Identifying Patients with Rare Disease Using Electronic Health Record Data: The Kaiser Permanente Southern California Membranous Nephropathy Cohort

Sun, Amy Z; Shu, Y. C.; Harrison, Teresa N.; Hever, Aviv; Jacobsen, Steven J.; O’Shaughnessy, Michelle M.; Sim, John J.

doi:10.7812/tpp/19.126

Cited by 15 publications

(11 citation statements)

References 14 publications

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“…First, we developed a population-based approach on the basis of EHR data combined with targeted physician adjudication to identify and characterize long-term outcomes of adults with primary NS. This approach could be applied by other health systems to identify adults with primary NS, and future efforts leveraging validated natural language processing algorithms and other machine-learning methods on unstructured EHR data could facilitate even more efficient population-level identification of primary NS, by avoiding the need for manual adjudication 35 36 Second, the substantial excess risk of ESKD with primary NS and particularly in those with FSGS or MN highlight the need for careful surveillance in these patients, optimizing control of risk factors for kidney disease progression, and identification of novel etiology-specific therapies.…”

Section: Discussionmentioning

confidence: 99%

Primary Nephrotic Syndrome and Risks of ESKD, Cardiovascular Events, and Death: The Kaiser Permanente Nephrotic Syndrome Study

Tan

Chertow

et al. 2021

JASN

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Background Few population-based data exist about adults with primary nephrotic syndrome. Methods To evaluate kidney, cardiovascular, and mortality outcomes in adults with primary nephrotic syndrome, we identified adults within an integrated health care delivery system (Kaiser Permanente Northern California) with nephrotic-range proteinuria or diagnosed nephrotic syndrome between 1996-2012. Nephrologists reviewed medical records for clinical presentation, laboratory findings, and biopsy results to confirm primary nephrotic syndrome and assigned etiology. We identified a 1:100 time-matched cohort of adults without diabetes, diagnosed nephrotic syndrome, or proteinuria as controls to compare rates of end-stage kidney disease (ESKD), cardiovascular outcomes, and death through 2014, using multivariable Cox regression. Results We confirmed 907 cases of primary nephrotic syndrome (655 definite and 252 presumed cases of focal segmental glomerulosclerosis [FSGS, 40%], membranous nephropathy [40%], and minimal change disease [20%]). Mean age was 49 years; 43% were women. Adults with primary nephrotic syndrome had higher adjusted rates of ESKD (adjusted hazard ratio [aHR], 19.63; 95% confidence interval [95% CI], 12.76 to 30.20), acute coronary syndrome (aHR 2.58; 95% CI, 1.89 to 3.52), heart failure (aHR 3.01; 95%CI, 2.16 to 4.19), ischemic stroke (aHR 1.80; 95%CI,1.06 to 3.05), venous thromboembolism (aHR 2.56; 95%CI, 1.35 to 4.85), and death (aHR 1.34; 95%CI, 1.09 to 1.64) versus controls. Excess ESKD risk was significantly higher for FSGS and membranous nephropathy than for presumed minimal change disease. The three etiologies of primary nephrotic syndrome did not differ significantly in terms of cardiovascular outcomes and death. Conclusions Adults with primary nephrotic syndrome experience higher adjusted rates of ESKD, cardiovascular outcomes, and death, with significant variation by underlying etiology in risk for developing ESKD.

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Section: Discussionmentioning

confidence: 99%

Primary Nephrotic Syndrome and Risks of ESKD, Cardiovascular Events, and Death: The Kaiser Permanente Nephrotic Syndrome Study

Tan

Chertow

et al. 2021

JASN

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“…Nonetheless, the trend in total heart failure prevalence in Germany over the last decade is rather flat and cannot explain the increases observed for CA [28]. On the other hand, rare diseases such as amyloidosis in general might be rather under-coded which leads to underestimation of CA prevalence and incidence as reported for other rare disease [30]. Nonetheless, assuming that these general limitations of the data source do not change relevantly within 10 years our findings on the temporal trend will not be impacted relevantly.…”

Section: Limitationsmentioning

confidence: 88%

Epidemiology of cardiac amyloidosis in Germany: a retrospective analysis from 2009 to 2018

et al. 2022

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Background Improved imaging modalities contributed to increasing awareness of cardiac amyloidosis. Contemporary data on frequency trends in Germany are lacking. Methods In a retrospective study using health claims data of a German statutory health insurance, patients with diagnostic codes of amyloidosis and concomitant heart failure between 2009 and 2018 were identified. Results Prevalence increased from 15.5 to 47.6 per 100,000 person-years, and incidence increased from 4.8 to 11.6 per 100,000 person-years, with a continuous steepening in the slope of incidence trend. In patients with amyloidosis and heart failure age and proportion of men significantly increased, whereas the frequency of myeloma and nephrotic syndrome significantly decreased over time. Median (IQR) survival time after first diagnosis was 2.5 years (0.5–6 years), with a 9% (95% CI 2–15%, p = 0.008) reduced risk of death in the second compared to the first 5 years of observation. In the 2 years prior and 1 year after diagnosis, mean total health care costs were 6568 €, 11,872 € and 21,955 € per person and year. Conclusion The rise in cardiac amyloidosis has continuously accelerated in the last decade. Considering the adverse outcome and high health care burden, further effort should be put on early detection of the disease to implement available treatment.

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“…Previous research has typically focused on specific rare conditions. Sun et al [42] used ICD-9 codes to identify membranous nephropathy patients in the Kaiser Permanente health system, while Dickey et al [43] used exome sequencing from the UKB to investigate whether erythropoietic protoporphyria may be under-diagnosed. The UKB [44] has also been analyzed more broadly, with rare variants in JAK2 and F11 associated to groups of myeloproliferative disease and congenital coagulation defects, respectively.…”

Section: Discussionmentioning

confidence: 99%

Enhanced rare disease mapping for phenome-wide genetic association in the UK Biobank

et al. 2022

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Background Rare diseases collectively affect up to 10% of the population, but often lack effective treatment, and typically little is known about their pathophysiology. Major challenges include suboptimal phenotype mapping and limited statistical power. Population biobanks, such as the UK Biobank, recruit many individuals who can be affected by rare diseases; however, investigation into their utility for rare disease research remains limited. We hypothesized the UK Biobank can be used as a unique population assay for rare diseases in the general population. Methods We constructed a consensus mapping between ICD-10 codes and ORPHA codes for rare diseases, then identified individuals with each rare condition in the UK Biobank, and investigated their age at recruitment, sex bias, and comorbidity distributions. Using exome sequencing data from 167,246 individuals of European ancestry, we performed genetic association controlling for case/control imbalance (SAIGE) to identify potential rare pathogenic variants for each disease. Results Using our mapping approach, we identified and characterized 420 rare diseases affecting 23,575 individuals in the UK Biobank. Significant genetic associations included JAK2 V617F for immune thrombocytopenic purpura (p = 1.24 × 10−13) and a novel CALR loss of function variant for essential thrombocythemia (p = 1.59 × 10−13). We constructed an interactive resource highlighting demographic information (http://www-personal.umich.edu/~mattpat/rareDiseases.html) and demonstrate transferability by applying our mapping to a medical claims database. Conclusions Enhanced disease mapping and increased power from population biobanks can elucidate the demographics and genetic associations for rare diseases.

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Identifying Patients with Rare Disease Using Electronic Health Record Data: The Kaiser Permanente Southern California Membranous Nephropathy Cohort

Cited by 15 publications

References 14 publications

Primary Nephrotic Syndrome and Risks of ESKD, Cardiovascular Events, and Death: The Kaiser Permanente Nephrotic Syndrome Study

Primary Nephrotic Syndrome and Risks of ESKD, Cardiovascular Events, and Death: The Kaiser Permanente Nephrotic Syndrome Study

Epidemiology of cardiac amyloidosis in Germany: a retrospective analysis from 2009 to 2018

Enhanced rare disease mapping for phenome-wide genetic association in the UK Biobank

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