e18080 Background: Implementation of electronic health records (EHRs) has engendered a large quan... more e18080 Background: Implementation of electronic health records (EHRs) has engendered a large quantity of machine-readable data. However, different practices choose different EHR vendors and the same vendor product may be implemented differently at each practice. Motivated by the desire to facilitate appropriate integration of data, our goal was to describe and quantify the consistency and variation of structured data within EHRs. Methods: De-identified and aggregated CancerLinQ data from 47 practices regarding the standards and variability of structured data including race, diagnoses, encounters, cancer staging, selected cancer-relevant medications, lab values and biomarkers were analyzed. EHR represented included ARIA, MOSAIQ, Allscripts, Centricity, Epic, Intellidose, NextGen, and OncoEMR. Results: De-identified EHR implementations included 23 A, 12 B, C and 5 other vendors. Only 6 practices (13%) used non-standard race representation. All practices used ICD-9/10 for diagnoses. There was variability in coding of encounters. Sixteen practices always used CPT, 5 practices always used SNOMED CT and 26 practices used multiple standards. Multiple staging systems were used. An average of 48% (range 11%-; including patients staged more than once) of patient records included coded staging information. Only one practice used a standard (LOINC) for laboratory data. No standards were used for medications ordered/administered or biomarkers. The table shows the number of distinct names for selected lab tests, medications and biomarkers across systems. Conclusions: In this cross-sectional sample, standards are used consistently for diagnoses and encounter data, often for race and rarely for medications, laboratory tests or biomarkers.[Table: see text]
2032 Background: 30-50% of patients with non-early NSCLC will eventually develop BM, with a media... more 2032 Background: 30-50% of patients with non-early NSCLC will eventually develop BM, with a median survival of less than one year from BM diagnosis. There are no widely accepted clinical risk models for development of BM in patients without them at baseline. We predicted the binary risk of BM using clinical and genetic factors from a large multi-institutional cohort. Methods: Stage II-IV NSCLC patients from the AACR Project GENIE Biopharma Consortium dataset were eligible. This consisted of 4 academic institutions who curated clinical data of patients who had somatic next-generation tumor sequencing (NGS) between 2015-2017. We excluded patients who had BM at baseline, died within 30 days of NSCLC diagnosis, or did not undergo brain imaging. Covariates included demographics, anticancer therapies (received up to 90 days prior to BM development and within 5 years from NSCLC diagnosis), and NGS data; radiotherapy (RT) data were not available. NGS features included mutations and copy number alterations. These features were restricted to those classified as oncogenic by OncoKB. Univariate feature selection with Fisher’s test (p<.1) was performed on medication and genetic features. We compared 5 different machine learning models for prediction: random forest (RF), support vector machine (SVM), lasso regression, ridge regression, and an ensemble classifier. We split our data into training and test sets. 10-fold cross-validation was done on the training set for parameter tuning. The area under the receiver-operating curve (AUC) is reported on the test set. Results: 956 patients were included, 192 (20%) in the test set. Univariate features associated with BM were treatment with etoposide, Asian race, presence of bone metastases at NSCLC diagnosis, mutations in TP53 and EGFR, amplifications of ERBB2 and EGFR, and deletions of RB1, CDKN2A and CDKN2B. Univariate features inversely associated with BM were older age, treatment with nivolumab, vinorelbine, alectinib, pembrolizumab, atezolizumab, and gemcitabine, as well as mutations in NOTCH1 and KRAS. Ridge regression had the best AUC, 0.73 (Table). Conclusions: We achieved reasonable prediction performance using commonly obtained clinical and genomic information in non-early NSCLC. The biologic role of the associated alterations deserves further scrutiny; this study replicates similar findings for EGFR and KRAS in a much smaller cohort. Certain subsets of NSCLC patients may benefit from increased surveillance for BM and transition to drug therapies known to effectively cross the blood-brain barrier, e.g., nivolumab and alectinib. Inclusion of additional covariates, e.g., brain RT, may further improve model performance.[Table: see text]
10535 Background: Homologous recombination is a major mechanism of defective DNA repair, but it r... more 10535 Background: Homologous recombination is a major mechanism of defective DNA repair, but it remains uncertain whether homologous repair deficient (HRD) tumors have favorable prognosis or are more/less likely to respond to treatment than tumors lacking such mutations. Objective: To determine whether lung (NSCLC) and colorectal (CRC) HRD+ tumors have better survival or response to chemotherapy than HRD- tumors. Methods: Patients with de novo stage IV NSCLC or CRC who had next generation sequencing (NGS) between 2015-2018 from one of four cancer centers were identified. Records were curated using the PRISSMM framework to ascertain treatment, overall survival (OS) and progression free survival based on imaging (PFS-I) and oncologists’ notes (PFS-M). Each NSCLC or CRC tumor was categorized as HRD+ if NGS revealed an oncogenic/likely oncogenic mutation in: ATM, BAP1, BARD1, BLM, BRCA1, BRCA2, BRIP1, CHEK2, FAM175A, FANCA, FANCC, NBN, PALB2, RAD50, RAD51, RAD51C, RTEL1, or MRE11A based...
e18746 Background: Most patients with cancer and COVID-19 will survive the acute illness. The lon... more e18746 Background: Most patients with cancer and COVID-19 will survive the acute illness. The longer-term impacts of COVID-19 on patients with cancer remain incompletely described. Methods: Using COVID-19 and Cancer Consortium registry data thru 12/31/2021, we examined outcomes of long-term COVID-19 survivors with post-acute sequelae of SARS-CoV-2 infection (PASC aka “long COVID”). PASC was defined as having recovered w/ complications or having died w/ ongoing infection 90+ days from original diagnosis; absence of PASC was defined as having fully recovered by 90 days, with 90+ days of follow-up. Patients with SARS-CoV-2 re-infection and records with low quality data were excluded. Results: 858 of 3710 of included patients (23%) met PASC criteria. Median follow-up (IQR) for PASC and recovered patients was 180 (98-217) and 180 (90-180) days, respectively. The PASC group had a higher rate of baseline comorbidities and poor performance status (Table). Cancer types, status, and recent an...
Summary Members of the taxane class of chemotherapies, staples of cancer treatment since the 1990... more Summary Members of the taxane class of chemotherapies, staples of cancer treatment since the 1990s, can induce chemotherapy-induced peripheral neuropathy (CIPN), a potentially irreversible outcome related to cumulative exposure. Switching between taxanes is often clinically necessary; however, different taxanes have different efficacies, toxicities, and dosing strategies, necessitating an evidence-based schema focused on toxicity. We performed a systematic review and meta-analysis of the literature on docetaxel and paclitaxel, extracting cumulative dose, rates of CIPN, and subject demographics, thereby establishing their dose-toxo-equivalence relationship through a Bayesian meta-analysis model, calculating doses of the two drugs that are expected to have comparable rates of CIPN, along with credible intervals. Our final model, based on 169 studies, produces credible interval widths that provide guidance within one treatment cycle. In practice, this model provides a framework under which oncologists can make treatment switching and dosing decisions, hopefully reducing patient risk of CIPN.
12035 Background: In-hospital mortality among patients with cancer (pts) and COVID-19 infection i... more 12035 Background: In-hospital mortality among patients with cancer (pts) and COVID-19 infection is high. The frequency of, and factors associated with, do-not-resuscitate (DNR) or do-not-intubate (DNI) orders at hospital admission (HA), and their correlation with care, has not been well studied. In November 2020, we began collecting this information for pts who were hospitalized at initial presentation in the CCC19 registry (NCT04354701). Methods: We investigated: 1. the frequency of, and factors associated with, DNR/DNI orders at HA; 2. change in code status during HA; and 3. the correlation between DNR/DNI orders and palliative care consultation (PC), mortality or length of stay (LOS). We included hospitalized, adult pts with cancer and COVID-19 from 57 participating sites. Reported characteristics include age, ECOG performance status (PS), and cancer status. Comparative statistics include 2-sided Wilcoxon rank sum and Fisher’s exact tests. Results: 744 pts had known baseline and/...
Studies in health technology and informatics, 2019
Natural language processing (NLP) technologies have been successfully applied to cancer research ... more Natural language processing (NLP) technologies have been successfully applied to cancer research by enabling automated phenotypic information extraction from narratives in electronic health records (EHRs) such as pathology reports; however, developing customized NLP solutions requires substantial effort. To facilitate the adoption of NLP in cancer research, we have developed a set of customizable modules for extracting comprehensive types of cancer-related information in pathology reports (e.g., tumor size, tumor stage, and biomarkers), by leveraging the existing CLAMP system, which provides user-friendly interfaces for building customized NLP solutions for individual needs. Evaluation using annotated data at Vanderbilt University Medical Center showed that CLAMP-Cancer could extract diverse types of cancer information with good F-measures (0.80-0.98). We then applied CLAMP-Cancer to an information extraction task at Mayo Clinic and showed that we can quickly build a customized NLP ...
Importance Real-world data sets that combine clinical and genomic data may be subject to left tru... more Importance Real-world data sets that combine clinical and genomic data may be subject to left truncation (when potential study participants are not included because they have already passed the milestone of interest at the time of study recruitment). The lapse between diagnosis and molecular testing can present analytic challenges and threaten the validity and interpretation of survival analyses. Observations Effects of ignoring left truncation when estimating overall survival are illustrated using data from the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC), and a straightforward risk-set adjustment approach is described. Ignoring left truncation results in overestimation of overall survival: unadjusted median survival estimates from diagnosis among patients with stage IV non-small cell lung cancer or stage IV colorectal cancer were overestimated by more than 1 year. Conclusions and Relevance Clinicogenomic data are a valuable resource for evaluation of real-world cancer outcomes and should be analyzed using appropriate methods to maximize their potential. Analysts must become adept at application of appropriate statistical methods to ensure valid, meaningful, and generalizable research findings.
Studies linking genomic and phenomic data are subject to selection biases, including delayed entr... more Studies linking genomic and phenomic data are subject to selection biases, including delayed entry or immortal time bias. Delayed entry can be problematic for time-to-event analyses, but utilization of appropriate statistical methods to account for delayed entry are underutilized. Delayed entry commonly occurs when genomic sequencing results are obtained after the start time for survival estimation. To evaluate the impact of left truncation on overall survival (OS) estimates, we explored outcomes in patients with de novo stage IV non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) from the AACR GENIE Biopharma Collaborative, who had genomic sequencing within a specified timeframe. We analyzed OS from diagnosis and from start of the most common first-line regimen, carboplatin/pemetrexed for NSCLC (N = 212 patients) and FOLFOX for CRC (N = 369 patients). We compared median OS using standard Kaplan-Meier methods to median OS using left truncation methods to account for delay...
8534 Background: The most widely used multiple myeloma (MM) staging system, the Revised Internati... more 8534 Background: The most widely used multiple myeloma (MM) staging system, the Revised International Staging System (R-ISS), is based on lactate dehydrogenase, albumin, cytogenetics, and beta-2 microglobulin (B2M). B2M has limited clinical utility, is often only obtained to compute R-ISS, and is often a send-out test. Prior studies have shown that elevated red cell distribution width (RDW), a common test that is part of the routine complete blood count, is associated with reduced overall survival (OS) in MM. We hypothesized that a MM staging system could be constructed replacing B2M with RDW. Methods: Patients treated at Vanderbilt University Medical Center from 2000 to 2018 with cancer registry-confirmed MM diagnoses were included. OS was computed by registry-curated death and diagnosis dates; living patients were censored at date last known alive or of last follow up. A Cox proportional hazards model determining the independent effects of R-ISS, age, and RDW on OS was built. An a...
9622 Background: Molecular tumor profiling has become an integral component of oncology practice ... more 9622 Background: Molecular tumor profiling has become an integral component of oncology practice but linked genomic-phenomic data remain scarce. Recurrence, treatment response and progression are not structured consistently in medical records and this deficit has been a roadblock to discovery of biomarkers that are associated with favorable outcomes. Methods: The Genomics Evidence Neoplasia Information Exchange (GENIE) consortium is an AACR sponsored project to link and share genomic and phenomic data to promote discovery in precision medicine. 3 cancer centers that routinely perform somatic tumor profiling for advanced cancers agreed to curate anti-neoplastic treatment exposures and outcomes including recurrence, progression, response and survival using a standard method. 6 cancer types (lung, colorectal, breast, prostate, pancreas and bladder) were selected and a REDCAP database captures anti-neoplastic treatments, and specific elements from pathology, radiology and oncology repor...
e20553 Background: Although modern therapeutics for multiple myeloma (MM) have resulted in improv... more e20553 Background: Although modern therapeutics for multiple myeloma (MM) have resulted in improved overall survival (OS) in recent years, patients who present with an acute disease-related complication often have poor outcomes. We sought to compare the OS of patients diagnosed with MM in or shortly after hospitalization with those diagnosed in the outpatient setting. Methods: Patients treated for MM at Vanderbilt University Medical Center (VUMC) between 2000 and 2018 were included. OS was computed from date of diagnosis; patients still alive were censored at date last known alive or of last follow-up. Baseline laboratory and cytogenetic data were used to calculate Revised International Staging System (R-ISS) stage; age was also recorded. Dates of inpatient notes and encounter codes were identified and compared to date of diagnosis to identify patients diagnosed within 30 days of an inpatient stay; patients whose first encounter at VUMC was 30 days or more after their diagnosis date...
e18907Background: Basic and clinical science suffer from a reproducibility crisis, causing many t... more e18907Background: Basic and clinical science suffer from a reproducibility crisis, causing many to ask whether current standards for statistical significance (P < .05) are too generous. Anecdotally...
Hormonal therapy is an effective, but challenging, long-term treatment for patients with hormone-... more Hormonal therapy is an effective, but challenging, long-term treatment for patients with hormone-receptor-positive breast cancer. Raising the rate of patients who initiate therapy may be possible by characterizing the factors that influence a patient's decision. We hypothesized that online patient portal messages convey such factors. To investigate this hypothesis, we focused on breast cancer patients who were prescribed hormonal therapy at Vanderbilt University Medical Center and sent messages through the portal between diagnosis and therapy initiation. We first conducted a topic modeling analysis to generate the main themes of portal messages. We subsequently applied survival analysis to learn the association between the factors conveyed in messages, in term of semantic word groups, and the time elapsed from diagnosis to therapy initiation. We found that consulting with healthcare providers increased the probability of therapy initiation, while mentions of symptoms or negative...
e18080 Background: Implementation of electronic health records (EHRs) has engendered a large quan... more e18080 Background: Implementation of electronic health records (EHRs) has engendered a large quantity of machine-readable data. However, different practices choose different EHR vendors and the same vendor product may be implemented differently at each practice. Motivated by the desire to facilitate appropriate integration of data, our goal was to describe and quantify the consistency and variation of structured data within EHRs. Methods: De-identified and aggregated CancerLinQ data from 47 practices regarding the standards and variability of structured data including race, diagnoses, encounters, cancer staging, selected cancer-relevant medications, lab values and biomarkers were analyzed. EHR represented included ARIA, MOSAIQ, Allscripts, Centricity, Epic, Intellidose, NextGen, and OncoEMR. Results: De-identified EHR implementations included 23 A, 12 B, C and 5 other vendors. Only 6 practices (13%) used non-standard race representation. All practices used ICD-9/10 for diagnoses. There was variability in coding of encounters. Sixteen practices always used CPT, 5 practices always used SNOMED CT and 26 practices used multiple standards. Multiple staging systems were used. An average of 48% (range 11%-; including patients staged more than once) of patient records included coded staging information. Only one practice used a standard (LOINC) for laboratory data. No standards were used for medications ordered/administered or biomarkers. The table shows the number of distinct names for selected lab tests, medications and biomarkers across systems. Conclusions: In this cross-sectional sample, standards are used consistently for diagnoses and encounter data, often for race and rarely for medications, laboratory tests or biomarkers.[Table: see text]
2032 Background: 30-50% of patients with non-early NSCLC will eventually develop BM, with a media... more 2032 Background: 30-50% of patients with non-early NSCLC will eventually develop BM, with a median survival of less than one year from BM diagnosis. There are no widely accepted clinical risk models for development of BM in patients without them at baseline. We predicted the binary risk of BM using clinical and genetic factors from a large multi-institutional cohort. Methods: Stage II-IV NSCLC patients from the AACR Project GENIE Biopharma Consortium dataset were eligible. This consisted of 4 academic institutions who curated clinical data of patients who had somatic next-generation tumor sequencing (NGS) between 2015-2017. We excluded patients who had BM at baseline, died within 30 days of NSCLC diagnosis, or did not undergo brain imaging. Covariates included demographics, anticancer therapies (received up to 90 days prior to BM development and within 5 years from NSCLC diagnosis), and NGS data; radiotherapy (RT) data were not available. NGS features included mutations and copy number alterations. These features were restricted to those classified as oncogenic by OncoKB. Univariate feature selection with Fisher’s test (p&lt;.1) was performed on medication and genetic features. We compared 5 different machine learning models for prediction: random forest (RF), support vector machine (SVM), lasso regression, ridge regression, and an ensemble classifier. We split our data into training and test sets. 10-fold cross-validation was done on the training set for parameter tuning. The area under the receiver-operating curve (AUC) is reported on the test set. Results: 956 patients were included, 192 (20%) in the test set. Univariate features associated with BM were treatment with etoposide, Asian race, presence of bone metastases at NSCLC diagnosis, mutations in TP53 and EGFR, amplifications of ERBB2 and EGFR, and deletions of RB1, CDKN2A and CDKN2B. Univariate features inversely associated with BM were older age, treatment with nivolumab, vinorelbine, alectinib, pembrolizumab, atezolizumab, and gemcitabine, as well as mutations in NOTCH1 and KRAS. Ridge regression had the best AUC, 0.73 (Table). Conclusions: We achieved reasonable prediction performance using commonly obtained clinical and genomic information in non-early NSCLC. The biologic role of the associated alterations deserves further scrutiny; this study replicates similar findings for EGFR and KRAS in a much smaller cohort. Certain subsets of NSCLC patients may benefit from increased surveillance for BM and transition to drug therapies known to effectively cross the blood-brain barrier, e.g., nivolumab and alectinib. Inclusion of additional covariates, e.g., brain RT, may further improve model performance.[Table: see text]
10535 Background: Homologous recombination is a major mechanism of defective DNA repair, but it r... more 10535 Background: Homologous recombination is a major mechanism of defective DNA repair, but it remains uncertain whether homologous repair deficient (HRD) tumors have favorable prognosis or are more/less likely to respond to treatment than tumors lacking such mutations. Objective: To determine whether lung (NSCLC) and colorectal (CRC) HRD+ tumors have better survival or response to chemotherapy than HRD- tumors. Methods: Patients with de novo stage IV NSCLC or CRC who had next generation sequencing (NGS) between 2015-2018 from one of four cancer centers were identified. Records were curated using the PRISSMM framework to ascertain treatment, overall survival (OS) and progression free survival based on imaging (PFS-I) and oncologists’ notes (PFS-M). Each NSCLC or CRC tumor was categorized as HRD+ if NGS revealed an oncogenic/likely oncogenic mutation in: ATM, BAP1, BARD1, BLM, BRCA1, BRCA2, BRIP1, CHEK2, FAM175A, FANCA, FANCC, NBN, PALB2, RAD50, RAD51, RAD51C, RTEL1, or MRE11A based...
e18746 Background: Most patients with cancer and COVID-19 will survive the acute illness. The lon... more e18746 Background: Most patients with cancer and COVID-19 will survive the acute illness. The longer-term impacts of COVID-19 on patients with cancer remain incompletely described. Methods: Using COVID-19 and Cancer Consortium registry data thru 12/31/2021, we examined outcomes of long-term COVID-19 survivors with post-acute sequelae of SARS-CoV-2 infection (PASC aka “long COVID”). PASC was defined as having recovered w/ complications or having died w/ ongoing infection 90+ days from original diagnosis; absence of PASC was defined as having fully recovered by 90 days, with 90+ days of follow-up. Patients with SARS-CoV-2 re-infection and records with low quality data were excluded. Results: 858 of 3710 of included patients (23%) met PASC criteria. Median follow-up (IQR) for PASC and recovered patients was 180 (98-217) and 180 (90-180) days, respectively. The PASC group had a higher rate of baseline comorbidities and poor performance status (Table). Cancer types, status, and recent an...
Summary Members of the taxane class of chemotherapies, staples of cancer treatment since the 1990... more Summary Members of the taxane class of chemotherapies, staples of cancer treatment since the 1990s, can induce chemotherapy-induced peripheral neuropathy (CIPN), a potentially irreversible outcome related to cumulative exposure. Switching between taxanes is often clinically necessary; however, different taxanes have different efficacies, toxicities, and dosing strategies, necessitating an evidence-based schema focused on toxicity. We performed a systematic review and meta-analysis of the literature on docetaxel and paclitaxel, extracting cumulative dose, rates of CIPN, and subject demographics, thereby establishing their dose-toxo-equivalence relationship through a Bayesian meta-analysis model, calculating doses of the two drugs that are expected to have comparable rates of CIPN, along with credible intervals. Our final model, based on 169 studies, produces credible interval widths that provide guidance within one treatment cycle. In practice, this model provides a framework under which oncologists can make treatment switching and dosing decisions, hopefully reducing patient risk of CIPN.
12035 Background: In-hospital mortality among patients with cancer (pts) and COVID-19 infection i... more 12035 Background: In-hospital mortality among patients with cancer (pts) and COVID-19 infection is high. The frequency of, and factors associated with, do-not-resuscitate (DNR) or do-not-intubate (DNI) orders at hospital admission (HA), and their correlation with care, has not been well studied. In November 2020, we began collecting this information for pts who were hospitalized at initial presentation in the CCC19 registry (NCT04354701). Methods: We investigated: 1. the frequency of, and factors associated with, DNR/DNI orders at HA; 2. change in code status during HA; and 3. the correlation between DNR/DNI orders and palliative care consultation (PC), mortality or length of stay (LOS). We included hospitalized, adult pts with cancer and COVID-19 from 57 participating sites. Reported characteristics include age, ECOG performance status (PS), and cancer status. Comparative statistics include 2-sided Wilcoxon rank sum and Fisher’s exact tests. Results: 744 pts had known baseline and/...
Studies in health technology and informatics, 2019
Natural language processing (NLP) technologies have been successfully applied to cancer research ... more Natural language processing (NLP) technologies have been successfully applied to cancer research by enabling automated phenotypic information extraction from narratives in electronic health records (EHRs) such as pathology reports; however, developing customized NLP solutions requires substantial effort. To facilitate the adoption of NLP in cancer research, we have developed a set of customizable modules for extracting comprehensive types of cancer-related information in pathology reports (e.g., tumor size, tumor stage, and biomarkers), by leveraging the existing CLAMP system, which provides user-friendly interfaces for building customized NLP solutions for individual needs. Evaluation using annotated data at Vanderbilt University Medical Center showed that CLAMP-Cancer could extract diverse types of cancer information with good F-measures (0.80-0.98). We then applied CLAMP-Cancer to an information extraction task at Mayo Clinic and showed that we can quickly build a customized NLP ...
Importance Real-world data sets that combine clinical and genomic data may be subject to left tru... more Importance Real-world data sets that combine clinical and genomic data may be subject to left truncation (when potential study participants are not included because they have already passed the milestone of interest at the time of study recruitment). The lapse between diagnosis and molecular testing can present analytic challenges and threaten the validity and interpretation of survival analyses. Observations Effects of ignoring left truncation when estimating overall survival are illustrated using data from the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC), and a straightforward risk-set adjustment approach is described. Ignoring left truncation results in overestimation of overall survival: unadjusted median survival estimates from diagnosis among patients with stage IV non-small cell lung cancer or stage IV colorectal cancer were overestimated by more than 1 year. Conclusions and Relevance Clinicogenomic data are a valuable resource for evaluation of real-world cancer outcomes and should be analyzed using appropriate methods to maximize their potential. Analysts must become adept at application of appropriate statistical methods to ensure valid, meaningful, and generalizable research findings.
Studies linking genomic and phenomic data are subject to selection biases, including delayed entr... more Studies linking genomic and phenomic data are subject to selection biases, including delayed entry or immortal time bias. Delayed entry can be problematic for time-to-event analyses, but utilization of appropriate statistical methods to account for delayed entry are underutilized. Delayed entry commonly occurs when genomic sequencing results are obtained after the start time for survival estimation. To evaluate the impact of left truncation on overall survival (OS) estimates, we explored outcomes in patients with de novo stage IV non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) from the AACR GENIE Biopharma Collaborative, who had genomic sequencing within a specified timeframe. We analyzed OS from diagnosis and from start of the most common first-line regimen, carboplatin/pemetrexed for NSCLC (N = 212 patients) and FOLFOX for CRC (N = 369 patients). We compared median OS using standard Kaplan-Meier methods to median OS using left truncation methods to account for delay...
8534 Background: The most widely used multiple myeloma (MM) staging system, the Revised Internati... more 8534 Background: The most widely used multiple myeloma (MM) staging system, the Revised International Staging System (R-ISS), is based on lactate dehydrogenase, albumin, cytogenetics, and beta-2 microglobulin (B2M). B2M has limited clinical utility, is often only obtained to compute R-ISS, and is often a send-out test. Prior studies have shown that elevated red cell distribution width (RDW), a common test that is part of the routine complete blood count, is associated with reduced overall survival (OS) in MM. We hypothesized that a MM staging system could be constructed replacing B2M with RDW. Methods: Patients treated at Vanderbilt University Medical Center from 2000 to 2018 with cancer registry-confirmed MM diagnoses were included. OS was computed by registry-curated death and diagnosis dates; living patients were censored at date last known alive or of last follow up. A Cox proportional hazards model determining the independent effects of R-ISS, age, and RDW on OS was built. An a...
9622 Background: Molecular tumor profiling has become an integral component of oncology practice ... more 9622 Background: Molecular tumor profiling has become an integral component of oncology practice but linked genomic-phenomic data remain scarce. Recurrence, treatment response and progression are not structured consistently in medical records and this deficit has been a roadblock to discovery of biomarkers that are associated with favorable outcomes. Methods: The Genomics Evidence Neoplasia Information Exchange (GENIE) consortium is an AACR sponsored project to link and share genomic and phenomic data to promote discovery in precision medicine. 3 cancer centers that routinely perform somatic tumor profiling for advanced cancers agreed to curate anti-neoplastic treatment exposures and outcomes including recurrence, progression, response and survival using a standard method. 6 cancer types (lung, colorectal, breast, prostate, pancreas and bladder) were selected and a REDCAP database captures anti-neoplastic treatments, and specific elements from pathology, radiology and oncology repor...
e20553 Background: Although modern therapeutics for multiple myeloma (MM) have resulted in improv... more e20553 Background: Although modern therapeutics for multiple myeloma (MM) have resulted in improved overall survival (OS) in recent years, patients who present with an acute disease-related complication often have poor outcomes. We sought to compare the OS of patients diagnosed with MM in or shortly after hospitalization with those diagnosed in the outpatient setting. Methods: Patients treated for MM at Vanderbilt University Medical Center (VUMC) between 2000 and 2018 were included. OS was computed from date of diagnosis; patients still alive were censored at date last known alive or of last follow-up. Baseline laboratory and cytogenetic data were used to calculate Revised International Staging System (R-ISS) stage; age was also recorded. Dates of inpatient notes and encounter codes were identified and compared to date of diagnosis to identify patients diagnosed within 30 days of an inpatient stay; patients whose first encounter at VUMC was 30 days or more after their diagnosis date...
e18907Background: Basic and clinical science suffer from a reproducibility crisis, causing many t... more e18907Background: Basic and clinical science suffer from a reproducibility crisis, causing many to ask whether current standards for statistical significance (P < .05) are too generous. Anecdotally...
Hormonal therapy is an effective, but challenging, long-term treatment for patients with hormone-... more Hormonal therapy is an effective, but challenging, long-term treatment for patients with hormone-receptor-positive breast cancer. Raising the rate of patients who initiate therapy may be possible by characterizing the factors that influence a patient's decision. We hypothesized that online patient portal messages convey such factors. To investigate this hypothesis, we focused on breast cancer patients who were prescribed hormonal therapy at Vanderbilt University Medical Center and sent messages through the portal between diagnosis and therapy initiation. We first conducted a topic modeling analysis to generate the main themes of portal messages. We subsequently applied survival analysis to learn the association between the factors conveyed in messages, in term of semantic word groups, and the time elapsed from diagnosis to therapy initiation. We found that consulting with healthcare providers increased the probability of therapy initiation, while mentions of symptoms or negative...
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Papers by Jeremy Warner