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A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva-Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean Mooney, Rachel Karchin (+1 others)
2014 PLoS Computational Biology  
To this end, we have designed a Bayesian probabilistic model to predict the probability of dichotomous phenotypes.  ...  Moreover, in a Critical Assessment of Genome Interpretation (CAGI) blinded prediction experiment, the models were used to match 77 PGP genomes to phenotypic profiles, generating the most accurate prediction  ...  Acknowledgments We thank the organizers of the Critical Assessment of Genome Interpretation (CAGI) experiment for motivating and encouraging our group to work on predicting phenotype from genotype, using  ... 
doi:10.1371/journal.pcbi.1003825 pmid:25188385 pmcid:PMC4154636 fatcat:gkz7l74qivd6hftb6xspsy2hvm

Probabilistic functional gene societies

Insuk Lee
2011 Progress in Biophysics and Molecular Biology  
This work was supported by grants from the National Research Foundation of Korea (NRF) funded by the Korea government (MEST) (No. 20100017649, 20100001818, 20090087951, 20100015754) and POSCO TJ Park  ...  The network-based approaches in medical and agricultural researches may bring a new paradigm to a more predictive and cost-effective genetic analysis to clinically and economically important phenotypes  ...  Noticeably we can predict many plant specific traits by associalogs from animals or yeast (Lee et al., 2010a) .  ... 
doi:10.1016/j.pbiomolbio.2011.01.003 pmid:21281658 fatcat:5p7pg6fzdrfmhhzmcnkg4msjzu

Genetic tests in major psychiatric disorders—integrating molecular medicine with clinical psychiatry—why is it so difficult?

U Demkow, T Wolańczyk
2017 Translational Psychiatry  
Selected approaches are presented, starting from currently used technologies (next-generation sequencing (NGS) and microarrays), followed by newer options (reverse phenotyping).  ...  To advance the field, we propose concerted cross-disciplinary effort to provide a diagnostic platform operating at the general level of genetic pathogenesis of complex-trait psychiatric disorders rather  ...  used to reliably predict the clinical outcome.  ... 
doi:10.1038/tp.2017.106 pmid:28608853 pmcid:PMC5537634 fatcat:64jaml4zmnbghantreut6d24n4

This Month in The Journal

Sarah Ratzel, Sara B. Cullinan
2014 American Journal of Human Genetics  
To better understand the results of this screen, they developed a probabilistic model that predicts that somatic individuals in whom the mutation originates before the germline lineage is established harbor  ...  In this study, Tabor et al. analyzed exome sequencing data from approximately 6,500 individuals from the NHLBI Exome Sequencing Project to evaluate the frequency of pathogenic variants with clinical utility  ... 
doi:10.1016/j.ajhg.2014.07.009 pmcid:PMC4129403 fatcat:ww4bmtfl4fdz7b4tn4h55sdiuq

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

Gholson J Lyon, Kai Wang
2012 Genome Medicine  
GJL is supported by funds from the Stanley Institute for Cognitive Genomics at Cold Spring Harbor Laboratory. KW is supported by NIH grant number HG006465. Published: 26 July 2012  ...  Acknowledgements We apologize to those whose work we could not cite due to reference limitations.  ...  (a) The probabilistic scoring approach collects relevant information from multiple data sources, and compiles a statistical model that ranks all genes in the genome by their likelihood of being disease  ... 
doi:10.1186/gm359 pmid:22830651 pmcid:PMC3580414 fatcat:c6ui7sn4gfetjbmvuqe4becloi

This Month in Genetics

Kathryn B. Garber
2013 American Journal of Human Genetics  
Probabilistic modeling indicated that there was a higher-than-expected mutation rate in the 44 genes sequenced in this study.  ...  Rosenfeld et al. used data from clinical samples collected by Signature Genomics over several years and compared these to more than 20,000 control samples in order to get penetrance estimates for specific  ... 
doi:10.1016/j.ajhg.2013.01.005 pmcid:PMC3567278 fatcat:6pdvg6w3mjeltfec622ehm3vsy

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

Li Zhang, Jingru Shi, Jian Ouyang, Riquan Zhang, Yiran Tao, Dongsheng Yuan, Chengkai Lv, Ruiyuan Wang, Baitang Ning, Ruth Roberts, Weida Tong, Zhichao Liu (+1 others)
2021 Genome Medicine  
A meta-voting prediction (MVP) score was developed to quantitively measure the pathogenic effect, which is based on the probabilistic value generated from the XGBoost algorithm.  ...  Conclusions The ability of the X-CNV framework to quantitatively prioritize functional, deleterious, and disease-causing CNV on a genome-wide basis outperformed current CNV-annotation tools and will have  ...  Acknowledgements We would like to thank Dr. Wenming Xiao from CDER/OND/OOD, FDA, U.S.A, for his valuable comments on the manuscript.  ... 
doi:10.1186/s13073-021-00945-4 pmid:34407882 pmcid:PMC8375180 fatcat:wwog4xtx6bbb7b4ra6fgjujlmy

Structural variation mutagenesis of the human genome: Impact on disease and evolution

James R. Lupski
2015 Environmental and Molecular Mutagenesis  
The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions  ...  distinct from chromosomal syndromes and single-gene Mendelian diseases.  ...  This phenomena was initially described from whole genome sequencing studies of ~800 cancers and referred to as "chromothripsis" -that was proposed to result from a shattering process and then a gluing  ... 
doi:10.1002/em.21943 pmid:25892534 pmcid:PMC4609214 fatcat:cuvxho7syrcpznldeuyqyfldi4

Deep Learning Models for Predicting Phenotypic Traits and Diseases from Omics Data [chapter]

Md. Mohaiminul Islam, Yang Wang, Pingzhao Hu
2018 Artificial Intelligence - Emerging Trends and Applications  
predict whether a patient has certain disease or its subtypes.  ...  We also demonstrate the superiority of our proposed DNN models over the SVM model for predicting triglyceride concentrations.  ...  [4] to build a probabilistic Bayesian model to predict the dichotomous traits (e.g., glaucoma, Corn's disease, prostate cancer).  ... 
doi:10.5772/intechopen.75311 fatcat:p2b5g35zyzbc3eusvcxeeareja

Clinically Relevant Functional Annotation of Genotype

C. A. MacRae, R. S. Vasan
2014 Circulation: Cardiovascular Genetics  
Recent genome wide association studies have revealed large numbers of loci that contribute to the common heritable variation in many disease traits, and whole-genome sequencing has uncovered a wealth of  ...  rare variation, even within a single individual, on a scale previously unimagined. 1 Article see p 8 Such a deluge of genomic variation vastly exceeds our ability to model the phenotypic consequences  ...  Calum A. MacRae and Ramachandran S. Vasan Clinically Relevant Functional Annotation of Genotype  ... 
doi:10.1161/circgenetics.114.000506 pmid:24550428 pmcid:PMC4188549 fatcat:qdk6chrpk5bapkntxuufhbku5e

Molecular genetic testing and the future of clinical genomics

Sara Huston Katsanis, Nicholas Katsanis
2013 Nature reviews genetics  
Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics.  ...  to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities.  ...  Most emerging clinical genome-sequencing paradigms focus on a narrow phenotypic band in order to probe its genetic architecture in detail.  ... 
doi:10.1038/nrg3493 pmid:23681062 pmcid:PMC4461364 fatcat:kv6bvs6gprbgrhuckdle3ma7eu

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation [article]

Nicole M. Ferraro, Benjamin J. Strober, Jonah Einson, Xin Li, Francois Aguet, Alvaro N. Barbeira, Stephane E Castel, Joe R. Davis, Austin T. Hilliard, Bence Kotis, YoSon Park, Alexandra J. Scott (+11 others)
2019 bioRxiv   pre-print
We further develop Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function.  ...  Together, we provide a comprehensive analysis of the transcriptomic impact of rare variation and a framework to prioritize functional rare variants and assess their trait relevance.  ...  Acknowledgements We thank members of the Lappalainen, Mohammadi, Montgomery, and Battle labs for helpful discussions and feedback, and the artists of the graphics that we modified in Fig. 1 A, found  ... 
doi:10.1101/786053 fatcat:tyc2dthbwfchtgxlnjvwawoosa

Machine Learning techniques and Polygenic Risk Score application to prediction genetic diseases

Nibeth Mena Mamani
2020 Advances in Distributed Computing and Artificial Intelligence Journal  
For the last 10 years and after important discoveries such as genomic understanding of the human being, there has been a considerable increase in the interest on research risk prediction models associated  ...  and investigated in order to have a greater precision in the prediction of genetic diseases.  ...  Nibeth Mena Mamani Genome-Wide Association Studies -GWAS Thanks to the Next Generation Sequencing (NGS), which allows sequencing of the entire genome, a big leap from gene association study to Genome-wide  ... 
doi:10.14201/adcaij202091514 fatcat:zqknfibmb5fh5neg3w3ae5bdfy

Transcriptomic signatures across human tissues identify functional rare genetic variation

Nicole M Ferraro, Benjamin J Strober, Jonah Einson, Nathan S Abell, Francois Aguet, Alvaro N Barbeira, Margot Brandt, Maja Bucan, Stephane E Castel, Joe R Davis, Emily Greenwald, Gaelen T Hess (+27 others)
2020 Science  
We developed Watershed, a probabilistic model that integrates multiple genomic and transcriptomic signals to predict variant function, validated these predictions in additional cohorts and through experimental  ...  Rare genetic variants are abundant across the human genome, and identifying their function and phenotypic impact is a major challenge.  ...  P.N. reports investigator-initiated research grants from Amgen, Apple, and Boston Scientific and is a scientific adviser to Apple and Blackstone Life Sciences.  ... 
doi:10.1126/science.aaz5900 pmid:32913073 pmcid:PMC7646251 fatcat:woalmwti2nayrpaz26kr6wxfam

Probabilistic latent semantic analysis applied to whole bacterial genomes identifies common genomic features

Julija Rusakovica, Jennifer Hallinan, Anil Wipat, Paolo Zuliani
2014 Journal of Integrative Bioinformatics  
Probabilistic Latent Semantic Indexing (PLSA) is an extention of LSA [3]. PLSA is based on a mixture decomposition derived from a latent class model.  ...  We characterised genome-scale amino acid sequences in terms of their components, and then investigated the relationships between genomes and tokens and the phenotypes they generated.  ...  The development of algorithms to identify the potential clinical phenotype of the bacteria from their genome sequence would facilitate rapid diagnosis and guide treatment decisions.  ... 
doi:10.2390/biecoll-jib-2014-243 pmid:24980693 fatcat:3i43kk67ebfdfpskf6o773v7xy
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