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. 2022 Sep 1;17(9):e0272522. doi: 10.1371/journal.pone.0272522

An Overview of Cancer in the First 315,000 All of Us Participants

Briseis Aschebrook-Kilfoy 1,2,3,*, Paul Zakin 1,2, Andrew Craver 1,2, Sameep Shah 1,2, Muhammad G Kibriya 1,2, Elizabeth Stepniak 1,2, Andrea Ramirez 4, Cheryl Clark 5, Elizabeth Cohn 6, Lucila Ohno-Machado 7, Mine Cicek 8, Eric Boerwinkle 9, Sheri D Schully 10, Stephen Mockrin 11, Kelly Gebo 12, Kelsey Mayo 10, Francis Ratsimbazafy 10, Alan Sanders 13, Raj C Shah 14, Maria Argos 15, Joyce Ho 16, Karen Kim 3,17, Martha Daviglus 18, Philip Greenland 16, Habibul Ahsan 1,2,3; On behalf of the All of Us Research Program Investigators
Editor: Alvaro Galli19
PMCID: PMC9436122  PMID: 36048778

Abstract

Introduction

The NIH All of Us Research Program will have the scale and scope to enable research for a wide range of diseases, including cancer. The program’s focus on diversity and inclusion promises a better understanding of the unequal burden of cancer. Preliminary cancer ascertainment in the All of Us cohort from two data sources (self-reported versus electronic health records (EHR)) is considered.

Materials and methods

This work was performed on data collected from the All of Us Research Program’s 315,297 enrolled participants to date using the Researcher Workbench, where approved researchers can access and analyze All of Us data on cancer and other diseases. Cancer case ascertainment was performed using data from EHR and self-reported surveys across key factors. Distribution of cancer types and concordance of data sources by cancer site and demographics is analyzed.

Results and discussion

Data collected from 315,297 participants resulted in 13,298 cancer cases detected in the survey (in 89,261 participants), 23,520 cancer cases detected in the EHR (in 203,813 participants), and 7,123 cancer cases detected across both sources (in 62,497 participants). Key differences in survey completion by race/ethnicity impacted the makeup of cohorts when compared to cancer in the EHR and national NCI SEER data.

Conclusions

This study provides key insight into cancer detection in the All of Us Research Program and points to the existing strengths and limitations of All of Us as a platform for cancer research now and in the future.

Introduction

Cancer was the leading cause of death in the United States after cardiovascular diseases in 2020, with over 600,000 cancer-related deaths and a further 1.8 million expected diagnoses [1–5]. Although treatments are improving and personalized medicine promises advancements, cancer diagnoses are expected to increase substantially over the next decade, due mainly to the aging population in the US and modifiable behavioral/lifestyle factors [1,2,6]. The risk of developing cancer depends on the complex interplay of factors including genes, age, and gender, lifestyle and behavioral factors such as diet, energy balance, physical activity, tobacco and alcohol use; endogenous factors such as hormones and growth factors; medication and drug use; infectious agents; and environmental exposures [1,6]. Precision medicine and precision health, which consider the patient as an individual, hold promise for cancer research [7–10]. For instance, individuals with similar diagnoses often receive the same treatment despite observations that efficacy varies by patient. Additionally, new approaches to precision prevention and early detection, informed by an enriched understanding of the etiology and natural history of cancer, could improve clinical interventions.

With over one million participants, the All of Us Research Program will have the scale to enable research on myriad diseases, especially cancer [11–13]. The program’s focus on diversity and inclusion promises to shed light on US cancer inequities, as fewer than 2% of cancer studies have been powered to consider race/ethnicity [14,15]. Given its diversity and large sample size, All of Us may have the statistical power to answer questions about the causes of cancer and drivers of disparities and identify opportunities for precision prevention.

Researchers currently have access to data from over 315K All of Us participants through the Researcher Workbench. Although the program does not target enrollment by health status, the sample to date includes a sufficient number of participants with a history of cancer, prevalent cancers, and incident cancers to enable systematic studies of cancer risk, outcomes, medication effects, and therapeutic approaches across environmental, social, genomic, and economic contexts. This demonstration project examines the distribution and characterization of cancer in All of Us and compares these numbers to expected national rates reported by the Surveillance, Epidemiology, and End Results (SEER) Program [16] and distribution in the US population.

Materials and methods

All of us research projects

The goals, recruitment methods and sites, and scientific rationale for All of Us have been described previously [17]. Demonstration projects were designed to establish the value of the cohort by describing the cohort and replicating previous findings for validation [18]. The work described here was proposed by Consortium members, reviewed and overseen by the program’s Science Committee, and was confirmed as meeting criteria for non-human subjects research by the All of Us Institutional Review Board. The initial release of data and tools used in this work was published in 2020 [18].

This work was performed using the All of Us Researcher Workbench, a cloud-based platform where approved researchers can access and analyze All of Us data. At the time of analysis, the All of Us data included survey responses, Electronic Health Records (EHR), and physical measurements (PM). These three types of data are collected either at an All of Us affiliated health care provider organization (HPO) or through a “direct-volunteer” mechanism. HPOs include regional medical centers, federally qualified health centers, and the Veterans Health Administration. HPOs recruit the majority of program participants–mainly persons affiliated with their center. The direct-volunteer route allows those who are not HPO patients to enroll online and visit a designated health clinic, blood bank, laboratory, or health care provider organization to have their PM collected. All three data types (survey, PM, and EHR) were mapped to the Observational Health and Medicines Outcomes Partnership (OMOP) common data model v 5.2 maintained by the Observational Health and Data Sciences Initiative (OHDSI) collaborative

To protect participant privacy, a series of data transformations were applied. These included data suppression of codes with a high risk of identification such as military status; generalization of categories, including age, sex at birth, gender identity, sexual orientation, and race; and date shifting by a random (less than one year) number of days, implemented consistently across each participant record. Documentation on privacy implementation and creation of the CDR is available in the All of Us Registered Tier CDR Data Dictionary [19]. The Researcher Workbench currently offers tools with a user interface (UI) built for selecting groups of participants (Cohort Builder), creating datasets for analysis (Dataset Builder), and Workspaces with Jupyter Notebooks (Notebooks) to analyze data. The Notebooks enable use of saved datasets and direct query using R and Python 3 programming languages.

Study population

Participant-provided information for our analysis was derived from the surveys described above. The full text of these surveys is available in the Survey Explorer found in the All of Us Research Hub, a publicly available website designed to support researchers [20]. The Basics survey elicits demographic information including age, race/ethnicity, education, marital status, household income, and geography. The Lifestyle survey collects tobacco use data. Personal Medical History collects self-reported cancer history, including cancer type(s), life stage at diagnosis, and whether the participant is currently seeing a health care provider and/or receiving cancer treatment. The Basics and Lifestyle surveys are collected at baseline, whereas Personal Medical History is collected during retention efforts 3 months after enrollment.

Cancer diagnosis data were also derived from participant EHR. Diagnoses were determined using SNOMED CT codes and mapped to OMOP concept ID by the All of Us DRC. SNOMED CT codes for cancers and subtypes were combined to reflect the categories used for national reporting, including SEER and the North American Association of Central Cancer Registries (NACCR). EHR data also include procedures, medications, laboratory tests, and health care provider visits. We used the following cancers/cancer sites in our analysis: bladder (93689003), leukemia (93143009), non-Hodgkin’s lymphoma (118601006), myeloma (109989006), bone (93725000), brain (93727008), breast (372137005), cervix (372024009), colon (93761005), endocrine system (371983001), endometrium (10708511000119100), esophagus (371984007), eye (371986009), head/neck (372123001), kidney (93849006), lung (93880001), oral cavity (372001002), ovary (93934004), pancreas (372003004), prostate (93974005), rectum (93984006), stomach (372014001), and thyroid (94098005).

Categories of time from diagnosis were taken from the Personal Medical History survey, which asks: “About how old were you when you were first told you had this condition?” Response categories were child (0–11), adolescent (12–17), adult (18–64), older adult (65–74), and elderly (75+).

Time from diagnosis in the EHR was calculated as the current date minus the date of diagnosis, reported in years (mean, SD, and median).

Treatment type was reported for persons with a history of cancer from the EHR using the following SNOMED codes: surgery (1623, 11600, 11601, 11602, 11603, 11604, 11606, 11620, 11621, 11622, 11624, 11626, 11640, 11641, 11642, 11643, 11644, 11646, 17260, 17261, 17262, 17263, 17264, 17266, 17270, 17272, 17273, 17274, 17276, 17280, 17281, 17282, 17283, 17284, 17286, 370612006), radiotherapy (108290001), chemotherapy (38216008), immunotherapy (64644003), hormone therapy (10324, 72143, L02BB, L02BG), and stem cell transplant (41.04, 41.05, 41.06, 41.07, 41.08).

National comparison

We compared the observed frequency of cancer reported in All of Us to National Cancer Institute’s SEER 18 Registries Database, November 2018 submission [21], to analyze cancer frequency overall and by site based on cases diagnosed in 2016 among residents of the areas included in the 18 registries covering ∼28% of the United States population. We reported the frequency of diagnosis in 2016 by assessing the limited duration 26-year cancer prevalence to determine the relative frequency and percent contribution of each cancer type to all cancers in the population by evaluating prevalence data representing the first invasive tumor site. Limited-Duration Prevalence represents the proportion of people alive on a certain day who had a diagnosis of the disease within the past x years (e.g. x = 5, 10 or 20 years). We chose the most recent year of diagnosis given the period for which All of Us has been conducting enrollment. Skin cancer (melanoma of the skin) was excluded from the “total cancer” calculation for SEER cancers and from the analysis since the All of Us survey data does not differentiate between melanoma and non-melanoma skin cancer. Invasive cancer was coded using the International Classification of Diseases for Oncology, third edition (ICD-O-3) [22].

Data analysis

We generated descriptive statistics and prevalence for the most common cancers and used Chi-square tests to test the difference in the categorical distribution of data source types (survey data, EHR, and both) across the key demographic and lifestyle categories. The percent distribution of cancer types was calculated as the number of cases per site/total number of cancer cases in each respective dataset. Results are stratified by race/ethnicity and sex at birth to consider the demographic-specific distributions in cancer types. Cancer frequency was calculated using SEER*Stat 8.3.9 [23].

Results

Table 1 shows the distribution of the baseline characteristics of all participants (N = 315,297), and by those with a cancer outcome as captured from the EHR (N = 203,813 participants with EHR; including N = 23,520 cancer cases), via self-report in the survey database (N = 89,261 completed Personal Medical History survey; including N = 13,298 cancer cases), and from participants with both survey and EHR data (N = 62,497 participants with both data types; including N = 7,123 cancer cases). Personal Medical History survey completion varies considerably, with older, female, and non-Hispanic Whites more likely to provide data than the population with available EHR (that more closely reflects the larger All of Us participant population). Differences across key demographic factors in data availability (survey data and/or EHR) are reflected in the distribution of cancer from the different data sources. Specifically, 84.8% of cancers from the Personal Medical History survey were reported by non-Hispanic Whites, 5.0% by Blacks, and 4.7% by Hispanics compared to 67.1%, 14.3%, and 12.2% respectively captured from the EHR. Non-Hispanic Whites are overwhelmingly represented among those with both self-report and EHR data (75.8%) compared to 51.5% representation in the overall All of Us study population. All p-values for the chi-square values comparing the distributions are <0.001 except the comparison of EMR versus total (which is 0.002).

Table 1. Comparison of characteristics of participants with cancer to the broader All of Us study population using self-reported survey data and electronic health record.

  Overall AoU Population Participants with survey data Cancer from survey % of persons with history of cancer Participants with EHR Cancer from EHR % of persons with history of cancer Participants with survey and EHR data Cancer from survey and EHR data % of persons with history of cancer
  N % N N prevalence N N prevalence N N prevalence
Total 315,297   89,261 13,298 14.9% 203,813 23,520 11.5% 62,497 7,123 11.4%
Age 20–35 65,173 20.7% 14,919 370 2.5% 39,035 719 1.8% 9,506 150 1.6%
35–50 71,695 22.8% 17,293 1,271 7.3% 44,621 2,374 5.3% 11,732 592 5.0%
50–65 97,126 30.8% 25,999 3,924 15.1% 63,821 7,517 11.8% 18,500 2,028 11.0%
65+ 76,835 24.4% 30,679 7,731 25.2% 53,938 12,873 23.9% 22,572 4,353 19.3%
Gender Female 191,114 60.6% 58,726 8,397 14.3% 124,735 13,994 11.2% 41,565 4,420 10.6%
Male 119,750 38.0% 29,935 4,778 16.0% 76,162 9,183 12.1% 20,472 2,631 12.9%
Other 3,866 1.2% 560 117 20.9% 490 55 11.2% 424 69 16.3%
Race/Ethnicity NH White 162,330 51.5% 67,991 11,276 16.6% 105,678 15,776 14.9% 47,345 6,125 12.9%
Black/AA 66,954 21.2% 6,746 669 9.9% 41,595 3,361 8.1% 4,971 328 6.6%
Hispanic 59,283 18.8% 7,846 628 8.0% 40,217 2,870 7.1% 5,667 294 5.2%
Asian 10,276 3.3% 3,000 207 6.9% 5,679 447 7.9% 1,903 107 5.6%
Other 2,177 0.7% 495 54 10.9% 1,392 145 10.4% 354 29 8.2%
>1 population 4,950 1.6% 1,527 152 10.0% 3,076 243 7.9% 1,001 61 6.1%
None of these 3,343 1.1% 750 111 14.8% 2,178 211 9.7% 537 53 9.9%
No answer 2,127 0.7% 657 162 24.7% 2,247 311 13.8% 521 ~ ~
Education <HS 31,984 10.2% 1,922 163 8.5% 21,280 1,533 7.2% 1,632 70 4.3%
HS/GED 64,006 20.3% 7,545 1,027 13.6% 42,601 3,607 8.5% 5,815 553 9.5%
Some college 80,110 25.4% 20,221 3,134 15.5% 52,832 5,909 11.2% 14,566 1,584 10.9%
College 131,462 41.7% 59,036 8,885 15.1% 82,174 12,028 14.6% 40,083 4,367 10.9%
No answer 2,006 0.6% 424 71 16.7% 3,401 335 9.9% 324 ~ ~
Annual Household Income <$35K 111,266 35.3% 17,864 2,233 12.5% 72,496 6,014 8.3% 12,929 1,032 8.0%
$35-75K 55,902 17.7% 21,087 3,152 14.9% 35,819 4,598 12.8% 14,694 1,644 11.2%
$75-150K 53,380 16.9% 25,574 3,929 15.4% 33,358 4,941 14.8% 17,436 2,160 12.4%
$150K+ 23,130 10.3% 16,584 2,607 15.7% 19,797 3,221 16.3% 11,253 1,466 13.0%
No answer 29,672 13.2% 6,545 1,131 17.3% 29,000 3,443 11.9% 4,990 682 13.7%
Smoking Frequency Not at all 66,334 53.3% 24,669 4,946 20.0% 46,168 8,097 17.5% 17,745 2,723 15.3%
Some days 17,857 14.3% 1,990 221 11.1% 11,618 774 6.7% 1,435 98 6.8%
Every day 38,129 30.6% 3,739 498 13.3% 24,609 1,375 5.6% 2,703 195 7.2%
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*Skin cancer is excluded from the analysis as it is not differentiated as malignant/non-malignant/melanoma in AoU survey.

** Less than 20 cancers are excluded from analysis and indicated as ~.

Table 2 shows that All of Us participants’ EHR data indicate a history of breast cancer most frequently (N = 6,474; 27.5% of cases) followed by blood cancers (N = 4,841; 20.6%) and prostate cancer (N = 3,971; 16.9%). This mirrors the most common self-reported cancers (from the survey) for breast cancer (N = 4,062; 30.5%) and prostate cancer (N = 2,165; 16.3%) but not for blood cancer (N = 483; 9.9%). There are N = 2,499 individuals with breast cancer documented from both the survey and EHR data sources, followed by N = 1,304 individuals with prostate cancer cases, and followed by N = 657 blood cancer cases. Prevalence is broken down by cancer site showing the difference in contribution to disease burden by data source.

Table 2. The relative distribution and prevalence of cancer cases by type in the All of Us Research Program from self-reported survey data and electronic health record overall.

  EHR Survey Data EHR + Survey
N % dist prevalence N % dist prevalence N % dist prevalence
Population 203,813 89,261 62,497
Total Cancers 23,520 - 11.54% 13,298 - 14.90% 7,123 - 11.40%
Bladder 983 4.18% 0.48% 483 3.63% 0.54% 301 4.23% 0.48%
Blood 4,841 20.58% 2.38% 1,113 8.37% 1.25% 657 9.22% 1.05%
Bone 350 1.49% 0.17% 181 1.36% 0.20% 107 1.50% 0.17%
Brain 612 2.60% 0.30% 182 1.37% 0.20% 102 1.43% 0.16%
Breast 6,474 27.53% 3.18% 4,062 30.55% 4.55% 2,499 35.08% 4.00%
Cervix 576 2.45% 0.28% 869 6.53% 0.97% 172 2.41% 0.28%
Colon & Rectum 2,601 11.06% 1.28% 722 5.43% 0.81% 385 5.41% 0.62%
Endocrine System 1,887 8.02% 0.93% 129 0.97% 0.14% 63 0.88% 0.10%
Endometrium 1,364 5.80% 0.67% 459 3.45% 0.51% 212 2.98% 0.34%
Esophagus 230 0.98% 0.11% 110 0.83% 0.12% 60 0.84% 0.10%
Eye 123 0.52% 0.06% 66 0.50% 0.07% 28 0.39% 0.04%
Head & Neck 1,698 7.22% 0.83% 333 2.50% 0.37% 155 2.18% 0.25%
Kidney 1,266 5.38% 0.62% 487 3.66% 0.55% 313 4.39% 0.50%
Lung 1,081 4.60% 0.53% 463 3.48% 0.52% 283 3.97% 0.45%
Ovary 786 3.34% 0.39% 348 2.62% 0.39% 207 2.91% 0.33%
Pancreas 548 2.33% 0.27% 119 0.89% 0.13% 77 1.08% 0.12%
Prostate 3,971 16.88% 1.95% 2,165 16.28% 2.43% 1,304 18.31% 2.09%
Stomach 320 1.36% 0.16% 76 0.57% 0.09% 35 0.49% 0.06%
Thyroid 1,648 7.01% 0.81% 924 6.95% 1.04% 573 8.04% 0.92%
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*Skin cancer is excluded from the analysis as it is not differentiated as malignant/non-malignant/melanoma in AoU survey.

Table 3 presents cancer type distribution from each data source by race and ethnicity, with N = 6,125 cancer cases detected in both data sources for non-Hispanic Whites compared to N = 328 cancer cases in African Americans and N = 294 cancer cases in Hispanics. Differences in the distribution of cancer types between survey data and EHR are observed by race/ethnicity (both within and between race/ethnicity, comparing non-Hispanic Whites, Blacks, and Hispanics (<0.001)). The prevalence of cancer subsequently varies by race/ethnicity in each data source as well as reported here.

Table 3. The relative distribution and prevalence of cancer cases by type in the All of Us Research Program from self-reported survey data and electronic medical record by race/ethnicity.

NH-White African American/Black
EHR Survey data EHR + Survey EHR Survey data EHR + survey
N % dist prevalence N % dist prevalence N % dist prevalence N % dist prevalence N % dist prevalence N % dist prevalence
Population 105,678 67,991 47,345 41,515 6,746 4,971
Total Cancer 15,776 - 14.9% 11,276 - 16.6% 6,125 - 12.9% 3,361 - 8.1% 669 - 9.9% 328 - 6.6%
Bladder 783 4.96% 0.74% 440 3.90% 0.65% 279 4.56% 0.59% 84 2.5% 0.20% ~ NA ~ ~ NA ~
Blood 3,136 19.88% 2.97% 983 8.72% 1.45% 583 9.52% 1.23% 730 21.7% 1.76% 30 4.5% 0.44% ~ NA ~
Bone 229 1.45% 0.22% 142 1.26% 0.21% 86 1.40% 0.18% 41 1.2% 0.10% ~ NA ~ ~ NA ~
Brain 398 2.52% 0.38% 151 1.34% 0.22% 89 1.45% 0.19% 92 2.7% 0.22% ~ NA ~ ~ NA ~
Breast 4,382 27.78% 4.15% 3,422 30.35% 5.03% 2,124 34.68% 4.49% 875 26.0% 2.11% 210 31.4% 3.11% 125 38.1% 2.51%
Cervix 282 1.79% 0.27% 711 6.31% 1.05% 148 2.42% 0.31% 143 4.3% 0.34% 51 7.6% 0.76% ~ NA ~
Colon & Rectum 1,683 10.67% 1.59% 604 5.36% 0.89% 330 5.39% 0.70% 398 11.8% 0.96% 43 6.4% 0.64% 18 5.5% ~
Endocrine System 1,221 7.74% 1.16% 104 0.92% 0.15% 56 0.91% 0.12% 213 6.3% 0.51% ~ NA ~ ~ NA ~
Endometrium 788 4.99% 0.75% 399 3.54% 0.59% 187 3.05% 0.39% 268 8.0% 0.65% 19 2.8% ~ ~ NA ~
Esophagus 166 1.05% 0.16% 93 0.82% 0.14% 52 0.85% 0.11% 23 0.7% 0.06% ~ NA ~ ~ NA ~
Eye 92 0.58% 0.09% 62 0.55% 0.09% 27 0.44% 0.06% 13 0.4% ~ ~ NA ~ ~ NA ~
Head & Neck 1,559 9.88% 1.48% 296 2.63% 0.44% 138 2.25% 0.29% 23 0.7% 0.06% ~ NA ~ ~ NA ~
Kidney 817 5.18% 0.77% 399 3.54% 0.59% 258 4.21% 0.54% 212 6.3% 0.51% 31 4.6% 0.46% 22 6.7% 0.44%
Lung 700 4.44% 0.66% 389 3.45% 0.57% 244 3.98% 0.52% 219 6.5% 0.53% 25 3.7% 0.37% ~ NA ~
Other Site NA NA ~ 1,499 13.29% 2.20% 601 9.81% 1.27% ~ NA ~ 90 13.5% 1.33% 42 12.8% 0.84%
Ovary 501 3.18% 0.47% 284 2.52% 0.42% 170 2.78% 0.36% 103 3.1% 0.25% 25 3.7% 0.37% ~ NA ~
Pancreas 346 2.19% 0.33% 94 0.83% 0.14% 61 1.00% 0.13% 76 2.3% 0.18% ~ NA ~ ~ NA ~
Prostate 2,837 17.98% 2.68% 1,915 16.98% 2.82% 1,155 18.86% 2.44% 605 18.0% 1.46% 114 17.0% 1.69% 60 18.3% 1.21%
Stomach 174 1.10% 0.16% 59 0.52% 0.09% 29 0.47% 0.06% 51 1.5% 0.12% ~ NA ~ ~ NA ~
Thyroid 1,068 6.77% 1.01% 798 7.08% 1.17% 493 8.05% 1.04% 182 5.4% 0.44% 33 4.9% 0.00% 15 4.6% ~
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*Skin cancer is excluded from the analysis as it is not differentiated as malignant/non-malignant/melanoma in AoU survey.

** Less than 20 cancers are excluded from analysis and indicated as ~.

Table 4 compares the distribution of cancer sites from All of Us survey data and EHR to the expected distribution nationally, based on recent SEER reports of the 26-year limited duration prevalence in 2018. The most common cancer types in SEER (based on contribution to total cancers) are breast cancer (19.9%), prostate cancer (17.6%), blood cancers (11.4%), and colorectal cancers (8.4%). The percent contribution to the cancer burden nationally (as illustrated by SEER data) from each cancer site differs significantly from the EHR site distribution (p<0.001) and the self-reported distribution (p<0.001). As expected, the percent of persons enrolled into All of Us largely from medical centers have a higher proportion of prevalent cancer (11.54% in EHR and 14.90% in survey) than in the US population reported by SEER (4.43%).

Table 4. Comparison of relative distribution and prevalence of cancer cases by type in the All of Us Research Program to SEER’s 26-year limited duration prevalence.

  EHR Survey Data EHR + Survey SEER 26-year prevalence
N % dist prevalence N % dist prevalence N % dist prevalence N % dist prevalence
Population 203,813 89,261 62,497 325,836,757
Total Cancers 23,520 - 11.54% 13,298 - 14.90% 7,123 - 11.40% 14,419,319 4.43%
Bladder 983 4.18% 0.48% 483 3.63% 0.54% 301 4.23% 0.48% 555,999 3.86% 0.17%
Blood 4,841 20.58% 2.38% 1,113 8.37% 1.25% 657 9.22% 1.05% 1,343,512 9.32% 0.41%
Bone 350 1.49% 0.17% 181 1.36% 0.20% 107 1.50% 0.17% 33,086 0.23% 0.01%
Brain 612 2.60% 0.30% 182 1.37% 0.20% 102 1.43% 0.16% 129,633 0.90% 0.04%
Breast 6,474 27.53% 3.18% 4,062 30.55% 4.55% 2,499 35.08% 4.00% 3,096,156 21.47% 0.95%
Cervix 576 2.45% 0.28% 869 6.53% 0.97% 172 2.41% 0.28% 182,868 1.27% 0.06%
Colon & Rectum 2,601 11.06% 1.28% 722 5.43% 0.81% 385 5.41% 0.62% 1,134,250 7.87% 0.35%
Endocrine System 1,887 8.02% 0.93% 129 0.97% 0.14% 63 0.88% 0.10% 70,825 0.49% 0.02%
Endometrium 1,364 5.80% 0.67% 459 3.45% 0.51% 212 2.98% 0.34% 632,326 4.39% 0.19%
Esophagus 230 0.98% 0.11% 110 0.83% 0.12% 60 0.84% 0.10% 21,960 0.15% 0.01%
Eye 123 0.52% 0.06% 66 0.50% 0.07% 28 0.39% 0.04% ~ ~ ~
Head & Neck 1,698 7.22% 0.83% 333 2.50% 0.37% 155 2.18% 0.25% 396,937 2.75% 0.12%
Kidney 1,266 5.38% 0.62% 487 3.66% 0.55% 313 4.39% 0.50% 451,550 3.13% 0.14%
Lung 1,081 4.60% 0.53% 463 3.48% 0.52% 283 3.97% 0.45% 423,209 2.94% 0.13%
Ovary 786 3.34% 0.39% 348 2.62% 0.39% 207 2.91% 0.33% 167,758 1.16% 0.05%
Pancreas 548 2.33% 0.27% 119 0.89% 0.13% 77 1.08% 0.12% 65,973 0.46% 0.02%
Prostate 3,971 16.88% 1.95% 2,165 16.28% 2.43% 1,304 18.31% 2.09% 3,017,103 20.92% 0.93%
Stomach 320 1.36% 0.16% 76 0.57% 0.09% 35 0.49% 0.06% 96,886 0.67% 0.03%
Thyroid 1,648 7.01% 0.81% 924 6.95% 1.04% 573 8.04% 0.92% 660,323 4.58% 0.20%
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*Skin cancer is excluded from the analysis as it is not differentiated as malignant/non-malignant/melanoma in AoU survey.

* SEER data is based on 5-year prevalence frequency counts of 1st invasive tumor.

Table 5 presents a description of the time from cancer diagnosis as reported in the EHR and survey database. The cancer with the shortest time from diagnosis in the EHR is lung cancer (mean = 5.85 years; SD = 4.46), and the longest time from diagnosis is for head and neck cancer (mean = 11.75 years; SD = 6.59). Across all cancer types, the most common period of diagnosis was adult, followed by older adult.

Table 5. Time from diagnosis of cancer cases and approximate age at diagnosis by type in the All of Us Research Program.

  AoU EHR N with timing of diagnosis Child Adolescent Adult Older Adult Elderly
Time between cancer diagnosis and enrollment, years
Cancer Site Mean SD Median N N % N % N % N % N %
Bladder 7.97 6 6.35 478 ~ NA ~ NA 249 50.00% 187 38.10% 39 10.80%
Blood 7.19 5.04 5.47 1,105 26 2.50% 24 0.90% 754 69.10% 246 21.90% 55 5.30%
Bone 8.62 6.57 6.59 180 ~ NA ~ NA 114 427.10% 40 135.70% ~ NA
Brain 8.83 6.68 6.78 181 9 4.90% ~ NA 140 76.90% ~ NA ~ NA
Breast 8.07 5.4 6.91 4,039 ~ NA ~ NA 3,328 81.90% 626 15.40% 83 2.00%
Cervix 8.42 6.16 6.59 863 ~ NA 23 2.60% 813 93.60% 21 2.40% ~ NA
Colon & Rectum 7.94 5.41 6.81 717 ~ NA ~ NA 535 74.10% 152 21.10% 27 3.70%
Endocrine System 8.19 5.65 6.81 128 ~ NA ~ NA 95 73.60% 23 17.80% ~ NA
Endometrium 7.6 5.66 5.84 457 ~ NA ~ NA 383 83.40% 66 14.40% ~ NA
Esophagus 6.55 4.92 5.17 110 ~ NA ~ NA 64 58.20% 42 38.20% ~ NA
Eye 7.09 5.22 5.73 66 ~ NA ~ NA 44 66.70% ~ NA ~ NA
Head & Neck 11.75 6.59 11.2 330 ~ NA ~ NA 222 66.70% 89 26.70% ~ NA
Kidney 7.19 5.29 5.81 485 ~ NA ~ NA 340 69.80% 118 24.20% ~ NA
Lung 5.85 4.46 4.38 459 ~ NA ~ NA 243 52.50% 172 37.10% 42 9.10%
Ovary 8.24 5.99 6.34 347 ~ NA ~ NA 296 85.10% 41 11.80% ~ NA
Pancreas 6.48 5.1 4.57 117 ~ NA ~ NA 71 59.70% 34 28.60% ~ NA
Prostate 7.95 5.44 6.57 2,157 ~ NA ~ NA 1,254 57.90% 807 37.30% 96 4.40%
Stomach 6.83 5.14 4.88 76 ~ NA ~ NA 59 77.60% ~ NA ~ NA
Thyroid 8.17 5.67 6.78 921 ~ NA ~ NA 789 85.40% 100 10.80% ~ NA
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*Skin cancer is excluded from the analysis as it is not differentiated as malignant/non-malignant/melanoma in AoU survey.

** Less than 20 cancers are excluded from analysis and indicated as ~.

Table 6 presents treatment types for cancer overall and by site. The most common treatment from the EHR is radiation (N = 7,422; 31.56%), followed by surgery (N = 5,975; 25.54%), hormone therapy (N = 3,962; 16.84%), chemotherapy (N = 842; 3.58%), immunotherapy (N = 470; 1.2%), and stem cell transplant (N = 127; 0.54%). Treatment type utilization varied by cancer site.

Table 6. Cancer treatment type overall and by site in the All of Us Research Program.

  Surgery Radiation Chemotherapy Immunotherapy Hormone Therapy Stem Cell Transplant
Cancer Site Total AoU EHR Cases N % N % N % N % N % N %
All Sites 23,520 5,975 25.4% 7,422 31.56% 842 3.58% 470 1.2% 3,962 16.84% 127 0.54%
Bladder 983 185 18.82% 130 13.22% 24 2.44% ~ ~ 48 4.88% ~ ~
Blood 4,841 666 13.76% 724 14.96% 322 6.65% 192 3.97% 210 4.34% 96 1.98%
Bone 350 98 28% 128 36.57% ~ ~ ~ ~ 39 11.14% ~ ~
Brain 612 192 31.37% 235 38.4% ~ ~ ~ ~ 29 4.74% ~ ~
Breast 6,474 1,075 16.6% 1,898 29.32% 132 2.04% 97 1.5% 2,445 37.77% ~ ~
Cervix 576 74 12.85% 132 22.92% ~ ~ ~ ~ 25 4.34% ~ ~
Colon & Rectum 2,601 455 17.49% 478 18.38% 83 3.19% 30 1.15% 127 4.88% ~ ~
Endocrine System 1,887 338 17.91% 502 26.6% 23 1.22% ~ ~ 95 5.03% ~ ~
Endometrium 1,364 194 14.22% 332 24.34% 23 1.68% ~ ~ 90 6.6% ~ ~
Esophagus 230 30 13.04% 79 34.35% ~ ~ ~ ~ ~ ~ ~ ~
Eye 123 23 18.7% 26 21.14% ~ ~ ~ ~ ~ ~ ~ ~
Head & Neck 1,698 916 53.95% 241 14.19% ~ ~ ~ ~ 71 4.18% ~ ~
Kidney 1,266 206 16.27% 175 13.82% ~ ~ ~ ~ 62 4.9% ~ ~
Lung 1,081 180 16.65% 343 31.73% 26 2.41% ~ ~ 61 5.64% ~ ~
Ovary 786 119 15.14% 124 15.78% 31 3.94% ~ ~ 62 7.89% ~ ~
Pancreas 548 78 14.23% 130 23.72% ~ ~ ~ ~ 29 5.29% ~ ~
Prostate 3,971 612 15.41% 879 22.14% 29 0.73% ~ ~ 421 10.6% ~ ~
Stomach 320 57 17.81% 76 23.75% ~ ~ ~ ~ ~ ~ ~ ~
Thyroid 1,648 286 17.35% 449 27.25% ~ 3.58% ~ ~ 77 4.67% ~ ~
Open in a new tab

*Skin cancer is excluded from the analysis as it is not differentiated as malignant/non-malignant/melanoma in AoU survey.

** Less than 20 cases are excluded from analysis and indicated as ~.

Conclusions

In this preliminary analysis of data from the All of Us Research Program, we report that the first 315K+ persons comprise a diverse population with a large number of prevalent cancer cases. As the goal of this effort is to inform studies on a variety of health conditions, including cancer, and to delineate information on risk factors and treatments, an early evaluation of cancers represented in the study population is warranted. Our findings have some key implications for cancer prevention, control, treatment, and outcomes research in the All of Us study population.

Our most notable finding is simple: although a diverse cohort is being enrolled, self-reported cancers are not being ascertained as frequently through the survey modules among underrepresented participants. As validation of diagnosis from EHR using manual verification or self-report is the gold standard to ensure accurate classification and minimize measurement error, the difference in valid case ascertainment by key factors like race is relevant for All of Us cancer research. The drop in cancer data detected from the survey or validated with survey data is associated with racial/ethnic differences in longitudinal retention. Although surveys are completed by a relatively older population, age doesn’t appear to be a key factor influencing differences in data collection. History of cancer is collected through a survey completed at least 90 days after enrollment in All of Us, with an overall medical history survey completion rate among underrepresented participants of 22% across the program compared to 42% in non-UBR participants. Some factors noted in the literature previously [24] that could be of relevance for differences in retention by race/ethnicity include language, literacy, cultural appropriateness, flexibility, ongoing incentives, communication, and of particular growing importance with increasingly electronic survey data collection is the digital divide. This has research implications for the cancer history data collected at follow-up as well as other key risk factor information including health care utilization, personal medical history, and family history. Our investigation shows that the impact of these factors on cancer disparities will be underreported even if cancer history can be obtained from the EHR of most underrepresented participants. All of Us leadership has changed survey module timeline and made Personal Medical History available at baseline, addressing some of the limitations noted here for prospective enrollees.

Furthermore, the difference in cancer ascertainment between survey modules and EHR modalities in underrepresented participants highlights the importance of technologies to integrate the medical records of direct volunteers. Sync for Science for obtaining EHRs from direct volunteers or other non-digital methods of collecting survey data could offer utility beyond the ability to confer medical record information for direct volunteers, as there are implications for inclusion and equity in the investigation of all diseases, including cancer.

The distribution of cancer sites between the two data sources when compared to SEER national statistics is impacted by exclusion of skin cancer from the All of Us cancer analyses. Skin cancer cases account for approximately half of the total cases reported in the survey data. These cases likely include both malignant and non-malignant skin cancers, which would introduce significantly different relative proportions of other cancers if included in the analysis. As restriction to malignant cases was not possible, we excluded all skin cancer cases from analysis.

Another point to consider is the grouping of blood cancers. Because the survey module asks about blood cancers generically, it is impossible to differentiate between myeloma, lymphoma, and leukemia in survey responses. This distinction can be deciphered from the EHR when available. The ability to distinguish these types will be crucial to many cancer researchers.

We further report on the time from diagnosis and the life stage to consider opportunities to collect incident cases or investigate hypotheses for more recent diagnoses. The utility of the life stage questions in etiology or outcomes research is unclear, as the groups (age ranges (child (0–11); adolescent (12–17); adult (18–64); older adult (65–74) and elderly (75+)) are quite broad in the survey. A more refined or consistent metric, such as date of cancer diagnosis, would aid investigation of various cancer-related hypotheses (such as being able to stratify by pre and post menopausal breast cancer. Presenting this data side-by-side highlights how distinct these metrics of diagnosis timing really are.

The All of Us Research Program is set to become one of the largest scientific efforts in U.S. history, and its emphasis on inclusion presents key opportunities to advance precision health and medicine and address disparities in research [25]. Despite the limitations noted in this report, this unprecedented depth of inclusion will confer an important resource for cancer research. All of Us was conceived to support studies of disease outcomes, medication effects, and other therapeutic approaches across various environmental, social, genomic, and economic contexts [26]. The scale and scope of its current cancer data will support extensive investigation of cancer-related hypotheses and enhance the pace of discovery and generalizability. The cohort’s expansion to 1 million participants will create further opportunities. Furthermore, feedback from demonstration projects such as this one will directly inform edits to existing surveys and development of reassessment modules.

In summary, the All of Us Research Program has collected significant cancer data from its first 315K participants. This preliminary investigation notes the most common cancers that will confer sufficient study power for research, especially once whole genome data is available for all participants. Considering our findings, the program might consider the implications of lower retention through survey completion among underrepresented participants on the resource’s utility for research on cancer and other diseases.

Acknowledgments

Past and Present All of Us Research Program Principal Investigators: Brian Ahmedani1; Christine D Cole Johnson1; Briseis Aschebrook-Kilfoy2; Habibul Ahsan2; Donna Antoine-LaVigne3; Glendora Singleton*3; Pamelia Watson-McGee3; Arnita Ford Norwood3; Hoda Anton-Culver4; Eric Topol5; Katie Baca-Motes5; Julia Moore-Vogel5; Steven Steinhubl5; Praduman Jain6; Mark Begale6; Neeta Jain6; David Klein6; Scott Sutherland6; James Wade*6; Bruce Korf7; Mona Fouad7; Beth Lewis7; David B Goldstein8; Louise Bier8; Ali G Gharavi8; George Hripcsak8; Eric Boerwinkle9; Murray H Brilliant10; Narayana Murali10; Scott Joseph Hebbring10; Elizabeth Burnside11; Dorothy Farrar-Edwards11; Yashoda Sharma12; Amy Taylor12; Carmen Chinea13; Liliana Lombardi Desa13; Nancy Jenks13; Steve Thibodeau14; Mine Cicek14; Eric Schlueter15; Beverly Wilson Holmes15; Maria Argos16; Martha Daviglus16; Robert Winn16; Paul Harris17; Consuelo Wilkins17; Dan Roden17; Joshua Denny17; Kim Doheny18; Debbie Nickerson19; Evan Eichler19; Gail Jarvik19; Gretchen Funk20; Sallie Hussey20; Anthony Philippakis21; Heidi Rehm21; Stacey Gabriel21; Richard Gibbs22; Edgar M Gil Rico23; David Glazer24; Jessica Burke25; Joyce Ho26, Philip Greenland26; Elizabeth Shenkman27; William R Hogan,27; Priscilla Igho-Pemu28; W Karlson29; Jordan Smoller29; Shawn N Murphy29; Margaret Elizabeth Ross30; Rainu Kaushal30; Eboni Winford31; Febe Wallace31; Parinda Khatri31; Vik Kheterpal32; Monica Kraft33; Francisco A Moreno33; Irving Kron33; Rachele Peterson33; Patricia Watkins Lattimore34; Cheryl Thomas34; Mitchell Lunn35; Juno Obedin-Maliver35; Oscar Marroquin36; Shyam Visweswaran36; Steven Reis36; Patrick McGovern37; Fatima Munoz38; Gregory Talavera38; George T O’Connor39; Christopher O’Donnell40; Lucila Ohno-Machado41; Greg Orr42; Fornessa Randal43; Andreas A Theodorou44; Eric Reiman44; Mercedita Roxas-Murray45; Louisa Stark46; Ronnie Tepp47; Alicia Zhou48; Scott Topper48; Rhonda Trousdale49; Phil Tsao50; Scott T Weiss51; David Wellis52; Jeffrey Whittle53; Amanda Wilson54; Stephan Zuchner55; Olveen Carrasquillo55; Margaret Pericak-Vance55; Michael E Zwick56; Megan Lewis57; Jen Uhrig57; May Okihiro58

Note

This is the list of individuals who were Principal Investigators or equivalent with the All of Us Research Program during the period that this paper was in development, October 1, 2019 –July 31, 2021.

+ Principal Investigator/Lead Author for the All of Us Research Program protocol (paul.a.harris@vumc.org)

Affiliations:

1. Henry Ford Health System, Detroit, Michigan, United States of America

2. University of Chicago Medical Center, Chicago, Illinois, United States of America

3. Jackson-Hinds Comprehensive Health Center, Jackson, Mississippi, United States of America

4. University of California, Irvine, Irvine, California, United States of America

5. Scripps Research Translational Institute, La Jolla, California, United States of America

6. Vibrent Health, Fairfax, Virginia, United States of America

7. University of Alabama at Birmingham, Birmingham, Alabama, United States of America

8. Columbia University, New York, New York, United States of America

9. University of Texas Health Science Center at Houston, Houston, Texas, United States of America

10. Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America

11. University of Wisconsin at Madison, Madison, Wisconsin, United States of America

12. Community Health Center, Inc., Middletown, Connecticut, United States of America

13. Sun River Health, New York, New York, United States of America

14. Mayo Clinic and Foundation, Rochester, Rochester, Minnesota, United States of America

15. Cooperative Health, Columbia, South Carolina, United States of America

16. University of Illinois at Chicago, Chicago, Illinois, United States of America

17. Vanderbilt University Medical Center, Nashville, Tennessee, United States of America

18. Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America

19. University of Washington, Seattle, Washington, United States of America

20. FiftyForward, Nashville, Tennessee, United States of America

21. Broad Institute, Cambridge, Massachusetts, United States of America

22. Baylor University, Waco, Texas, United States of America

23. National Alliance for Hispanic Health, Washington, DC, United States of America

24. Verily Life Sciences, San Francisco, California, United States of America

25. MITRE Corporation, McLean, Virginia, United States of America

26. Northwestern University, Chicago, Illinois, United States of America

27. University of Florida, Gainesville, Florida, United States of America

28. Morehouse School of Medicine, Atlanta, Atlanta, Georgia, United States of America

29. Partners Health Care, Boston, Massachusetts, United States of America

30. Cornell University, Weill Medical College, Ithaca, New York, United States of America

31. Cherokee Health Systems, Knoxville, Tennessee, United States of America

32. CareEvolution, Inc., Ann Arbor, Michigan, United States of America

33. University of Arizona, Tucson, Tucson, Arizona, United States of America

34. Delta Research and Educational Foundation, Washington, DC, United States of America

35. Stanford University, Palo Alto, California, United States of America

36. University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

37. Wondros, Los Angeles, California, United States of America

38. San Ysidro Health Center, San Ysidro, California, United States of America

39. Boston Medical Center, Boston, Massachusetts, United States of America

40. VA All of Us Coordinating Center, Boston, Boston, Massachusetts, United States of America

41. University of California, San Diego, La Jolla, California, United States of America

42. Walgreen Co., Deerfield, Illinois, United States of America

43. Asian Health Coalition, Chicago, Illinois, United States of America

44. Banner Health, Phoenix, Arizona, United States of America

45. Montage Marketing Group, Bethesda, Maryland, United States of America

46. University of Utah, Salt Lake City, Utah, United States of America

47. HCM Strategists, Austin, Texas, United States of America

48. Color Genomics, Inc., Burlingame, California, United States of America

49. NYC Health + Hospitals, New York, New York, United States of America

50. VA All of Us Coordinating Center—Palo Alto, Palo Alto, California, United States of America

51. Brigham and Women’s Hospital, Boston, Massachusetts, United States of America

52. San Diego Blood Bank, San Diego, California, United States of America

53. Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America

54. National Library of Medicine (NLM), Bethesda, Maryland, United States of America

55. University of Miami School of Medicine, Miami, Florida, United States of America

56. Emory University, Atlanta, Georgia, United States of America

57. Research Triangle Institute, Research Triangle Park, North Carolina, United States of America

58. Waianae Coast CHC, Waianae, Hawaii, United States of America

Data Availability

Data is owned by a third party, the All of Us Research Program. The data underlying this article were provided by the All of Us Research Program by permission that can be sought by scientists and the public alike. The Researcher Workbench is a cloud-based platform where registered researchers can access Registered and Controlled Tier data, including the data presented here. Researchers/citizen scientists must verify their identity and complete the All of Us Research Program data access process to access the Researcher Workbench and Registered Tier data. Once this process is completed, the data will be made available to all persons. More information on data access can be found in the All of Us Research Hub (https://www.researchallofus.org/) as is the option to register for access. The authors did not have any special access privileges to this data that other researchers would not have.

Funding Statement

All of Us is supported by grants through the National Institutes of Health Office of the Director: Regional Medical Centers: 1 OT2 OD026549; 1 OT2 OD026554; 1 OT2 OD026557; 1 OT2 OD026556; 1 OT2 OD026550; 1 OT2 OD 026552; 1 OT2 OD026553; 1 OT2 OD026548; 1 OT2 OD026551; 1 OT2 OD026555; 1 OT2 OD026552; IAA #: AOD 16037; Federally Qualified Health Centers: HHSN 263201600085U; Data and Research Center: 5 U2C OD023196; Biobank: 1 U24 OD023121; The Participant Center: U24 OD023176; Participant Technology Systems Center: 1 U24 OD023163; Communications and Engagement: 3 OT2 OD023205; 3 OT2 OD023206; Community Partners: 1 OT2 OD025277; 3 OT2 OD025315; 1 OT2 OD025337; 1 OT2 OD025276; and the All of Us Pilot: 1 OT2 OD023132. The Role of the Funder: The NIH funds the All of Us Research Program and has approved the Demonstration Projects. The Demonstration Project leadership reviewed the manuscript and are coauthors here. The funder (NIH specifically) had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

Data is owned by a third party, the All of Us Research Program. The data underlying this article were provided by the All of Us Research Program by permission that can be sought by scientists and the public alike. The Researcher Workbench is a cloud-based platform where registered researchers can access Registered and Controlled Tier data, including the data presented here. Researchers/citizen scientists must verify their identity and complete the All of Us Research Program data access process to access the Researcher Workbench and Registered Tier data. Once this process is completed, the data will be made available to all persons. More information on data access can be found in the All of Us Research Hub (https://www.researchallofus.org/) as is the option to register for access. The authors did not have any special access privileges to this data that other researchers would not have.

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