Phenotyping Algorithms Research Articles

Maize Phenotypic Parameters Based on the Constrained Region Point Cloud Phenotyping Algorithm as a Developed Method

As one of the world’s most crucial food crops, maize plays a pivotal role in ensuring food security and driving economic growth. The diversification of maize variety breeding is significantly enhancing the cumulative benefits in these areas. Precise measurement of phenotypic data is pivotal for the selection and breeding of maize varieties in cultivation and production. However, in outdoor environments, conventional phenotyping methods, including point cloud processing techniques based on region growing algorithms and clustering segmentation, encounter significant challenges due to the low density and frequent loss of point cloud data. These issues substantially compromise measurement accuracy and computational efficiency. Consequently, this paper introduces a Constrained Region Point Cloud Phenotyping (CRPCP) algorithm that proficiently detects the phenotypic traits of multiple maize plants in sparse outdoor point cloud data. The CRPCP algorithm consists primarily of three core components: (1) a constrained region growth algorithm for effective segmentation of maize stem point clouds in complex backgrounds; (2) a radial basis interpolation technique to bridge gaps in point cloud data caused by environmental factors; and (3) a multi-level parallel decomposition strategy leveraging scene blocking and plant instances to enable high-throughput real-time computation. The results demonstrate that the CRPCP algorithm achieves a segmentation accuracy of 96.2%. When assessing maize plant height, the algorithm demonstrated a strong correlation with manual measurements, evidenced by a coefficient of determination R2 of 0.9534, a root mean square error (RMSE) of 0.4835 cm, and a mean absolute error (MAE) of 0.383 cm. In evaluating the diameter at breast height (DBH) of the plants, the algorithm yielded an R2 of 0.9407, an RMSE of 0.0368 cm, and an MAE of 0.031 cm. Compared to the PointNet point cloud segmentation method, the CRPCP algorithm reduced segmentation time by more than 44.7%. The CRPCP algorithm proposed in this paper enables efficient segmentation and precise phenotypic measurement of low-density maize multi-plant point cloud data in outdoor environments. This algorithm offers an automated, high-precision, and highly efficient solution for large-scale field phenotypic analysis, with broad applicability in precision breeding, agronomic management, and yield prediction.

Developing an automated algorithm for identification of children and adolescents with diabetes using electronic health records from the OneFlorida+ clinical research network.

To develop an automated computable phenotype (CP) algorithm for identifying diabetes cases in children and adolescents usingelectronic health records (EHRs) from the UF Health System. The CP algorithm was iteratively derived based on structured data from EHRs (UF Health System 2012-2020). We randomly selected 536 presumed cases among individuals aged <18 years who had (1) glycated haemoglobin levels ≥ 6.5%; or (2) fasting glucose levels ≥126 mg/dL; or (3) random plasma glucose levels ≥200 mg/dL; or (4) a diabetes-related diagnosis code from an inpatient or outpatient encounter; or (5) prescribed, administered, or dispensed diabetes-related medication. Four reviewers independently reviewed the patient charts to determine diabetes status and type. Presumed cases without type 1 (T1D) or type 2 diabetes (T2D) diagnosis codes were categorized as non-diabetes/other types of diabetes. The rest were categorized as T1D if the most recent diagnosis was T1D, or otherwise categorized as T2D if the most recent diagnosis was T2D. Next, we applied a list of diagnoses and procedures that can determine diabetes type (e.g., steroid use suggests induced diabetes) to correct misclassifications from Step 1. Among the 536 reviewed cases, 159 and 64 had T1D and T2D, respectively. The sensitivity, specificity, and positive predictive values of the CP algorithm were 94%, 98% and 96%, respectively, for T1D and 95%, 95% and 73% for T2D. We developed a highly accurate EHR-based CP for diabetes in youth based on EHR data from UF Health. Consistent with prior studies, T2D was more difficult to identify using these methods.

Foundational model aided automatic high-throughput drug screening using self-controlled cohort study.

Developing medicine from scratch to governmental authorization and detecting adverse drug reactions (ADR) have barely been economical, expeditious, and risk-averse investments. The availability of large-scale observational healthcare databases and the popularity of large language models offer an unparalleled opportunity to enable automatic high-throughput drug screening for both repurposing and pharmacovigilance. To demonstrate a general workflow for automatic high-throughput drug screening with the following advantages: (i) the association of various exposure on diseases can be estimated; (ii) both repurposing and pharmacovigilance are integrated; (iii) accurate exposure length for each prescription is parsed from clinical texts; (iv) intrinsic relationship between drugs and diseases are removed jointly by bioinformatic mapping and large language model - ChatGPT; (v) causal-wise interpretations for incidence rate contrasts are provided. Using a self-controlled cohort study design where subjects serve as their own control group, we tested the intention-to-treat association between medications on the incidence of diseases. Exposure length for each prescription is determined by parsing common dosages in English free text into a structured format. Exposure period starts from initial prescription to treatment discontinuation. A same exposure length preceding initial treatment is the control period. Clinical outcomes and categories are identified using existing phenotyping algorithms. Incident rate ratios (IRR) are tested using uniformly most powerful (UMP) unbiased tests. We assessed 3,444 medications on 276 diseases on 6,613,198 patients from the Clinical Practice Research Datalink (CPRD), an UK primary care electronic health records (EHR) spanning from 1987 to 2018. Due to the built-in selection bias of self-controlled cohort studies, ingredients-disease pairs confounded by deterministic medical relationships are removed by existing map from RxNorm and nonexistent maps by calling ChatGPT. A total of 16,901 drug-disease pairs reveals significant risk reduction, which can be considered as candidates for repurposing, while a total of 11,089 pairs showed significant risk increase, where drug safety might be of a concern instead. This work developed a data-driven, nonparametric, hypothesis generating, and automatic high-throughput workflow, which reveals the potential of natural language processing in pharmacoepidemiology. We demonstrate the paradigm to a large observational health dataset to help discover potential novel therapies and adverse drug effects. The framework of this study can be extended to other observational medical databases.

Clinical Phenotyping for Prognosis and Immunotherapy Guidance in Bacterial Sepsis and COVID-19.

It is suggested that sepsis may be classified into four clinical phenotypes, using an algorithm employing 29 admission parameters. We applied a simplified phenotyping algorithm among patients with bacterial sepsis and severe COVID-19 and assessed characteristics and outcomes of the derived phenotypes. Retrospective analysis of data from prospective clinical studies. Greek ICUs and Internal Medicine departments. We analyzed 1498 patients, 620 with bacterial sepsis and 878 with severe COVID-19. We implemented a six-parameter algorithm (creatinine, lactate, aspartate transaminase, bilirubin, C-reactive protein, and international normalized ratio) to classify patients with bacterial sepsis intro previously defined phenotypes. Patients with severe COVID-19, included in two open-label immunotherapy trials were subsequently classified. Heterogeneity of treatment effect of anakinra was assessed. The primary outcome was 28-day mortality. The algorithm validated the presence of the four phenotypes across the cohort of bacterial sepsis and the individual studies included in this cohort. Phenotype α represented younger patients with low risk of death, β was associated with high comorbidity burden, and δ with the highest mortality. Phenotype assignment was independently associated with outcome, even after adjustment for Charlson Comorbidity Index. Phenotype distribution and outcomes in severe COVID-19 followed a similar pattern. A simplified algorithm successfully identified previously derived phenotypes of bacterial sepsis, which were predictive of outcome. This classification may apply to patients with severe COVID-19 with prognostic implications.

Evaluation of a Multi-Component Phenotype Algorithm for Systemic Lupus Erythematosus across the PCORnet, OMOP, and i2b2 Common Data Models

The aim of this study was to evaluate the performance of a computable phenotype for systemic lupus erythematosus (SLE) patients when it is ported from a local data warehouse to the i2b2, OMOP, and PCORnet CDMs. We adapted the SLE phenotype to the Northwestern Medicine (NM) Enterprise Data Warehouse (EDW) and NU i2b2, OMOP, and PCORnet instances. Each of the phenotype’s 17 components were determined by a rules-based algorithm built on diagnosis, medication, lab, and procedure codes. We assessed the phenotype over 168 clinician-confirmed SLE patients and 100 healthy controls and calculated agreement between the EDW and CDMs for overall SLE classification, individual SLICC criteria membership, and individual code occurrence level aggregates - count, first and last date, lab values using Cohen’s kappa (Cκ) and intraclass correlation coefficients (ICC). For overall SLE classification, agreement of the OMOP and PCORnet datamarts with the EDW was high (Cκ 0.928, 0.802, respectively) while that of i2b2 was low (Cκ 0.328). For the panel of SLICC criteria, OMOP had high agreement for 14/17 SLICC criteria (Cκ 0.792-1.000). PCORnet had high agreement for 13/17 criteria (Cκ 0.708-1.000). i2b2 had high agreement for 10/17 criteria (Cκ 0.813-1.000) with the exception of lab-based criteria. While agreement between the EDW and CDMs at the level of individual codes was relatively poor, agreement at the levels of overall SLE classification and individual SLICC criteria were reasonably high for OMOP and PCORnet, suggesting that inconsistencies at a micro, code level become less apparent at the macro, phenotype level.

Accurately identifying incident cases of venous thromboembolism in the electronic health record: Performance of a novel phenotyping algorithm

BackgroundAccurate identification of incident venous thromboembolism (VTE) for quality improvement and health services research is challenging. The purpose of this study was to evaluate the performance of a novel incident VTE phenotyping algorithm defined using standard terminologies, requiring three key indicators documented in the electronic health record (EHR): VTE diagnostic code, VTE-related imaging procedure code, and anticoagulant medication code. MethodsRetrospective chart reviews were conducted to assess the performance of the algorithm using a random sample of phenotype(+) and phenotype(−) diagnostic encounters from primary care practices and acute care sites affiliated with five hospitals across a large integrated care delivery system in Massachusetts. The performance of the algorithm was evaluated by calculating the positive predictive value (PPV), negative predictive value (NPV), sensitivity, and specificity, using the phenotype(+) and phenotype(−) diagnostic encounters sample and target population data. ResultsBased on gold-standard manual chart review, the algorithm had a PPV of 95.2 % (95 % CI: 93.1–96.8 %), NPV of 97.1 % (95 % CI: 95.3–98.4 %), sensitivity of 91.7 % (95 % CI: 90.8–92.6 %), and specificity of 98.4 % (95 % CI: 98.1–98.6 %). The algorithm systematically misclassified a low number of specific types of encounters, highlighting potential areas for improvement. ConclusionsThis novel phenotyping algorithm offers an accurate approach for identifying incident VTE in general populations using EHR data and standard terminologies, and accurately identifies the specific encounter and date of diagnosis of the incident VTE. This approach can be used for measurement of incident VTE to drive quality improvement, research to expand the evidence, and development of quality metrics and clinical decision support to improve the diagnostic process.

Abstract P365: Prevalence of Hypertension in Minnesota Adults in 2023 Using Data from a Statewide Electronic Health Record Consortium

Background: Data on prevalence of hypertension in the United States come primarily from in-person data collected by the National Health and Nutrition Examination Survey and self-reports in the Behavioral Risk Factor Surveillance Survey. Electronic phenotypic algorithms for hypertension that include diagnosis codes, blood pressure values, and antihypertensive treatment have been proposed and tested. Objective: To describe prevalence of hypertension in Minnesota adults using data from a statewide electronic health record (EHR) consortium, the Minnesota EHR Consortium (MNEHRC). Methods: Data from 11 health systems participating in the MNEHRC were standardized to a common data model allowing for distributed querying of EHR data. Data were de-duplicated using a one-way hash algorithm. Preliminary prevalence of hypertension in 2023 was estimated in Minnesota residents with ≥ 1 encounter in the past 3 years who had ≥1 diagnosis of hypertension in the past 5 years. Medicaid insurance status was determined via linkage with state enrollment files. Residential addresses of patients were geocoded to census tracts and social vulnerability index (SVI) of census tracts was determined. Results: Among 4,369,470 Minnesotan age 18 and older in 2023, 23.6% had hypertension based on ≥1 diagnosis code. Prevalence increased with age, was higher in men (26% vs. 22% in women), and adjusted for age and sex was highest in Black (30%) and Native American (27%) compared with White (23%) and Hispanic (21%) Minnesotans. Within each race/ethnic group, those insured by Medicaid had a higher adjusted hypertension prevalence than those with other insurance types. The prevalence of hypertension in census tracts with moderate to high SVI ranged from 3% to 43%, but on average was similar to the statewide prevalence of 24% (see image 1). Prevalence of hypertension in race/ethnicity, sex, and age subgroups in higher SVI census tracts was similar to the statewide prevalence in those subgroups. Conclusions: The prevalence of hypertension in Minnesota was described in detail by demographic characteristics, geography and social vulnerability. Future work will expand the electronic hypertension phenotype and examine quality of care.

Genetic and mechanistic evaluation of an individual with para-Bombay phenotype associated with a compound heterozygote comprising two novel FUT1 variants.

As is well documented, the para-Bombay phenotype is typically characterized by the reduction or absence of ABH antigens on red blood cells but the presence of corresponding antigens in saliva. Herein, the underlying molecular mechanism of an individual with para-Bombay AB phenotype combined with two novel variants of the FUT1 gene was investigated. ABH antigens and antibodies were detected in the serum of the proband using conventional serological methods. The coding region nucleotides of the ABO, FUT1, and FUT2 genes were directly sequenced by polymerase chain reaction. Moreover, the FUT1 haploid type in the proband was analyzed by TA clone sequencing. The 3D structure of wild-type and mutant fucosyltransferases were simulated and analyzed using Phyre2 and Pymol software. Lastly, the effect of missense substitution on the function of fucosyltransferase was predicted by the Polymorphism Phenotyping algorithm (PolyPhen-2) and MutationTaster. ABH antigens were noted to be absent on the surface of red blood cells of the proband. The ABO genotype was ABO*A1.02/ABO*B.01, while the FUT2 genotype was FUT2*01/FUT2*c.357T. Interestingly, two novel missense variants (c.289G>A, p.Ala97Thr and c.575G>C, p.Arg192Pro) and one synonymous SNP (c.840G>A) were identified in the FUT1 gene. Furthermore, c.289G>A was detected in one haploid type, whereas c.575G>C and c.840G>A were discovered in another haploid type. Meanwhile, in silico analysis revealed that amino acid substitution caused by missense variants altered the partial spatial structure of the α-helices where residues 97 and 298 were located using 3D homology modeling software. Finally, both missense variants were defined as probably damaging based on PolyPhen-2 prediction. Two novel FUT1 variants were identified in a Chinese individual with para-Bombay AB phenotype, which can expand our understanding of the molecular mechanism underlying the para-Bombay phenotype and contribute to improving the safety of blood transfusion.

Validation of an acute respiratory infection phenotyping algorithm to support robust computerised medical record-based respiratory sentinel surveillance, England, 2023.

IntroductionRespiratory sentinel surveillance systems leveraging computerised medical records (CMR) use phenotyping algorithms to identify cases of interest, such as acute respiratory infection (ARI). The Oxford-Royal College of General Practitioners Research and Surveillance Centre (RSC) is the English primary care-based sentinel surveillance network.AimThis study describes and validates the RSC's new ARI phenotyping algorithm.MethodsWe developed the phenotyping algorithm using a framework aligned with international interoperability standards. We validated our algorithm by comparing ARI events identified during the 2022/23 influenza season in England through use of both old and new algorithms. We compared clinical codes commonly used for recording ARI.ResultsThe new algorithm identified an additional 860,039 cases and excluded 52,258, resulting in a net increase of 807,781 cases (33.84%) of ARI compared to the old algorithm, with totals of 3,194,224 cases versus 2,386,443 cases. Of the 860,039 newly identified cases, the majority (63.7%) were due to identification of symptom codes suggestive of an ARI diagnosis not detected by the old algorithm. The 52,258 cases incorrectly identified by the old algorithm were due to inadvertent identification of chronic, recurrent, non-infectious and other non-ARI disease.ConclusionWe developed a new ARI phenotyping algorithm that more accurately identifies cases of ARI from the CMR. This will benefit public health by providing more accurate surveillance reports to public health authorities. This new algorithm can serve as a blueprint for other CMR-based surveillance systems wishing to develop similar phenotyping algorithms.

External Validation of an Electronic Phenotyping Algorithm Detecting Attention to High Body Mass Index in Pediatric Primary Care.

The lack of feasible and meaningful measures of clinicians' behavior hinders efforts to assess and improve obesity management in pediatric primary care. In this study, we examined the external validity of a novel algorithm, previously validated in a single geographic region, using structured electronic health record (EHR) data to identify phenotypes of clinicians' attention to elevated body mass index (BMI) and weight-related comorbidities. We extracted structured EHR data for 300 randomly selected 6- to 12-year-old children with elevated BMI seen for well-child visits from June 2018 to May 2019 at pediatric primary care practices affiliated with Yale. Using diagnosis codes, laboratory orders, referrals, and medications adapted from the original algorithm, we categorized encounters as having evidence of attention to BMI only, weight-related comorbidities only, or both BMI and comorbidities. We evaluated the algorithm's sensitivity and specificity for detecting any attention to BMI and/or comorbidities using chart review as the reference standard. The adapted algorithm yielded a sensitivity of 79.2% and specificity of 94.0% for identifying any attention to high BMI/comorbidities in clinical documentation. Of 86 encounters labeled as "no attention" by the algorithm, 83% had evidence of attention in free-text components of the progress note. The likelihood of classification as "any attention" by both chart review and the algorithm varied by BMI category and by clinician type (p < 0.001). The electronic phenotyping algorithm had high specificity for detecting attention to high BMI and/or comorbidities in structured EHR inputs. The algorithm's performance may be improved by incorporating unstructured data from clinical notes.

Validation of a Major and Clinically Relevant Nonmajor Bleeding Phenotyping Algorithm on Electronic Health Records.

Bleeding is an important health outcome of interest in epidemiological studies. We aimed to develop and validate rule-based algorithms to identify (1) major bleeding and (2) all clinically relevant bleeding (CRB) (composite of major and all clinically relevant nonmajor bleeding) within real-world electronic healthcare data. We took a random sample (n = 1630) of inpatient admissions to Singapore public healthcare institutions in 2019 and 2020, stratifying by hospital and year. We included patients of all age groups, sex, and ethnicities. Presence of major bleeding and CRB were ascertained by two annotators through chart review. A total of 630 and 1000 records were used for algorithm development and validation, respectively. We formulated two algorithms: sensitivity- and positive predictive value (PPV)-optimized algorithms. A combination of hemoglobin test patterns and diagnosis codes were used in the final algorithms. During validation, diagnosis codes alone yielded low sensitivities for major bleeding (0.16) and CRB (0.24), although specificities and PPV were high (>0.97). For major bleeding, the sensitivity-optimized algorithm had much higher sensitivity and negative predictive values (NPVs) (sensitivity = 0.94, NPV = 1.00), however false positive rates were also relatively high (specificity = 0.90, PPV = 0.34). PPV-optimized algorithm had improved specificity and PPV (specificity = 0.96, PPV = 0.52), with little reduction in sensitivity and NPV (sensitivity = 0.88, NPV = 0.99). For CRB events, our algorithms had lower sensitivities (0.50-0.56). The use of diagnosis codes alone misses many genuine major bleeding events. We have developed major bleeding algorithms with high sensitivities, which can ascertain events within populations of interest.

Development of Interoperable Computable Phenotype Algorithms for Adverse Events of Special Interest to Be Used for Biologics Safety Surveillance: Validation Study.

Adverse events associated with vaccination have been evaluated by epidemiological studies and more recently have gained additional attention with the emergency use authorization of several COVID-19 vaccines. As part of its responsibility to conduct postmarket surveillance, the US Food and Drug Administration continues to monitor several adverse events of special interest (AESIs) to ensure vaccine safety, including for COVID-19. This study is part of the Biologics Effectiveness and Safety Initiative, which aims to improve the Food and Drug Administration's postmarket surveillance capabilities while minimizing public burden. This study aimed to enhance active surveillance efforts through a rules-based, computable phenotype algorithm to identify 5 AESIs being monitored by the Center for Disease Control and Prevention for COVID-19 or other vaccines: anaphylaxis, Guillain-Barré syndrome, myocarditis/pericarditis, thrombosis with thrombocytopenia syndrome, and febrile seizure. This study examined whether these phenotypes have sufficiently high positive predictive value (PPV) to ensure that the cases selected for surveillance are reasonably likely to be a postbiologic adverse event. This allows patient privacy, and security concerns for the data sharing of patients who had nonadverse events can be properly accounted for when evaluating the cost-benefit aspect of our approach. AESI phenotype algorithms were developed to apply to electronic health record data at health provider organizations across the country by querying for standard and interoperable codes. The codes queried in the rules represent symptoms, diagnoses, or treatments of the AESI sourced from published case definitions and input from clinicians. To validate the performance of the algorithms, we applied them to electronic health record data from a US academic health system and provided a sample of cases for clinicians to evaluate. Performance was assessed using PPV. With a PPV of 93.3%, our anaphylaxis algorithm performed the best. The PPVs for our febrile seizure, myocarditis/pericarditis, thrombocytopenia syndrome, and Guillain-Barré syndrome algorithms were 89%, 83.5%, 70.2%, and 47.2%, respectively. Given our algorithm design and performance, our results support continued research into using interoperable algorithms for widespread AESI postmarket detection.

Estimating disease burden using national linked electronic health records: a study using an English population-based cohort.

Electronic health records (EHRs) have the potential to be used to produce detailed disease burden estimates. In this study we created disease estimates using national EHR for three high burden conditions, compared estimates between linked and unlinked datasets and produced stratified estimates by age, sex, ethnicity, socio-economic deprivation and geographical region. EHRs containing primary care (Clinical Practice Research Datalink), secondary care (Hospital Episode Statistics) and mortality records (Office for National Statistics) were used. We used existing disease phenotyping algorithms to identify cases of cancer (breast, lung, colorectal and prostate), type 1 and 2 diabetes, and lower back pain. We calculated age-standardised incidence of first cancer, point prevalence for diabetes, and primary care consultation prevalence for low back pain. 7.2 million people contributing 45.3 million person-years of active follow-up between 2000-2014 were included. CPRD-HES combined and CPRD-HES-ONS combined lung and bowel cancer incidence estimates by sex were similar to cancer registry estimates. Linked CPRD-HES estimates for combined Type 1 and Type 2 diabetes were consistently higher than those of CPRD alone, with the difference steadily increasing over time from 0.26% (2.99% for CPRD-HES vs. 2.73 for CPRD) in 2002 to 0.58% (6.17% vs. 5.59) in 2013. Low back pain prevalence was highest in the most deprived quintile and when compared to the least deprived quintile the difference in prevalence increased over time between 2000 and 2013, with the largest difference of 27% (558.70 per 10,000 people vs 438.20) in 2013. We use national EHRs to produce estimates of burden of disease to produce detailed estimates by deprivation, ethnicity and geographical region. National EHRs have the potential to improve disease burden estimates at a local and global level and may serve as more automated, timely and precise inputs for policy making and global burden of disease estimation.

Clinical and allergological characteristics of patients with severe bronchial asthma in the regional registry and phenotyping principles for the targeted therapy choice

Introduction. Severe asthma targeted therapy effectiveness depends on precise targeting of the selected drug to the key link in pathogenesis. Therefore, severe asthma phenotyping in real clinical practice is relevant.Aim. To determine main clinical and allergological characteristics of patients with severe asthma and to establish important phenotyping signs determined choice of a targeted drug for severe asthma treatment.Materials and methods. The prospective and retrospective study involved patients (n = 198) of the Sverdlovsk region registry receiving targeted therapy of severe asthma. Considering clinical and allergological picture, allergic, non-allergic eosinophilic and mixed severe asthma phenotypes were identified. Clinical and laboratory characteristics of phenotypes were described. A phenotyping algorithm was developed.Results. In the register of patients (n = 198) with severe asthma, non-allergic eosinophilic asthma was 46.5%, allergic – 34.8%, mixed – 18.7%. Significant signs for phenotyping were identified: age of asthma onset, proven allergy, Phadiatop ImmunoCAP level and blood eosinophils on baseline, concomitant allergic rhinitis, chronic rhinosinusitis with nasal polyps and hyper-sensitivity to NSAIDs. The main signs of allergic severe asthma determined: early onset, proven allergy and a positive result of Phadiatop ImmunoCAP (the probability of allergic phenotype increases with Phadiatop ≥ 1.53 PAU/l). Signs of non-allergic eosinophilic asthma were eosinophilia ≥ 150 cells/µl, absence of allergy, concomitant chronic rhinosinusitis with nasal polyps and hypersensitivity to NSAIDs, late onset (after 30 years). Signs were identified for mixed asthma: presence of proven allergy or latent sensitization in combination with high level of Phadiatop ImmunoCAP, late onset, eosinophilia ≥ 300 cells/µl, chronic rhinosinusitis with nasal polyps, hypersensitivity NSAIDs.Conclusions. The algorithm for severe asthma phenotyping based on the isolation of eosinophilia of allergic and non-allergic origin is proposed. Severe asthma phenotyping, which can be carried out in real clinical practice, should facilitate the selection of an initial targeted drug.

Performance of Phenotype Algorithms for the Identification of Opioid-Exposed Infants.

Observational studies examining outcomes among opioid-exposed infants are limited by phenotype algorithms that may under identify opioid-exposed infants without neonatal opioid withdrawal syndrome (NOWS). We developed and validated the performance of different phenotype algorithms to identify opioid-exposed infants using electronic health record data. We developed phenotype algorithms for the identification of opioid-exposed infants among a population of birthing person-infant dyads from an academic health care system (2010-2022). We derived phenotype algorithms from combinations of 6 unique indicators of in utero opioid exposure, including those from the infant record (NOWS or opioid-exposure diagnosis, positive toxicology) and birthing person record (opioid use disorder diagnosis, opioid drug exposure record, opioid listed on medication reconciliation, positive toxicology). We determined the positive predictive value (PPV) and 95% confidence interval for each phenotype algorithm using medical record review as the gold standard. Among 41 047 dyads meeting exclusion criteria, we identified 1558 infants (3.80%) with evidence of at least 1 indicator for opioid exposure and 32 (0.08%) meeting all 6 indicators of the phenotype algorithm. Among the sample of dyads randomly selected for review (n = 600), the PPV for the phenotype requiring only a single indicator was 95.4% (confidence interval: 93.3-96.8) with varying PPVs for the other phenotype algorithms derived from a combination of infant and birthing person indicators (PPV range: 95.4-100.0). Opioid-exposed infants can be accurately identified using electronic health record data. Our publicly available phenotype algorithms can be used to conduct research examining outcomes among opioid-exposed infants with and without NOWS.

Air pollution exposure, accelerated biological aging, and increased thyroid dysfunction risk: Evidence from a nationwide prospective study

BackgroundLong-term air pollution exposure is a major health concern, yet its associations with thyroid dysfunction (hyperthyroidism and hypothyroidism) and biological aging remain unclear. We aimed to determine the association of long-term air pollution exposure with thyroid dysfunction and to investigate the potential roles of biological aging. MethodsA prospective cohort study was conducted on 432,340 participants with available data on air pollutants including particulate matter (PM2.5, PM10, and PM2.5-10), nitrogen dioxide (NO2), and nitric oxide (NO) from the UK Biobank. An air pollution score was calculated using principal component analysis to reflect joint exposure to these pollutants. Biological aging was assessed using the Klemera-Doubal method biological age and the phenotypic age algorithms. The associations of individual and joint air pollutants with thyroid dysfunction were estimated using the Cox proportional hazards regression model. The roles of biological aging were explored using interaction and mediation analyses. ResultsDuring a median follow-up of 12.41 years, 1,721 (0.40 %) and 9,296 (2.15 %) participants developed hyperthyroidism and hypothyroidism, respectively. All air pollutants were observed to be significantly associated with an increased risk of incident hypothyroidism, while PM2.5, PM10, and NO2 were observed to be significantly associated with an increased risk of incident hyperthyroidism. The hazard ratios (HRs) for hyperthyroidism and hypothyroidism were 1.15 (95 % confidence interval: 1.00–1.32) and 1.15 (1.08–1.22) for individuals in the highest quartile compared with those in the lowest quartile of air pollution score, respectively. Additionally, we noticed that individuals with higher pollutant levels and biologically older generally had a higher risk of incident thyroid dysfunction. Moreover, accelerated biological aging partially mediated 1.9 %–9.4 % of air pollution-associated thyroid dysfunction. ConclusionsDespite the possible underestimation of incident thyroid dysfunction, long-term air pollution exposure may increase the risk of incident thyroid dysfunction, particularly in biologically older participants, with biological aging potentially involved in the mechanisms.

A general framework for developing computable clinical phenotype algorithms.

To present a general framework providing high-level guidance to developers of computable algorithms for identifying patients with specific clinical conditions (phenotypes) through a variety of approaches, including but not limited to machine learning and natural language processing methods to incorporate rich electronic health record data. Drawing on extensive prior phenotyping experiences and insights derived from 3 algorithm development projects conducted specifically for this purpose, our team with expertise in clinical medicine, statistics, informatics, pharmacoepidemiology, and healthcare data science methods conceptualized stages of development and corresponding sets of principles, strategies, and practical guidelines for improving the algorithm development process. We propose 5 stages of algorithm development and corresponding principles, strategies, and guidelines: (1) assessing fitness-for-purpose, (2) creating gold standard data, (3) feature engineering, (4) model development, and (5) model evaluation. This framework is intended to provide practical guidance and serve as a basis for future elaboration and extension.

An algorithm to identify patients aged 0–3 with rare genetic disorders

BackgroundWith over 7000 Mendelian disorders, identifying children with a specific rare genetic disorder diagnosis through structured electronic medical record data is challenging given incompleteness of records, inaccurate medical diagnosis coding, as well as heterogeneity in clinical symptoms and procedures for specific disorders. We sought to develop a digital phenotyping algorithm (PheIndex) using electronic medical records to identify children aged 0–3 diagnosed with genetic disorders or who present with illness with an increased risk for genetic disorders.ResultsThrough expert opinion, we established 13 criteria for the algorithm and derived a score and a classification. The performance of each criterion and the classification were validated by chart review. PheIndex identified 1,088 children out of 93,154 live births who may be at an increased risk for genetic disorders. Chart review demonstrated that the algorithm achieved 90% sensitivity, 97% specificity, and 94% accuracy.ConclusionsThe PheIndex algorithm can help identify when a rare genetic disorder may be present, alerting providers to consider ordering a diagnostic genetic test and/or referring a patient to a medical geneticist.

Development and validation of a race-agnostic computable phenotype for kidney health in adult hospitalized patients.

Standard race adjustments for estimating glomerular filtration rate (GFR) and reference creatinine can yield a lower acute kidney injury (AKI) and chronic kidney disease (CKD) prevalence among African American patients than non-race adjusted estimates. We developed two race-agnostic computable phenotypes that assess kidney health among 139,152 subjects admitted to the University of Florida Health between 1/2012-8/2019 by removing the race modifier from the estimated GFR and estimated creatinine formula used by the race-adjusted algorithm (race-agnostic algorithm 1) and by utilizing 2021 CKD-EPI refit without race formula (race-agnostic algorithm 2) for calculations of the estimated GFR and estimated creatinine. We compared results using these algorithms to the race-adjusted algorithm in African American patients. Using clinical adjudication, we validated race-agnostic computable phenotypes developed for preadmission CKD and AKI presence on 300 cases. Race adjustment reclassified 2,113 (8%) to no CKD and 7,901 (29%) to a less severe CKD stage compared to race-agnostic algorithm 1 and reclassified 1,208 (5%) to no CKD and 4,606 (18%) to a less severe CKD stage compared to race-agnostic algorithm 2. Of 12,451 AKI encounters based on race-agnostic algorithm 1, race adjustment reclassified 591 to No AKI and 305 to a less severe AKI stage. Of 12,251 AKI encounters based on race-agnostic algorithm 2, race adjustment reclassified 382 to No AKI and 196 (1.6%) to a less severe AKI stage. The phenotyping algorithm based on refit without race formula performed well in identifying patients with CKD and AKI with a sensitivity of 100% (95% confidence interval [CI] 97%-100%) and 99% (95% CI 97%-100%) and a specificity of 88% (95% CI 82%-93%) and 98% (95% CI 93%-100%), respectively. Race-agnostic algorithms identified substantial proportions of additional patients with CKD and AKI compared to race-adjusted algorithm in African American patients. The phenotyping algorithm is promising in identifying patients with kidney disease and improving clinical decision-making.

Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users.

Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. We describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.