<scp>IncidencePrevalence</scp>: An R package to calculate population‐level incidence rates and prevalence using the <scp>OMOP</scp> common data model

Raventós, Berta; Català, Martí; Du, Mike; Guo, Yuchen; Black, Adam; Inberg, Ger; Li, Xintong; López‐Güell, Kim; Newby, Danielle; de Ridder, Maria; Barboza, Cesar; Duarte‐Salles, Talita; Verhamme, Katia; Rijnbeek, Peter; Prieto Alhambra, Daniel; Burn, Edward

doi:10.1002/pds.5717

Cited by 4 publications

(1 citation statement)

References 20 publications

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“…Incidence rates (IR) with 95% confidence intervals (CI) were calculated for all endocrine treatments and treatment-related outcomes monthly, and within the pre-pandemic, lockdown, and post-lockdown periods across the entire observation period using the IncidencePrevalence R package [11]. Patients with breast cancer or prostate cancer who were diagnosed within the observation period contributed time-at-risk, and as such contributed to the ‘denominator population’, until the earliest of a record of the endocrine treatment / treatment-related outcome, transfer out of the database, end of the study period or death.…”

Section: Statistical Analysesmentioning

confidence: 99%

Collateral effects of the COVID-19 pandemic on endocrine treatments for breast and prostate cancer in the UK: implications for bone health

Barclay,

Català,

Jödicke

et al. 2023

Preprint

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BackgroundThe COVID-19 pandemic affected cancer screening, diagnosis and treatment pathways. This study examined the impact of the pandemic on incidence and trends of endocrine treatments in patients with breast or prostate cancer; and endocrine treatment-related side-effects.MethodsPopulation-based cohort study using UK primary care Clinical Practice Research Datalink (CPRD) GOLD database. There were 13,701 newly diagnosed breast cancer patients and 12,221 prostate cancer patients with ≥1-year data availability since diagnosis between January 2017-June 2022. Incidence rates (IR) and incidence rate ratios (IRR) were calculated across multiple time periods before and after lockdown to examine the impact of changing social restrictions on endocrine treatments and treatment-related outcomes, including osteopenia, osteoporosis and bisphosphonate prescriptions.ResultsIn patients with breast cancer, aromatase inhibitor prescriptions increased during lockdown compared to pre-pandemic (IRR: 1.22 [95% Confidence Interval: 1.11-1.34]), followed by a decrease post-first lockdown (IRR: 0.79 [95%CI: 0.69-0.89]). In patients with prostate cancer, first-generation antiandrogen prescriptions increased compared to pre-pandemic (IRR: 1.23 [95% CI: 1.08-1.4]). For breast cancer patients on aromatase inhibitors, diagnoses of osteopenia, osteoporosis and bisphosphonate prescriptions were reduced across all lockdown periods compared to pre-pandemic (IRR range: 0.31-0.62).ConclusionDuring the first two years of the pandemic, newly diagnosed breast and prostate cancer patients were prescribed more endocrine treatments compared to pre-pandemic, due to restrictions on hospital procedures replacing surgeries with bridging therapies. But breast cancer patients had fewer diagnoses of osteopenia and osteoporosis, and bisphosphonate prescriptions. These patients should be followed up in the coming years for signs of bone thinning. Evidence of poorer management of treatment-related side-effects will allow us to determine whether there is a need to better allocate resources to patients at high risk for bone-related complications.

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Section: Statistical Analysesmentioning

confidence: 99%

Collateral effects of the COVID-19 pandemic on endocrine treatments for breast and prostate cancer in the UK: implications for bone health

Barclay,

Català,

Jödicke

et al. 2023

Preprint

Self Cite

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Incident Use of Hydroxychloroquine for the Treatment of Rheumatoid Arthritis and Systemic Lupus Erythematosus During the COVID‐19 Pandemic

Mercadé‐Besora,

Guo,

et al. 2024

Arthritis Care & Research

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ObjectiveWe studied whether the use of hydroxychloroquine (HCQ) for COVID‐19 resulted in supply shortages for patients with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE).MethodsWe used US claims data (IQVIA PHARMETRICS® Plus for Academics [PHARMETRICS]) and hospital electronic records from Spain (IMASIS) to estimate monthly rates of HCQ use between January 2019 and March 2022, in the general population, and in RA and SLE patients. Methotrexate (MTX) was use was estimated as a control.ResultsOver 13.5 million individuals (13,311,811 PHARMETRICS, 207,646 IMASIS) were included in the general population cohort. RA and SLE cohorts enrolled 135,259 and 39,295 patients respectively, in PHARMETRICS. Incidence of MTX and HCQ were stable before March 2020. On March 2020, the incidence of HCQ increased by 9‐ and 67‐fold in PHARMETRICS and IMASIS respectively, to decrease in May 2020. Usage rates of HCQ went back to pre‐pandemic trends in Spain, but remained high in the US, mimicking waves of COVID‐19. No significant changes in HCQ use were noted among patients with RA and SLE. MTX use rates decreased during HCQ approval period for COVID‐19 treatment.ConclusionsUse of HCQ increased dramatically in the general population in both Spain and the US during March and April 2020. While Spain returned to pre‐pandemic rates after the first wave, use of HCQ remained high and followed waves of COVID‐19 in the US. However, we found no evidence of general shortages in the use of HCQ for both RA and SLE in the US.This article is protected by copyright. All rights reserved.

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Incidence, prevalence, and survival of lung cancer in the United Kingdom from 2000-2021: a population-based cohort study

Corby,

Barclay,

Tan

et al. 2024

Preprint

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BackgroundLung cancer is the leading cause of cancer-associated mortality worldwide. In the UK, there has been a major reduction in smoking, the leading risk factor for lung cancer, as well as the introduction of the new screening in 2023. Therefore, an up-to-date assessment of the trends of lung cancer is required in the UK.MethodsWe performed a population-based cohort study using the UK primary care Clinical Practice Research Datalink (CPRD) GOLD database, compared with CPRD Aurum. Participants aged 18+ years, with one-year of prior data availability, were included. We estimated lung cancer incidence rates (IR), period prevalence (PP), and survival at one-, five– and ten years after diagnosis using the Kaplan-Meier method.ResultsOverall, 11,388,117 participants, with 45,563 lung cancer cases were studied. The incidence rate of lung cancer was 52.0 (95% CI 51.5 to 52.5) per 100,000 person-years, with incidence increasing from 2000 to 2021, especially in females aged over 50, and males aged over 80, with the highest incidence rate in people aged 80-89. Period prevalence in 2021 was 0.18%, with the largest rise seen in participants aged over 60. Median survival post-diagnosis increased from 6.6 months in those diagnosed between 2000-2004 to 10 months between 2015-2019. Both short and long-term survival was higher in younger cohorts, with 82.7% one-year survival in those aged 18-29, versus 24.2% in the age 90+ cohort. Throughout the study period, survival was longer in females, with a larger increase in survival over time than in males.ConclusionThe incidence and prevalence of lung cancer diagnoses in the UK have increased, especially in female and older populations, with a small increase in median survival. With the introduction of the UK lung cancer screening programme, this study will enable future comparisons of overall disease burden, so the overall impact may be seen.

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IncidencePrevalence: An R package to calculate population‐level incidence rates and prevalence using the OMOP common data model

Cited by 4 publications

References 20 publications

Collateral effects of the COVID-19 pandemic on endocrine treatments for breast and prostate cancer in the UK: implications for bone health

Collateral effects of the COVID-19 pandemic on endocrine treatments for breast and prostate cancer in the UK: implications for bone health

Incident Use of Hydroxychloroquine for the Treatment of Rheumatoid Arthritis and Systemic Lupus Erythematosus During the COVID‐19 Pandemic

Incidence, prevalence, and survival of lung cancer in the United Kingdom from 2000-2021: a population-based cohort study

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