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Variability in assigning pathogenicity to incidental findings: insights from LDLR sequence linked to the electronic health record in 1013 individuals.
Safarova MS, Klee EW, Baudhuin LM, Winkler EM, Kluge ML, Bielinski SJ, Olson JE, Kullo IJ. Safarova MS, et al. Eur J Hum Genet. 2017 Apr;25(4):410-415. doi: 10.1038/ejhg.2016.193. Epub 2017 Feb 1. Eur J Hum Genet. 2017. PMID: 28145427 Free PMC article.
Knowledge of variant pathogenicity is key to implementing genomic medicine. We describe variability between expert reviewers in assigning pathogenicity to sequence variants in LDLR, the causal gene in the majority of cases of familial hypercholesterolemia. .. …
Knowledge of variant pathogenicity is key to implementing genomic medicine. We describe variability between expert revi …
Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations.
Ge T, Irvin MR, Patki A, Srinivasasainagendra V, Lin YF, Tiwari HK, Armstrong ND, Benoit B, Chen CY, Choi KW, Cimino JJ, Davis BH, Dikilitas O, Etheridge B, Feng YA, Gainer V, Huang H, Jarvik GP, Kachulis C, Kenny EE, Khan A, Kiryluk K, Kottyan L, Kullo IJ, Lange C, Lennon N, Leong A, Malolepsza E, Miles AD, Murphy S, Namjou B, Narayan R, O'Connor MJ, Pacheco JA, Perez E, Rasmussen-Torvik LJ, Rosenthal EA, Schaid D, Stamou M, Udler MS, Wei WQ, Weiss ST, Ng MCY, Smoller JW, Lebo MS, Meigs JB, Limdi NA, Karlson EW. Ge T, et al. Genome Med. 2022 Jun 29;14(1):70. doi: 10.1186/s13073-022-01074-2. Genome Med. 2022. PMID: 35765100 Free PMC article.
BACKGROUND: Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately afflicts communities of color. Leveraging existing large-scale genome-wide association studies (GWAS), polygenic risk scores (PRS) have sh …
BACKGROUND: Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately affli …
The landscape of the methodology in drug repurposing using human genomic data: a systematic review.
Wang L, Lu Y, Li D, Zhou Y, Yu L, Mesa Eguiagaray I, Campbell H, Li X, Theodoratou E. Wang L, et al. Brief Bioinform. 2024 Jan 22;25(2):bbad527. doi: 10.1093/bib/bbad527. Brief Bioinform. 2024. PMID: 38279645
Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of nov …
Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.
Groza T, Wu H, Dinger ME, Danis D, Hilton C, Bagley A, Davids JR, Luo L, Lu Z, Robinson PN. Groza T, et al. Bioinformatics. 2023 Dec 1;39(12):btad716. doi: 10.1093/bioinformatics/btad716. Bioinformatics. 2023. PMID: 38001031 Free PMC article.
MOTIVATION: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other …
MOTIVATION: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical litera …
Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining.
Shameer K, Perez-Rodriguez MM, Bachar R, Li L, Johnson A, Johnson KW, Glicksberg BS, Smith MR, Readhead B, Scarpa J, Jebakaran J, Kovatch P, Lim S, Goodman W, Reich DL, Kasarskis A, Tatonetti NP, Dudley JT. Shameer K, et al. BMC Med Inform Decis Mak. 2018 Sep 14;18(Suppl 3):79. doi: 10.1186/s12911-018-0653-3. BMC Med Inform Decis Mak. 2018. PMID: 30255805 Free PMC article.
To implement individualized interventions, it is necessary to predict those individuals at highest risk for 30-day readmission. In this study, our aim was to conduct a data-driven investigation to find the pharmacological factors influencing 30-day all-cause, intra- and in …
To implement individualized interventions, it is necessary to predict those individuals at highest risk for 30-day readmission. In th …
Imputation and quality control steps for combining multiple genome-wide datasets.
Verma SS, de Andrade M, Tromp G, Kuivaniemi H, Pugh E, Namjou-Khales B, Mukherjee S, Jarvik GP, Kottyan LC, Burt A, Bradford Y, Armstrong GD, Derr K, Crawford DC, Haines JL, Li R, Crosslin D, Ritchie MD. Verma SS, et al. Front Genet. 2014 Dec 11;5:370. doi: 10.3389/fgene.2014.00370. eCollection 2014. Front Genet. 2014. PMID: 25566314 Free PMC article.
The electronic MEdical Records and GEnomics (eMERGE) network brings together DNA biobanks linked to electronic health records (EHRs) from multiple institutions. ...A number of challenges were encountered due to the complexity of using two differ …
The electronic MEdical Records and GEnomics (eMERGE) network brings together DNA biobanks linked to electronic healt
Prototype of a Standards-Based EHR and Genetic Test Reporting Tool Coupled with HL7-Compliant Infobuttons.
Crump JK, Del Fiol G, Williams MS, Freimuth RR. Crump JK, et al. AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:330-339. eCollection 2018. AMIA Jt Summits Transl Sci Proc. 2018. PMID: 29888091 Free PMC article.
However, genetic information is often ambiguous and difficult to understand, and clinicians have reported low-self-efficacy in integrating genetics into their care routine. The Health Level Seven (HL7) Infobutton standard helps to integrate online knowledge resources withi …
However, genetic information is often ambiguous and difficult to understand, and clinicians have reported low-self-efficacy in integrating g …
Data model harmonization for the All Of Us Research Program: Transforming i2b2 data into the OMOP common data model.
Klann JG, Joss MAH, Embree K, Murphy SN. Klann JG, et al. PLoS One. 2019 Feb 19;14(2):e0212463. doi: 10.1371/journal.pone.0212463. eCollection 2019. PLoS One. 2019. PMID: 30779778 Free PMC article.
We previously demonstrated this ontology system can drive data reconfiguration, to transform data into new formats without site-specific programming. We previously implemented this on our 12-site Accessible Research Commons for Health (ARCH) network to transform i2b …
We previously demonstrated this ontology system can drive data reconfiguration, to transform data into new formats without site-specific pro …
Implementing Algorithm-Guided Warfarin Dosing in an Ethnically Diverse Patient Population Using Electronic Health Records and Preemptive CYP2C9 and VKORC1 Genetic Testing.
Obeng AO, Kaszemacher T, Abul-Husn NS, Gottesman O, Vega A, Waite E, Myers K, Cho J, Bottinger EP, Ellis SB, Scott SA. Obeng AO, et al. Clin Pharmacol Ther. 2016 Nov;100(5):427-430. doi: 10.1002/cpt.425. Epub 2016 Aug 18. Clin Pharmacol Ther. 2016. PMID: 27393744 Free PMC article.
To facilitate multiethnic algorithm-guided warfarin dosing using preemptive genetic testing, we developed a strategy that accounts for the complexity of race and leverages electronic health records for algorithm variables and deploying point-of-care do …
To facilitate multiethnic algorithm-guided warfarin dosing using preemptive genetic testing, we developed a strategy that accounts for the c …