Singapore General Hospital

BACKGROUND: A worldwide outbreak of severe acute respiratory syndrome (SARS) has been associated with exposures originating from a single ill health care worker from Guangdong Province, China. We conducted studies to identify the etiologic agent of this outbreak. METHODS: We received clinical specimens from patients in seven countries and tested them, using virus-isolation techniques, electron-microscopical and histologic studies, and molecular and serologic assays, in an attempt to identify a wide range of potential pathogens. RESULTS: None of the previously described respiratory pathogens were consistently identified. However, a novel coronavirus was isolated from patients who met the case definition of SARS. Cytopathological features were noted in Vero E6 cells inoculated with a throat-swab specimen. Electron-microscopical examination revealed ultrastructural features characteristic of coronaviruses. Immunohistochemical and immunofluorescence staining revealed reactivity with group I coronavirus polyclonal antibodies. Consensus coronavirus primers designed to amplify a fragment of the polymerase gene by reverse transcription-polymerase chain reaction (RT-PCR) were used to obtain a sequence that clearly identified the isolate as a unique coronavirus only distantly related to previously sequenced coronaviruses. With specific diagnostic RT-PCR primers we identified several identical nucleotide sequences in 12 patients from several locations, a finding consistent with a point-source outbreak. Indirect fluorescence antibody tests and enzyme-linked immunosorbent assays made with the new isolate have been used to demonstrate a virus-specific serologic response. This virus may never before have circulated in the U.S. population. CONCLUSIONS: A novel coronavirus is associated with this outbreak, and the evidence indicates that this virus has an etiologic role in SARS. Because of the death of Dr. Carlo Urbani, we propose that our first isolate be named the Urbani strain of SARS-associated coronavirus.

Abstract Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature 1 . Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium 2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses 3–15 , enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated—but distinct—DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.

Abstract Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale 1–3 . Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter 4 ; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation 5,6 ; analyses timings and patterns of tumour evolution 7 ; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity 8,9 ; and evaluates a range of more-specialized features of cancer genomes 8,10–18 .

Importance: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019 and has spread globally with sustained human-to-human transmission outside China. Objective: To report the initial experience in Singapore with the epidemiologic investigation of this outbreak, clinical features, and management. Design, Setting, and Participants: Descriptive case series of the first 18 patients diagnosed with polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection at 4 hospitals in Singapore from January 23 to February 3, 2020; final follow-up date was February 25, 2020. Exposures: Confirmed SARS-CoV-2 infection. Main Outcomes and Measures: Clinical, laboratory, and radiologic data were collected, including PCR cycle threshold values from nasopharyngeal swabs and viral shedding in blood, urine, and stool. Clinical course was summarized, including requirement for supplemental oxygen and intensive care and use of empirical treatment with lopinavir-ritonavir. Results: Among the 18 hospitalized patients with PCR-confirmed SARS-CoV-2 infection (median age, 47 years; 9 [50%] women), clinical presentation was an upper respiratory tract infection in 12 (67%), and viral shedding from the nasopharynx was prolonged for 7 days or longer among 15 (83%). Six individuals (33%) required supplemental oxygen; of these, 2 required intensive care. There were no deaths. Virus was detectable in the stool (4/8 [50%]) and blood (1/12 [8%]) by PCR but not in urine. Five individuals requiring supplemental oxygen were treated with lopinavir-ritonavir. For 3 of the 5 patients, fever resolved and supplemental oxygen requirement was reduced within 3 days, whereas 2 deteriorated with progressive respiratory failure. Four of the 5 patients treated with lopinavir-ritonavir developed nausea, vomiting, and/or diarrhea, and 3 developed abnormal liver function test results. Conclusions and Relevance: Among the first 18 patients diagnosed with SARS-CoV-2 infection in Singapore, clinical presentation was frequently a mild respiratory tract infection. Some patients required supplemental oxygen and had variable clinical outcomes following treatment with an antiretroviral agent.

BACKGROUND: Patients with neutropenia resulting from chemotherapy for acute myelogenous leukemia or the myelodysplastic syndrome are at high risk for difficult-to-treat and often fatal invasive fungal infections. METHODS: In this randomized, multicenter study involving evaluators who were unaware of treatment assignments, we compared the efficacy and safety of posaconazole with those of fluconazole or itraconazole as prophylaxis for patients with prolonged neutropenia. Patients received prophylaxis with each cycle of chemotherapy until recovery from neutropenia and complete remission, until occurrence of an invasive fungal infection, or for up to 12 weeks, whichever came first. We compared the incidence of proven or probable invasive fungal infections during treatment (the primary end point) between the posaconazole and fluconazole or itraconazole groups; death from any cause and time to death were secondary end points. RESULTS: A total of 304 patients were randomly assigned to receive posaconazole, and 298 patients were randomly assigned to receive fluconazole (240) or itraconazole (58). Proven or probable invasive fungal infections were reported in 7 patients (2%) in the posaconazole group and 25 patients (8%) in the fluconazole or itraconazole group (absolute reduction in the posaconazole group, -6%; 95% confidence interval, -9.7 to -2.5%; P<0.001), fulfilling statistical criteria for superiority. Significantly fewer patients in the posaconazole group had invasive aspergillosis (2 [1%] vs. 20 [7%], P<0.001). Survival was significantly longer among recipients of posaconazole than among recipients of fluconazole or itraconazole (P=0.04). Serious adverse events possibly or probably related to treatment were reported by 19 patients (6%) in the posaconazole group and 6 patients (2%) in the fluconazole or itraconazole group (P=0.01). The most common treatment-related adverse events in both groups were gastrointestinal tract disturbances. CONCLUSIONS: In patients undergoing chemotherapy for acute myelogenous leukemia or the myelodysplastic syndrome, posaconazole prevented invasive fungal infections more effectively than did either fluconazole or itraconazole and improved overall survival. There were more serious adverse events possibly or probably related to treatment in the posaconazole group. (ClinicalTrials.gov number, NCT00044486 [ClinicalTrials.gov].).

BACKGROUND AND METHODS: In preliminary trials, lamivudine, an oral nucleoside analogue, has shown promise for the treatment of chronic hepatitis B. We conducted a one-year, double-blind trial of lamivudine in 358 Chinese patients with chronic hepatitis B. The patients were randomly assigned to receive 25 mg of lamivudine (142 patients), 100 mg of lamivudine (143), or placebo (73) orally once daily. The patients underwent liver biopsies before entering the study and after completing the assigned treatment regimen. The primary end point was a reduction of at least two points in the Knodell necroinflammatory score. RESULTS: Hepatic necroinflammatory activity improved by two points or more in 56 percent of the patients receiving 100 mg of lamivudine, 49 percent of those receiving 25 mg of lamivudine, and 25 percent of those receiving placebo (P<0.001 and P=0.001, respectively, for the comparisons of lamivudine treatment with placebo). Necroinflammatory activity worsened in 7 percent of the patients receiving 100 mg of lamivudine, 8 percent of those receiving 25 mg, and 26 percent of those receiving placebo. The 100-mg dose of lamivudine was associated with a reduced progression of fibrosis (P=0.01 for the comparison with placebo) and with the highest rate of hepatitis B e antigen (HBeAg) seroconversion (loss of HBeAg, development of antibody to HBeAg, and undetectable HBV DNA) (16 percent), the greatest suppression of HBV DNA (98 percent reduction at week 52 as compared with the base-line value), and the highest rate of sustained normalization of alanine aminotransferase levels (72 percent). Ninety-six percent of the patients completed the study. The incidence of adverse events was similar in all groups, and there were few serious events. CONCLUSIONS: In a one-year study, lamivudine was associated with substantial histologic improvement in many patients with chronic hepatitis B. A daily dose of 100 mg was more effective than a daily dose of 25 mg.

BACKGROUND: Treatment with dasatinib, a highly potent BCR-ABL kinase inhibitor, has resulted in high rates of complete cytogenetic response and progression-free survival among patients with chronic myeloid leukemia (CML) in the chronic phase, after failure of imatinib treatment. We assessed the efficacy and safety of dasatinib, as compared with imatinib, for the first-line treatment of chronic-phase CML. METHODS: In a multinational study, 519 patients with newly diagnosed chronic-phase CML were randomly assigned to receive dasatinib at a dose of 100 mg once daily (259 patients) or imatinib at a dose of 400 mg once daily (260 patients). The primary end point was complete cytogenetic response by 12 months, confirmed on two consecutive assessments at least 28 days apart. Secondary end points, including major molecular response, were tested at a significance level of 0.0001 to adjust for multiple comparisons. RESULTS: After a minimum follow-up of 12 months, the rate of confirmed complete cytogenetic response was higher with dasatinib than with imatinib (77% vs. 66%, P=0.007), as was the rate of complete cytogenetic response observed on at least one assessment (83% vs. 72%, P=0.001). The rate of major molecular response was higher with dasatinib than with imatinib (46% vs. 28%, P<0.0001), and responses were achieved in a shorter time with dasatinib (P<0.0001). Progression to the accelerated or blastic phase of CML occurred in 5 patients who were receiving dasatinib (1.9%) and in 9 patients who were receiving imatinib (3.5%). The safety profiles of the two treatments were similar. CONCLUSIONS: Dasatinib, administered once daily, as compared with imatinib, administered once daily, induced significantly higher and faster rates of complete cytogenetic response and major molecular response. Since achieving complete cytogenetic response within 12 months has been associated with better long-term, progression-free survival, dasatinib may improve the long-term outcomes among patients with newly diagnosed chronic-phase CML. (ClinicalTrials.gov number, NCT00481247.)

OBJECTIVE: Early operative debridement is a major determinant of outcome in necrotizing fasciitis. However, early recognition is difficult clinically. We aimed to develop a novel diagnostic scoring system for distinguishing necrotizing fasciitis from other soft tissue infections based on laboratory tests routinely performed for the evaluation of severe soft tissue infections: the Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC) score. DESIGN: Retrospective observational study of patients divided into a developmental cohort (n = 314) and validation cohort (n = 140) SETTING: Two teaching tertiary care hospitals. PATIENTS: One hundred forty-five patients with necrotizing fasciitis and 309 patients with severe cellulitis or abscesses admitted to the participating hospitals. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The developmental cohort consisted of 89 consecutive patients admitted for necrotizing fasciitis. Control patients (n = 225) were randomly selected from patients admitted with severe cellulitis or abscesses during the same period. Hematologic and biochemical results done on admission were converted into categorical variables for analysis. Univariate and multivariate logistic regression was used to select significant predictors. Total white cell count, hemoglobin, sodium, glucose, serum creatinine, and C-reactive protein were selected. The LRINEC score was constructed by converting into integer the regression coefficients of independently predictive factors in the multiple logistic regression model for diagnosing necrotizing fasciitis. The cutoff value for the LRINEC score was 6 points with a positive predictive value of 92.0% and negative predictive value of 96.0%. Model performance was very good (Hosmer-Lemeshow statistic, p =.910); area under the receiver operating characteristic curve was 0.980 and 0.976 in the developmental and validation cohorts, respectively. CONCLUSIONS: The LRINEC score is a robust score capable of detecting even clinically early cases of necrotizing fasciitis. The variables used are routinely measured to assess severe soft tissue infections. Patients with a LRINEC score of > or = 6 should be carefully evaluated for the presence of necrotizing fasciitis.

BACKGROUND: Current treatments for chronic hepatitis B are suboptimal. In the search for improved therapies, we compared the efficacy and safety of pegylated interferon alfa plus lamivudine, pegylated interferon alfa without lamivudine, and lamivudine alone for the treatment of hepatitis B e antigen (HBeAg)-positive chronic hepatitis B. METHODS: A total of 814 patients with HBeAg-positive chronic hepatitis B received either peginterferon alfa-2a (180 microg once weekly) plus oral placebo, peginterferon alfa-2a plus lamivudine (100 mg daily), or lamivudine alone. The majority of patients in the study were Asian (87 percent). Most patients were infected with hepatitis B virus (HBV) genotype B or C. Patients were treated for 48 weeks and followed for an additional 24 weeks. RESULTS: After 24 weeks of follow-up, significantly more patients who received peginterferon alfa-2a monotherapy or peginterferon alfa-2a plus lamivudine than those who received lamivudine monotherapy had HBeAg seroconversion (32 percent vs. 19 percent [P<0.001] and 27 percent vs. 19 percent [P=0.02], respectively) or HBV DNA levels below 100,000 copies per milliliter (32 percent vs. 22 percent [P=0.01] and 34 percent vs. 22 percent [P=0.003], respectively). Sixteen patients receiving peginterferon alfa-2a (alone or in combination) had hepatitis B surface antigen (HBsAg) seroconversion, as compared with 0 in the group receiving lamivudine alone (P=0.001). The most common adverse events were those known to occur with therapies based on interferon alfa. Serious adverse events occurred in 4 percent, 6 percent, and 2 percent of patients receiving peginterferon alfa-2a monotherapy, combination therapy, and lamivudine monotherapy, respectively. Two patients receiving lamivudine monotherapy had irreversible liver failure after the cessation of treatment--one underwent liver transplantation, and the other died. CONCLUSIONS: In patients with HBeAg-positive chronic hepatitis B, peginterferon alfa-2a offers superior efficacy over lamivudine, on the basis of HBeAg seroconversion, HBV DNA suppression, and HBsAg seroconversion.

Chronic kidney disease is a progressive disease with no cure and high morbidity and mortality that occurs commonly in the general adult population, especially in people with diabetes and hypertension. Preservation of kidney function can improve outcomes and can be achieved through non-pharmacological strategies (eg, dietary and lifestyle adjustments) and chronic kidney disease-targeted and kidney disease-specific pharmacological interventions. A plant-dominant, low-protein, and low-salt diet might help to mitigate glomerular hyperfiltration and preserve renal function for longer, possibly while also leading to favourable alterations in acid-base homoeostasis and in the gut microbiome. Pharmacotherapies that alter intrarenal haemodynamics (eg, renin-angiotensin-aldosterone pathway modulators and SGLT2 [SLC5A2] inhibitors) can preserve kidney function by reducing intraglomerular pressure independently of blood pressure and glucose control, whereas other novel agents (eg, non-steroidal mineralocorticoid receptor antagonists) might protect the kidney through anti-inflammatory or antifibrotic mechanisms. Some glomerular and cystic kidney diseases might benefit from disease-specific therapies. Managing chronic kidney disease-associated cardiovascular risk, minimising the risk of infection, and preventing acute kidney injury are crucial interventions for these patients, given the high burden of complications, associated morbidity and mortality, and the role of non-conventional risk factors in chronic kidney disease. When renal replacement therapy becomes inevitable, an incremental transition to dialysis can be considered and has been proposed to possibly preserve residual kidney function longer. There are similarities and distinctions between kidney-preserving care and supportive care. Additional studies of dietary and pharmacological interventions and development of innovative strategies are necessary to ensure optimal kidney-preserving care and to achieve greater longevity and better health-related quality of life for these patients.

A paramyxovirus virus termed Nipah virus has been identified as the etiologic agent of an outbreak of severe encephalitis in people with close contact exposure to pigs in Malaysia and Singapore. The outbreak was first noted in late September 1998 and by mid-June 1999, more than 265 encephalitis cases, including 105 deaths, had been reported in Malaysia, and 11 cases of encephalitis or respiratory illness with one death had been reported in Singapore. Electron microscopic, serologic, and genetic studies indicate that this virus belongs to the family Paramyxoviridae and is most closely related to the recently discovered Hendra virus. We suggest that these two viruses are representative of a new genus within the family Paramyxoviridae. Like Hendra virus, Nipah virus is unusual among the paramyxoviruses in its ability to infect and cause potentially fatal disease in a number of host species, including humans.

Preface to the Second Edition Preface to the First Edition 1. Basic Design Considerations 2. The Normal Distribution 3. Comparing Independent Groups for Binary, Ordered Categorical and Continuous Data 4. Comparing Paired Groups for Binary, Ordered Categorical and Continuous Outcomes 5. Demonstrating Equivalence 6. Confidence Intervals 7. Post-Marketing Surveillance 8. The Correlation Coefficient 9. Comparing Two Survival Curves 10. Phase II Trials 11. Observer Agreement Studies 12. Randomization Cumalative References Author Index Subject Index

The concept of 'idiopathic' Parkinson's disease (PD) as a single entity has been challenged with the identification of several clinical subtypes, pathogenic genes and putative causative environmental agents. In addition to classic motor symptoms, non-motor manifestations (such as rapid eye movement sleep disorder, anosmia, constipation and depression) appear at prodromic/premotor stage and evolve, along with cognitive impairment and dysautonomia, as the disease progresses, often dominating the advanced stages of the disease. The key molecular pathogenic mechanisms include α-synuclein misfolding and aggregation, mitochondrial dysfunction, impairment of protein clearance (associated with deficient ubiquitin-proteasome and autophagy-lysosomal systems), neuroinflammation and oxidative stress. The involvement of dopaminergic as well as noradrenergic, glutamatergic, serotonergic and adenosine pathways provide insights into the rich and variable clinical phenomenology associated with PD and the possibility of alternative therapeutic approaches beyond traditional dopamine replacement therapies.One of the biggest challenges in the development of potential neuroprotective therapies has been the lack of reliable and sensitive biomarkers of progression. Immunotherapies such as the use of vaccination or monoclonal antibodies directed against aggregated, toxic α-synuclein.as well as anti-aggregation or protein clearance strategies are currently investigated in clinical trials. The application of glucagon-like peptide one receptor agonists, specific PD gene target agents (such as GBA or LRRK2 modifiers) and other potential disease modifying drugs provide cautious optimism that more effective therapies are on the horizon. Emerging therapies, such as new symptomatic drugs, innovative drug delivery systems and novel surgical interventions give hope to patients with PD about their future outcomes and prognosis.

Abstract Cancer develops through a process of somatic evolution 1,2 . Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes 3 . Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) 4 , we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.

The classification of breast tumours continues to evolve, with the integration of new knowledge from research rapidly being translated into clinical practice. Major changes are shown in Table 1. In this volume of the World Health Organization (WHO) classification of tumours series’ fifth edition, which is an update of the fourth-edition breast tumours volume published in 2012,1 the descriptions of breast tumours follow the familiar systematic approach of previous volumes, with the content now organised in sequence from benign epithelial proliferations and precursors, through benign neoplasms, to in-situ and invasive breast cancer, followed by mesenchymal and haematolymphoid neoplasms, tumours of the male breast, and genetic tumour syndromes. A brief introduction prefaces the content pertaining to each major tumour group, to provide a general perspective and highlight key modifications. In the current volume, information on epidemiology, imaging, clinical features, grading, staging, molecular testing for hormone receptors and ERBB2 (HER2), post-therapy effects, core needle biopsy and fine-needle aspiration considerations, molecular pathology and genomics is now presented in the general overview that introduces the sections on invasive breast carcinoma (IBC), rather than in the first chapter as in the previous edition. Core biopsy diagnosis, an important preoperative tool, is addressed across multiple sections. The importance of molecular pathology in aiding diagnosis is recognised, with a specific subsection for each tumour type. Essential and desirable diagnostic criteria are also included, to reinforce key histopathological clues. Invasive breast cancers are still organised into chapters by their morphological subtypes, which remain clinically relevant. However, as the majority of cases are of no special type (NST), additional prognostic and predictive factors that aid significantly in treatment and outcome stratification are also focused on and reviewed in more depth in the invasive carcinoma overview section. The overview acknowledges the treatment-relevant subtypes of invasive carcinoma [based on oestrogen receptor (ER) and HER2 status], and new data are added to support the differences in pathogenesis, treatment response and prognosis of these clinically relevant groupings. Updates in defining and testing hormone receptor and HER2 status are presented, and there are updated sections on additional assays and parameters used in prediction and prognosis (including proliferation markers, androgen receptor, response to neoadjuvant therapy, gene expression assays, tumour-infiltrating lymphocytes (TILs), prognostic scoring systems, and programmed death-ligand 1 testing). The overview section of the molecular classification of breast cancers is also updated to include more recent data supporting classification schemes that have prognostic associations (including the intrinsic subtypes, integrative cluster subgroups, triple-negative subclassifications, and mutation-based profiling). Standard prognostic indicators, such as tumour size, lymph node status, and Nottingham grade, continue to be highly relevant. An important change in this edition is the conversion of mitotic count from the traditional denominator of 10 high-power fields to a defined area expressed in mm2. This serves to standardise the true area over which mitoses are enumerated, because different microscopes have high-power fields of different sizes. This change will also be helpful for anyone reporting using digital systems. The score thresholds for mitotic counts based on the diameter of the high-power field and its corresponding area are shown in Table 2. Updates to the ‘Invasive breast carcinoma, NST’ section include a revised definition of the mixed NST–special subtype (now expanded to include cases with 10–90% special subtype admixed with NST, with a recommendation to include parameters regarding both components). Classification of several patterns previously recognised as separate special rare subtypes have moved under the NST umbrella as ‘special morphological patterns’. Carcinomas previously classified as the special subtype ‘carcinoma with medullary features’ (including medullary carcinoma, atypical medullary carcinoma, and invasive carcinoma NST with medullary features) have suffered from poor interobserver reproducibility and overlap in features with carcinomas that have basal-like molecular profiles and carcinomas associated with BRCA1 mutations. In addition, the increasing affirmation of the prognostic importance of TILs in high-grade breast cancers in explaining their good prognosis, including high-grade cancers not meeting strict medullary criteria, reduces the requirement for discrete separation of these tumours, which exist along a morphological continuum. Therefore, for clinical purposes, it is now proposed to consider carcinomas with a medullary pattern as representing one end of the spectrum of the TIL-rich IBC-NSTs rather than a distinct morphological subtype, and to use the term ‘IBC-NST with medullary pattern’. In addition, oncocytic, lipid-rich, glycogen-rich clear cell, and sebaceous carcinomas, which are rarely encountered, are also now recognised as special patterns of NST along with carcinoma with osteoclast-like stromal giant cells, pleomorphic carcinoma, and choriocarcinomatous and melanotic patterns. Inflammatory, bilateral and non-synchronous breast carcinomas are also now recognised as distinct clinical presentations rather than special subtypes of breast cancer. As well as classic lobular carcinoma in situ (LCIS), the pleomorphic and florid subtypes are now recognised. Pleomorphic LCIS shows marked nuclear atypia, and may include apocrine features, whereas in florid LCIS there is marked distension of terminal duct lobular units or ducts, often forming a mass-like appearance. It is now recognised that some invasive lobular carcinomas may be associated with extracellular mucin production. Although neuroendocrine neoplasms (NENs) are allocated their own section, harmonised with those of other organ systems on the basis of a recent WHO workshop report,2 it must be emphasised that true primary neuroendocrine tumours (NETs) of the breast remain uncommon and poorly defined. According to the proposed consensus terminology, well-differentiated NETs broadly correspond to grade 1 (carcinoid-like) and grade 2 (atypical carcinoid-like) tumours (regarded as carcinomas in the breast), whereas poorly differentiated neuroendocrine carcinomas (NECs) are typified by small-cell and large-cell carcinoma. Many breast tumours that show varying degrees of neuroendocrine differentiation belong to recognised entities, such as hypercellular mucinous carcinoma and solid papillary carcinoma of both in-situ and invasive types. Small-cell NEC does arise in the breast, often admixed with invasive carcinoma NST. Large-cell NEC has been added as an entity arising in the breast, albeit encountered very rarely. For well-differentiated NETs resembling carcinoid or atypical carcinoid tumour, it is prudent to exclude metastasis from another site. It is recommended that the classification of breast tumours showing neuroendocrine expression be based on the recognisable morphological tumour type, such as invasive carcinoma NST, mucinous carcinoma, or solid papillary carcinoma.3 Because some degree of neuroendocrine expression is relatively common in invasive breast cancer NST, most breast cancers with neuroendocrine expression will ultimately be classified as invasive carcinoma NST with neuroendocrine differentiation. Only if neuroendocrine histological features and neuroendocrine marker expression are distinct or uniform enough to classify a cancer as one of the rare NETs or NECs of the breast should NEN terminology be used. NET or NEC of the breast are currently treated on the basis of standard breast cancer parameters (such as ER and HER2 status). The new WHO classification is not advocating routine evaluation for neuroendocrine markers in breast cancers. One important change in the classification of fibroepithelial tumours is the removal of well-differentiated liposarcoma as a histological criterion of malignancy in breast phyllodes tumours in the absence of additional supporting microscopic alterations. Evidence has emerged that these abnormal adipocyte populations residing within phyllodes tumours do not harbour the MDM2 aberrations that characterise well-differentiated liposarcomas elsewhere. In light of the consensus opinion that this heterologous element does not have metastatic potential, it was agreed that its presence alone should not warrant a malignant grade in phyllodes tumours unless there are other histological changes of malignancy. A new entity included in this volume is mucinous cystadenocarcinoma, a unique invasive malignancy with a relatively good prognosis, featuring luminal mucin and cytomorphology resembling pancreatobiliary and ovarian mucinous cystadenocarcinoma. The entity ‘tall cell carcinoma with reversed polarity’ is introduced in the section about rare and salivary gland-type tumours, as there have been multiple reports of this entity, previously termed ‘breast tumour resembling the tall cell variant of papillary thyroid carcinoma’ as well as ‘solid papillary carcinoma with reverse polarity’, with these descriptions united by the consistent finding of IDH2 and PIK3CA mutations.4 The new terminology of ‘tall cell carcinoma with reversed polarity’ incorporates portions of earlier terms used to describe this entity—‘tall cell’ and ‘reversed polarity’. This revised term was a consensus agreement achieved during the WHO Editorial Board Meeting. It was also felt that having ‘papillary thyroid carcinoma’ in the terminology may be confusing and misleading. Periductal stromal tumour is now considered to be a variant of phyllodes tumour. Mesenchymal tumours, haematolymphoid tumours and genetic tumour syndromes are covered in dedicated chapters in alignment with the approach being taken throughout this fifth edition of the series. Tumour classification is a dynamic process, integrating multiple sources of information that have emerged since the previous WHO update. Digital pathology, which is becoming widely available, may enable the application of new artificial intelligence and computer learning tools to refine breast and other tumour classifications that will ultimately facilitate appropriate therapy and accurate prognostication. No authors reported any conflicts of interest to the International Agency for Research on Cancer (IARC) that would affect their participation in forming the classification. The content of this article represents the personal views of the authors, and does not represent the views of the authors’ employers and associated institutions. Where authors are identified as personnel of the IARC/WHO, the authors alone are responsible for the views expressed in this article, and they do not necessarily represent the decisions, policy or views of the IARC/WHO. The authors are standing and expert members of the WHO Classification of Tumours Editorial Board, or the IARC Secretariat. This commentary is based on the introduction to tumours of the breast. All authors were involved in the conception of the article, writing the article, and reviewing the final version.

INTRODUCTION: The Asian Pacific Association for the Study of the Liver (APASL) convened an international working party on the management of hepatocellular carcinoma (HCC) in December 2008 to develop consensus recommendations. METHODS: The working party consisted of expert hepatologist, hepatobiliary surgeon, radiologist, and oncologist from Asian-Pacific region, who were requested to make drafts prior to the consensus meeting held at Bali, Indonesia on 4 December 2008. The quality of existing evidence and strength of recommendations were ranked from 1 (highest) to 5 (lowest) and from A (strongest) to D (weakest), respectively, according to the Oxford system of evidence-based approach for developing the consensus statements. RESULTS: Participants of the consensus meeting assessed the quality of cited studies and assigned grades to the recommendation statements. Finalized recommendations were presented at the fourth APASL single topic conference on viral-related HCC at Bali, Indonesia and approved by the participants of the conference.

Breast cancer is a heterogeneous disease with varied morphological appearances, molecular features, behavior, and response to therapy. Current routine clinical management of breast cancer relies on the availability of robust clinical and pathological prognostic and predictive factors to support clinical and patient decision making in which potentially suitable treatment options are increasingly available. One of the best-established prognostic factors in breast cancer is histological grade, which represents the morphological assessment of tumor biological characteristics and has been shown to be able to generate important information related to the clinical behavior of breast cancers. Genome-wide microarray-based expression profiling studies have unraveled several characteristics of breast cancer biology and have provided further evidence that the biological features captured by histological grade are important in determining tumor behavior. Also, expression profiling studies have generated clinically useful data that have significantly improved our understanding of the biology of breast cancer, and these studies are undergoing evaluation as improved prognostic and predictive tools in clinical practice. Clinical acceptance of these molecular assays will require them to be more than expensive surrogates of established traditional factors such as histological grade. It is essential that they provide additional prognostic or predictive information above and beyond that offered by current parameters. Here, we present an analysis of the validity of histological grade as a prognostic factor and a consensus view on the significance of histological grade and its role in breast cancer classification and staging systems in this era of emerging clinical use of molecular classifiers.

These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

Abstract Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters—fluke-positive CCAs (clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3′ untranslated region deletion as a mechanism of FGFR2 upregulation. Integration of noncoding promoter mutations with protein–DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores—mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics, and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer. Significance: Integrated whole-genome and epigenomic analysis of CCA on an international scale identifies new CCA driver genes, noncoding promoter mutations, and structural variants. CCA molecular landscapes differ radically by etiology, underscoring how distinct cancer subtypes in the same organ may arise through different extrinsic and intrinsic carcinogenic processes. Cancer Discov; 7(10); 1116–35. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 1047

Abstract A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes 1–7 . Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types 8 . Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions—as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2–7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and—in liver cancer—frequently activate the telomerase gene TERT . A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.