Nomograms in oncology: more than meets the eye Balachandran, Vinod P, Dr; Gonen, Mithat, PhD; Smith, J Joshua, MD ...
The lancet oncology,
04/2015, Volume:
16, Issue:
4
Journal Article
Peer reviewed
Open access
Summary Nomograms are widely used as prognostic devices in oncology and medicine. With the ability to generate an individual probability of a clinical event by integrating diverse prognostic and ...determinant variables, nomograms meet our desire for biologically and clinically integrated models and fulfill our drive towards personalised medicine. Rapid computation through user-friendly digital interfaces, together with increased accuracy, and more easily understood prognoses compared with conventional staging, allow for seamless incorporation of nomogram-derived prognosis to aid clinical decision making. This has led to the appearance of many nomograms on the internet and in medical journals, and an increase in nomogram use by patients and physicians alike. However, the statistical foundations of nomogram construction, their precise interpretation, and evidence supporting their use are generally misunderstood. This issue is leading to an under-appreciation of the inherent uncertainties regarding nomogram use. We provide a systematic, practical approach to evaluating and comprehending nomogram-derived prognoses, with particular emphasis on clarifying common misconceptions and highlighting limitations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Although neoadjuvant chemoradiotherapy achieves low local recurrence rates in clinical stages II to III rectal cancer, it delays administration of optimal chemotherapy. We evaluated preoperative ...infusional fluorouracil, leucovorin, and oxaliplatin (FOLFOX)/bevacizumab with selective rather than consistent use of chemoradiotherapy.
Thirty-two patients with clinical stages II to III rectal cancer participated in this single-center phase II trial. All were candidates for low anterior resection with total mesorectal excision (TME). Patients were to receive six cycles of FOLFOX, with bevacizumab included for cycles 1 to 4. Patients with stable/progressive disease were to have radiation before TME, whereas responders were to have immediate TME. Postoperative radiation was planned if R0 resection was not achieved. Postoperative FOLFOX × 6 was recommended, but adjuvant regimens were left to clinician discretion. The primary outcome was R0 resection rate.
Between April 2007 and December 2008, 32 (100%) of 32 study participants had R0 resections. Two did not complete preoperative chemotherapy secondary to cardiovascular toxicity. Both had preoperative chemoradiotherapy and then R0 resections. Of 30 patients completing preoperative chemotherapy, all had tumor regression and TME without preoperative chemoradiotherapy. The pathologic complete response rate to chemotherapy alone was 8 of 32 (25%; 95% CI, 11% to 43%). The 4-year local recurrence rate was 0% (95% CI, 0% to 11%); the 4-year disease-free survival was 84% (95% CI, 67% to 94%).
For selected patients with clinical stages II to III rectal cancer, neoadjuvant chemotherapy and selective radiation does not seem to compromise outcomes. Preoperative Radiation or Selective Preoperative Radiation and Evaluation Before Chemotherapy and TME (PROSPECT), a randomized phase III trial to validate this experience, is now open in the US cooperative group network.
Bayesian nonparametric (BNP) models are becoming increasingly important in psychology, both as theoretical models of cognition and as analytic tools. However, existing tutorials tend to be at a level ...of abstraction largely impenetrable by non-technicians. This tutorial aims to help beginners understand key concepts by working through important but often omitted derivations carefully and explicitly, with a focus on linking the mathematics with a practical computation solution for a Dirichlet Process Mixture Model (DPMM)—one of the most widely used BNP methods. Abstract concepts are made explicit and concrete to non-technical readers by working through the theory that gives rise to them. A publicly accessible computer program written in the statistical language R is explained line-by-line to help readers understand the computation algorithm. The algorithm is also linked to a construction method called the Chinese Restaurant Process in an accessible tutorial in this journal (Gershman and Blei, 2012). The overall goals are to help readers understand more fully the theory and application so that they may apply BNP methods in their own work and leverage the technical details in this tutorial to develop novel methods.
•Mathematical derivations essential to the development of Dirichlet Process are provided.•An accessible pedagogy for complex and abstract mathematics in DP modeling.•A publicly accessible computer program in R is explained line-by-line.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Group 2 innate lymphoid cells (ILC2s) regulate inflammation and immunity in mammalian tissues
. Although ILC2s are found in cancers of these tissues
, their roles in cancer immunity and immunotherapy ...are unclear. Here we show that ILC2s infiltrate pancreatic ductal adenocarcinomas (PDACs) to activate tissue-specific tumour immunity. Interleukin-33 (IL33) activates tumour ILC2s (TILC2s) and CD8
T cells in orthotopic pancreatic tumours but not heterotopic skin tumours in mice to restrict pancreas-specific tumour growth. Resting and activated TILC2s express the inhibitory checkpoint receptor PD-1. Antibody-mediated PD-1 blockade relieves ILC2 cell-intrinsic PD-1 inhibition to expand TILC2s, augment anti-tumour immunity, and enhance tumour control, identifying activated TILC2s as targets of anti-PD-1 immunotherapy. Finally, both PD-1
TILC2s and PD-1
T cells are present in most human PDACs. Our results identify ILC2s as anti-cancer immune cells for PDAC immunotherapy. More broadly, ILC2s emerge as tissue-specific enhancers of cancer immunity that amplify the efficacy of anti-PD-1 immunotherapy. As ILC2s and T cells co-exist in human cancers and share stimulatory and inhibitory pathways, immunotherapeutic strategies to collectively target anti-cancer ILC2s and T cells may be broadly applicable.
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IJS, KISLJ, NUK, UL, UM, UPUK
CAR T cells expressing anti-CD19 and signaling molecules CD28 and CD3-zeta chain induced complete remission in 83% of patients with refractory ALL. Patients with a low disease burden had longer ...survival and a lower rate of toxic effects than those with a high disease burden.
Sixteen patients with mismatch repair–deficient, locally advanced rectal cancer were enrolled in a pilot study in which 6 months of neoadjuvant anti–PD-1 therapy was to be followed by surgical ...resection. Twelve patients have completed treatment and have had at least 6 months of follow-up; all 12 had a clinical complete response. All imaging tests and biopsies have shown no viable tumor.
Background
While multiple Asian and a few Western retrospective series have demonstrated the feasibility and safety of robotic-assisted gastrectomy for gastric cancer, its reliability for thorough ...resection, especially for locoregional disease, has not yet been firmly established, and reported learning curves vary widely. To support wider implementation of robotic gastrectomy, we evaluated the learning curve for this approach, assessed its oncologic feasibility, and created a selection model predicting the likelihood of conversion to open surgery in a US patient population.
Patients and Methods
We retrospectively reviewed data on all consecutive patients who underwent robotic gastrectomy at a high-volume institution between May 2012 and March 2019.
Results
Of the 220 patients with gastric cancer selected to undergo curative-intent robotic gastrectomy, surgery was completed using robotics in 159 (72.3%). The median number of removed lymph nodes was 28, and ≥ 15 lymph nodes were removed in 94% of procedures. Surgical time decreased steadily over the first 60–80 cases. Complications were generally minor: 7% of patients experienced complications of grade 3 or higher, with an anastomotic leak rate of 2% and mortality rate 0.9%. Factors predicting conversion to open surgery included neoadjuvant chemotherapy, BMI ≥ 31 kg/m
2
, and tumor size ≥ 6 cm.
Conclusions
These findings support the safety and oncologic feasibility of robotic gastrectomy for selected patients with gastric cancer. Proficiency can be achieved by 20 cases and mastery by 60–80 cases. Ideal candidates for this approach are patients with few comorbidities, BMI < 31 kg/m
2
, and tumors < 6 cm.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
The identification of somatic activating mutations in JAK2 (refs 1–4) and in the thrombopoietin receptor gene (MPL) in most patients with myeloproliferative neoplasm (MPN) led to the clinical ...development of JAK2 kinase inhibitors. JAK2 inhibitor therapy improves MPN-associated splenomegaly and systemic symptoms but does not significantly decrease or eliminate the MPN clone in most patients with MPN. We therefore sought to characterize mechanisms by which MPN cells persist despite chronic inhibition of JAK2. Here we show that JAK2 inhibitor persistence is associated with reactivation of JAK–STAT signalling and with heterodimerization between activated JAK2 and JAK1 or TYK2, consistent with activation of JAK2 in trans by other JAK kinases. Further, this phenomenon is reversible: JAK2 inhibitor withdrawal is associated with resensitization to JAK2 kinase inhibitors and with reversible changes in JAK2 expression. We saw increased JAK2 heterodimerization and sustained JAK2 activation in cell lines, in murine models and in patients treated with JAK2 inhibitors. RNA interference and pharmacological studies show that JAK2-inhibitor-persistent cells remain dependent on JAK2 protein expression. Consequently, therapies that result in JAK2 degradation retain efficacy in persistent cells and may provide additional benefit to patients with JAK2-dependent malignancies treated with JAK2 inhibitors.
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DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Decision curve analysis is a novel method for evaluating diagnostic tests, prediction models and molecular markers. It combines the mathematical simplicity of accuracy measures, such as sensitivity ...and specificity, with the clinical applicability of decision analytic approaches. Most critically, decision curve analysis can be applied directly to a data set, and does not require the sort of external data on costs, benefits and preferences typically required by traditional decision analytic techniques.
In this paper we present several extensions to decision curve analysis including correction for overfit, confidence intervals, application to censored data (including competing risk) and calculation of decision curves directly from predicted probabilities. All of these extensions are based on straightforward methods that have previously been described in the literature for application to analogous statistical techniques.
Simulation studies showed that repeated 10-fold crossvalidation provided the best method for correcting a decision curve for overfit. The method for applying decision curves to censored data had little bias and coverage was excellent; for competing risk, decision curves were appropriately affected by the incidence of the competing risk and the association between the competing risk and the predictor of interest. Calculation of decision curves directly from predicted probabilities led to a smoothing of the decision curve.
Decision curve analysis can be easily extended to many of the applications common to performance measures for prediction models. Software to implement decision curve analysis is provided.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Intratumor heterogeneity is a major clinical problem because tumor cell subtypes display variable sensitivity to therapeutics and may play different roles in progression. We previously characterized ...2 cell populations in human breast tumors with distinct properties: CD44+CD24- cells that have stem cell-like characteristics, and CD44-CD24+ cells that resemble more differentiated breast cancer cells. Here we identified 15 genes required for cell growth or proliferation in CD44+CD24- human breast cancer cells in a large-scale loss-of-function screen and found that inhibition of several of these (IL6, PTGIS, HAS1, CXCL3, and PFKFB3) reduced Stat3 activation. We found that the IL-6/JAK2/Stat3 pathway was preferentially active in CD44+CD24- breast cancer cells compared with other tumor cell types, and inhibition of JAK2 decreased their number and blocked growth of xenografts. Our results highlight the differences between distinct breast cancer cell types and identify targets such as JAK2 and Stat3 that may lead to more specific and effective breast cancer therapies.
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