Junjun / Goodhand, Peter / North, Kathryn / Birney, Ewan

Cell genomics

2022 Volume 1, Issue 2

Abstract: The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic ... ...

Abstract	The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
Language	English
Publishing date	2022-02-24
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2021.100029
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Article ; Online: Extreme downregulation of chromosome Y and Alzheimer's disease in men.

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Article ; Online: Extreme Downregulation of Chromosome Y and Cancer Risk in Men.

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Article ; Online: A quality control portal for sequencing data deposited at the European genome-phenome archive.

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Article ; Online: The European Genome-phenome Archive in 2021.

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Article ; Online: The Data Use Ontology to streamline responsible access to human biomedical datasets.

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Article ; Online: GA4GH: International policies and standards for data sharing across genomic research and healthcare.

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