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A scalable, aggregated genotypic-phenotypic database for human disease variation

2019 Database: The Journal of Biological Databases and Curation  
To effectively share comprehensive, integrated genotypic-phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy.  ...  We hope that this database will help researchers and scientists explore genotype-phenotype correlations in hereditary cancer, identify novel variants for functional analysis and enable data-driven drug  ...  Acknowledgements We would like to thank Sunil Bodapati, Scott Topper, Lindsey Jones and Jill Hagenkord for helpful discussions; Huy Hong for design expertise; and Linda Jiang for consumer expertise.  ... 
doi:10.1093/database/baz013 pmid:30759220 pmcid:PMC6372842 fatcat:zb5stoxhv5cvlooz3q3n7gpmjq

The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design

Paul Lacaze, Mark Pinese, Warren Kaplan, Andrew Stone, Marie-Jo Brion, Robyn L. Woods, Martin McNamara, John J. McNeil, Marcel E. Dinger, David M. Thomas
2018 European Journal of Human Genetics  
the database.  ...  Aged and healthy populations are more likely to be selectively depleted of pathogenic alleles and therefore particularly suitable as a reference population for the major diseases of clinical and public  ...  To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/.  ... 
doi:10.1038/s41431-018-0279-z pmid:30353151 pmcid:PMC6336775 fatcat:stg2ewiycrar3k5zo4j2nleyia

FROG - Fingerprinting Genomic Variation Ontology

E. Abinaya, Pankaj Narang, Anshu Bhardwaj, Kumarasamy Thangaraj
2015 PLoS ONE  
Genetic variations play a crucial role in differential phenotypic outcomes.  ...  Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant.  ...  Acknowledgments The authors thank Rakesh Kumar, CSIR-OSDD Unit, Delhi, for setting up FROG web-interface and Dr. Vipin Singh, AMITY University, Noida, Delhi, for critical comments on the manuscript.  ... 
doi:10.1371/journal.pone.0134693 pmid:26244889 pmcid:PMC4526677 fatcat:zizjjzcmajezjenj3aodbnidza

Scalable Newborn Screening Solutions: Bioinformatics and Next-Generation Sequencing

Nicole Ruiz-Schultz, Bryce Asay, Andreas Rohrwasser
2021 International Journal of Neonatal Screening  
This is especially true for disorders lacking robust biomarkers for detection in primary screening methods and for disorders requiring genotyping or sequencing as a second-tier and/or diagnostic test.  ...  Barriers to the incorporation of NGS and bioinformatics within NBS are discussed, and ideas for a regional bioinformatics model and shared variant repository are presented as potential solutions.  ...  A targeted panel approach for detection of disease-causing variants in disorders where genotype-phenotype associations are well characterized (e.g., CF, phenylketonuria, VLCAD deficiency) can be a more  ... 
doi:10.3390/ijns7040063 pmid:34698050 fatcat:p3hz4lq2jrgurbt7ewaacnon4i

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research

Teri A. Manolio, Douglas M. Fowler, Lea M. Starita, Melissa A. Haendel, Daniel G. MacArthur, Leslie G. Biesecker, Elizabeth Worthey, Rex L. Chisholm, Eric D. Green, Howard J. Jacob, Howard L. McLeod, Dan Roden (+19 others)
2017 Cell  
To facilitate such collaborations, we recommend prioritizing clinically relevant genes for functional studies, developing reference variant-phenotype databases, adopting phenotype description standards  ...  Genome sequencing has revolutionized the diagnosis of genetic diseases.  ...  Although variants in orthologous genes can produce similar phenotypes across model organisms and humans-indeed, this is the major value of model organism studies for understanding human variation-even  ... 
doi:10.1016/j.cell.2017.03.005 pmid:28340351 pmcid:PMC5511379 fatcat:gg4f555uo5edbaibtz6y5mjvme

Recent advances in predicting gene–disease associations

Kenneth Opap, Nicola Mulder
2017 F1000Research  
Singhal A, Simmons M, Lu Z: Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine. PLoS Comput Biol. 2016; 12(11): e1005017.  ...  Piñero J, Queralt-Rosinach N, Bravo À, et al.: DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database (Oxford). 2015; 2015: bav028.  ...  The review of Brookes and Robinson 12 lists some of the databases that contain genotype-phenotype data in relation to human health.  ... 
doi:10.12688/f1000research.10788.1 pmid:28529714 pmcid:PMC5414807 fatcat:hzph7zrm55ecje7fsp2yfk66uq

Computational tools for discovery and interpretation of expression quantitative trait loci

Fred A Wright, Andrey A Shabalin, Ivan Rusyn
2012 Pharmacogenomics (London)  
concept in genomics to a mature area of investigation, with important connections to genome-wide association studies for human disease, pharmacogenomics and toxicogenomics.  ...  The classical genetic methods for linkage or association mapping were adapted to eQTL analyses, with attendant challenges of scalability presented by thousands of expression quantitative traits [16] .  ...  Review information, genotype and phenotype; and a .DAT file with annotation for the .PED file.  ... 
doi:10.2217/pgs.11.185 pmid:22304583 pmcid:PMC3295835 fatcat:pvjzp7kyurfw7h2uzslblauqa4

Novel bioinformatic developments for exome sequencing

Stefan H. Lelieveld, Joris A. Veltman, Christian Gilissen
2016 Human Genetics  
similar phenotypic and genotypic profiles though a number of databases http://www.matchmakerexchange.org/ Phenotypes Phenotips A software tool for collecting and analyzing phenotypic information  ...  In addition, a need for population-specific databases of variation will remain, especially for those populations that are poorly represented in the large public databases (Tennessen et al. 2012) .  ... 
doi:10.1007/s00439-016-1658-6 pmid:27075447 pmcid:PMC4883269 fatcat:h4hz4xgarfbdti33ctqwyxncny

Semantically enabling pharmacogenomic data for the realization of personalized medicine

Matthias Samwald, Adrien Coulet, Iker Huerga, Robert L Powers, Joanne S Luciano, Robert R Freimuth, Frederick Whipple, Elgar Pichler, Eric Prud'hommeaux, Michel Dumontier, M Scott Marshall
2012 Pharmacogenomics (London)  
Of special interest are those curated databases that describe associations between genotypes and phenotypes in humans (some examples are provided in TABLE 2).  ...  Information resources for pharmacogenomics A number of public domain databases are available that can provide key information relevant for understanding genetic variation and its potential impact on disease  ... 
doi:10.2217/pgs.11.179 pmid:22256869 pmcid:PMC3957334 fatcat:q7o2vfijn5hmlasoaskcjjopkq

REVEAL--visual eQTL analytics

G. Jager, F. Battke, K. Nieselt
2012 Bioinformatics  
Based on these, certain genotypes can be connected with specific phenotypic outcomes to infer causal associations of genetic variation, expression and disease.  ...  Typical eQTL analyses involve three types of data: sequence-based data reflecting the genotypic variations, gene expression data and meta-data describing the phenotype.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge Alexander Herbig, Julian Heinrich and Corinna Vehlow for constructive discussions. Funding: DFG Priority Program 1335 Scalable Visual Analytics.  ... 
doi:10.1093/bioinformatics/bts382 pmid:22962479 pmcid:PMC3436809 fatcat:fsjo2zsajzajtdnvnhtbnkpnj4

New approaches to establish genetic causality

Elizabeth M. McNally, Alfred L. George
2015 Trends in cardiovascular medicine  
Whether one is seeking to discover the molecular basis for a disease in a research setting or trying to interpret results from a clinical genetic test, predicting the phenotypic effect of genetic variation  ...  The resulting avalanche of information on the molecular causes of these disorders has prompted a revolution in our understanding of disease mechanisms and provided new avenues for diagnoses.  ...  In Mendelian disorders, rare genetic variants confer a major portion of disease risk making it feasible to construct a tighter genotype-phenotype relationship than what is seen with GWAS.  ... 
doi:10.1016/j.tcm.2015.02.013 pmid:25864169 pmcid:PMC4560679 fatcat:by7xnhvvpbbpfh6etuxxscd4c4

Innovative Genomic Collaboration Using the GENESIS (GEM.app) Platform

Michael Gonzalez, Marni J. Falk, Xiaowu Gai, Richard Postrel, Rebecca Schüle, Stephan Zuchner
2015 Human Mutation  
Secondly, GENESIS (GEM.app) has grown to nearly 600 registered users from 44 countries, who have collectively achieved 62 gene identifications or published studies that have expanded phenotype/genotype  ...  Firstly, GEM.app has been renamed to GENESIS since it is now part of 'The Genesis Project' (501c3), a non-for-profit foundation that is committed to providing the best technology to enable research scientists  ...  It was further supported by the European Union within the 7th European Community Framework Program through funding for the E-Rare Network NEUROLIPID (01GM1408B to RS), and a Marie Curie International Outgoing  ... 
doi:10.1002/humu.22836 pmid:26173844 pmcid:PMC4682547 fatcat:cnvkarmk6fbwhmdnqrcsvtsteu

The Medical Genome Reference Bank: a whole-genome data resource of 4,000 healthy elderly individuals. Rationale and cohort design [article]

Paul Lacaze, Mark Pinese, Warren Kaplan, Andrew Stone, Marie-Jo Brion, Robyn L Woods, Martin McNamara, John J McNeil, Marcel E Dinger, David M Thomas
2018 bioRxiv   pre-print
the database.  ...  Aged and healthy populations are more likely to be selectively depleted of pathogenic alleles, and therefore particularly suitable as a reference populations for the major diseases of clinical and public  ...  disease phenotypes.  ... 
doi:10.1101/274019 fatcat:hung7ywkijhhtb4inxoi4jqjja

HGVA: the Human Genome Variation Archive

Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo (+1 others)
2017 Nucleic Acids Research  
reference for identifying disease-causing genotypes.  ...  High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential  ...  ACKNOWLEDGEMENTS We are indebted to Kathy Stirrups for reviewing the English of the manuscript.  ... 
doi:10.1093/nar/gkx445 pmid:28535294 pmcid:PMC5570161 fatcat:nh6pq2brofgibotoqjtsh5jqqq

Some experiences and opportunities for big data in translational research

Christopher G. Chute, Mollie Ullman-Cullere, Grant M. Wood, Simon M. Lin, Min He, Jyotishman Pathak
2013 Genetics in Medicine  
ACKNOWLEDGMENTS We are grateful for the grant support in part from the National Human Genome Research Institute as eMERGE consortium members, specifically U01-HG06379 (Mayo Clinic) and U01-HG006389 (Marshfield  ...  However, the recognition that the rate-limiting step for genotype-to-phenotype associations was resoundingly on the phenotyping side prompted the National Human Genome Research Institute to propose the  ...  , particularly into a single record 11 for the database of Genotypes and Phenotypes (dbGaP). 12 These problems included temporal and platform differences, manifest in surprising and underdocumented heterogeneity  ... 
doi:10.1038/gim.2013.121 pmid:24008998 pmcid:PMC3906918 fatcat:ayzsjqtp35fupfwazpwbnwuisa
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