A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease.

The study of de novo point mutations (new germline mutations arising from the gametes of the parents) remained largely static until the arrival of next-generation sequencing technologies, which made both whole-exome sequencing (WES) and whole-genome sequencing (WGS) feasible in practical terms. Single nucleotide polymorphism genotyping arrays have been used to identify de novo copy-number variants in a number of common neurodevelopmental conditions such as schizophrenia and autism. By contrast, as point mutations and microlesions occurring de novo are refractory to analysis by these microarray-based methods, little was known about either their frequency or impact upon neurodevelopmental disease, until the advent of WES. De novo point mutations have recently been implicated in schizophrenia, autism and mental retardation through the WES of case-parent trios. Taken together, these findings strengthen the hypothesis that the occurrence of de novo mutations could account for the high prevalence of such diseases that are associated with a marked reduction in fecundity. De novo point mutations are also known to be responsible for many sporadic cases of rare dominant mendelian disorders such as Kabuki syndrome, Schinzel-Giedion syndrome and Bohring-Opitz syndrome. These disorders share a common feature in that they are all characterized by intellectual disability. In summary, recent WES studies of neurodevelopmental and neuropsychiatric disease have provided new insights into the role of de novo mutations in these disorders. Our knowledge of de novo mutations is likely to be further accelerated by WGS. However, the collection of case-parent trios will be a prerequisite for such studies. This review aims to discuss recent developments in the study of de novo mutations made possible by technological advances in DNA sequencing.

Integrating next-generation sequencing into the diagnostic testing of inherited cancer predisposition.

The clinical application of next-generation sequencing (NGS) as a diagnostic tool has become increasingly evident. The coupling of NGS technologies with new genomic sequence enrichment methods has made the sequencing of panels of target genes technically feasible, at the same time as making such an approach cost-effective for diagnostic applications. In this article, we discuss recent studies that have applied NGS in the diagnostic setting in relation to hereditary cancer.

Trastuzumab and beyond: sequencing cancer genomes and predicting molecular networks.

Life diversity can now be clearly explored with the next-generation DNA sequencing technology, allowing the discovery of genetic variants among individuals, patients and tumors. However, beyond causal mutations catalog completion, systems medicine is essential to link genotype to phenotypic cancer diversity towards personalized medicine. Despite advances with traditional single genes molecular research, including rare mutations in BRCA1/2 and CDH1 for primary prevention and trastuzumab for treating HER2-overexpressing breast and gastric tumors, overall, treatment failure and death rates are still alarmingly high. Revolution in sequencing reveals that, now both a huge number and widespread variability of driver mutations, including single-nucleotide polymorphisms, genomic rearrangements and copy-number changes involved in breast cancer development. All these genetic alterations result in a heterogeneous deregulation of signaling pathways, including EGFR, HER2, VEGF, Wnt/Notch, TGF and others.Cancer initiation, progression and metastases are driven by complex molecular networks rather than linear genotype-phenotype relationship. Therefore, clinical expectations by traditional molecular research strategies targeting single genes and single signaling pathways are likely minimal. This review discusses the necessity of molecular networks modeling to understand complex gene-gene, protein-protein and gene-environment interactions. Moreover, the potential of systems clinico-biological approaches to predict intracellular signaling pathways components networks and cancer heterogeneous cells within an individual tumor is described. A flowchart specific for three steps in cancer evolution separately tumorigenesis, early-stage and advanced-stage breast cancer is presented. Using reverse engineering starting with the integration of available established clinical, environmental, treatment and oncological outcomes (survival and death) data and then the still incomplete but progressively accumulating genotypic data into computational networks modeling may lead to bionetworks-based discovery of robust biomarkers and highly effective cancer drugs targets.

Pathological serosa and node-based classification accurately predicts gastric cancer recurrence risk and outcome, and determines potential and limitation of a Japanese-style extensive surgery for Western patients: a prospective with quality control 10-year follow-up study.

UICC classification accurately predicts overall survival but not recurrence-risk. We report here data of overall and first site-specific recurrence following curative surgery useful for the development of recurrence-oriented preventive target therapies. Patients who underwent resection for gastric cancer were stratified according to curability of surgery [curative (R0) vs non-curative resection], extent of surgery [limited (D1) vs extended (D2) node dissection] and pathological nodal/serosal status. The intent-to-treat principle, log-rank test and Cox regression analysis were used for statistical analysis of time-to-event (recurrence, death) endpoints. Curative resection only produced a chance of cure whereas survival was very poor following non-curative resection (P < 0.0001). For D2 R0 subgroup of patients, a pathological serosa and a node state-based classification into three groups, proved to be of clinical implication. Risk of recurrence after a median follow-up of 92 months was low among patients with both serosa and node-negative cancer (first group; 11%), moderate among those with either serosa or node-positive cancer (second group; 53%) and very high among those with both serosa and node-positive cancer (third group; 83%). In multivariate analysis, the relative risks of recurrence and death from gastric cancer among patients in the second and third groups, as compared to those in the first, were 7.07 (95% CI, 2.36-21.17; P = 0.0002) and 16.19 (95% CI, 5.76-45.54; P < 0.0001) respectively. First site-specific recurrence analysis revealed: low rate of loco-regional recurrence alone (12%), serosa state determinant factor of the site-recurrence (peritoneal for serosa-positive and haematogenous for serosa-negative cancers) and dramatic increase of all types of recurrence by the presence of nodal metastases. Our findings demonstrate that a pathological serosa- and node-based classification is very simple and predicts accurately site-specific recurrence-risks. Furthermore they reveal that risk of recurrence following curative D2 surgery alone is low for serosa- and node-negative cancers, but very high in serosa- and node-positive cancers suggesting the need for new therapeutic strategies in this subgroup of patients.

Distal gastric cancer and extensive surgery: a new evaluation method based on the study of the status of residual lymph nodes after limited surgery.

BACKGROUND: Curative resection (R0) is the treatment of choice for distal gastric cancer, but it is unclear whether this operation should include a total gastrectomy (TG) with splenectomy and extended (D2) lymph node dissection. A new concept was developed based on the fact that residual metastatic lymph nodes after a limited (D1) subtotal gastrectomy (SG) may be the source of fatal relapse. We conducted a prospective study on patients who had undergone a D2 TG to evaluate whether certain stations left behind after a D1 SG contain metastasis. METHODS: We studied 1207 nodes obtained from 35 eligible patients who underwent a TG within 2 years. Of these patients, 29 fulfilled the criterion for a D2 dissection with curative potential. Numbers of retrieved and tumor-containing nodes by each station according to the Japanese Research Society for Gastric Cancer were documented prospectively in a standardized protocol. All lymph nodes were studied in sections smaller than 2 mm, but emphasis was given to the study of nodes from stations 1 and 2 (paracardial right and left), station 10 (splenic hilum), and stations 7 through 12 (around celiac axis, and in hepatoduodenal ligament) that can be dissected with a TG, splenectomy, and D2 dissection, respectively. For quality control of D2 dissection, the numbers of nodes retrieved by each compartment II nodal station (7-12) documented by a pathologist were used and compared with proposed reference values. Long-term survival and cumulative risk of relapse were calculated in terms of lymph node status and presence of metastasis in compartment II nodes. RESULTS: A mean total node yield of 37.4 from stations 1-12 and 11.4 from compartment II (stations 7-12) was obtained from 29 patients who had a D2 TG with curative intent. A substantial variation in node yields was found, and sometimes several stations contained no lymph nodes, which suggested an important cause of noncompliance (no yield of lymph nodes detected by the pathologist from that indicated for dissection stations) and difficulties for quality control. No positive node was detected in stations 1, 2, and 10 among patients who had a curative TG with splenectomy. However, substantially high was the incidence of metastasis in compartment II nodes, which was detected in one third of patients with node-positive disease. After 10 years of follow-up, overall survival and relapse rates among R0 D2 patients with negative compartment II nodes (pN0/pN1 disease) were 47% and 44%, respectively. CONCLUSIONS: Our results suggest the necessity of D2 dissection, but not of TG with splenectomy, to achieve an R0 resection for patients with distal gastric carcinoma. A large prospective study based on our protocol and findings may clarify whether a D2 R0 resection would result in a survival benefit.

Current status and future perspectives in gastric cancer management.

Gastric cancer is still a major health problem and a leading cause of cancer mortality despite a worldwide decline in incidence. Environmental and Helicobacter pylori (Hp) acting early in life in a multistep and multifactorial process may cause intestinal type carcinomas, whereas genetic abnormalities are related more to the diffuse type of disease. Primarily due to early detection of the disease, the results of treatment for gastric cancer have improved in Japan, Korea and several specialized Western centres. Surgery offers excellent long-term survival results for early gastric cancer (EGC). Advances in diagnostic and treatment technology have contributed to a trend towards minimal invasive surgery such as endoscopic mucosal resection (EMR) and laparoscopic surgery for selected mucosal cancers. In the Western world, however, more than 80% of patients at diagnosis have an advanced gastric cancer with a poor prognosis. The aim of surgery is complete removal of the tumour (UICC R0-resection), which is known to be the only proven, effective treatment modality and the most important treatment-related prognostic factor. Gastrectomy with preservation of the spleen and pancreas in most cases is the standard procedure. However, at present there is no consensus about the optimal extent of lymph-node dissection. The hypothesis that extended (D2) lymph-node dissection leads to improved survival has not been confirmed in randomized trials. Results from specialized centres and ongoing multi-institutional randomized trials, however, indicate that D2 dissection, with preservation of the spleen and pancreas, can be performed with the same safety as a D1 dissection. Furthermore, in 50% of patients with node-positive disease, the extraperigastric N2 nodes are involved (N2 disease) and thus an R0-resection is achievable only by a D2 node dissection resulting in a 5-year survival of about 30% for such patients. However, even after a D2 node dissection with curative potential, disease recurs in two-thirds of patients with locally advanced gastric cancer (LAGC) and is rapidly fatal. The need for an adjuvant treatment is obvious, but at present there is no such treatment of proven effectiveness. Promising results with preoperative chemotherapy, which increases the R0-resection rate, and intra-or early postoperative intraperitoneal chemohyperthermia to prevent peritoneal dissemination have been reported. However, randomized trials are necessary before these combined treatments become widely accepted. Present data indicate that the treatment of gastric cancer has become more and more sophisticated with a tailored therapy for individual cases. Treatment includes a broad spectrum of therapeutic options from EMR for selected mucosal cancers to aggressive combined treatment for LAGC. Precise knowledge of patterns of recurrence and metastases, critical evaluation of clinicopathologic variables, integration of high technology into diagnosis to predict accurately pre-treatment staging, and the surgeon's ability to perform minimally invasive surgery and D2 node dissection technique are necessary for an appropriate treatment option. All these prerequisites are best ensured by management in experienced surgical oncology units.