Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes.

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes.

Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.

An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses.

Coronavirus Disease 2019 has emerged as a significant global concern, triggering harsh public health restrictions in a successful bid to curb its exponential growth. As discussion shifts towards relaxation of these restrictions, there is significant concern of second-wave resurgence. The key to managing these outbreaks is early detection and intervention, and yet there is a significant lag time associated with usage of laboratory confirmed cases for surveillance purposes. To address this, syndromic surveillance can be considered to provide a timelier alternative for first-line screening. Existing syndromic surveillance solutions are however typically focused around a known disease and have limited capability to distinguish between outbreaks of individual diseases sharing similar syndromes. This poses a challenge for surveillance of COVID-19 as its active periods tend to overlap temporally with other influenza-like illnesses. In this study we explore performing sentinel syndromic surveillance for COVID-19 and other influenza-like illnesses using a deep learning-based approach. Our methods are based on aberration detection utilizing autoencoders that leverages symptom prevalence distributions to distinguish outbreaks of two ongoing diseases that share similar syndromes, even if they occur concurrently. We first demonstrate that this approach works for detection of outbreaks of influenza, which has known temporal boundaries. We then demonstrate that the autoencoder can be trained to not alert on known and well-managed influenza-like illnesses such as the common cold and influenza. Finally, we applied our approach to 2019-2020 data in the context of a COVID-19 syndromic surveillance task to demonstrate how implementation of such a system could have provided early warning of an outbreak of a novel influenza-like illness that did not match the symptom prevalence profile of influenza and other known influenza-like illnesses.

Clinical concept extraction: A methodology review.

BACKGROUND: Concept extraction, a subdomain of natural language processing (NLP) with a focus on extracting concepts of interest, has been adopted to computationally extract clinical information from text for a wide range of applications ranging from clinical decision support to care quality improvement. OBJECTIVES: In this literature review, we provide a methodology review of clinical concept extraction, aiming to catalog development processes, available methods and tools, and specific considerations when developing clinical concept extraction applications. METHODS: Based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a literature search was conducted for retrieving EHR-based information extraction articles written in English and published from January 2009 through June 2019 from Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and the ACM Digital Library. RESULTS: A total of 6,686 publications were retrieved. After title and abstract screening, 228 publications were selected. The methods used for developing clinical concept extraction applications were discussed in this review.

HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology.

BACKGROUND: In precision medicine, deep phenotyping is defined as the precise and comprehensive analysis of phenotypic abnormalities, aiming to acquire a better understanding of the natural history of a disease and its genotype-phenotype associations. Detecting phenotypic relevance is an important task when translating precision medicine into clinical practice, especially for patient stratification tasks based on deep phenotyping. In our previous work, we developed node embeddings for the Human Phenotype Ontology (HPO) to assist in phenotypic relevance measurement incorporating distributed semantic representations. However, the derived HPO embeddings hold only distributed representations for IS-A relationships among nodes, hampering the ability to fully explore the graph. METHODS: In this study, we developed a framework, HPO2Vec+, to enrich the produced HPO embeddings with heterogeneous knowledge resources (i.e., DECIPHER, OMIM, and Orphanet) for detecting phenotypic relevance. Specifically, we parsed disease-phenotype associations contained in these three resources to enrich non-inheritance relationships among phenotypic nodes in the HPO. To generate node embeddings for the HPO, node2vec was applied to perform node sampling on the enriched HPO graphs based on random walk followed by feature learning over the sampled nodes to generate enriched node embeddings. Four HPO embeddings were generated based on different graph structures, which we hereafter label as HPOEmb-Original, HPOEmb-DECIPHER, HPOEmb-OMIM, and HPOEmb-Orphanet. We evaluated the derived embeddings quantitatively through an HPO link prediction task with four edge embeddings operations and six machine learning algorithms. The resulting best embeddings were then evaluated for patient stratification of 10 rare diseases using electronic health records (EHR) collected at Mayo Clinic. We assessed our framework qualitatively by visualizing phenotypic clusters and conducting a use case study on primary hyperoxaluria (PH), a rare disease, on the task of inferring relevant phenotypes given 22 annotated PH related phenotypes. RESULTS: The quantitative link prediction task shows that HPOEmb-Orphanet achieved an optimal AUROC of 0.92 and an average precision of 0.94. In addition, HPOEmb-Orphanet achieved an optimal F1 score of 0.86. The quantitative patient similarity measurement task indicates that HPOEmb-Orphanet achieved the highest average detection rate for similar patients over 10 rare diseases and performed better than other similarity measures implemented by an existing tool, HPOSim, especially for pairwise patients with fewer shared common phenotypes. The qualitative evaluation shows that the enriched HPO embeddings are generally able to detect relationships among nodes with fine granularity and HPOEmb-Orphanet is particularly good at associating phenotypes across different disease systems. For the use case of detecting relevant phenotypic characterizations for given PH related phenotypes, HPOEmb-Orphanet outperformed the other three HPO embeddings by achieving the highest average P@5 of 0.81 and the highest P@10 of 0.79. Compared to seven conventional similarity measurements provided by HPOSim, HPOEmb-Orphanet is able to detect more relevant phenotypic pairs, especially for pairs not in inheritance relationships. CONCLUSION: We drew the following conclusions based on the evaluation results. First, with additional non-inheritance edges, enriched HPO embeddings can detect more associations between fine granularity phenotypic nodes regardless of their topological structures in the HPO graph. Second, HPOEmb-Orphanet not only can achieve the optimal performance through link prediction and patient stratification based on phenotypic similarity, but is also able to detect relevant phenotypes closer to domain expert's judgments than other embeddings and conventional similarity measurements. Third, incorporating heterogeneous knowledge resources do not necessarily result in better performance for detecting relevant phenotypes. From a clinical perspective, in our use case study, clinical-oriented knowledge resources (e.g., Orphanet) can achieve better performance in detecting relevant phenotypic characterizations compared to biomedical-oriented knowledge resources (e.g., DECIPHER and OMIM).

Ensembles of natural language processing systems for portable phenotyping solutions.

BACKGROUND: Manually curating standardized phenotypic concepts such as Human Phenotype Ontology (HPO) terms from narrative text in electronic health records (EHRs) is time consuming and error prone. Natural language processing (NLP) techniques can facilitate automated phenotype extraction and thus improve the efficiency of curating clinical phenotypes from clinical texts. While individual NLP systems can perform well for a single cohort, an ensemble-based method might shed light on increasing the portability of NLP pipelines across different cohorts. METHODS: We compared four NLP systems, MetaMapLite, MedLEE, ClinPhen and cTAKES, and four ensemble techniques, including intersection, union, majority-voting and machine learning, for extracting generic phenotypic concepts. We addressed two important research questions regarding automated phenotype recognition. First, we evaluated the performance of different approaches in identifying generic phenotypic concepts. Second, we compared the performance of different methods to identify patient-specific phenotypic concepts. To better quantify the effects caused by concept granularity differences on performance, we developed a novel evaluation metric that considered concept hierarchies and frequencies. Each of the approaches was evaluated on a gold standard set of clinical documents annotated by clinical experts. One dataset containing 1,609 concepts derived from 50 clinical notes from two different institutions was used in both evaluations, and an additional dataset of 608 concepts derived from 50 case report abstracts obtained from PubMed was used for evaluation of identifying generic phenotypic concepts only. RESULTS: For generic phenotypic concept recognition, the top three performers in the NYP/CUIMC dataset are union ensemble (F1, 0.634), training-based ensemble (F1, 0.632), and majority vote-based ensemble (F1, 0.622). In the Mayo dataset, the top three are majority vote-based ensemble (F1, 0.642), cTAKES (F1, 0.615), and MedLEE (F1, 0.559). In the PubMed dataset, the top three are majority vote-based ensemble (F1, 0.719), training-based (F1, 0.696) and MetaMapLite (F1, 0.694). For identifying patient specific phenotypes, the top three performers in the NYP/CUIMC dataset are majority vote-based ensemble (F1, 0.610), MedLEE (F1, 0.609), and training-based ensemble (F1, 0.585). In the Mayo dataset, the top three are majority vote-based ensemble (F1, 0.604), cTAKES (F1, 0.531) and MedLEE (F1, 0.527). CONCLUSIONS: Our study demonstrates that ensembles of natural language processing can improve both generic phenotypic concept recognition and patient specific phenotypic concept identification over individual systems. Among the individual NLP systems, each individual system performed best when they were applied in the dataset that they were primary designed for. However, combining multiple NLP systems to create an ensemble can generally improve the performance. Specifically, the ensemble can increase the results reproducibility across different cohorts and tasks, and thus provide a more portable phenotyping solution compared to individual NLP systems.

Detecting Lifestyle Risk Factors for Chronic Kidney Disease With Comorbidities: Association Rule Mining Analysis of Web-Based Survey Data.

BACKGROUND: The rise in the number of patients with chronic kidney disease (CKD) and consequent end-stage renal disease necessitating renal replacement therapy has placed a significant strain on health care. The rate of progression of CKD is influenced by both modifiable and unmodifiable risk factors. Identification of modifiable risk factors, such as lifestyle choices, is vital in informing strategies toward renoprotection. Modification of unhealthy lifestyle choices lessens the risk of CKD progression and associated comorbidities, although the lifestyle risk factors and modification strategies may vary with different comorbidities (eg, diabetes, hypertension). However, there are limited studies on suitable lifestyle interventions for CKD patients with comorbidities. OBJECTIVE: The objectives of our study are to (1) identify the lifestyle risk factors for CKD with common comorbid chronic conditions using a US nationwide survey in combination with literature mining, and (2) demonstrate the potential effectiveness of association rule mining (ARM) analysis for the aforementioned task, which can be generalized for similar tasks associated with noncommunicable diseases (NCDs). METHODS: We applied ARM to identify lifestyle risk factors for CKD progression with comorbidities (cardiovascular disease, chronic pulmonary disease, rheumatoid arthritis, diabetes, and cancer) using questionnaire data for 450,000 participants collected from the Behavioral Risk Factor Surveillance System (BRFSS) 2017. The BRFSS is a Web-based resource, which includes demographic information, chronic health conditions, fruit and vegetable consumption, and sugar- or salt-related behavior. To enrich the BRFSS questionnaire, the Semantic MEDLINE Database was also mined to identify lifestyle risk factors. RESULTS: The results suggest that lifestyle modification for CKD varies among different comorbidities. For example, the lifestyle modification of CKD with cardiovascular disease needs to focus on increasing aerobic capacity by improving muscle strength or functional ability. For CKD patients with chronic pulmonary disease or rheumatoid arthritis, lifestyle modification should be high dietary fiber intake and participation in moderate-intensity exercise. Meanwhile, the management of CKD patients with diabetes focuses on exercise and weight loss predominantly. CONCLUSIONS: We have demonstrated the use of ARM to identify lifestyle risk factors for CKD with common comorbid chronic conditions using data from BRFSS 2017. Our methods can be generalized to advance chronic disease management with more focused and optimized lifestyle modification of NCDs.

Discovering associations between problem list and practice setting.

BACKGROUND: The Health Information Technology for Economic and Clinical Health Act (HITECH) has greatly accelerated the adoption of electronic health records (EHRs) with the promise of better clinical decisions and patients' outcomes. One of the core criteria for "Meaningful Use" of EHRs is to have a problem list that shows the most important health problems faced by a patient. The implementation of problem lists in EHRs has a potential to help practitioners to provide customized care to patients. However, it remains an open question on how to leverage problem lists in different practice settings to provide tailored care, of which the bottleneck lies in the associations between problem list and practice setting. METHODS: In this study, using sampled clinical documents associated with a cohort of patients who received their primary care at Mayo Clinic, we investigated the associations between problem list and practice setting through natural language processing (NLP) and topic modeling techniques. Specifically, after practice settings and problem lists were normalized, statistical χ2 test, term frequency-inverse document frequency (TF-IDF) and enrichment analysis were used to choose representative concepts for each setting. Then Latent Dirichlet Allocations (LDA) were used to train topic models and predict potential practice settings using similarity metrics based on the problem concepts representative of practice settings. Evaluation was conducted through 5-fold cross validation and Recall@k, Precision@k and F1@k were calculated. RESULTS: Our method can generate prioritized and meaningful problem lists corresponding to specific practice settings. For practice setting prediction, recall increases from 0.719 (k = 2) to 0.931 (k = 10), precision increases from 0.882 (k = 2) to 0.931 (k = 10) and F1 increases from 0.790 (k = 2) to 0.931 (k = 10). CONCLUSION: To our best knowledge, our study is the first attempting to discover the association between the problem lists and hospital practice settings. In the future, we plan to investigate how to provide more tailored care by utilizing the association between problem list and practice setting revealed in this study.

Rare disease knowledge enrichment through a data-driven approach.

BACKGROUND: Existing resources to assist the diagnosis of rare diseases are usually curated from the literature that can be limited for clinical use. It often takes substantial effort before the suspicion of a rare disease is even raised to utilize those resources. The primary goal of this study was to apply a data-driven approach to enrich existing rare disease resources by mining phenotype-disease associations from electronic medical record (EMR). METHODS: We first applied association rule mining algorithms on EMR to extract significant phenotype-disease associations and enriched existing rare disease resources (Human Phenotype Ontology and Orphanet (HPO-Orphanet)). We generated phenotype-disease bipartite graphs for HPO-Orphanet, EMR, and enriched knowledge base HPO-Orphanet + and conducted a case study on Hodgkin lymphoma to compare performance on differential diagnosis among these three graphs. RESULTS: We used disease-disease similarity generated by the eRAM, an existing rare disease encyclopedia, as a gold standard to compare the three graphs with sensitivity and specificity as (0.17, 0.36, 0.46) and (0.52, 0.47, 0.51) for three graphs respectively. We also compared the top 15 diseases generated by the HPO-Orphanet + graph with eRAM and another clinical diagnostic tool, the Phenomizer. CONCLUSIONS: Per our evaluation results, our approach was able to enrich existing rare disease knowledge resources with phenotype-disease associations from EMR and thus support rare disease differential diagnosis.

A clinical text classification paradigm using weak supervision and deep representation.

BACKGROUND: Automatic clinical text classification is a natural language processing (NLP) technology that unlocks information embedded in clinical narratives. Machine learning approaches have been shown to be effective for clinical text classification tasks. However, a successful machine learning model usually requires extensive human efforts to create labeled training data and conduct feature engineering. In this study, we propose a clinical text classification paradigm using weak supervision and deep representation to reduce these human efforts. METHODS: We develop a rule-based NLP algorithm to automatically generate labels for the training data, and then use the pre-trained word embeddings as deep representation features for training machine learning models. Since machine learning is trained on labels generated by the automatic NLP algorithm, this training process is called weak supervision. We evaluat the paradigm effectiveness on two institutional case studies at Mayo Clinic: smoking status classification and proximal femur (hip) fracture classification, and one case study using a public dataset: the i2b2 2006 smoking status classification shared task. We test four widely used machine learning models, namely, Support Vector Machine (SVM), Random Forest (RF), Multilayer Perceptron Neural Networks (MLPNN), and Convolutional Neural Networks (CNN), using this paradigm. Precision, recall, and F1 score are used as metrics to evaluate performance. RESULTS: CNN achieves the best performance in both institutional tasks (F1 score: 0.92 for Mayo Clinic smoking status classification and 0.97 for fracture classification). We show that word embeddings significantly outperform tf-idf and topic modeling features in the paradigm, and that CNN captures additional patterns from the weak supervision compared to the rule-based NLP algorithms. We also observe two drawbacks of the proposed paradigm that CNN is more sensitive to the size of training data, and that the proposed paradigm might not be effective for complex multiclass classification tasks. CONCLUSION: The proposed clinical text classification paradigm could reduce human efforts of labeled training data creation and feature engineering for applying machine learning to clinical text classification by leveraging weak supervision and deep representation. The experimental experiments have validated the effectiveness of paradigm by two institutional and one shared clinical text classification tasks.

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication.

BACKGROUND: Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the domestication syndrome. Here, we use signatures persisting in dog genomes to identify genes and pathways possibly altered by the selective pressures of domestication. RESULTS: Whole-genome SNP analyses of 43 globally distributed village dogs and 10 wolves differentiated signatures resulting from domestication rather than breed formation. We identified 246 candidate domestication regions containing 10.8 Mb of genome sequence and 429 genes. The regions share haplotypes with ancient dogs, suggesting that the detected signals are not the result of recent selection. Gene enrichments highlight numerous genes linked to neural crest and central nervous system development as well as neurological function. Read depth analysis suggests that copy number variation played a minor role in dog domestication. CONCLUSIONS: Our results identify genes that act early in embryogenesis and can confer phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development as the targets of selection during domestication. These differences reflect the phenotypes of the domestication syndrome, which can be explained by alterations in the migration or activity of neural crest cells during development. We propose that initial selection during early dog domestication was for behavior, a trait influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.

A comparison of word embeddings for the biomedical natural language processing.

BACKGROUND: Word embeddings have been prevalently used in biomedical Natural Language Processing (NLP) applications due to the ability of the vector representations being able to capture useful semantic properties and linguistic relationships between words. Different textual resources (e.g., Wikipedia and biomedical literature corpus) have been utilized in biomedical NLP to train word embeddings and these word embeddings have been commonly leveraged as feature input to downstream machine learning models. However, there has been little work on evaluating the word embeddings trained from different textual resources. METHODS: In this study, we empirically evaluated word embeddings trained from four different corpora, namely clinical notes, biomedical publications, Wikipedia, and news. For the former two resources, we trained word embeddings using unstructured electronic health record (EHR) data available at Mayo Clinic and articles (MedLit) from PubMed Central, respectively. For the latter two resources, we used publicly available pre-trained word embeddings, GloVe and Google News. The evaluation was done qualitatively and quantitatively. For the qualitative evaluation, we randomly selected medical terms from three categories (i.e., disorder, symptom, and drug), and manually inspected the five most similar words computed by embeddings for each term. We also analyzed the word embeddings through a 2-dimensional visualization plot of 377 medical terms. For the quantitative evaluation, we conducted both intrinsic and extrinsic evaluation. For the intrinsic evaluation, we evaluated the word embeddings' ability to capture medical semantics by measruing the semantic similarity between medical terms using four published datasets: Pedersen's dataset, Hliaoutakis's dataset, MayoSRS, and UMNSRS. For the extrinsic evaluation, we applied word embeddings to multiple downstream biomedical NLP applications, including clinical information extraction (IE), biomedical information retrieval (IR), and relation extraction (RE), with data from shared tasks. RESULTS: The qualitative evaluation shows that the word embeddings trained from EHR and MedLit can find more similar medical terms than those trained from GloVe and Google News. The intrinsic quantitative evaluation verifies that the semantic similarity captured by the word embeddings trained from EHR is closer to human experts' judgments on all four tested datasets. The extrinsic quantitative evaluation shows that the word embeddings trained on EHR achieved the best F1 score of 0.900 for the clinical IE task; no word embeddings improved the performance for the biomedical IR task; and the word embeddings trained on Google News had the best overall F1 score of 0.790 for the RE task. CONCLUSION: Based on the evaluation results, we can draw the following conclusions. First, the word embeddings trained from EHR and MedLit can capture the semantics of medical terms better, and find semantically relevant medical terms closer to human experts' judgments than those trained from GloVe and Google News. Second, there does not exist a consistent global ranking of word embeddings for all downstream biomedical NLP applications. However, adding word embeddings as extra features will improve results on most downstream tasks. Finally, the word embeddings trained from the biomedical domain corpora do not necessarily have better performance than those trained from the general domain corpora for any downstream biomedical NLP task.

Clinical information extraction applications: A literature review.

BACKGROUND: With the rapid adoption of electronic health records (EHRs), it is desirable to harvest information and knowledge from EHRs to support automated systems at the point of care and to enable secondary use of EHRs for clinical and translational research. One critical component used to facilitate the secondary use of EHR data is the information extraction (IE) task, which automatically extracts and encodes clinical information from text. OBJECTIVES: In this literature review, we present a review of recent published research on clinical information extraction (IE) applications. METHODS: A literature search was conducted for articles published from January 2009 to September 2016 based on Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and ACM Digital Library. RESULTS: A total of 1917 publications were identified for title and abstract screening. Of these publications, 263 articles were selected and discussed in this review in terms of publication venues and data sources, clinical IE tools, methods, and applications in the areas of disease- and drug-related studies, and clinical workflow optimizations. CONCLUSIONS: Clinical IE has been used for a wide range of applications, however, there is a considerable gap between clinical studies using EHR data and studies using clinical IE. This study enabled us to gain a more concrete understanding of the gap and to provide potential solutions to bridge this gap.

Recommending Education Materials for Diabetic Questions Using Information Retrieval Approaches.

BACKGROUND: Self-management is crucial to diabetes care and providing expert-vetted content for answering patients' questions is crucial in facilitating patient self-management. OBJECTIVE: The aim is to investigate the use of information retrieval techniques in recommending patient education materials for diabetic questions of patients. METHODS: We compared two retrieval algorithms, one based on Latent Dirichlet Allocation topic modeling (topic modeling-based model) and one based on semantic group (semantic group-based model), with the baseline retrieval models, vector space model (VSM), in recommending diabetic patient education materials to diabetic questions posted on the TuDiabetes forum. The evaluation was based on a gold standard dataset consisting of 50 randomly selected diabetic questions where the relevancy of diabetic education materials to the questions was manually assigned by two experts. The performance was assessed using precision of top-ranked documents. RESULTS: We retrieved 7510 diabetic questions on the forum and 144 diabetic patient educational materials from the patient education database at Mayo Clinic. The mapping rate of words in each corpus mapped to the Unified Medical Language System (UMLS) was significantly different (P<.001). The topic modeling-based model outperformed the other retrieval algorithms. For example, for the top-retrieved document, the precision of the topic modeling-based, semantic group-based, and VSM models was 67.0%, 62.8%, and 54.3%, respectively. CONCLUSIONS: This study demonstrated that topic modeling can mitigate the vocabulary difference and it achieved the best performance in recommending education materials for answering patients' questions. One direction for future work is to assess the generalizability of our findings and to extend our study to other disease areas, other patient education material resources, and online forums.

POKR: Building a Computable Heterogeneous Knowledge Resource for Precision Oncology.

Precision oncology is expected to improve selection of targeted therapies, tailored to individual patients and ultimately improve cancer patients' outcomes. Several cancer genetics knowledge databases have been successfully developed for such purposes, including CIViC and OncoKB, with active community-based curations and scoring of genetic-treatment evidences. Although many studies were conducted based on each knowledge base respectively, the integrative analysis across both knowledge bases remains largely unexplored. Thus, there exists an urgent need for a heterogeneous precision oncology knowledge resource with computational power to support drug repurposing discovery in a timely manner, especially for life-threatening cancer. In this pilot study, we built a heterogeneous precision oncology knowledge resource (POKR) by integrating CIViC and OncoKB, in order to incorporate unique information contained in each knowledge base and make associations amongst biomedical entities (e.g., gene, drug, disease) computable and measurable via training POKR graph embeddings. All the relevant codes, database dump files, and pre-trained POKR embeddings can be accessed through the following URL: https://github.com/shenfc/POKR.

Advances of Drugs Electroanalysis Based on Direct Electrochemical Redox on Electrodes: A Review.

The strong development of mankind is inseparable from the proper use of drugs, and the electroanalytical research of drugs occupies an important position in the field of analytical chemistry. This review mainly elaborates the research progress of drugs electroanalysis based on direct electrochemical redox on various electrodes for the recent decade from 2011 to 2021. At first, we summarize some frequently used electrochemical data processing and electrochemical mechanism research derivation methods in the literature. Then, according to the drug therapeutic and application/usage purposes, the research progress of drugs electrochemical analysis is classified and discussed, where we focus on drugs electrochemical reaction mechanism. At the same time, the comparisons of electrochemical sensing performance of the drugs on various electrodes from recent studies are listed, so that readers can more intuitively compare and understand the electroanalytical sensing performance of each modified electrode for each of the drug. Finally, this review discusses the shortcomings and prospects of the drugs electroanalysis based on direct electrochemical redox research.

PO2RDF: representation of real-world data for precision oncology using resource description framework.

BACKGROUND: Next-generation sequencing provides comprehensive information about individuals' genetic makeup and is commonplace in precision oncology practice. Due to the heterogeneity of individual patient's disease conditions and treatment journeys, not all targeted therapies were initiated despite actionable mutations. To better understand and support the clinical decision-making process in precision oncology, there is a need to examine real-world associations between patients' genetic information and treatment choices. METHODS: To fill the gap of insufficient use of real-world data (RWD) in electronic health records (EHRs), we generated a single Resource Description Framework (RDF) resource, called PO2RDF (precision oncology to RDF), by integrating information regarding genes, variants, diseases, and drugs from genetic reports and EHRs. RESULTS: There are a total 2,309,014 triples contained in the PO2RDF. Among them, 32,815 triples are related to Gene, 34,695 triples are related to Variant, 8,787 triples are related to Disease, 26,154 triples are related to Drug. We performed two use case analyses to demonstrate the usability of the PO2RDF: (1) we examined real-world associations between EGFR mutations and targeted therapies to confirm existing knowledge and detect off-label use. (2) We examined differences in prognosis for lung cancer patients with/without TP53 mutations. CONCLUSIONS: In conclusion, our work proposed to use RDF to organize and distribute clinical RWD that is otherwise inaccessible externally. Our work serves as a pilot study that will lead to new clinical applications and could ultimately stimulate progress in the field of precision oncology.

Family History Extraction From Synthetic Clinical Narratives Using Natural Language Processing: Overview and Evaluation of a Challenge Data Set and Solutions for the 2019 National NLP Clinical Challenges (n2c2)/Open Health Natural Language Processing (OHNLP) Competition.

BACKGROUND: As a risk factor for many diseases, family history (FH) captures both shared genetic variations and living environments among family members. Though there are several systems focusing on FH extraction using natural language processing (NLP) techniques, the evaluation protocol of such systems has not been standardized. OBJECTIVE: The n2c2/OHNLP (National NLP Clinical Challenges/Open Health Natural Language Processing) 2019 FH extraction task aims to encourage the community efforts on a standard evaluation and system development on FH extraction from synthetic clinical narratives. METHODS: We organized the first BioCreative/OHNLP FH extraction shared task in 2018. We continued the shared task in 2019 in collaboration with the n2c2 and OHNLP consortium, and organized the 2019 n2c2/OHNLP FH extraction track. The shared task comprises 2 subtasks. Subtask 1 focuses on identifying family member entities and clinical observations (diseases), and subtask 2 expects the association of the living status, side of the family, and clinical observations with family members to be extracted. Subtask 2 is an end-to-end task which is based on the result of subtask 1. We manually curated the first deidentified clinical narrative from FH sections of clinical notes at Mayo Clinic Rochester, the content of which is highly relevant to patients' FH. RESULTS: A total of 17 teams from all over the world participated in the n2c2/OHNLP FH extraction shared task, where 38 runs were submitted for subtask 1 and 21 runs were submitted for subtask 2. For subtask 1, the top 3 runs were generated by Harbin Institute of Technology, ezDI, Inc., and The Medical University of South Carolina with F1 scores of 0.8745, 0.8225, and 0.8130, respectively. For subtask 2, the top 3 runs were from Harbin Institute of Technology, ezDI, Inc., and University of Florida with F1 scores of 0.681, 0.6586, and 0.6544, respectively. The workshop was held in conjunction with the AMIA 2019 Fall Symposium. CONCLUSIONS: A wide variety of methods were used by different teams in both tasks, such as Bidirectional Encoder Representations from Transformers, convolutional neural network, bidirectional long short-term memory, conditional random field, support vector machine, and rule-based strategies. System performances show that relation extraction from FH is a more challenging task when compared to entity identification task.

Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2.

Gene duplication is a major mechanism for the evolution of gene novelty, and copy-number variation makes a major contribution to inter-individual genetic diversity. However, most approaches for studying copy-number variation rely upon uniquely mapping reads to a genome reference and are unable to distinguish among duplicated sequences. Specialized approaches to interrogate specific paralogs are comparatively slow and have a high degree of computational complexity, limiting their effective application to emerging population-scale data sets. We present QuicK-mer2, a self-contained, mapping-free approach that enables the rapid construction of paralog-specific copy-number maps from short-read sequence data. This approach is based on the tabulation of unique k-mer sequences from short-read data sets, and is able to analyze a 20X coverage human genome in approximately 20 min. We applied our approach to newly released sequence data from the 1000 Genomes Project, constructed paralog-specific copy-number maps from 2457 unrelated individuals, and uncovered copy-number variation of paralogous genes. We identify nine genes where none of the analyzed samples have a copy number of two, 92 genes where the majority of samples have a copy number other than two, and describe rare copy number variation effecting multiple genes at the APOBEC3 locus.

The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records.

OBJECTIVE: The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task track 3, focused on medical concept normalization (MCN) in clinical records. This track aimed to assess the state of the art in identifying and matching salient medical concepts to a controlled vocabulary. In this paper, we describe the task, describe the data set used, compare the participating systems, present results, identify the strengths and limitations of the current state of the art, and identify directions for future research. MATERIALS AND METHODS: Participating teams were provided with narrative discharge summaries in which text spans corresponding to medical concepts were identified. This paper refers to these text spans as mentions. Teams were tasked with normalizing these mentions to concepts, represented by concept unique identifiers, within the Unified Medical Language System. Submitted systems represented 4 broad categories of approaches: cascading dictionary matching, cosine distance, deep learning, and retrieve-and-rank systems. Disambiguation modules were common across all approaches. RESULTS: A total of 33 teams participated in the MCN task. The best-performing team achieved an accuracy of 0.8526. The median and mean performances among all teams were 0.7733 and 0.7426, respectively. CONCLUSIONS: Overall performance among the top 10 teams was high. However, several mention types were challenging for all teams. These included mentions requiring disambiguation of misspelled words, acronyms, abbreviations, and mentions with more than 1 possible semantic type. Also challenging were complex mentions of long, multi-word terms that may require new ways of extracting and representing mention meaning, the use of domain knowledge, parse trees, or hand-crafted rules.