Citations

Abstract Background: DEPendency of association on the number of Top Hits (DEPTH) is an approach to identify candidate susceptibility regions by considering the risk signals from overlapping groups of sequential variants across the genome. Methods: We applied a DEPTH analysis using a sliding window of 200 SNPs to colorectal cancer data from the Colon Cancer Family Registry (CCFR; 5,735 cases and 3,688 controls), and Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO; 8,865 cases and 10,285 controls) studies. A DEPTH score > 1 was used to identify candidate susceptibility regions common to both analyses. We compared DEPTH results against those from conventional genome-wide association study (GWAS) analyses of these two studies as well as against 132 published susceptibility regions. Results: Initial DEPTH analysis revealed 2,622 (CCFR) and 3,686 (GECCO) candidate susceptibility regions, of which 569 were common to both studies. Bootstrapping revealed 40 and 49 candidate susceptibility regions in the CCFR and GECCO data sets, respectively. Notably, DEPTH identified at least 82 regions that would not be detected using conventional GWAS methods, nor had they been identified by previous colorectal cancer GWASs. We found four reproducible candidate susceptibility regions (2q22.2, 2q33.1, 6p21.32, 13q14.3). The highest DEPTH scores were in the human leukocyte antigen locus at 6p21 where the strongest associated SNPs were rs762216297, rs149490268, rs114741460, and rs199707618 for the CCFR data, and rs9270761 for the GECCO data. Conclusions: DEPTH can identify candidate susceptibility regions for colorectal cancer not identified using conventional analyses of larger datasets. Impact: DEPTH has potential as a powerful complementary tool to conventional GWAS analyses for discovering susceptibility regions within the genome.

Abstract Background: The genotoxin colibactin, produced by Escherichia coli containing the pks island, is associated with a tumor single base substitution (SBS) mutational signature SBS88. It is unknown whether lifestyle and environmental factors related to gut dysbiosis impact colorectal cancer (CRC) risk and survival differently by colibactin signature status. Methods: Utilizing the resources of the Genetic Epidemiology of Colorectal cancer Consortium and Colon Cancer Family Registry (GECCO-CCFR), a consortium including both case-control and cohort study designs, SBS88 tumor mutational signature was measured in 4308 CRC cases who were microsatellite stable (MSS) and had at least five somatic single nucleotide variants for signature decomposition. Associations of 13 lifestyle and environmental factors with CRC risk by colibactin signature status were assessed using logistic and multinomial regression; associations with CRC survival were assessed using Cox proportional hazards regression. Results: 392 (9%) of the 4308 MSS tumors were positive for SBS88. Having a BMI ≥30 kg/m2 (versus a BMI 18.5-24.9 kg/m2) was strongly associated with worse CRC-specific survival among those with the SBS88 signature, but not among those with SBS88 negative CRC [further adjusted hazard ratio (HR) = 3.40 95% confidence interval (CI) 1.47, 7.84, and HR = 0.97 95% CI 0.78, 1.21, respectively, P for heterogeneity = 0.066]. Associations of fruit intake with CRC risk may be differential by SBS88 status. In minimally adjusted models, those in the highest quartile of fruit intake (versus the first quartile) had 0.53 (95% CI 0.37, 0.76) times the risk of SBS88 positive CRC, as opposed to 0.75 (95% CI 0.66, 0.85) times the risk of SBS88 negative CRC (P for heterogeneity = 0.047). Among cohort studies specifically, associations between CRC risk and BMI, alcohol, and fruit intake also differed by SBS88 status (P for heterogeneity ranging 0.02-0.05). Conclusions: Higher BMI may be associated with worse CRC-specific survival among those with SBS88 positive tumors. BMI, alcohol, and dietary factors may be differentially associated with CRC risk based on SBS88 status. Citation Format: Claire Elizabeth Thomas, Peter Georgeson, Conghui Qu, Robert S. Steinfelder, Daniel D. Buchanan, Mark A. Jenkins, Andrea Gsur, Jane C. Figueiredo, Polly A. Newcomb, Peter T. Campbell, Christina Newton, Caroline Y. Um, Lisa Boardman, Victor Moreno, Jenny Chang-Claude, Michael Hoffmeister, Marc J. Gunter, Andrew T. Chan, Shuji Ogino, Ellen L. Goode, Brigid Lynch, Yohannes A. Melaku, Steven Gallinger, Sonja I. Berndt, Wen-Yi Huang, Ulrike Peters, Amanda I. Phipps. Lifestyle and environmental factors in relation to colorectal cancer risk and survival by colibactin tumor mutational signature status [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6453.

OBJECTIVE Spondylolisthesis is a common operative disease in the United States, but robust predictive models for patient outcomes remain limited. The development of models that accurately predict postoperative outcomes would be useful to help identify patients at risk of complicated postoperative courses and determine appropriate healthcare and resource utilization for patients. As such, the purpose of this study was to develop k-nearest neighbors (KNN) classification algorithms to identify patients at increased risk for extended hospital length of stay (LOS) following neurosurgical intervention for spondylolisthesis. METHODS The Quality Outcomes Database (QOD) spondylolisthesis data set was queried for patients receiving either decompression alone or decompression plus fusion for degenerative spondylolisthesis. Preoperative and perioperative variables were queried, and Mann-Whitney U-tests were performed to identify which variables would be included in the machine learning models. Two KNN models were implemented (k = 25) with a standard training set of 60%, validation set of 20%, and testing set of 20%, one with arthrodesis status (model 1) and the other without (model 2). Feature scaling was implemented during the preprocessing stage to standardize the independent features. RESULTS Of 608 enrolled patients, 544 met prespecified inclusion criteria. The mean age of all patients was 61.9 ± 12.1 years (± SD), and 309 (56.8%) patients were female. The model 1 KNN had an overall accuracy of 98.1%, sensitivity of 100%, specificity of 84.6%, positive predictive value (PPV) of 97.9%, and negative predictive value (NPV) of 100%. Additionally, a receiver operating characteristic (ROC) curve was plotted for model 1, showing an overall area under the curve (AUC) of 0.998. Model 2 had an overall accuracy of 99.1%, sensitivity of 100%, specificity of 92.3%, PPV of 99.0%, and NPV of 100%, with the same ROC AUC of 0.998. CONCLUSIONS Overall, these findings demonstrate that nonlinear KNN machine learning models have incredibly high predictive value for LOS. Important predictor variables include diabetes, osteoporosis, socioeconomic quartile, duration of surgery, estimated blood loss during surgery, patient educational status, American Society of Anesthesiologists grade, BMI, insurance status, smoking status, sex, and age. These models may be considered for external validation by spine surgeons to aid in patient selection and management, resource utilization, and preoperative surgical planning.

OBJECTIVE The purpose of this study was to evaluate the performance of different supervised machine learning algorithms to predict achievement of minimum clinically important difference (MCID) in neck pain after surgery in patients with cervical spondylotic myelopathy (CSM). METHODS This was a retrospective analysis of the prospective Quality Outcomes Database CSM cohort. The data set was divided into an 80% training and a 20% test set. Various supervised learning algorithms (including logistic regression, support vector machine, decision tree, random forest, extra trees, gaussian naïve Bayes, k–nearest neighbors, multilayer perceptron, and extreme gradient boosted trees) were evaluated on their performance to predict achievement of MCID in neck pain at 3 and 24 months after surgery, given a set of predicting baseline features. Model performance was assessed with accuracy, F1 score, area under the receiver operating characteristic curve, precision, recall/sensitivity, and specificity. RESULTS In total, 535 patients (46.9%) achieved MCID for neck pain at 3 months and 569 patients (49.9%) achieved it at 24 months. In each follow-up cohort, 501 patients (93.6%) were satisfied at 3 months after surgery and 569 patients (100%) were satisfied at 24 months after surgery. Of the supervised machine learning algorithms tested, logistic regression demonstrated the best accuracy (3 months: 0.76 ± 0.031, 24 months: 0.773 ± 0.044), followed by F1 score (3 months: 0.759 ± 0.019, 24 months: 0.777 ± 0.039) and area under the receiver operating characteristic curve (3 months: 0.762 ± 0.027, 24 months: 0.773 ± 0.043) at predicting achievement of MCID for neck pain at both follow-up time points, with fair performance. The best precision was also demonstrated by logistic regression at 3 (0.724 ± 0.058) and 24 (0.780 ± 0.097) months. The best recall/sensitivity was demonstrated by multilayer perceptron at 3 months (0.841 ± 0.094) and by extra trees at 24 months (0.817 ± 0.115). Highest specificity was shown by support vector machine at 3 months (0.952 ± 0.013) and by logistic regression at 24 months (0.747 ± 0.18). CONCLUSIONS Appropriate selection of models for studies should be based on the strengths of each model and the aims of the studies. For maximally predicting true achievement of MCID in neck pain, of all the predictions in this balanced data set the appropriate metric for the authors’ study was precision. For both short- and long-term follow-ups, logistic regression demonstrated the highest precision of all models tested. Logistic regression performed consistently the best of all models tested and remains a powerful model for clinical classification tasks.

Abstract Colorectal cancer risk can be impacted by genetic, environmental, and lifestyle factors, including diet and obesity. Gene-environment interactions (G × E) can provide biological insights into the effects of obesity on colorectal cancer risk. Here, we assessed potential genome-wide G × E interactions between body mass index (BMI) and common SNPs for colorectal cancer risk using data from 36,415 colorectal cancer cases and 48,451 controls from three international colorectal cancer consortia (CCFR, CORECT, and GECCO). The G × E tests included the conventional logistic regression using multiplicative terms (one degree of freedom, 1DF test), the two-step EDGE method, and the joint 3DF test, each of which is powerful for detecting G × E interactions under specific conditions. BMI was associated with higher colorectal cancer risk. The two-step approach revealed a statistically significant G×BMI interaction located within the Formin 1/Gremlin 1 (FMN1/GREM1) gene region (rs58349661). This SNP was also identified by the 3DF test, with a suggestive statistical significance in the 1DF test. Among participants with the CC genotype of rs58349661, overweight and obesity categories were associated with higher colorectal cancer risk, whereas null associations were observed across BMI categories in those with the TT genotype. Using data from three large international consortia, this study discovered a locus in the FMN1/GREM1 gene region that interacts with BMI on the association with colorectal cancer risk. Further studies should examine the potential mechanisms through which this locus modifies the etiologic link between obesity and colorectal cancer. Significance: This gene-environment interaction analysis revealed a genetic locus in FMN1/GREM1 that interacts with body mass index in colorectal cancer risk, suggesting potential implications for precision prevention strategies.

Study Design. External validation using prospectively collected data. Objectives. To determine the model performance of “Dialogue Support” (DS) in predicting outcomes after lumbar spine surgery. Summary of Background Data. To help clinicians discuss risk versus benefit with patients considering lumbar fusion surgery, DS has been made available online. As DS was created using a Swedish sample, there is a need to study how well DS performs in alternative populations. Patients and Methods. Preoperative data from patients enrolled in the Quality Outcomes Database were entered into DS. The probability for each patient to report satisfaction, achieve success (leg pain improvement ≥3), or have no leg pain 12 months after surgery was extracted and compared with their actual 12-month postoperative data. The ability of DS to identify patients in the Quality Outcomes Database who report satisfaction, achieve success, or have no leg pain 12 months after surgery was determined using Receiver operating characteristic curve analysis, goodness-of-fit tests, and calibration plots. Results. There was a significant improvement in all outcomes in 23,928 cases included in the analysis from baseline to 12 months postoperative. Most (84%) reported satisfaction, 67% achieved success, and 44% were pain-free 12 months postoperative. Receiver operating characteristic analysis showed that DS had a low ability to predict satisfaction [area under the curve (AUC) = 0.606], success (AUC = 0.546), and being pain-free (AUC = 0.578) at 12 months postoperative; poor fit for satisfaction (<0.001) and being pain-free (P = 0.004), but acceptable fit for success (P = 0.052). Calibration plots showed underestimation for satisfaction and success, but acceptable estimates for being pain-free. Conclusion. DS is not directly transferable to predict satisfaction and success after lumbar surgery in a US population. This may be due to differences in patient characteristics, weights of the variables included, or the exclusion of unknown variables associated with outcomes. Future studies to better understand and improve the transferability of these models are needed.

OBJECTIVE The Quality Outcomes Database (QOD) was established in 2012 by the NeuroPoint Alliance, a nonprofit organization supported by the American Association of Neurological Surgeons. Currently, the QOD has launched six different modules to cover a broad spectrum of neurosurgical practice—namely lumbar spine surgery, cervical spine surgery, brain tumor, stereotactic radiosurgery (SRS), functional neurosurgery for Parkinson’s disease, and cerebrovascular surgery. This investigation aims to summarize research efforts and evidence yielded through QOD research endeavors. METHODS The authors identified all publications from January 1, 2012, to February 18, 2023, that were produced by using data collected prospectively in a QOD module without a prespecified research purpose in the context of quality surveillance and improvement. Citations were compiled and presented along with comprehensive documentation of the main study objective and take-home message. RESULTS A total of 94 studies have been produced through QOD efforts during the past decade. QOD-derived literature has been predominantly dedicated to spinal surgical outcomes, with 59 and 22 studies focusing on lumbar and cervical spine surgery, respectively, and 6 studies focusing on both. More specifically, the QOD Study Group—a research collaborative between 16 high-enrolling sites—has yielded 24 studies on lumbar grade 1 spondylolisthesis and 13 studies on cervical spondylotic myelopathy, using two focused data sets with high data accuracy and long-term follow-up. The more recent neuro-oncological QOD efforts, i.e., the Tumor QOD and the SRS Quality Registry, have contributed 5 studies, providing insights into the real-world neuro-oncological practice and the role of patient-reported outcomes. CONCLUSIONS Prospective quality registries are an important resource for observational research, yielding clinical evidence to guide decision-making across neurosurgical subspecialties. Future directions of the QOD efforts include the development of research efforts within the neuro-oncological registries and the American Spine Registry—which has now replaced the inactive spinal modules of the QOD—and the focused research on high-grade lumbar spondylolisthesis and cervical radiculopathy.

OBJECTIVE The American Spine Registry (ASR) is a collaborative effort between the American Academy of Orthopaedic Surgeons and the American Association of Neurological Surgeons. The goal of this study was to evaluate how representative the ASR is of the national practice with spinal procedures, as recorded in the National Inpatient Sample (NIS). METHODS The authors queried the NIS and the ASR for cervical and lumbar arthrodesis cases performed during 2017–2019. International Classification of Diseases, 10th Revision and Current Procedural Terminology codes were used to identify patients undergoing cervical and lumbar procedures. The two groups were compared for the overall proportion of cervical and lumbar procedures, age distribution, sex, surgical approach features, race, and hospital volume. Outcomes available in the ASR, such as patient-reported outcomes and reoperations, were not analyzed due to nonavailability in the NIS. The representativeness of the ASR compared to the NIS was assessed via Cohen’s d effect sizes, and absolute standardized mean differences (SMDs) of < 0.2 were considered trivial, whereas > 0.5 were considered moderately large. RESULTS A total of 24,800 arthrodesis procedures were identified in the ASR for the period between January 1, 2017, and December 31, 2019. During the same time period, 1,305,360 cases were recorded in the NIS. Cervical fusions comprised 35.9% of the ASR cohort (8911 cases) and 36.0% of the NIS cohort (469,287 cases). The two databases presented trivial differences in terms of patient age and sex for all years of interest across both cervical and lumbar arthrodeses (SMD < 0.2). Trivial differences were also noted in the distribution of open versus percutaneous procedures of the cervical and lumbar spine (SMD < 0.2). Among lumbar cases, anterior approaches were more common in the ASR than in the NIS (32.1% vs 22.3%, SMD = 0.22), but the discrepancy among cervical cases in the two databases was trivial (SMD = 0.03). Small differences were illustrated in terms of race, with SMDs < 0.5, and a more significant discrepancy was identified in the geographic distribution of participating sites (SMDs of 0.7 and 0.74 for cervical and lumbar cases, respectively). For both of these measures, SMDs in 2019 were smaller than those in 2018 and 2017. CONCLUSIONS The ASR and NIS databases presented a very high similarity in proportions of cervical and lumbar spine surgeries, as well as similar distributions of age and sex, and distribution of open versus endoscopic approach. Slight discrepancies in anterior versus posterior approach among lumbar cases and patient race, and more significant discrepancies in geographic representation were also identified, yet decreasing trends in differences suggested the improving representativeness of the ASR over the course of time and its progressive growth. These conclusions are important to underline the external validity of quality investigations and research conclusions to be drawn from analyses in which the ASR is used.

Screening for colorectal cancer (CRC) is effective in reducing CRC related mortality. Current screening methods include endoscopy based and biomarker based approaches. This guideline is a joint official statement of the Asian Pacific Association of Gastroenterology (APAGE) and the Asian Pacific Society of Digestive Endoscopy (APSDE), developed in response to the increasing use of, and accumulating supportive evidence for the role of, non-invasive biomarkers for the diagnosis of CRC and its precursor lesions. A systematic review of 678 publications and a two stage Delphi consensus process involving 16 clinicians in various disciplines was undertaken to develop 32 evidence based and expert opinion based recommendations for the use of faecal immunochemical tests, faecal based tumour biomarkers or microbial biomarkers, and blood based tumour biomarkers for the detection of CRC and adenoma. Comprehensive up-to-date guidance is provided on indications, patient selection and strengths and limitations of each screening tool. Future research to inform clinical applications are discussed alongside objective measurement of research priorities. This joint APAGE–APSDE practice guideline is intended to provide an up-to-date guide to assist clinicians worldwide in utilising non-invasive biomarkers for CRC screening; it has particular salience for clinicians in the Asia-Pacific region.