The Interlaboratory Robustness Of Next-Generation Sequencing (IRON) Study Phase II: Deep-Sequencing Analyses Of Hematological Malignancies Performed In 8,867 Cases By An International Network Involving 27 Laboratories

Introduction: Amplicon deep-sequencing using second-generation sequencing technology is an innovative molecular diagnostic technique and enables a highly-sensitive detection of mutations. As an international consortium we had investigated previously the robustness, precision, and reproducibility of 454 amplicon next-generation sequencing (NGS) across 10 laboratories from 8 countries (Leukemia, 2011;25:1840-8).

Aims: In Phase II of the study, we established distinct working groups for various hematological malignancies, i.e. acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), and multiple myeloma. Currently, 27 laboratories from 13 countries are part of this research consortium. In total, 74 gene targets were selected by the working groups and amplicons were developed for a NGS deep-sequencing assay (454 Life Sciences, Branford, CT). A data analysis pipeline was developed to standardize mutation interpretation both for accessing raw data (Roche Amplicon Variant Analyzer, 454 Life Sciences) and variant interpretation (Sequence Pilot, JSI Medical Systems, Kippenheim, Germany).

Results: We will report on the design, standardization, quality control aspects, landscape of mutations, as well as the prognostic and predictive utility of this assay in a cohort of 8,867 cases. Overall, 1,146 primer sequences were designed and tested. In detail, for example in AML, 924 cases had been screened for CEBPA mutations. RUNX1 mutations were analyzed in 1,888 cases applying the deep-sequencing read counts to study the stability of such mutations at relapse and their utility as a biomarker to detect residual disease. Analyses of DNMT3A (n=1,041) were focused to perform landscape investigations and to address the prognostic relevance. Additionally, this working group is focusing on TET2, ASXL1, and TP53 analyses. A novel prognostic model is being developed allowing stratification of AML into prognostic subgroups based on molecular markers only. In ALL, 1,124 pediatric and adult cases have been screened, including 763 assays for TP53 mutations both at diagnosis and relapse of ALL. Pediatric and adult leukemia expert labs developed additional content to study the mutation incidence of other B and T lineage markers such as IKZF1, JAK2, IL7R, PAX5, EP300, LEF1, CRLF2, PHF6, WT1, JAK1, PTEN, AKT1, IL7R, NOTCH1, CREBBP, or FBXW7. Further, the molecular landscape of CLL is changing rapidly. As such, a separate working group focused on analyses including NOTCH1, SF3B1, MYD88, XPO1, FBXW7 and BIRC3. Currently, 922 cases were screened to investigate the range of mutational burden of NOTCH1 mutations for their prognostic relevance. In MDS, RUNX1 mutation analyses were performed in 977 cases. The prognostic relevance of TP53 mutations in MDS was assessed in additional 327 cases, including isolated deletions of chromosome 5q. Next, content was developed targeting genes of the cellular splicing component, e.g. SF3B1, SRSF2, U2AF1, and ZRSR2. In BCR-ABL1-negative MPN, nine genes of interest (JAK2, MPL, TET2, CBL, KRAS, EZH2, IDH1, IDH2, ASXL1) have been analyzed in a cohort of 155 primary myelofibrosis cases searching for novel somatic mutations and addressing their relevance for disease progression and leukemia transformation. Moreover, an assay was developed and applied to CMML cases allowing the simultaneous analysis of 25 leukemia-associated target genes in a single sequencing run using just 20 ng of starting DNA. Finally, nine laboratories are studying CML, applying ultra-deep sequencing of the BCR-ABL1 tyrosine kinase domain. Analyses were performed on 615 cases investigating the dynamics of expansion of mutated clones under various tyrosine kinase inhibitor therapies.

Conclusion: Molecular characterization of hematological malignancies today requires high diagnostic sensitivity and specificity. As part of the IRON-II study, a network of laboratories analyzed a variety of disease entities applying amplicon-based NGS assays. Importantly, the consortium not only standardized assay design for disease-specific panels, but also achieved consensus on a common data analysis pipeline for mutation interpretation. Distinct working groups have been forged to address scientific tasks and in total 8,867 cases had been analyzed thus far.

Guidance for laboratories performing molecular pathology for cancer patients

Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.

Merely Birds of Passage: Lady Hariot Dufferin's Travel Writings and Medical Work in India, 1884-88

This article examines the travel writings and medical work in India of Lady Hariot Dufferin, Vicereine of India between 1884 and 1888. Lady Dufferin accompanied her husband, the Viceroy Lord Dufferin, through various social and political engagements in India, and carved her own niche in colonial and postcolonial history as a pioneer in the medical training of women in India. The article examines her travel writings on India and explores the nature of her complicity in the Raj, as well as the gendered nature of the separate public role she created for herself in relation to her 'zenana work' in providing medical care for the women of India. The author suggests that, through her work, Lady Dufferin challenges and extends the theoretical paradigms of postcolonialist and feminist critiques of empire.

Why people experiencing acute myocardial infarction delay seeking medical assistance

Background: Delay time from onset of symptoms of myocardial infarction to seeking medical assistance can have life- 31 threatening consequences. A number of factors have been associated with delay, but there is little evidence regarding the predictive 32 value of these indices. Aim: To explore potential predictors of patient delay from onset of symptoms to time medical assistance 33 was sought in a consecutive sample of patients admitted to CCU with acute myocardial infarction. Methods: The Cardiac Denial 34 of Impact Scale, Health Locus of Control Scale, Health Value Scale and Pennebaker Inventory of Limbic Languidness were 35 administered to 62 patients between 3 and 6 days after admission. Results: Attribution of symptoms to heart disease and health 36 locus of control had a significant predictive effect on patients seeking help within 60 min, while previous experience of heart 37 disease did not. Conclusion: Assisting individuals to recognise the potential for symptoms to have a cardiac origin is an important 38 objective. Interventions should take into account the variety of cognitive and behavioural factors involved in decision making.

Belief, Knowledge and Expertise. The emergence of the lay expert in medical sociology

The paper has three main aims. First, to trace – through the pages of the Journal – the changing ways in which lay understandings of health and illness have been represented during the 1979-2002 period. Second, to say something about the limits of lay knowledge (and particularly lay expertise) in matters of health and medicine. Third, to call for a re-assessment of what lay people can offer to a democratised and customer sensitive system of health care and to attempt to draw a boundary around the domain of expertise. In following through on those aims, the author calls upon data derived from three current projects. These latter concern the diagnosis of Alzheimer’s disease in people with Down’s syndrome; the development of an outcome measure for people who have suffered a traumatic brain injury; and a study of why older people might reject annual influenza vaccinations. Key words: Lay health beliefs, lay expertise, Alzheimer’s, Traumatic Brain Injury, Vaccinations

The impact of curricular change on medical students' knowledge of anatomy

Background: In recent years, following the publication of Tomorrow's Doctors, the undergraduate medical curriculum in most UK medical schools has undergone major revision. This has resulted in a significant reduction in the time allocated to the teaching of the basic medical sciences, including anatomy. However, it is not clear what impact these changes have had on medical students' knowledge of surface anatomy. Aim: This study aimed to assess the impact of these curricular changes on medical students' knowledge of surface anatomy. Setting: Medical student intakes for 1995-98 at the Queen's University of Belfast, UK. Methods: The students were invited to complete a simple examination paper testing their knowledge of surface anatomy. Results from the student intake of 1995, which undertook a traditional, 'old' curriculum, were compared with those from the student intakes of 1996-98, which undertook a new, 'systems-based' curriculum. To enhance linear response and enable the use of linear models for analysis, all data were adjusted using probit transformations of the proportion (percentage) of correct answers for each item and each year group. Results: The student intake of 1995 (old curriculum) were more likely to score higher than the students who undertook the new, systems-based curriculum. Conclusion: The introduction of the new, systems-based course has had a negative impact on medical students' knowledge of surface anatomy.

Development of a Complex Intervention for Secondary Prevention of Coronary Heart Disease in Primary Care Using the UK Medical Research Council Framework

Objective: To apply the UK Medical Research Council (MRC) framework for development and evaluation of trials of complex interventions to a primary healthcare intervention to promote secondary prevention of coronary heart disease. Study Design: Case report of intervention development. Methods: First, literature relating to secondary prevention and lifestyle change was reviewed. Second, a preliminary intervention was modeled, based on literature findings and focus group interviews with patients (n = 23) and staff (n = 29) from 4 general practices. Participants’ experiences of and attitudes toward key intervention components were explored. Third, the preliminary intervention was pilot-tested in 4 general practices. After delivery of the pilot intervention, practitioners evaluated the training sessions, and qualitative data relating to experiences of the intervention were collected using semistructured interviews with staff (n = 10) and patient focus groups (n = 17). Results: Literature review identified 3 intervention components: a structured recall system, practitioner training, and patient information. Initial qualitative data identified variations in recall system design, training requirements (medication prescribing, facilitating behavior change), and information appropriate to the prospective study participants. Identifying detailed structures within intervention components clarified how the intervention could be tailored to individual practice, practitioner, and patient needs while preserving the theoretical functions of the components. Findings from the pilot phase informed further modeling of the intervention, reducing administrative time, increasing practical content of training, and omitting unhelpful patient information. Conclusion: Application of the MRC framework helped to determine the feasibility and development of a complex intervention for primary care research.

Characterization and optimization of experimental variables within a reproducible bladder encrustation model and in vitro evaluation of the efficacy of urease inhibitors for the prevention of medical device-related encrustation

This study presents a reproducible, cost-effective in vitro encrustation model and, furthermore, describes the effects of components of the artificial urine and the presence of agents that modify the action of urease on encrustation on commercially available ureteral stents. The encrustation model involved the use of small-volume reactors (700 mL) containing artificial urine and employing an orbital incubator (at 37 degrees C) to ensure controlled stirring. The artificial urine contained sources of calcium and magnesium (both as chlorides), albumin and urease. Alteration of the ratio (% w/w) of calcium salt to magnesium salt affected the mass of encrustation, with the greatest encrustation noted whenever magnesium was excluded from the artificial urine. Increasing the concentration of albumin, designed to mimic the presence of protein in urine, significantly decreased the mass of both calcium and magnesium encrustation until a plateau was observed. Finally, exclusion of urease from the artificial urine significantly reduced encrustation due to the indirect effects of this enzyme on pH. Inclusion of the urease inhibitor, acetohydroxamic acid, or urease substrates (methylurea or ethylurea) into the artificial medium markedly reduced encrustation on ureteral stents. In conclusion, this study has described the design of a reproducible, cost-effective in vitro encrustation model. Encrustation was markedly reduced on biomaterials by the inclusion of agents that modify the action of urease. These agents may, therefore, offer a novel clinical approach to the control of encrustation on urological medical devices. (c) 2005 Wiley Periodicals, Inc.