New approaches to open problems in gene expression microarray data

In the past decade, the advent of efficient genome sequencing tools and high-throughput experimental biotechnology has lead to enormous progress in the life science. Among the most important innovations is the microarray tecnology. It allows to quantify the expression for thousands of genes simultaneously by measurin the hybridization from a tissue of interest to probes on a small glass or plastic slide. The characteristics of these data include a fair amount of random noise, a predictor dimension in the thousand, and a sample noise in the dozens. One of the most exciting areas to which microarray technology has been applied is the challenge of deciphering complex disease such as cancer. In these studies, samples are taken from two or more groups of individuals with heterogeneous phenotypes, pathologies, or clinical outcomes. these samples are hybridized to microarrays in an effort to find a small number of genes which are strongly correlated with the group of individuals. Eventhough today methods to analyse the data are welle developed and close to reach a standard organization (through the effort of preposed International project like Microarray Gene Expression Data -MGED- Society [1]) it is not unfrequant to stumble in a clinician's question that do not have a compelling statistical method that could permit to answer it.The contribution of this dissertation in deciphering disease regards the development of new approaches aiming at handle open problems posed by clinicians in handle specific experimental designs. In Chapter 1 starting from a biological necessary introduction, we revise the microarray tecnologies and all the important steps that involve an experiment from the production of the array, to the quality controls ending with preprocessing steps that will be used into the data analysis in the rest of the dissertation. While in Chapter 2 a critical review of standard analysis methods are provided stressing most of problems that In Chapter 3 is introduced a method to adress the issue of unbalanced design of miacroarray experiments. In microarray experiments, experimental design is a crucial starting-point for obtaining reasonable results. In a two-class problem, an equal or similar number of samples it should be collected between the two classes. However in some cases, e.g. rare pathologies, the approach to be taken is less evident. We propose to address this issue by applying a modified version of SAM [2]. MultiSAM consists in a reiterated application of a SAM analysis, comparing the less populated class (LPC) with 1,000 random samplings of the same size from the more populated class (MPC) A list of the differentially expressed genes is generated for each SAM application. After 1,000 reiterations, each single probe given a "score" ranging from 0 to 1,000 based on its recurrence in the 1,000 lists as differentially expressed. The performance of MultiSAM was compared to the performance of SAM and LIMMA [3] over two simulated data sets via beta and exponential distribution. The results of all three algorithms over low- noise data sets seems acceptable However, on a real unbalanced two-channel data set reagardin Chronic Lymphocitic Leukemia, LIMMA finds no significant probe, SAM finds 23 significantly changed probes but cannot separate the two classes, while MultiSAM finds 122 probes with score >300 and separates the data into two clusters by hierarchical clustering. We also report extra-assay validation in terms of differentially expressed genes Although standard algorithms perform well over low-noise simulated data sets, multi-SAM seems to be the only one able to reveal subtle differences in gene expression profiles on real unbalanced data. In Chapter 4 a method to adress similarities evaluation in a three-class prblem by means of Relevance Vector Machine [4] is described. In fact, looking at microarray data in a prognostic and diagnostic clinical framework, not only differences could have a crucial role. In some cases similarities can give useful and, sometimes even more, important information. The goal, given three classes, could be to establish, with a certain level of confidence, if the third one is similar to the first or the second one. In this work we show that Relevance Vector Machine (RVM) [2] could be a possible solutions to the limitation of standard supervised classification. In fact, RVM offers many advantages compared, for example, with his well-known precursor (Support Vector Machine - SVM [3]). Among these advantages, the estimate of posterior probability of class membership represents a key feature to address the similarity issue. This is a highly important, but often overlooked, option of any practical pattern recognition system. We focused on Tumor-Grade-three-class problem, so we have 67 samples of grade I (G1), 54 samples of grade 3 (G3) and 100 samples of grade 2 (G2). The goal is to find a model able to separate G1 from G3, then evaluate the third class G2 as test-set to obtain the probability for samples of G2 to be member of class G1 or class G3. The analysis showed that breast cancer samples of grade II have a molecular profile more similar to breast cancer samples of grade I. Looking at the literature this result have been guessed, but no measure of significance was gived before.

Fattori di rischio biomeccanico e valori limite di esposizione (TLV-ACGIH®) nell’ambito dello studio di coorte della sindrome del tunnel carpale occupazionale

OBIETTIVI: Per esplorare il contributo dei fattori di rischio biomeccanico, ripetitività (hand activity level – HAL) e forza manuale (peak force - PF), nell’insorgenza della sindrome del tunnel carpale (STC), abbiamo studiato un’ampia coorte di lavoratori dell’industria, utilizzando come riferimento il valore limite di soglia (TLV©) dell’American Conference of Governmental Industrial Hygienists (ACGIH). METODI: La coorte è stata osservata dal 2000 al 2011. Abbiamo classificato l’esposizione professionale rispetto al limite di azione (AL) e al TLV dell’ACGIH in: “accettabile” (sotto AL), “intermedia” (tra AL e TLV) e “inaccettabile” (sopra TLV). Abbiamo considerato due definizioni di caso: 1) sintomi di STC; 2) sintomi e positività allo studio di conduzione nervosa (SCN). Abbiamo applicato modelli di regressione di Poisson aggiustati per sesso, età, indice di massa corporea e presenza di patologie predisponenti la malattia. RISULTATI: Nell’intera coorte (1710 lavoratori) abbiamo trovato un tasso di incidenza (IR) di sintomi di STC di 4.1 per 100 anni-persona; un IR di STC confermata dallo SCN di 1.3 per 100 anni-persona. Gli esposti “sopra TLV” presentano un rischio di sviluppare sintomi di STC di 1.76 rispetto agli esposti “sotto AL”. Un andamento simile è emerso per la seconda definizione di caso [incidence rate ratios (IRR) “sopra TLV”, 1.37 (intervallo di confidenza al 95% (IC95%) 0.84–2.23)]. Gli esposti a “carico intermedio” risultano a maggior rischio per la STC [IRR per i sintomi, 3.31 (IC95% 2.39–4.59); IRR per sintomi e SCN positivo, 2.56 (IC95% 1.47–4.43)]. Abbiamo osservato una maggior forza di associazione tra HAL e la STC. CONCLUSIONI: Abbiamo trovato un aumento di rischio di sviluppare la STC all’aumentare del carico biomeccanico: l’aumento di rischio osservato già per gli esposti a “carico intermedio” suggerisce che gli attuali valori limite potrebbero non essere sufficientemente protettivi per alcuni lavoratori. Interventi di prevenzione vanno orientati verso attività manuali ripetitive.