Annual Report to the Nation on the Status of Cancer, part 2: Early assessment of the COVID-19 pandemic's impact on cancer diagnosis.

BACKGROUND: With access to cancer care services limited because of coronavirus disease 2019 control measures, cancer diagnosis and treatment have been delayed. The authors explored changes in the counts of US incident cases by cancer type, age, sex, race, and disease stage in 2020. METHODS: Data were extracted from selected US population-based cancer registries for diagnosis years 2015-2020 using first-submission data from the North American Association of Central Cancer Registries. After a quality assessment, the monthly numbers of newly diagnosed cancer cases were extracted for six cancer types: colorectal, female breast, lung, pancreas, prostate, and thyroid. The observed numbers of incident cancer cases in 2020 were compared with the estimated numbers by calculating observed-to-expected (O/E) ratios. The expected numbers of incident cases were extrapolated using Joinpoint trend models. RESULTS: The authors report an O/E ratio <1.0 for major screening-eligible cancer sites, indicating fewer newly diagnosed cases than expected in 2020. The O/E ratios were lowest in April 2020. For every cancer site except pancreas, Asians/Pacific Islanders had the lowest O/E ratio of any race group. O/E ratios were lower for cases diagnosed at localized stages than for cases diagnosed at advanced stages. CONCLUSIONS: The current analysis provides strong evidence for declines in cancer diagnoses, relative to the expected numbers, between March and May of 2020. The declines correlate with reductions in pathology reports and are greater for cases diagnosed at in situ and localized stage, triggering concerns about potential poor cancer outcomes in the coming years, especially in Asians/Pacific Islanders. PLAIN LANGUAGE SUMMARY: To help control the spread of coronavirus disease 2019 (COVID-19), health care organizations suspended nonessential medical procedures, including preventive cancer screening, during early 2020. Many individuals canceled or postponed cancer screening, potentially delaying cancer diagnosis. This study examines the impact of the COVID-19 pandemic on the number of newly diagnosed cancer cases in 2020 using first-submission, population-based cancer registry database. The monthly numbers of newly diagnosed cancer cases in 2020 were compared with the expected numbers based on past trends for six cancer sites. April 2020 had the sharpest decrease in cases compared with previous years, most likely because of the COVID-19 pandemic.

Impact on the Volume of Pathology Reports Before and During the COVID-19 Pandemic in SEER Cancer Registries.

INTRODUCTION: Health care procedures including cancer screening and diagnosis were interrupted due to the COVID-19 pandemic. The extent of this impact on cancer care in the United States is not fully understood. We investigated pathology report volume as a reflection of trends in oncology services pre-pandemic and during the pandemic. METHODS: Electronic pathology reports were obtained from 11 U.S. central cancer registries from NCI's SEER Program. The reports were sorted by cancer site and document type using a validated algorithm. Joinpoint regression was used to model temporal trends from January 2018 to February 2020, project expected counts from March 2020 to February 2021 and calculate observed-to-expected ratios. Results were stratified by sex, age, cancer site, and report type. RESULTS: During the first 3 months of the pandemic, pathology report volume decreased by 25.5% and 17.4% for biopsy and surgery reports, respectively. The 12-month O/E ratio (March 2020-February 2021) was lowest for women (O/E 0.90) and patients 65 years and older (O/E 0.91) and lower for cancers with screening (melanoma skin, O/E 0.86; breast, O/E 0.88; lung O/E 0.89, prostate, O/E 0.90; colorectal, O/E 0.91) when compared with all other cancers combined. CONCLUSIONS: These findings indicate a decrease in cancer diagnosis, likely due to the COVID-19 pandemic. This decrease in the number of pathology reports may result in a stage shift causing a subsequent longer-term impact on survival patterns. IMPACT: Investigation on the longer-term impact of the pandemic on pathology services is vital to understand if cancer care delivery levels continue to be affected.

Data-driven choice of a model selection method in joinpoint regression.

Selecting the number of change points in segmented line regression is an important problem in trend analysis, and there have been various approaches proposed in the literature. We first study the empirical properties of several model selection procedures and propose a new method based on two Schwarz type criteria, a classical Bayes Information Criterion (BIC) and the one with a harsher penalty than BIC (BIC3). The proposed rule is designed to use the former when effect sizes are small and the latter when the effect sizes are large and employs the partial R2 to determine the weight between BIC and BIC3. The proposed method is computationally much more efficient than the permutation test procedure that has been the default method of Joinpoint software developed for cancer trend analysis, and its satisfactory performance is observed in our simulation study. Simulations indicate that the proposed method performs well in keeping the probability of correct selection at least as large as that of BIC3, whose performance is comparable to that of the permutation test procedure, and improves BIC3 when it performs worse than BIC. The proposed method is applied to the U.S. prostate cancer incidence and mortality rates.

Interpreting cancer incidence trends: challenges due to the COVID-19 pandemic.

The considerable deficit in cancer diagnoses in 2020 due to COVID-19 pandemic disruptions in health care can pose challenges in the estimation and interpretation of long-term cancer trends. Using Surveillance, Epidemiology, and End Results (SEER) (2000-2020) data, we demonstrate that inclusion of the 2020 incidence rates in joinpoint models to estimate trends can result in a poorer fit to the data and less accurate or less precise trend estimates, providing challenges in the interpretation of the estimates as a cancer control measure. To measure the decline in 2020 relative to 2019 cancer incidence rates, we used the percent change of rates in 2020 compared with 2019. Overall, SEER cancer incidence rates dropped approximately 10% in 2020, but for thyroid cancer the decrease was as large as 18% after adjusting for reporting delay. The 2020 SEER incidence data are available in all SEER released products, except for joinpoint estimates of trends and lifetime risk of developing cancer.

Twenty years since Joinpoint 1.0: Two major enhancements, their justification, and impact.

Since its release of Version 1.0 in 1998, Joinpoint software developed for cancer trend analysis by a team at the US National Cancer Institute has received a considerable attention in the trend analysis community and it became one of most widely used software for trend analysis. The paper published in Statistics in Medicine in 2000 (a previous study) describes the permutation test procedure to select the number of joinpoints, and Joinpoint Version 1.0 implemented the permutation procedure as the default model selection method and employed parametric methods for the asymptotic inference of the model parameters. Since then, various updates and extensions have been made in Joinpoint software. In this paper, we review basic features of Joinpoint, summarize important updates of Joinpoint software since its first release in 1998, and provide more information on two major enhancements. More specifically, these enhancements overcome prior limitations in both the accuracy and computational efficiency of previously used methods. The enhancements include: (i) data driven model selection methods which are generally more accurate under a broad range of data settings and more computationally efficient than the permutation test and (ii) the use of the empirical quantile method for construction of confidence intervals for the slope parameters and the location of the joinpoints, which generally provides more accurate coverage than the prior parametric methods used. We show the impact of these changes in cancer trend analysis published by the US National Cancer Institute.

Updated Methodology for Projecting U.S.- and State-Level Cancer Counts for the Current Calendar Year: Part II: Evaluation of Incidence and Mortality Projection Methods.

BACKGROUND: The American Cancer Society (ACS) and the NCI collaborate every 5 to 8 years to update the methods for estimating the numbers of new cancer cases and deaths in the current year for the U.S. and individual states. Herein, we compare our current projection methodology with the next generation of statistical models. METHODS: A validation study was conducted comparing current projection methods (vector autoregression for incidence; Joinpoint regression for mortality) with the Bayes state-space method and novel Joinpoint algorithms. Incidence data from 1996-2010 were projected to 2014 using two inputs: modeled data and observed data with modeled where observed were missing. For mortality, observed data from 1995 to 2009, 1996 to 2010, 1997 to 2011, and 1998 to 2012, each projected 3 years forward to 2012 to 2015. Projection methods were evaluated using the average absolute relative deviation (AARD) between observed counts (2014 for incidence, 2012-2015 for mortality) and estimates for 47 cancer sites nationally and 21 sites by state. RESULTS: A novel Joinpoint model provided a good fit for both incidence and mortality, particularly for the most common cancers in the U.S. Notably, the AARD for cancers with cases in 2014 exceeding 49,000 for this model was 3.4%, nearly half that of the current method (6.3%). CONCLUSIONS: A data-driven Joinpoint algorithm had versatile performance at the national and state levels and will replace the ACS's current methods. IMPACT: This methodology provides estimates of cancer data that are not available for the current year, thus continuing to fill an important gap for advocacy, research, and public health planning.

Updated Methodology for Projecting U.S.- and State-Level Cancer Counts for the Current Calendar Year: Part I: Spatio-temporal Modeling for Cancer Incidence.

BACKGROUND: The American Cancer Society (ACS) and the NCI collaborate every 5-8 years to update the methods for estimating numbers of new cancer cases and deaths in the current year in the United States and in every state and the District of Columbia. In this article, we reevaluate the statistical method for estimating unavailable historical incident cases which are needed for projecting the current year counts. METHODS: We compared the current county-level model developed in 2012 (M0) with three new models, including a state-level mixed effect model (M1) and two state-level hierarchical Bayes models with varying random effects (M2 and M3). We used 1996-2014 incidence data for 16 sex-specific cancer sites to fit the models. An average absolute relative deviation (AARD) comparing the observed with the model-specific predicted counts was calculated for each site. Models were also cross-validated for six selected sex-specific cancer sites. RESULTS: For the cross-validation, the AARD ranged from 2.8% to 33.0% for M0, 3.3% to 31.1% for M1, 6.6% to 30.5% for M2, and 10.4% to 393.2% for M3. M1 encountered the least technical issues in terms of model convergence and running time. CONCLUSIONS: The state-level mixed effect model (M1) was overall superior in accuracy and computational efficiency and will be the new model for the ACS current year projection project. IMPACT: In addition to predicting the unavailable state-level historical incidence counts for cancer surveillance, the updated algorithms have broad applicability for disease mapping and other activities of public health planning, advocacy, and research.

On the application, reporting, and sharing of in silico simulations for genetic studies.

In silico simulations play an indispensable role in the development and application of statistical models and methods for genetic studies. Simulation tools allow for the evaluation of methods and investigation of models in a controlled manner. With the growing popularity of evolutionary models and simulation-based statistical methods, genetic simulations have been applied to a wide variety of research disciplines such as population genetics, evolutionary genetics, genetic epidemiology, ecology, and conservation biology. In this review, we surveyed 1409 articles from five journals that publish on major application areas of genetic simulations. We identified 432 papers in which genetic simulations were used and examined the targets and applications of simulation studies and how these simulation methods and simulated data sets are reported and shared. Whereas a large proportion (30%) of the surveyed articles reported the use of genetic simulations, only 28% of these genetic simulation studies used existing simulation software, 2% used existing simulated data sets, and 19% and 12% made source code and simulated data sets publicly available, respectively. Moreover, 15% of articles provided no information on how simulation studies were performed. These findings suggest a need to encourage sharing and reuse of existing simulation software and data sets, as well as providing more information regarding the performance of simulations.

Measuring progress against cancer in the Azores, Portugal: Incidence, survival, and mortality trends and projections to 2025.

BACKGROUND: Measuring progress against cancer is more accurate when trends in incidence, survival, and mortality are interpreted simultaneously. Our study aims to analyze how these key metrics have evolved over time in the Azores, Portugal. METHODS: Data for incident cases diagnosed in 1997-2016 and followed up through December 31, 2017 were obtained from the Azores Cancer Registry. Data for cancer deaths that occurred in 1991-2016 were obtained from Statistics Portugal. To estimate temporal trends, we applied a joinpoint model to age-adjusted rates. We estimated five-year net survival within the framework of relative survival using the Pohar-Perme estimator and predicted the number of cases and deaths in 2025. RESULTS: In men, incidence and mortality decreased for stomach, larynx, and prostate cancer. In women, mortality decreased for breast and cervical cancer. Five-year relative survival improved for several cancers, with the most pronounced improvements for prostate cancer in men and colorectal cancer in women (24.1 and 27.9 percentage point absolute increase, respectively). Conversely, incidence and mortality increased for colorectal cancer in men and lung cancer in women. The incidence and mortality burdens are both expected to increase in 2025. CONCLUSION: Overall, progress against cancer in the Azores has been mixed, and much of the progress has been driven by advances in treatment. Statistics for lung cancer in women and colorectal cancer in men are a call to action for policymakers. Reducing tobacco use and tackling the obesity epidemic are the two public health priorities for cancer control within the region.

Regional differences in tobacco smoking and lung cancer in Portugal in 2018: a population-based analysis using nationwide incidence and mortality data.

OBJECTIVES: This study aims to estimate the proportion of lung cancer cases and deaths attributable to tobacco smoking in Portugal in 2018, complemented by trends in incidence and mortality, by sex and region. DESIGN: Cancer cases for 1998-2011 and cancer deaths for 1991-2018 were obtained from population-based registries and Statistics Portugal, respectively. We projected cases for 2018 and used reported deaths for the same year to estimate, using Peto's method, the number and proportion of lung cancer cases and deaths caused by tobacco smoking in 2018. We calculated the age-adjusted incidence and mortality rates in each year of diagnosis and death. We fitted a joinpoint regression to the observed data to estimate the annual percentage change (APC) in the rates. SETTING: Portugal. RESULTS: In 2018, an estimated 3859 cases and 3192 deaths from lung cancer were attributable to tobacco smoking in Portugal, with men presenting a population attributable fraction (PAF) of 82.6% (n=3064) for incidence and 84.1% (n=2749) for mortality, while in women those values were 51.0% (n=795) and 42.7% (n=443), respectively. In both sexes and metrics, the Azores were the region with the highest PAF and the Centre with the lowest. During 1998-2011, the APC for incidence ranged from 0.6% to 3.0% in men and 3.6% to 7.9% in women, depending on region, with mortality presenting a similar pattern between sexes. CONCLUSION: Exposure to tobacco smoking has accounted for most of the lung cancer cases and deaths estimated in Portugal in 2018. Differential patterns of tobacco consumption across the country, varying implementation of primary prevention programmes and differences in personal cancer awareness may have contributed to the disparities observed. Primary prevention of lung cancer remains a public health priority, particularly among women.

The Joinpoint-Jump and Joinpoint-Comparability Ratio Model for Trend Analysis with Applications to Coding Changes in Health Statistics.

Analysis of trends in health data collected over time can be affected by instantaneous changes in coding that cause sudden increases/decreases, or "jumps," in data. Despite these sudden changes, the underlying continuous trends can present valuable information related to the changing risk profile of the population, the introduction of screening, new diagnostic technologies, or other causes. The joinpoint model is a well-established methodology for modeling trends over time using connected linear segments, usually on a logarithmic scale. Joinpoint models that ignore data jumps due to coding changes may produce biased estimates of trends. In this article, we introduce methods to incorporate a sudden discontinuous jump in an otherwise continuous joinpoint model. The size of the jump is either estimated directly (the Joinpoint-Jump model) or estimated using supplementary data (the Joinpoint-Comparability Ratio model). Examples using ICD-9/ICD-10 cause of death coding changes, and coding changes in the staging of cancer illustrate the use of these models.

CP*Trends: An Online Tool for Comparing Cohort and Period Trends Across Cancer Sites.

Cohort or period components of trends can provide a rationale for new research or point to clues on the effectiveness of control strategies. Graphical display of trends guides models that quantify the experience of a population. In this paper, a method for smoothing rates by single year of age and year is developed and displayed to show the contributions of period and cohort to trends. The magnitude of the contribution of period and/or cohort in a model for trends may be assessed by the percentage of deviance explained and the relative contributions of cohort (C) and period (P) individually, known as the C-P score. The method is illustrated using Surveillance, Epidemiology, and End Results data (1975-2014) on lung and bronchial cancer mortality in females and prostate and colorectal cancer incidence in males. Smoothed age-period and age-cohort rates provide a useful first step in studies of etiology and the impact of disease control without imposing a restrictive model. We found that, in this data set, cohort predominates for female lung and bronchial cancer and period predominates for male prostate cancer. However, the effects change with age for male colorectal cancer incidence, indicating an age shift in relevant exposures. These methods are applied on an interactive website for both incidence and mortality at over 20 cancer sites in the United States.

Early estimates of cancer incidence for 2015: Expanding to include estimates for white and black races.

BACKGROUND: The National Cancer Institute's cancer incidence estimates through 2015 from the Surveillance, Epidemiology, and End Results (SEER) registries' November 2017 submission are released in April 2018. METHODS: Early estimates (February 2017) of cancer incidence rates and trends from the SEER 18 registries for diagnoses in 2000 through 2015 were evaluated with a revised delay-adjustment model, which was used to adjust for the undercount of cases in the early release. For the first time, early estimates were produced for race (whites and blacks) along with estimates for new sites: the oral cavity and pharynx, leukemia, and myeloma. RESULTS: Model validation comparing delay-adjusted rates and trends through 2014 and using 2016 submissions showed good agreement. Differences in trends through 2015 in comparison with those through 2014 were evident. The rate of female breast cancer rose significantly from 2004 to 2015 by 0.3% per year (annual percent change [APC] = 0.3%); the prior trend through 2014 (the same magnitude) was not yet significant. The female colon and rectum cancer trend for whites became flat after previously declining. Lung and bronchus cancer for whites showed a significant decline (APC for males = -2.3%, 2012-2015; APC for females = -0.7%, 2011-2015). Thyroid cancer for black females changed from a continuous rise to a flat final segment (APC = 1.6%, not significant, 2011-2015). Both kidney and renal pelvis cancer (APC = 1.5%, 2011-2015) and childhood cancers (APC = 0.5%, 2000-2015) for white males showed a significant rise in the final segments from previously flat trends. Kidney and renal pelvis cancer for black males showed a change from a significant rise to a flat trend. CONCLUSIONS: The early release of SEER data continues to be useful as a preliminary estimate of the most current cancer incidence trends. Cancer 2018;124:2192-204. © 2018 American Cancer Society.

Improved confidence interval for average annual percent change in trend analysis.

This paper considers an improved confidence interval for the average annual percent change in trend analysis, which is based on a weighted average of the regression slopes in the segmented line regression model with unknown change points. The performance of the improved confidence interval proposed by Muggeo is examined for various distribution settings, and two new methods are proposed for further improvement. The first method is practically equivalent to the one proposed by Muggeo, but its construction is simpler, and it is modified to use the t-distribution instead of the standard normal distribution. The second method is based on the empirical distribution of the residuals and the resampling using a uniform random sample, and its satisfactory performance is indicated by a simulation study. Copyright © 2017 John Wiley & Sons, Ltd.

Early estimates of SEER cancer incidence, 2014.

BACKGROUND: Cancer incidence rates and trends for cases diagnosed through 2014 using data reported to the Surveillance, Epidemiology, and End Results (SEER) program in February 2016 and a validation of rates and trends for cases diagnosed through 2013 and submitted in February 2015 using the November 2015 submission are reported. New cancer sites include the pancreas, kidney and renal pelvis, corpus and uterus, and childhood cancer sites for ages birth to 19 years inclusive. METHODS: A new reporting delay model is presented for these estimates for more consistent results with the model used for the usual November SEER submissions, adjusting for the large case undercount in the February submission. Joinpoint regression methodology was used to assess trends. Delay-adjusted rates and trends were checked for validity between the February 2016 and November 2016 submissions. RESULTS: Validation revealed that the delay model provides similar estimates of eventual counts using either February or November submission data. Trends declined through 2014 for prostate and colon and rectum cancer for males and females, male and female lung cancer, and cervical cancer. Thyroid cancer and liver and intrahepatic bile duct cancer increased. Pancreas (male and female) and corpus and uterus cancer demonstrated a modest increase. Slight increases occurred for male kidney and renal pelvis, and for all childhood cancer sites for ages birth to 19 years. CONCLUSIONS: Evaluating early cancer data submissions, adjusted for reporting delay, produces timely and valid incidence rates and trends. The results of the current study support using delay-adjusted February submission data for valid incidence rate and trend estimates over several data cycles. Cancer 2017;123:2524-34. © 2017 American Cancer Society.

Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes.

BACKGROUND: Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways. RESULTS: A bottom-up graphic Gaussian model (GGM) algorithm was developed for constructing ML-hGRN operating above a biological pathway using small- to medium-sized microarray or RNA-seq data sets. The algorithm first placed genes of a pathway at the bottom layer and began to construct a ML-hGRN by evaluating all combined triple genes: two pathway genes and one regulatory gene. The algorithm retained all triple genes where a regulatory gene significantly interfered two paired pathway genes. The regulatory genes with highest interference frequency were kept as the second layer and the number kept is based on an optimization function. Thereafter, the algorithm was used recursively to build a ML-hGRN in layer-by-layer fashion until the defined number of layers was obtained or terminated automatically. CONCLUSIONS: We validated the algorithm and demonstrated its high efficiency in constructing ML-hGRNs governing biological pathways. The algorithm is instrumental for biologists to learn the hierarchical regulators associated with a given biological pathway from even small-sized microarray or RNA-seq data sets.

Preliminary estimates of SEER cancer incidence for 2013.

BACKGROUND: This article presents a first look at rates and trends for cases in the Surveillance, Epidemiology, and End Results (SEER) program diagnosed through 2013 using the February 2015 submission, and a validation of rates and trends from the February 2014 submission using the subsequent November 2014 submission. To the authors' knowledge, this is the second time SEER has published trends based on the early February submission. Three new cancer sites were added: cervix, thyroid, and liver/ intrahepatic bile duct. METHODS: A reporting delay model adjusted for the undercount of cases, which is substantially larger for the February than the subsequent November submission, was used. Joinpoint regression methodology was used to assess trends. Delay-adjusted rates and trends were checked to assess validity between the February and November 2014 submissions. RESULTS: The validation of rates and trends from the February and November 2014 submissions demonstrated even better agreement than the previously reported comparison between the February and November 2013 submissions, thereby affording additional confidence that the delay-adjusted February submission data can be used to produce valid estimates of incidence trends. Trends for cases diagnosed through 2013 revealed more rapid declines in female colon and rectal cancer and prostate cancer. A plateau in female melanoma trends and a slowing of the increases in thyroid cancer and male liver/intrahepatic bile duct cancer trends were observed. CONCLUSIONS: Analysis of early cancer data submissions can provide a preliminary indication of differences in incidence trends with an additional year of data. Although the delay adjustment correction adjusts for underreporting of cases, caution should be exercised when interpreting the results in this early submission. Cancer 2016;122:1579-87. © 2016 American Cancer Society.

Early estimates of SEER cancer incidence for 2012: Approaches, opportunities, and cautions for obtaining preliminary estimates of cancer incidence.

BACKGROUND: The National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) program collects and publishes population-based cancer incidence data from registries covering approximately 28% (seer.cancer.gov/registries/data.html) of the US population. SEER incidence rates are released annually in April from data submitted the prior November. The time needed to identify, consolidate, clean, and submit data requires the latest diagnosis year included to be 3 years before release. Approaches, opportunities, and cautions for an earlier release of data based on a February submission are described. METHODS: First, cases submitted in February for the latest diagnosis year represented 92% to 98% of those in the following November submission. A reporting delay model was used to statistically adjust counts in recent diagnosis years for cases projected in the future. February submissions required larger adjustment factors than November submissions. Second, trends were checked to assess the validity. RESULTS: Most cancer sites had similar annual percent change (APC) trends for February and November 2013. Male colon and rectum cancer and female lung and bronchus cancer showed an acceleration in declining APC trends only in February. Average annual percent change (AAPC) trends for the 2 submissions were similar for all sites. CONCLUSIONS: For the first time, preliminary 2012 incidence rates, based on February submissions, are provided. An accelerated decline starting in 2008 for male colon and rectum cancer rates and male lung cancer rates did not persist when 2012 data were added. An earlier release of SEER data is possible. Caution must be exercised when one is interpreting changing trends. Use of the more conservative AAPC is advised.