Molecular diagnosis of the myeloproliferative neoplasms: UK guidelines for the detection of JAK2 V617F and other relevant mutations

Molecular genetic assays for the detection of the JAK2 V617F (c.1849G>T) and other pathogenetic mutations within JAK2 exon 12 and MPL exon 10 are part of the routine diagnostic workup for patients presenting with erythrocytosis, thrombocytosis or otherwise suspected to have a myeloproliferative neoplasm. A wide choice of techniques are available for the detection of these mutations, leading to potential difficulties for clinical laboratories in deciding upon the most appropriate assay, which can lead to problems with inter-laboratory standardization. Here, we discuss the most important issues for a clinical diagnostic laboratory in choosing a technique, particularly for detection of the JAK2 V617F mutation at diagnosis. The JAK2 V617F detection assay should be both specific and sensitive enough to detect a mutant allele burden as low as 13%. Indeed, the use of sensitive assays increases the detection rate of the JAK2 V617F mutation within myeloproliferative neoplasms. Given their diagnostic relevance, it is also beneficial and relatively straightforward to screen JAK2 V617F negative patients for JAK2 exon 12 mutations (in the case of erythrocytosis) or MPL exon 10 mutations (thrombocytosis or myelofibrosis) using appropriate assays. Molecular results should be considered in the context of clinical findings and other haematological or laboratory results.

JAK2V617F homozygosity arises commonly and recurrently in PV and ET, but PV is characterized by expansion of a dominant homozygous subclone

Subclones homozygous for JAK2V617F are more common in polycythemia vera (PV) than essential thrombocythemia (ET), but their prevalence and significance remain unclear. The JAK2 mutation status of 6495 BFU-E, grown in low erythropoietin conditions, was determined in 77 patients with PV or ET. Homozygous-mutant colonies were common in patients with JAK2V617F-positive PV and were surprisingly prevalent in JAK2V617F-positive ET and JAK2 exon 12-mutated PV. Using microsatellite PCR to map loss-of-heterozygosity breakpoints within individual colonies, we demonstrate that recurrent acquisition of JAK2V617F homozygosity occurs frequently in both PV and ET. PV was distinguished from ET by expansion of a dominant homozygous subclone, the selective advantage of which is likely to reflect additional genetic or epigenetic lesions. Our results suggest a model in which development of a dominant JAK2V617F-homzygous subclone drives erythrocytosis in many PV patients, with alternative mechanisms operating in those with small or undetectable homozygous-mutant clones.

Ireland

‘Islands constitute natural unities; sea channels constitute natural divisions’. So wrote Kevin Howard (2006: 9) with particular reference to the two largest islands of the British Isles: Great Britain and Ireland. However, at the time of writing, the political unity of Great Britain is being called into question, while Ireland has been divided since the 1920s. Part of the island of Ireland is united not with the rest of the island, but with Great Britain across the other side of the ‘natural division’ that is the Irish Sea, for Ireland’s history, development and political structures have long been moulded by Great Britain. The journey to this ‘unnatural’ unity and the associated division of Ireland forms the material for this chapter.

On the Assumption of Bivariate Normality in Selection Models: A Copula Approach Applied to Estimating HIV Prevalence

Background: Heckman-type selection models have been used to control HIV prevalence estimates for selection bias when participation in HIV testing and HIV status are associated after controlling for observed variables. These models typically rely on the strong assumption that the error terms in the participation and the outcome equations that comprise the model are distributed as bivariate normal.
Methods: We introduce a novel approach for relaxing the bivariate normality assumption in selection models using copula functions. We apply this method to estimating HIV prevalence and new confidence intervals (CI) in the 2007 Zambia Demographic and Health Survey (DHS) by using interviewer identity as the selection variable that predicts participation (consent to test) but not the outcome (HIV status).
Results: We show in a simulation study that selection models can generate biased results when the bivariate normality assumption is violated. In the 2007 Zambia DHS, HIV prevalence estimates are similar irrespective of the structure of the association assumed between participation and outcome. For men, we estimate a population HIV prevalence of 21% (95% CI = 16%–25%) compared with 12% (11%–13%) among those who consented to be tested; for women, the corresponding figures are 19% (13%–24%) and 16% (15%–17%).
Conclusions: Copula approaches to Heckman-type selection models are a useful addition to the methodological toolkit of HIV epidemiology and of epidemiology in general. We develop the use of this approach to systematically evaluate the robustness of HIV prevalence estimates based on selection models, both empirically and in a simulation study.

Statin use after diagnosis of breast cancer and survival: a population-based cohort study

BACKGROUND: Preclinical studies have shown that statins, particularly simvastatin, can prevent growth in breast cancer cell lines and animal models. We investigated whether statins used after breast cancer diagnosis reduced the risk of breast cancer-specific, or all-cause, mortality in a large cohort of breast cancer patients.

METHODS: A cohort of 17,880 breast cancer patients, newly diagnosed between 1998 and 2009, was identified from English cancer registries (from the National Cancer Data Repository). This cohort was linked to the UK Clinical Practice Research Datalink, providing prescription records, and to the Office of National Statistics mortality data (up to 2013), identifying 3694 deaths, including 1469 deaths attributable to breast cancer. Unadjusted and adjusted hazard ratios (HRs) for breast cancer-specific, and all-cause, mortality in statin users after breast cancer diagnosis were calculated using time-dependent Cox regression models. Sensitivity analyses were conducted using multiple imputation methods, propensity score methods and a case-control approach.

RESULTS: There was some evidence that statin use after a diagnosis of breast cancer had reduced mortality due to breast cancer and all causes (fully adjusted HR = 0.84 [95% confidence interval = 0.68-1.04] and 0.84 [0.72-0.97], respectively). These associations were more marked for simvastatin 0.79 (0.63-1.00) and 0.81 (0.70-0.95), respectively.

CONCLUSIONS: In this large population-based breast cancer cohort, there was some evidence of reduced mortality in statin users after breast cancer diagnosis. However, these associations were weak in magnitude and were attenuated in some sensitivity analyses.

Am I shrinking? On clothing size and body size.

Comment on: Hughes LA, Schouten LJ, Goldbohm RA, van den Brandt PA, Weijenberg MP. Self-reported clothing size as a proxy measure for body size. Epidemiology. 2009 Sep;20(5):673-6. PMID: 19451821

Simulation-Based Finite-Sample Tests for Heteroskedasticity and ARCH Effects.

A wide range of tests for heteroskedasticity have been proposed in the econometric and statistics literature. Although a few exact homoskedasticity tests are available, the commonly employed procedures are quite generally based on asymptotic approximations which may not provide good size control in finite samples. There has been a number of recent studies that seek to improve the reliability of common heteroskedasticity tests using Edgeworth, Bartlett, jackknife and bootstrap methods. Yet the latter remain approximate. In this paper, we describe a solution to the problem of controlling the size of homoskedasticity tests in linear regression contexts. We study procedures based on the standard test statistics [e.g., the Goldfeld-Quandt, Glejser, Bartlett, Cochran, Hartley, Breusch-Pagan-Godfrey, White and Szroeter criteria] as well as tests for autoregressive conditional heteroskedasticity (ARCH-type models). We also suggest several extensions of the existing procedures (sup-type of combined test statistics) to allow for unknown breakpoints in the error variance. We exploit the technique of Monte Carlo tests to obtain provably exact p-values, for both the standard and the new tests suggested. We show that the MC test procedure conveniently solves the intractable null distribution problem, in particular those raised by the sup-type and combined test statistics as well as (when relevant) unidentified nuisance parameter problems under the null hypothesis. The method proposed works in exactly the same way with both Gaussian and non-Gaussian disturbance distributions [such as heavy-tailed or stable distributions]. The performance of the procedures is examined by simulation. The Monte Carlo experiments conducted focus on : (1) ARCH, GARCH, and ARCH-in-mean alternatives; (2) the case where the variance increases monotonically with : (i) one exogenous variable, and (ii) the mean of the dependent variable; (3) grouped heteroskedasticity; (4) breaks in variance at unknown points. We find that the proposed tests achieve perfect size control and have good power.

L’adoption intrafamiliale réalisée en Haïti par des Haïtiens québécois vivant à Montréal

La protection des enfants dans les pays en développement constitue encore aujourd’hui une problématique qui continue à alimenter la préoccupation et des débats sur l’avenir des enfants à l’échelle nationale et internationale. En dépit des interventions répétées des organismes internationaux œuvrant dans le domaine de la protection des enfants à travers le monde, les conditions socioéconomiques de millions d’enfants ne cessent d’empirer, laissant ainsi leur avenir dans une incertitude accablante. Le souci de secourir ces enfants a ouvert la voie à l’amplification du phénomène d’adoption internationale qui témoigne d’une forme de «solidarité» internationale en faveur des enfants à travers le monde mais qui finit par s’imposer comme une forme de protection sociale qui transcende les frontières nationales. En Haïti, la précarité des conditions de vie a permis la mise en action d’un ensemble de stratégies d’entraide se reposant sur des liens communautaires forts qui se veut une sorte de soupape pour amortir les impacts sur les membres de la famille, mais qui s’étend parfois sur toute la communauté. Dans cette dynamique, l’enfant bénéficie d’une attention soutenue. Ainsi, certains membres de la diaspora haïtienne en Amérique du Nord, plus précisément à Montréal ont procédé à l’adoption dans leur famille élargie en Haïti. L’objectif de cette recherche est donc de dégager une appréhension de l’adoption intrafamiliale en Haïti, plus particulièrement celle réalisée par des haïtiens vivants à Montréal. Mais de manière spécifique, nous visons à : 1) comprendre la nature des décisions d’adopter et sa spécificité en contexte d’adoption intrafamiliale chez les adoptants québécois originaires d’Haïti, 2) établir les étapes et le contexte des démarches d’adoption qui caractérisent les projets des adoptants haïtiens québécois et 3) comprendre dans quelle mesure la protection des enfants fait partie du désir d’adopter chez ces adoptants en dégageant leur point de vue. Cette recherche nous a permis de comprendre que l’adoption intrafamiliale en Haïti est marquée par une grande diversité de motivations tels que le désir d’enfants, le sauvetage des enfants, la redevance sociale, la réussite sociale de l’enfant, l’accès à l’éducation, le désengagement social, le souci de maintenir à distance l’esprit de clan et le don d’enfants. Si ces motifs visent pour la plupart à la protection de l’enfant, ils sont aussi en lien avec la culture haïtienne qui voit dans celui-ci une véritable lueur d’espoir pour l’amélioration des conditions de vie des parents dans leurs vieux jours.

Attitudes et comportements alimentaires des athlètes québécoises pratiquant un sport esthétique à un haut niveau : caractéristiques personnelles et comparaison à un groupe de contrôle

La pratique d’un sport de type esthétique est aujourd’hui considérée par plusieurs (Sundgot-Borgen & Torstveit, 2004; Thompson & Sherman, 2010) comme un facteur de risque à l’adoption d’attitudes et de comportements alimentaires inappropriés à l’égard de l’alimentation et de l’image corporelle (ACIAI) et ultimement au développement d’un trouble des conduites alimentaires (TCA). Les études actuelles portant sur cette problématique rapportent toutefois des résultats contradictoires. De plus, certains aspects méthodologiques associés notamment à l’hétérogénéité des échantillons limitent la portée interprétative de ces résultats. Afin de pallier les limites actuelles des écrits empiriques, cette thèse a pour but de tracer le portrait de la problématique des désordres alimentaires chez les jeunes athlètes québécoises de haut niveau en sport esthétique. Pour ce faire, un échantillon homogène de 145 adolescentes âgées de 12 à 19 ans a été constitué soit 52 athlètes de haut niveau et 93 non-athlètes. Les sports représentés sont le patinage artistique, la nage synchronisée et le ballet. À partir de cet échantillon, deux études sont réalisées. L’objectif de la première étude est de comparer l’intensité des ACIAI et la prévalence des TCA dans les deux groupes à l’aide de deux questionnaires soit le Eating Disorder Examination Questionnaire (EDE-Q) et le Eating Disorder Inventory-3 (EDI-3). Les résultats obtenus suggèrent qu’il n’y a pas de différence significative entre les athlètes et les non-athlètes de l’échantillon en ce qui a trait à l’intensité des ACIAI et à la prévalence des TCA. La deuxième étude est constituée de deux objectifs. Tout d’abord, comparer les deux groupes relativement aux caractéristiques personnelles suivantes : l’insatisfaction de l’image corporelle (IIC), le sentiment d’efficacité personnelle envers l’alimentation normative (SEP-AN) et l’image corporelle (SEP-IC), le perfectionnisme (P), l’ascétisme (As), la dysrégulation émotionnelle (DÉ) et le déficit intéroceptif (DI). De nature plus exploratoire, le second objectif de cette étude est de décrire et de comparer les caractéristiques personnelles qui sont associées aux ACIAI dans chacun des groupes. Afin de réaliser ces objectifs, deux autres questionnaires ont été utilisés soit le Eating Disorder Recovery Self-efficacy Questionnaire-f (EDRSQ-f) et le Body Shape Questionnaire (BSQ). En somme, les analyses indiquent que les athlètes de l’échantillon présentent des niveaux plus faibles de SEP-AN et de DÉ. Ce faisant, elles auraient moins confiance en leur capacité à maintenir une alimentation normative, mais réguleraient plus efficacement leurs émotions que les adolescentes non-athlètes. Une fois l’âge et l’indice de masse corporelle contrôlés, les résultats démontrent également que le SEP-AN et l’IIC contribuent à prédire dans chaque groupe les ACIAI tels que mesurés par la recherche de minceur. Le SEP-AN a aussi été associé dans les deux groupes à l’intensité des symptômes boulimiques. Les modèles obtenus diffèrent cependant quant aux variables prédictives principales. Chez les athlètes de l’échantillon, l’intensité des conduites boulimiques est associée à la DÉ alors qu’elle est davantage liée au DI chez les adolescentes non sportives. Enfin, en plus de discuter et de comparer l’ensemble de ces résultats aux autres travaux disponibles, les apports distinctifs de la thèse et les principales limites des études sont abordés. Des pistes sont également suggérées afin d’orienter les recherches futures et des implications cliniques sont proposées.

Ultrasonic Study Of The Elastic Properties And Phase Transitions In Selected Mixed Sulphate Crystals

The thesis investigated the elastic properties and phase transitions in selected mixed sulphate crystals – Lithium Hydrazinium Sulphate [LiN2H2SO4], Lithium Ammonium Sulphate [LiNH4SO4] and Lithium Potassium Sulphate [LiKSO4] – using ultrasonic technique. The pulse echo overlap technique has been used for measuring ultrasonic velocity and its dependence on temperature along different directions with waves of longitudinal and transverse polarizations. Two major numerical techniques and the corresponding computer programs developed as part of present work are presented in this thesis. All the 9 elastic constants of LHS are determined accurately from ultrasonic measurements and applying misorientation correction refines the constants. Ultrasonic measurements are performed in LAS to determine the elastic constants and to study the low temperature phase transitions. Temperature variation studies of elastic constant of LAS are performed for 6 different modes of propagation for heating and cooling at low temperatures. All the 5 independent elastic constants of LPS is determined using ultrasonic measurements. It is concluded that LPS crystal does not undergo a phase transition near this temperature. A comparison of the three crystals studied shows that LPS has maximum number of phase transitions and LHS has the least number. It is interesting to note that LPS has the simplest formula unit among the three. There is considerable scope for the future work on these crystals and others belonging to the sulphate family.

Unusual autofluorescence characteristic of cultured red-rain cells

The red cells found in the red rain in Kerala, India are now considered as a possible case of extraterrestrial life form. These cells can undergo rapid replication even at an extreme high temperature of 300 deg C. They can also be cultured in diverse unconventional chemical substrates. The molecular composition of these cells is yet to be identified. This paper reports the unusual autofluorescence characteristic of the cultured red rain cells. A spectrofluorimetric study has been performed to investigate this, which shows a systematic shift of the fluorescence emission peak wavelength as the excitation wavelength is increased. Conventional biomolecules are not known to have this property. Details of this investigation and the results are discussed.