Next-generation sequencing: a change of paradigm in molecular diagnostic validation

Next-generation sequencing (NGS) is beginning to show its full potential for diagnostic and therapeutic applications. In particular, it is enunciating its capacity to contribute to a molecular taxonomy of cancer, to be used as a standard approach for diagnostic mutation detection, and to open new treatment options that are not exclusively organ-specific. If this is the case, how much validation is necessary and what should be the validation strategy, when bringing NGS into the diagnostic/clinical practice? This validation strategy should address key issues such as: what is the overall extent of the validation? Should essential indicators of test performance such as sensitivity of specificity be calculated for every target or sample type? Should bioinformatic interpretation approaches be validated with the same rigour? What is a competitive clinical turnaround time for a NGS-based test, and when does it become a cost-effective testing proposition? While we address these and other related topics in this commentary, we also suggest that a single set of international guidelines for the validation and use of NGS technology in routine diagnostics may allow us all to make a much more effective use of resources.

Exploratory factor analysis in validation studies : Uses and recommendations

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Do logbooks influence recall of physical activity in validation studies?

Purpose: To examine whether physical activity logbooks influence estimates of validity of 7-d recall physical activity questionnaires. Methods: A  convenience sample of 551 adults aged 18–75 yr wore an MTI  accelerometer for seven consecutive days and were then randomly administered two of four 7-d recall physical activity questionnaires that varied in length and format (Active Australia Survey (AAS), long and short  International Physical Activity Questionnaires (IPAQ-L and IPAQ-S), and Behavioral Risk Factor Surveillance System (BRFSS)). A subsample of 75% concurrently completed a physical activity logbook. Results: Correlations (rho) between self-reported and measured duration of moderate- and vigorous-intensity activity and total activity were similar among participants who received a logbook and those who did not for each of the four instruments. There was also no interaction between assessment method (survey, accelerometer) and the assignment of a logbook. For the IPAQ-L, however, variability in the difference between accelerometer data and responses to the vigorous items was smaller among those assigned a logbook (F = 4.128, df = 260, P = 0.043). Overall, there were no differences in percent agreement or kappa for participation in sufficient levels of physical activity according to receipt of a logbook for any of the surveys. Conclusion: The process of self-monitoring through completion of a logbook does not appear to influence estimates of validity for brief or long questionnaires with global questions. Whereas the magnitude of error in accuracy of recall of particular types of activity may be reduced by completion of a logbook that is similar in structure to the survey being validated, this does not appear to influence overall estimates of validity.

The psychometric properties of the brief Other as Shamer Scale for Children (OAS‐C) : preliminary validation studies in a sample of Portuguese children

Shame is a social emotion with adaptive functions involved in human be-havior and social interactions. This emotion is regarded as an involuntary response associated with increased self-awareness, loss of status and self-devaluation (Gilbert, 1998), that may render individuals more prone to psychopathology (Gilbert, 1998; Pinto-Gouveia & Matos, 2011). Thus, identifying and assessing feelings of shame in childhood is essential in addressing the actual impact of shame on individual’s developmental trajectory. The Other As Shamer Scale (OAS; Goss, Gilbert & Allan, 1994) is a widely used measure of external shame, adapted and translated to several languages — including Portuguese (Matos, Pinto-Gouveia, Gilbert, Duarte & Figueiredo, 2015) — to adult and to adolescent populations (OASB-A - Other As Shamer Brief for adolescents; translated and adapted by Cunha, Xavier, Cherpe & Pinto-Gouveia, 2014). The current study aims to adapt and to explore the psychometric proper-ties of the brief OAS in a sample of Portuguese children attending to elementary schools.

Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma.

We have used whole exome sequencing to compare a group of presentation t(4;14) with t(11;14) cases of myeloma to define the mutational landscape. Each case was characterized by a median of 24.5 exonic nonsynonymous single-nucleotide variations, and there was a consistently higher number of mutations in the t(4;14) group, but this number did not reach statistical significance. We show that the transition and transversion rates in the 2 subgroups are similar, suggesting that there was no specific mechanism leading to mutation differentiating the 2 groups. Only 3% of mutations were seen in both groups, and recurrently mutated genes include NRAS, KRAS, BRAF, and DIS3 as well as DNAH5, a member of the axonemal dynein family. The pattern of mutation in each group was distinct, with the t(4;14) group being characterized by deregulation of chromatin organization, actin filament, and microfilament movement. Recurrent RAS pathway mutations identified subclonal heterogeneity at a mutational level in both groups, with mutations being present as either dominant or minor subclones. The presence of subclonal diversity was confirmed at a single-cell level using other tumor-acquired mutations. These results are consistent with a distinct molecular pathogenesis underlying each subgroup and have important impacts on targeted treatment strategies. The Medical Research Council Myeloma IX trial is registered under ISRCTN68454111.

The reliability of information on work-related injuries available from hospitalisation data in Australia

Objective: To examine the reliability of work-related activity coding for injury-related hospitalisations in Australia. Method: A random sample of 4373 injury-related hospital separations from 1 July 2002 to 30 June 2004 were obtained from a stratified random sample of 50 hospitals across 4 states in Australia. From this sample, cases were identified as work-related if they contained an ICD-10-AM work-related activity code (U73) allocated by either: (i) the original coder; (ii) an independent auditor, blinded to the original code; or (iii) a research assistant, blinded to both the original and auditor codes, who reviewed narrative text extracted from the medical record. The concordance of activity coding and number of cases identified as work-related using each method were compared. Results: Of the 4373 cases sampled, 318 cases were identified as being work-related using any of the three methods for identification. The original coder identified 217 and the auditor identified 266 work-related cases (68.2% and 83.6% of the total cases identified, respectively). Around 10% of cases were only identified through the text description review. The original coder and auditor agreed on the assignment of work-relatedness for 68.9% of cases. Conclusions and Implications: The current best estimates of the frequency of hospital admissions for occupational injury underestimate the burden by around 32%. This is a substantial underestimate that has major implications for public policy, and highlights the need for further work on improving the quality and completeness of routine, administrative data sources for a more complete identification of work-related injuries.

Validation of the WHOQOL-BREF among women following childbirth

Background: There is an increasing interest in measuring quality of life (QOL) in clinical settings and in clinical trials. None of the commonly used QOL instrument have been validated for use postnatally. Aim: To assess the psychometric properties of the 26-item WHOQOL-BREF among women following childbirth. Methods: Using a prospective cohort design we recruited 320 women within the first few days of childbirth. At six weeks postpartum, participants were asked to complete the WHOQOL-BREF, the Edinburgh Postnatal Depression Index and the Australian Unity Wellbeing Index. Validation of the WHOQOL-BREF included an analysis of internal consistency, discriminate validity, convergent validity and an examination of the domain structure. Results: 221 (69.1%) women returned their six-week questionnaire. All domains of the WHOQOL-BREF met reliability standards (alpha coefficient exceeding 0.70). The questionnaire discriminated well between known groups (depressed and non-depressed women. P = <0.000) and demonstrated satisfactory correlations with the Australian Unity Wellbeing index (r = >0.45). The domain structure of the WHOQOL-BREF was also valid in this population of new mothers, with moderate to high correlation between individual items and the domain structure to which the items were originally assigned. Conclusion: The WHOQOL-BRF is well-accepted and valid instrument in this population and may be used in postnatal clinical settings or for assessing intervention effects in research studies.

Validation of the interRAI Cognitive Performance Scale against independent clinical diagnosis and the Mini-Mental State Examination in older hospitalized patients

Objective To compare the diagnostic accuracy of the interRAI Acute Care (AC) Cognitive Performance Scale (CPS2) and the Mini-Mental State Examination (MMSE), against independent clinical diagnosis for detecting dementia in older hospitalized patients. Design, Setting, and Participants The study was part of a prospective observational cohort study of patients aged ≥70 years admitted to four acute hospitals in Queensland, Australia, between 2008 and 2010. Recruitment was consecutive and patients expected to remain in hospital for ≥48 hours were eligible to participate. Data for 462 patients were available for this study. Measurements Trained research nurses completed comprehensive geriatric assessments and administered the interRAI AC and MMSE to patients. Two physicians independently reviewed patients’ medical records and assessments to establish the diagnosis of dementia. Indicators of diagnostic accuracy included sensitivity, specificity, predictive values, likelihood ratios and areas under receiver (AUC) operating characteristic curves. Results 85 patients (18.4%) were considered to have dementia according to independent clinical diagnosis. The sensitivity of the CPS2 [0.68 (95%CI: 0.58–0.77)] was not statistically different to the MMSE [0.75 (0.64–0.83)] in predicting physician diagnosed dementia. The AUCs for the 2 instruments were also not statistically different: CPS2 AUC = 0.83 (95%CI: 0.78–0.89) and MMSE AUC = 0.87 (95%CI: 0.83–0.91), while the CPS2 demonstrated higher specificity [0.92 95%CI: 0.89–0.95)] than the MMSE [0.82 (0.77–0.85)]. Agreement between the CPS2 and clinical diagnosis was substantial (87.4%; κ=0.61). Conclusion The CPS2 appears to be a reliable screening tool for assessing cognitive impairment in acutely unwell older hospitalized patients. These findings add to the growing body of evidence supporting the utility of the interRAI AC, within which the CPS2 is embedded. The interRAI AC offers the advantage of being able to accurately screen for both dementia and delirium without the need to use additional assessments, thus increasing assessment efficiency.

Validation of back-calculation equations for juvenile bluefish (Pomatomus saltatrix) with the use of tetracycline-marked otoliths

In recent years, a decrease in the abundance of bluefish (Pomatomus saltatrix) has been observed (Fahay et al., 1999; Munch and Conover, 2000) that has led to increased interest in a better understanding the life history of the species. Estimates of several young-of-the-year (YOY) life history characteristics, including the importance and use of estuaries as nursery habitat (Kendall and Walford, 1979) and size-dependant mortality (Hare and Cowen, 1997), are reliant upon the accuracy of growth determination. By using otoliths, it is possible to use back-calculation formulae (BCFs) to estimate the length at certain ages and stages of development for many species of fishes. Use of otoliths to estimate growth in this way can provide the same information as long-term laboratory experiments and tagging studies without the time and expense of rearing or recapturing fish. The difficulty in using otoliths in this way lies in validating that 1) there is constancy in the periodicity of the increment formation, and 2) there is no uncoupling of the relationship between somatic and otolith growth. To date there are no validation studies demonstrating the relationship between otolith growth and somatic growth for bluefish. Daily increment formation in otoliths has been documented for larval (Hare and Cowen, 1994) and juvenile bluefish (Nyman and Conover, 1988). Hare and Cowen (1995) found ageindependent variability in the ratio of otolith size to body length in early age bluefish, although these differences varied between ontogenetic stages. Furthermore, there have been no studies where an evaluation of back-calculation methods has been combined with a validation of otolithderived lengths for juvenile bluefish.

Psychometric evaluation and experimental validation of the statistics anxiety rating scale.

The Statistics Anxiety Rating Scale (STARS) was adapted into German to examine its psychometric properties (n = 400). Two validation studies (n = 66, n = 96) were conducted to examine its criterion-related validity. The psychometric properties of the questionnaire were very similar to those previously reported for the original English version in various countries and other language versions. Confirmatory factor analysis indicated 2 second-order factors: One was more closely related to anxiety and the other was more closely related to negative attitudes toward statistics. Predictive validity of the STARS was shown both in an experimental exam-like situation in the laboratory and during a real examination situation. Taken together, the findings indicate that statistics anxiety as assessed by the STARS is a useful construct that is more than just an expression of a more general disposition to anxiety.

Digital slide viewing for primary reporting in gastrointestinal pathology: a validation study

Despite the increasing availability of digital slide viewing, and numerous advantages associated with its application, a lack of quality validation studies is amongst the reasons for poor uptake in routine practice. This study evaluated primary digital pathology reporting in the setting of routine subspecialist gastrointestinal pathology, commonplace in most tissue pathology laboratories and representing one of the highest volume specialties in most laboratories. Individual digital and glass slide diagnoses were compared amongst three pathologists reporting in a gastrointestinal subspecialty team, in a prospective series of 100 consecutive diagnostic cases from routine practice in a large teaching hospital laboratory. The study included a washout period of at least 6 months. Discordant diagnoses were classified, and the study evaluated against recent College of American Pathologists (CAP) recommendations for evaluating digital pathology systems for diagnostic use. The study design met all 12 of the CAP recommendations. The 100 study cases generated 300 pairs of diagnoses, comprising 100 glass slide diagnoses and 100 digital diagnoses from each of the three study pathologists. 286 of 300 pairs of diagnoses were concordant, representing intraobserver concordance of 95.3 %, broadly comparable to rates previously published in this field. In ten of the 14 discordant pairs, the glass slide diagnosis was favoured; in four cases, the digital diagnosis was favoured, but importantly, the 14 discordant intraobserver diagnoses were considered to be of minor clinical significance. Interobserver, or viewing modality independent, concordance was found in 94 of the total of 100 study cases, providing a comparable baseline discordance rate expected in any second viewing of pathology material. These overall results support the safe use of digital pathology in primary diagnostic reporting in this setting

Consumers' need for uniqueness : scale development and validation

Consumers acquire and display material possessions for the purpose of feeling differentiated from other people and, thus, are targeted with a variety of marketing stimuli that attempt to enhance self‐perceptions of uniqueness. Because the pursuit of differentness (or counterconformity motivation) varies across individuals to influence consumer responses, we develop and validate a trait measure of consumers’ need for uniqueness. Consumers' need for uniqueness is defined as an individual’s pursuit of differentness relative to others that is achieved through the acquisition, utilization, and disposition of consumer goods for the purpose of developing and enhancing one’s personal and social identity. Following assessments of the scale’s latent structure, a series of validation studies examines the scale’s validity. The presentation of empirical work is followed by a discussion of how consumers' need for uniqueness could be used in better understanding consumer behavior and the role consumption plays in people’s expression of identity.

Translation, cultural adaptation to Brazil and validation of the venous leg ulcer quality of life questionnaire (VLU-QoL-Br)

Objetivo:traduzir o instrumento Venous legulcer quality of life questionnaire (VLU-QoL), adaptá-lo culturalmente para o português do Brasil e validá-lo com pacientes do Hospital das Clínicas da Faculdade de Medicina de Botucatu (FMB) da Universidade Estadual Paulista (Unesp). Métodos:o questionário foi traduzido por um tradutor profissional e por dois dermatologistas especialistas na área de úlceras venosas (UV), sendo reformulado em reunião com os três tradutores. O constructo (VLU-QoL-Br) foi submetido a pré-entrevista com 10 portadores de UV para a adaptação da linguagem. Posteriormente, foi aplicado em pacientes do HC-Unesp, e como teste-reteste para verificação de sua reprodutibilidade. Resultados:foram avaliados 82 pacientes, sendo 56 (68%) do sexo feminino. A idade média foi de 67,3 anos. O questionário foi traduzido, adaptado e aplicado aos pacientes. O constructo apresentou alta consistência interna (alfa= 0,94) e adequada correlação item-total. Quando avaliados os 32 retestes, observou-se correlação intraclasse para concordância de 0,78 (p < 0,01), indicando boa reprodutibilidade do constructo. A análise fatorial confirmatória corroborou as dimensões do questionário original: atividades, psicológico e sintomas. Escores do VLU-QoL-Br se associaram, independentemente, à área total das úlceras e a menor escolaridade dos sujeitos (p < 0,01). Conclusão:a tradução, a adaptação e a validação do questionário VLU-Qol-Br demonstrou boa performance psicométrica, permitindo seu uso clínico no Brasil. É importante avaliar seu desempenho em outras regiões e em diferentes amostras de indivíduos.

Validation of the weight concerns scale applied to Brazilian university students

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)