Defining Disease Phenotypes in Primary Care Electronic Health Records by a Machine Learning Approach: A Case Study in Identifying Rheumatoid Arthritis. by Shang-Ming Zhou, Fabiola Fernandez-Gutierrez, Jonathan Kennedy, Roxanne Cooksey, Mark Atkinson, Spiros Denaxas, Stefan Siebert, William G Dixon, Terence W O'Neill, Ernest Choy, Cathie Sudlow, UK Biobank Follow-up and Outcomes Group, Sinead Brophy

“…<h4>Objectives</h4>1) To use data-driven method to examine clinical codes (risk factors) of a medical condition in primary care electronic health records (EHRs) that can accurately predict a diagnosis of the condition in secondary care EHRs. 2) To develop and validate a disease phenotyping algorithm for rheumatoid arthritis using primary care EHRs.…”
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Loss of MTAP expression is strongly linked to homozygous 9p21 deletion, unfavorable tumor phenotype, and noninflamed microenvironment in urothelial bladder cancer by Natalia Gorbokon, Niklas Wößner, Viktoria Ahlburg, Henning Plage, Sebastian Hofbauer, Kira Furlano, Sarah Weinberger, Paul Giacomo Bruch, Simon Schallenberg, Florian Roßner, Sefer Elezkurtaj, Maximilian Lennartz, Niclas C Blessin, Andreas H Marx, Henrik Samtleben, Margit Fisch, Michael Rink, Marcin Slojewski, Krystian Kaczmarek, Thorsten Ecke, Tobias Klatte, Stefan Koch, Nico Adamini, Sarah Minner, Ronald Simon, Guido Sauter, Henrik Zecha, David Horst, Thorsten Schlomm, Lukas Bubendorf, Martina Kluth

“…Data were compared with data on tumor phenotype, patient survival, intratumoral lymphocyte subsets, and PD‐L1 expression. …”
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Enhancing human phenotype ontology term extraction through synthetic case reports and embedding-based retrieval: A novel approach for improved biomedical data annotation by Abdulkadir Albayrak, Yao Xiao, Piyush Mukherjee, Sarah S. Barnett, Cherisse A. Marcou, Steven N. Hart

“…With the increasing utilization of exome and genome sequencing in clinical and research genetics, accurate and automated extraction of human phenotype ontology (HPO) terms from clinical texts has become imperative. …”
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Case Report: Two years of compassionate use with Olipudase-alfa in a child with neurovisceral acid sphingomyelinase deficiency by Federica Deodato, Sara Boenzi, Benedetta Greco, Alessia Graziosi, Carlo Dionisi-Vici

“…ASMD presents a broad phenotypic spectrum with a continuum of severity, making it challenging to predict the phenotype in very young children and differentiate between acute and chronic neurovisceral disease. …”
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Identifying emergency presentations of chronic liver disease using routinely collected administrative hospital data by Jessica King, Vikram Bains, James Doidge, Jan Van Der Meulen, Kate Walker, William Bernal

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Genotype–phenotype correlations in inherited cardiomyopathies, their role in clinical decision-making, and implications in personalized cardiac medicine in multi-omics as well as d... by Yaqob Samir Taleb, Paras Memon, Aftab Jalbani, Nawaf Al-Anazi, Abdulkareem Al-Garni, Muneera Altaweel, Muhammad Aamir Khan, Muhammad Farooq Sabar, Zafar Iqbal

“…Understanding genotype–phenotype correlations in these conditions is vital for personalized cardiac medicine, enabling targeted therapeutic strategies and predictive diagnostics. …”
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Developing Laterality-Specific Computable Phenotypes from Electronic Health Record Data, Employing Treatment-Warranted Diabetic Macular Edema as a Use Case by Kaili Ding, MBBS, MS, Tracy Z. Lang, BS, Roberta McKean-Cowdin, PhD, Hossein Ameri, MD, PhD, Narsing A. Rao, MD, Brian C. Toy, MD

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Pathogenesis, Prognosis and Outcomes of Multiple Organ Failure in Newborns (Review) by A. V. Golomidov, E. V. Grigoriev, V. G. Moses, K. B. Moses

“…The pSOFA scale is suggested for predicting the outcome of MOF in full-term infants, while the nSOFA scale should be used in premature infants with low birth weight.…”
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DETERMINING THE SIZE OF THE POPULATION OF THE GENETIC ALGORITHM FOR THE PROBLEMS OF DISCRETE OPTIMIZATION IN CAD by V. V. Frolov

“…The model was obtained for the power range of the reference sets from 12 to 52, and allows to predict the size of the population beyond the limits of this range. …”
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Congenital hypotrichosis caused by compound heterozygous variants in the LSS gene in a Chinese patient with strabismus: case report by Linlin Bao, Linlin Bao, Qian Li, Zhicao Yue, Fang Yang, Fang Yang

“…Based on ACMG guidelines, both variants were classified as likely pathogenic, consistent with the patient's phenotype.ConclusionWe present a rare case of LSS-related hypotrichosis with strabismus and a novel c.386G&gt;A variant has not been reported, which broadens the understanding of LSS gene variants and their phenotypic spectrum, enhancing insights into the genotype-phenotype relationship in LSS-related conditions.…”
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Genomic profiling, implications for genotype-based treatment of 131 patients with phenylketonuria and characterization of novel p.Pro416Leu PAH variant by K. Klaassen, B. Kecman, S. Stankovic, J. Komazec, S. Pavlovic, Maja Stojiljkovic, M. Djordjevic

“…This study comprised genomic profiling and phenotypic characterization of 131 Serbian PKU patients along with implications for BH4 therapy. …”
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Patient Interaction Phenotypes With an Automated SMS Text Message–Based Program and Use of Acute Health Care Resources After Hospital Discharge: Observational Study by Klea Profka, Agnes Wang, Emily Schriver, Ashley Batugo, Anna U Morgan, Danielle Mowery, Eric Bressman

“…ObjectiveOur primary aim was to identify and characterize distinct patient interaction phenotypes with a postdischarge automated SMS text messaging program. …”
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Global genetic variations predict brain response to faces. by Erin W Dickie, Amir Tahmasebi, Leon French, Natasa Kovacevic, Tobias Banaschewski, Gareth J Barker, Arun Bokde, Christian Büchel, Patricia Conrod, Herta Flor, Hugh Garavan, Juergen Gallinat, Penny Gowland, Andreas Heinz, Bernd Ittermann, Claire Lawrence, Karl Mann, Jean-Luc Martinot, Frauke Nees, Thomas Nichols, Mark Lathrop, Eva Loth, Zdenka Pausova, Marcela Rietschel, Michal N Smolka, Andreas Ströhle, Roberto Toro, Gunter Schumann, Tomáš Paus, IMAGEN consortium, IMAGEN consortium, IMAGEN consortium

“…Here we estimated the proportion of phenotypic variance in the brain response to facial expressions explained by common genetic variance captured by ∼ 500,000 single nucleotide polymorphisms. …”
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Aberrant gene expression prediction across human tissues by Florian R. Hölzlwimmer, Jonas Lindner, Georgios Tsitsiridis, Nils Wagner, Francesco Paolo Casale, Vicente A. Yépez, Julien Gagneur

“…Furthermore, we show on UK Biobank blood traits that performing rare variant association testing using the continuous and tissue-specific AbExp variant scores instead of LOFTEE variant burden increases gene discovery sensitivity and enables improved phenotype predictions.…”
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A subregional prediction model for radiation-induced hypothyroidism by Wenting Ren, Ziqi Pan, Kuo Men, Bin Liang, Qingfeng Xu, Junlin Yi, Jianrong Dai

“…The phenotype and dosimetry parameters of each subregion were analyzed by AUC, T test and Delong test. …”
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Incorporating gene expression and environment for genomic prediction in wheat by Jia Liu, Jia Liu, Andrew Gock, Kerrie Ramm, Sandra Stops, Tanya Phongkham, Adam Norman, Russell Eastwood, Eric Stone, Shannon Dillon

“…Here we explored the role transcriptome data could play in enhancing GS in wheat.MethodsAcross 286 wheat lines, we integrated phenotype and multi-omic data from controlled environment and field experiments including ca. 40K single nucleotide polymorphisms (SNP), abundance data for ca. 50K transcripts as well as meta-data (e.g. categorical environments) to predict individual genetic merit for two agronomic traits, flowering time and height. …”
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BRCA1, BRCA2 mutations — future of predictive oncology: a review of literature by V. N. Dmitriev, I. V. Sukhoterin, I. I. Zybenko, T. V. Dmitrieva

“…In recent years, it has been demonstrated that breast cancer arising in BRCA1 and BRCA2 mutation carriers differs in its morphological, immuno- phenotypic and molecular characteristics from sporadic breast cancer. …”
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Clinicopathological and predictive value of MAIT cells in non-small cell lung cancer for immunotherapy by Dongyan Shi, Lin Lin, Yun Chen, Jian Liu, Lin Shi, Jinying Lu, Da Zhong, Meijuan Song, Wenhua You, Wen-Hui Li

“…Moreover, we found predictive value of circulating MAIT cells for anti-PD-1 immunotherapy in NSCLC patients.Conclusions MAIT cells shifted to an exhausted tumor-promoting phenotype in NSCLC patients and the circulating MAIT subset could be a predictor for patients who respond to anti-PD-1 immunotherapy.…”
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PI16 attenuates response to sorafenib and represents a predictive biomarker in hepatocellular carcinoma by Pusen Wang, Zhongyi Jiang, Xueni Liu, Kanru Yu, Chunguang Wang, Hao Li, Lin Zhong

“…Abstract Sorafenib has become the only FDA‐approved first‐line therapy for advanced hepatocellular carcinoma (HCC) for more than 10 years, but there is still no validated predictive or prognostic marker. Peptidase inhibitor 16 (PI16) is a functionally unknown gene in cancer research. …”
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Deep mutagenesis scanning using whole trimeric SARS-CoV-2 spike highlights the importance of NTD-RBD interactions in determining spike phenotype. by Ruthiran Kugathasan, Ksenia Sukhova, Maya Moshe, Paul Kellam, Wendy Barclay

“…These maps may fail to reflect interdomain interactions in the prediction of phenotypes. To try to improve on this, we developed a platform for deep mutational scanning using whole trimeric spike. …”
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