Key Points• This is the first study to validate the importance of NOTCH1 and SF3B1 gene mutations in the context of a randomized, prospective clinical trial.• Mutations in both genes are independent prognostic biomarkers, and therefore have clinical utility in the accurate risk-adapted stratification of CLL patients. Continuing Medical Education onlineThis activity has been planned and implemented in accordance with the Essential Areas and policies of the Accreditation Council for Continuing Medical Education through the joint sponsorship of Medscape, LLC and the American Society of Hematology. Medscape, LLC is accredited by the ACCME to provide continuing medical education for physicians. Medscape, LLC designates this Journal-based CME activity for a maximum of 1.0 AMA PRA Category 1 Credit(s) ™ . Physicians should claim only the credit commensurate with the extent of their participationin the activity. All other clinicians completing this activity will be issued a certificate of participation. To participate in this journal CME activity: (1) review the learning objectives and author disclosures; (2) study the education content; (3) take the post-test with a 70% minimum passing score and complete the evaluation at http://www.medscape.org/journal/blood; and (4) view/print certificate. For CME questions, see page 566. Disclosures Associate Editor John G. Gribben served as an advisor or consultant for Celgene and Roche and as a speaker or a member of a speakers bureau for Roche, Jensen, and Celgene. The authors and CME questions author Laurie Barclay, freelance writer and reviewer, Medscape, LLC, declare no competing financial interests. For personal use only. on May 9, 2018. by guest www.bloodjournal.org From Continuing Medical Education online Learning objectivesUpon completion of this activity, participants will be able to:1. Describe the frequency of NOTCH1 and SF3B1 mutations in patients with chronic lymphocytic leukemia (CLL), and their correlations with other genetic markers.2. Describe survival in CLL patients with NOTCH1 mutations, and the prognostic value of this mutation. 3. Describe survival in CLL patients with SF3B1 mutations, and the prognostic value of this mutation.

Cetuximab led to a significant increase in RR and OS in patients with KRAS/BRAF wild-type rectal cancer, but the primary end point of improved CR was not met.

The progressive elucidation of the molecular pathogenesis of cancer has fueled the rational development of targeted drugs for patient populations stratified by genetic characteristics. Here we discuss general challenges relating to molecular diagnostics and describe predictive biomarkers for personalized cancer medicine. We also highlight resistance mechanisms for epidermal growth factor receptor (EGFR) kinase inhibitors in lung cancer. We envisage a future requiring the use of longitudinal genome sequencing and other omics technologies alongside combinatorial treatment to overcome cellular and molecular heterogeneity and prevent resistance caused by clonal evolution.

Children with Down syndrome (DS) have a greatly increased risk of acute megakaryoblastic leukemia (AMKL) and acute lymphoblastic leukemia (ALL). Both DS-AMKL and the related transient myeloproliferative disorder (TMD) have GATA1 mutations as obligatory, early events. To identify mutations contributing to leukemogenesis in DS-ALL, we undertook sequencing of candidate genes, including IntroductionChildren with Down syndrome (DS), characterized by constitutional trisomy 21, have a 50-fold increased risk of developing acute leukemia in the first few years of life. 1,2 This comprises the normally extremely rare subtype acute megakaryoblastic leukemia (AMKL) as well as the common variety (B-cell precursor) of acute lymphoblastic leukemia (ALL). 2-4 Both DS-AMKL and the transient myeloproliferative disorder (TMD) that often precedes it are consistently associated with acquired mutations in the GATA1 gene. 5 Concordant GATA1 mutations in the blast cells of identical twins with TMD 6 and mutations in the neonatal blood spots of DS newborns 7 indicate that this is an early/prenatal event in DS leukemogenesis.Much less is known about the genetic events predisposing to DS-ALL. Candidate genes for activating mutations in DS-ALL include FLT3 and RAS, both mutated in high hyperdiploid ALL (with acquired trisomy 21), 8,9 PTPN11 and BRAF, mutated in B-cell precursor ALL. 10,11 An additional candidate is the JAK2 pseudokinase domain mutation JAK2⌬IREED, reported in a single case of DS-ALL. 12 A different JAK2 pseudokinase domain mutation, JAK2V617F, is frequently found in the myeloproliferative disorders (MPDs) and believed to be an initiating event. [13][14][15] Submicroscopic deletions that involve genes linked functionally to deregulation of cell cycling or B-cell differentiation were also implicated in the molecular pathogenesis of ALL. [16][17][18][19] In this study we undertook both sequencing of candidate genes and high-resolution singlenucleotide polymorphism (SNP) array analysis to identify genetic events associated with ALL in DS. Methods PatientsPatients' samples (Table S1, available on the Blood website; see the Supplemental Materials link at the top of the online article) were collected, informed consent was obtained in accordance with the Declaration of Helsinki, and the study was carried out with approval of the ethical review committee from all participating institutions. DNA was extracted from archival (frozen cell or cytogenetic-fixed pellet) leukemic samples. SequencingPrimers were designed to amplify the following candidate genes: FLT3 ITD, FLT3 kinase domain, KIT kinase domain, PTPN11, BRAF, NRAS, and KRAS (Table S2A). Exons 12 to 23 of the JAK2 gene were polymerase chain reaction (PCR)-amplified and sequenced using previously described primers. 13 All samples found to be mutated were PCR-amplified and sequenced in a second, independent experiment. Pyrosequencing was carried out in accordance to the manufacturer's instructions (Biotage AB, Uppsala, Sweden) using the primers shown in Table S2B. Ba/F3 prolifer...

Purpose: Mounting evidence supports the clinical significance of gene mutations and immunogenetic features in common mature B-cell malignancies.Experimental Design: We undertook a detailed characterization of the genetic background of splenic marginal zone lymphoma (SMZL), using targeted resequencing and explored potential clinical implications in a multinational cohort of 175 patients with SMZL.Results: We identified recurrent mutations in TP53 (16%), KLF2 (12%), NOTCH2 (10%), TNFAIP3 (7%), MLL2 (11%), MYD88 (7%), and ARID1A (6%), all genes known to be targeted by somatic mutation in SMZL. KLF2 mutations were early, clonal events, enriched in patients with del(7q) and IGHV1-2 Ã 04 B-cell receptor immunoglobulins, and were associated with a short median time to first treatment (0.12 vs. 1.11 years; P ¼ 0.01).In multivariate analysis, mutations in NOTCH2 [HR, 2.12; 95% confidence interval (CI), 1.02-4.4; P ¼ 0.044] and 100% germline IGHV gene identity (HR, 2.19; 95% CI, 1.05-4.55; P ¼ 0.036) were independent markers of short time to first treatment, whereas TP53 mutations were an independent marker of short overall survival (HR, 2.36; 95 % CI, 1.08-5.2; P ¼ 0.03). Conclusions:We identify key associations between gene mutations and clinical outcome, demonstrating for the first time that NOTCH2 and TP53 gene mutations are independent markers of reduced treatment-free and overall survival, respectively.

Background:Following chemo-radiotherapy (CCRT) for human papilloma virus positive (HPV+) locally advanced head and neck cancer, patients frequently undergo unnecessary neck dissection (ND) and/or repeated biopsies for abnormal PET-CT, which causes significant morbidity. We assessed the role of circulating HPV DNA in identifying ‘true’ residual disease.Methods:We prospectively recruited test (n=55) and validation (n=33) cohorts. HPV status was confirmed by E7 RT-PCR. We developed a novel amplicon-based next generation sequencing assay (HPV16-detect) to detect circulating HPV DNA. Circulating HPV DNA levels post-CCRT were correlated to disease response (PET-CT).Results:In pre-CCRT plasma, HPV-detect demonstrated 100% sensitivity and 93% specificity, and 90% sensitivity and 100% specificity for the test (27 HPV+) and validation (20 HPV+) cohorts, respectively. Thirty-six out of 37 patients (test and validation cohort) with complete samples-set had negative HPV-detect at end of treatment. Six patients underwent ND (3) and repeat primary site biopsies (3) for positive PET-CT but had no viable tumour. One patient had positive HPV-detect and positive PET-CT and liver biopsy, indicating 100% agreement for HPV-detect and residual cancer.Conclusions:We demonstrate that HPV16-detect is a highly sensitive and specific test for identification of HPV DNA in plasma at diagnosis. HPV DNA post-treatment correlates with clinical response.

SummaryMolecular testing for the BCR-ABL1 fusion gene by real time quantitative polymerase chain reaction (RT-qPCR) is the most sensitive routine approach for monitoring the response to therapy of patients with chronic myeloid leukaemia. In the context of tyrosine kinase inhibitor (TKI) therapy, the technique is most appropriate for patients who have achieved complete cytogenetic remission and can be used to define specific therapeutic milestones. To achieve this effectively, standardization of the laboratory procedures and the interpretation of results are essential. We present here consensus best practice guidelines for RT-qPCR testing, data interpretation and reporting that have been drawn up and agreed by a consortium of 21 testing laboratories in the United Kingdom and Ireland in accordance with the procedures of the UK Clinical Molecular Genetics Society.

Lung cancer diagnostics have progressed greatly in the previous decade. Development of molecular testing to identify an increasing number of potentially clinically actionable genetic variants, using smaller samples obtained via minimally invasive techniques, is a huge challenge. Tumour heterogeneity and cancer evolution in response to therapy means that repeat biopsies or circulating biomarkers are likely to be increasingly useful to adapt treatment as resistance develops. We highlight some of the current challenges faced in clinical practice for molecular testing of EGFR, ALK, and new biomarkers such as PDL1. Implementation of next generation sequencing platforms for molecular diagnostics in non-small-cell lung cancer is increasingly common, allowing testing of multiple genetic variants from a single sample. The use of next generation sequencing to recruit for molecularly stratified clinical trials is discussed in the context of the UK Stratified Medicine Programme and The UK National Lung Matrix Trial.