Classification and regression trees are machine-learning methods for constructing prediction models from data. The models are obtained by recursively partitioning the data space and fitting a simple prediction model within each partition. As a result, the partitioning can be represented graphically as a decision tree. Classification trees are designed for dependent variables that take a finite number of unordered values, with prediction error measured in terms of misclassification cost. Regression trees are for dependent variables that take continuous or ordered discrete values, with prediction error typically measured by the squared difference between the observed and predicted values. This article gives an introduction to the subject by reviewing some widely available algorithms and comparing their capabilities, strengths, and weakness in two examples. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 14-23 DOI: 10.1002/widm.8

This article is categorized under: 

Technologies > Classification
Technologies > Machine Learning
Technologies > Prediction
Technologies > Statistical Fundamentals

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Classification and regression trees

EASL-EORTC clinical practice guidelines : management of hepatocellular carcinoma

BackgroundSomatic mutations have the potential to encode “non-self” immunogenic antigens. We hypothesized that tumors with a large number of somatic mutations due to mismatch-repair defects may be susceptible to immune checkpoint blockade. MethodsWe conducted a phase 2 study to evaluate the clinical activity of pembrolizumab, an anti–programmed death 1 immune checkpoint inhibitor, in 41 patients with progressive metastatic carcinoma with or without mismatch-repair deficiency. Pembrolizumab was administered intravenously at a dose of 10 mg per kilogram of body weight every 14 days in patients with mismatch repair–deficient colorectal cancers, patients with mismatch repair–proficient colorectal cancers, and patients with mismatch repair–deficient cancers that were not colorectal. The coprimary end points were the immune-related objective response rate and the 20-week immune-related progression-free survival rate. ResultsThe immune-related objective response rate and immune-related progression-free survival ...

/pdf/pd-1-blockade-in-tumors-with-mismatch-repair-deficiency-1eb0ztv7j7.pdf

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

Background Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Results Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Conclusions Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.)

http://www.therenegadecell.com/wiki/images/0/0d/NEJM-2012-366%2810%29-883.pdf

Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.

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Cancer Genome Landscapes

The present invention provides antibodies which specifically bind to pancreatic adenocarcinoma upregulated factor (PAUF) protein and uses thereof

Antibody specifically binding to PAUF protein and use thereof

Prognostic value of tumor-to-parenchymal contrast enhancement ratio on portal venous-phase CT in pancreatic neuroendocrine neoplasms

Some clinical diagnoses such as sepsis, renal failure, metastatic cancer, house-bound lifestyle, and stroke are associated with worse prognosis after inhospital cardiac arrest (IHCA) [1-3]. But there are a few reports about chronic liver disease, Asian people, and the incidence of IHCA is rarely reported in the literature. The aim of this study was to evaluate the hospital mortality of adult patients who had experienced IHCA by underlying disease and the incidence of IHCA.

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Clinical outcome in patients who experienced inhospital cardiac arrest by underlying disease

Adenosquamous carcinoma is a rare histologic subtype of extrahepatic bile duct (EBD) carcinoma and limited information is available on its clinicopathologic characteristics. Twelve cases of adenosquamous carcinoma were collected from 3 institutions and their clinicopathologic characteristics were examined and compared with those of 176 EBD adenocarcinomas. The adenocarcinoma component was more often seen at the surface of the tumor (7 of 12 cases, 58%), while the squamous carcinoma component was slightly more frequent at the advanced edge (7 of 12 cases, 58%). Immunohistochemistry, available in 10 cases, revealed that S100A2 was positive in the squamous carcinoma component in all 10 cases (100%), while it was present in the adenocarcinoma component in only 2 of 10 cases (20%, chi-square test, p=0.001). S100A4 expression did not show any difference between the two components. Patients with adenosquamous carcinomas had worse survival (median survival, 11 months) than those with adenocarcinoma (median survival, 32 months; log-rank test, p=0.003). Patients with predominant squamous cell carcinoma component at the leading edge had worse survival than those without it. In conclusion, patients with adenosquamous carcinoma demonstrated worse survival than those with pure adenocarcinoma. S100A2 immunohistochemical staining may be helpful in detecting the squamous component.

Original Article Adenosquamous Carcinoma of Extrahepatic Bile Duct: Clinicopathologic Study of 12 Cases

Choledochal cyst has only rarely been encountered in association with pregnancy. The clinical manifestations are nonspecific and variable that makes it difficult to differentiate from physiologic changes in pregnancy. Consequently, diagnosis is often delayed until patients present with life-threatening complications. During pregnancy, symptoms of choledochal cyst may be developed by hormonal changes and the enlarged uterus. Because of the risk of fetal mortality and maternal morbidity, definitive surgical treatment should be delayed and step-by-step management should be carefully implemented to avoid complication until delivery. Herein, we report a case of enlarged, symptomatic choledochal cyst that developed in a 26-year-old pregnant woman. The temporal relationship between pregnancy and symptom development, as well as the biliary sludge formation in the enlarged cyst, suggest that the choledochal cyst was influenced by pregnancy. In order to buy time for fetal maturation, endoscopic ultrasonography-guided choledochoduodenostomy was performed for biliary decompression as a bridge to surgical excision.

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Seung-Mo Hong

Papers

Antibody specifically binding to PAUF protein and use thereof

Prognostic value of tumor-to-parenchymal contrast enhancement ratio on portal venous-phase CT in pancreatic neuroendocrine neoplasms

Clinical outcome in patients who experienced inhospital cardiac arrest by underlying disease

Original Article Adenosquamous Carcinoma of Extrahepatic Bile Duct: Clinicopathologic Study of 12 Cases

Symptomatic Choledochal Cyst in Association with Pregnancy Managed with EUS-guided Choledochoduodenostomy without Fluoroscopic Guidance