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Transthyretin amyloid cardiomyopathy, an often unrecognized cause of heart failure, is now treatable with a transthyretin stabilizer. It is therefore important to identify at-risk patients who can undergo targeted testing for earlier diagnosis and treatment, prior to the development of irreversible heart failure. Here we show that a random forest machine learning model can identify potential wild-type transthyretin amyloid cardiomyopathy using medical claims data. We derive a machine learning model in 1071 cases and 1071 non-amyloid heart failure controls and validate the model in three nationally representative cohorts (9412 cases, 9412 matched controls), and a large, single-center electronic health record-based cohort (261 cases, 39393 controls). We show that the machine learning model performs well in identifying patients with cardiac amyloidosis in the derivation cohort and all four validation cohorts, thereby providing a systematic framework to increase the suspicion of transthyretin cardiac amyloidosis in patients with heart failure. Transthyretin amyloid cardiomyopathy is a treatable but often unrecognized cause of heart failure. We derived and validated a machine learning model based on medical diagnostic codes that identifies heart failure patients at risk for wild-type transthyretin amyloid cardiomyopathy.

An 11-factor random forest model has been developed among ambulatory heart failure (HF) patients for identifying potential wild-type amyloidogenic TTR cardiomyopathy (wtATTR-CM). The model has not been evaluated in a large sample of patients hospitalized for HF. This study included Medicare beneficiaries aged ≥65 years hospitalized for HF in the Get With The Guidelines-HF® Registry from 2008-2019. Patients with and without a diagnosis of ATTR-CM were compared, as defined by inpatient and outpatient claims data within 6 months pre- or post-index hospitalization. Within a cohort matched 1:1 by age and sex, univariable logistic regression was used to evaluate relationships between ATTR-CM and each of the 11 factors of the established model. Discrimination and calibration of the 11-factor model were assessed. Among 205,545 patients (median age 81 years) hospitalized for HF across 608 hospitals, 627 patients (0.31%) had a diagnosis code for ATTR-CM. Univariable analysis within the 1:1 matched cohort of each of the 11-factors in the ATTR-CM model found pericardial effusion, carpal tunnel syndrome, lumbar spinal stenosis, and elevated serum enzymes (e.g., troponin elevation) to be strongly associated with ATTR-CM. The 11-factor model showed modest discrimination (c-statistic 0.65) and good calibration within the matched cohort. Among US patients hospitalized for HF, the number of patients with ATTR-CM defined by diagnosis codes on an inpatient/outpatient claim within 6 months of admission was low. Most factors within the prior 11-factor model were associated with greater odds of ATTR-CM diagnosis. In this population, the ATTR-CM model demonstrated modest discrimination.

ObjectiveThe aim of this study was to evaluate the potential real-world application of a machine learning (ML) algorithm, developed and trained on heart failure (HF) cohorts in the USA, to detect patients with undiagnosed wild type cardiac amyloidosis (ATTRwt) in the UK.DesignIn this retrospective observational study, anonymised, linked primary and secondary care data (Clinical Practice Research Datalink GOLD and Hospital Episode Statistics, respectively, were used to identify patients diagnosed with HF between 2009 and 2018 in the UK. International Classification of Diseases (ICD)-10 clinical modification codes were matched to equivalent Read (primary care) and ICD-10 WHO (secondary care) diagnosis codes used in the UK. In the absence of specific Read or ICD-10 WHO codes for ATTRwt, two proxy case definitions (definitive and possible cases) based on the degree of confidence that the contributing codes defined true ATTRwt cases were created using ML.Primary outcome measureAlgorithm performance was evaluated primarily using the area under the receiver operating curve (AUROC) by comparing the actual versus algorithm predicted case definitions at varying sensitivities and specificities.ResultsThe algorithm demonstrated strongest predictive ability when a combination of primary care and secondary care data were used (AUROC: 0.84 in definitive cohort and 0.86 in possible cohort). For primary care or secondary care data alone, performance ranged from 0.68 to 0.78.ConclusionThe ML algorithm, despite being developed in a US population, was effective at identifying patients that may have ATTRwt in a UK setting. Its potential use in research and clinical care to aid identification of patients with undiagnosed ATTRwt, possibly enabling earlier diagnosis in the disease pathway, should be investigated.

Background: Wild-type transthyretin amyloid cardiomyopathy (ATTR-CM) is a frequently under-recognized cause of heart failure (HF) in older patients. To improve identification of patients at risk for the disease, we initiated a pilot program in which 9 cardiac/non-cardiac phenotypes and 20 high-performing phenotype combinations predictive of wild-type ATTR-CM were operationalized in electronic health record (EHR) configurations at a large academic medical center. Methods: Inclusion criteria were age >50 years and HF; exclusion criteria were end-stage renal disease and prior amyloidosis diagnoses. The different Epic EHR configurations investigated were a clinical decision support tool (Best Practice Advisory) and operational/analytical reports (Clarity™, Reporting Workbench™, and SlicerDicer); the different data sources employed were problem list, visit diagnosis, medical history, and billing transactions. Results: With Clarity, among 45 051 patients with HF, 4006 patients (8.9%) had ⩾1 phenotype combination associated with increased risk of wild-type ATTR-CM. Across all data sources, 2 phenotypes (cardiomegaly; osteoarthrosis) and 2 combinations (carpal tunnel syndrome + HF; atrial fibrillation + heart block + cardiomegaly + osteoarthrosis) generated the highest proportions of patients for wild-type ATTR-CM screening. Conclusion: All EHR configurations tested were capable of operationalizing phenotypes or phenotype combinations to identify at-risk patients; the Clarity report was the most comprehensive.

Background Primary immunodeficiency (PI) is a group of heterogeneous disorders resulting from immune system defects. Over 70% of PI is undiagnosed, leading to increased mortality, co-morbidity and healthcare costs. Among PI disorders, combined immunodeficiencies (CID) are characterized by complex immune defects. Common variable immunodeficiency (CVID) is among the most common types of PI. In light of available treatments, it is critical to identify adult patients at risk for CID and CVID, before the development of serious morbidity and mortality. Methods We developed a deep learning-based method (named “TabMLPNet”) to analyze clinical history from nationally representative medical claims from electronic health records (Optum® data, covering all US), evaluated in the setting of identifying CID/CVID in adults. Further, we revealed the most important CID/CVID-associated antecedent phenotype combinations. Four large cohorts were generated: a total of 47,660 PI cases and (1:1 matched) controls. Results The sensitivity/specificity of TabMLPNet modeling ranges from 0.82-0.88/0.82-0.85 across cohorts. Distinctive combinations of antecedent phenotypes associated with CID/CVID are identified, consisting of respiratory infections/conditions, genetic anomalies, cardiac defects, autoimmune diseases, blood disorders and malignancies, which can possibly be useful to systematize the identification of CID and CVID. Conclusions We demonstrated an accurate method in terms of CID and CVID detection evaluated on large-scale medical claims data. Our predictive scheme can potentially lead to the development of new clinical insights and expanded guidelines for identification of adult patients at risk for CID and CVID as well as be used to improve patient outcomes on population level. Plain language summary Primary immunodeficiencies (PI) are disorders that weaken the immune system, increasing the incident of life-threatening infections, organ damage and the development of cancer and autoimmune diseases. Although PI is estimated to affect 1-2% of the global population, 70-90% of these patients remain undiagnosed. Many patients are diagnosed during adulthood, after other serious diseases have already developed. We developed a computational method to analyze the clinical history from a large group of people with and without PI. We focused on combined (CID) and common variable immunodeficiency (CVID), which are among the least studied and most common PI subtypes, respectively. We could identify people with CID or CVID and combinations of diseases and symptoms which could make it easier to identify CID or CVID. Our method could be used to more readily identify adults at risk of CID or CVID, enabling treatment to start earlier and their long-term health to be improved. Papanastasiou et al. develop a deep learning-based method to identify combined immunodeficiencies (CID) and common variable immunodeficiencies (CVID) from large-scale electronic health record data. Distinctive combinations of antecedent phenotypes associated with CID/CVID are identified that could improve early diagnosis.

Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE) sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.

Gene expression quantitative trait loci (eQTL) are useful for identifying single nucleotide polymorphisms (SNPs) associated with diseases. At times, a genetic variant may be associated with a master regulator involved in the manifestation of a disease. The downstream target genes of the master regulator are typically co-expressed and share biological function. Therefore, it is practical to screen for eQTLs by identifying SNPs associated with the targets of a transcript-regulator (TR). We used a multivariate regression with the gene expression of known targets of TRs and SNPs to identify TReQTLs in European (CEU) and African (YRI) HapMap populations. A nominal p-value of <1×10(-6) revealed 234 SNPs in CEU and 154 in YRI as TReQTLs. These represent 36 independent (tag) SNPs in CEU and 39 in YRI affecting the downstream targets of 25 and 36 TRs respectively. At a false discovery rate (FDR) = 45%, one cis-acting tag SNP (within 1 kb of a gene) in each population was identified as a TReQTL. In CEU, the SNP (rs16858621) in Pcnxl2 was found to be associated with the genes regulated by CREM whereas in YRI, the SNP (rs16909324) was linked to the targets of miRNA hsa-miR-125a. To infer the pathways that regulate expression, we ranked TReQTLs by connectivity within the structure of biological process subtrees. One TReQTL SNP (rs3790904) in CEU maps to Lphn2 and is associated (nominal p-value = 8.1×10(-7)) with the targets of the X-linked breast cancer suppressor Foxp3. The structure of the biological process subtree and a gene interaction network of the TReQTL revealed that tumor necrosis factor, NF-kappaB and variants in G-protein coupled receptors signaling may play a central role as communicators in Foxp3 functional regulation. The potential pleiotropic effect of the Foxp3 TReQTLs was gleaned from integrating mRNA-Seq data and SNP-set enrichment into the analysis.