Dario Basso

Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks.

Pediatric acute lymphoblastic leukemia (ALL) comprises genetically distinct subtypes. However, 25% of cases still lack defined genetic hallmarks. To identify genomic aberrancies in childhood ALL patients nonclassifiable by conventional methods, we performed a single nucleotide polymorphisms (SNP) array‐based genomic analysis of leukemic cells from 29 cases. The vast majority of cases analyzed (19/24, 79%) showed genomic abnormalities; at least one of them affected either genes involved in cell cycle regulation or in B‐cell development. The most relevant abnormalities were CDKN2A/9p21 deletions (7/24, 29%), ETV6 (TEL)/12p13 deletions (3/24, 12%), and intrachromosomal amplifications of chromosome 21 (iAMP21) (3/24, 12%). To identify variation in expression of genes directly or indirectly affected by recurrent genomic alterations, we integrated genomic and gene expression data generated by microarray analyses of the same samples. SMAD1 emerged as a down‐regulated gene in CDKN2A homozygous deleted cases compared with nondeleted. The JAG1 gene, encoding the Jagged 1 ligand of the Notch receptor, was among a list of differentially expressed (up‐regulated) genes in ETV6‐deleted cases. Our findings demonstrate that integration of genomic analysis and gene expression profiling can identify genetic lesions undetected by routine methods and potential novel pathways involved in B‐progenitor ALL pathogenesis.

Upregulation of translational machinery and distinct genetic subgroups characterise hyperdiploidy in multiple myeloma

Karyotypic instability, including numerical and structural chromosomal aberrations, represents a distinct feature of multiple myeloma (MM). About 40–50% of patients display hyperdiploidy, defined by recurrent trisomies of non‐random chromosomes. To molecularly characterise hyperdiploid (H) and nonhyperdiploid (NH) MM, we analysed the gene expression profiles of 66 primary tumours, and used fluorescence in situ hybridisation to investigate the major chromosomal alterations. The differential expression of 225 genes mainly involved in protein biosynthesis, transcriptional machinery and oxidative phosphorylation distinguished the 28 H‐MM from the 38 NH‐MM cases. The 204 upregulated genes in H‐MM mapped mainly to the chromosomes involved in hyperdiploidy, and the 29% upregulated genes in NH‐MM mapped to 16q. The identified transcriptional fingerprint was robustly validated on a publicly available gene expression dataset of 64 MM cases; and the global expression modulation of regions on the chromosomes involved in hyperdiploidy was verified using a self‐developed non‐parametric statistical method. H‐MM could be further divided into two distinct molecular and transcriptional entities, characterised by the presence of trisomy 11 and 1q‐extracopies/chromosome 13 deletion respectively. These data reinforce the importance of combining molecular cytogenetics and gene expression profiling to define a genomic framework for the study of MM pathogenesis and clinical management.

Transcriptional features of multiple myeloma patients with chromosome 1q gain

Abnormalities of chromosome 1 are among the most frequent chromosomal alterations in multiple myeloma (MM), being found in up to 45% of patients.1, 2 It has been reported that the short arm of chromosome 1 is preferentially involved in deletions, whereas the long arm is associated with amplification. The gain of 1q (1q/gain) can occur as isochromosomes, duplications or jumping translocations. It has been widely reported that 1q/gain MM patients are characterized by complex karyotypes and aggressive disease, and a close association with poor-risk genetic features, such as chromosome 13q deletion (13) and the t(4;14) translocation has also been described.1 It has been recently demonstrated that gains/amplification of 1q21 increase as the condition goes from smoldering to overt MM, thus suggesting that these regions contain critical genes for disease progression.2 These findings along with the limited information concerning specific transcriptional profiles prompted us to molecularly characterize 1q/gain MMs by FISH and microarray analyses.

A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions

MOTIVATION The systematic integration of expression profiles and other types of gene information, such as chromosomal localization, ontological annotations and sequence characteristics, still represents a challenge in the gene expression arena. In particular, the analysis of transcriptional data in context of the physical location of genes in a genome appears promising in detecting chromosomal regions with transcriptional imbalances often characterizing cancer. RESULTS A computational tool named locally adaptive statistical procedure (LAP), which incorporates transcriptional data and structural information for the identification of differentially expressed chromosomal regions, is described. LAP accounts for variations in the distance between genes and in gene density by smoothing standard statistics on gene position before testing the significance of their differential levels of gene expression. The procedure smooths parameters and computes p-values locally to account for the complex structure of the genome and to more precisely estimate the differential expression of chromosomal regions. The application of LAP to three independent sets of raw expression data allowed identifying differentially expressed regions that are directly involved in known chromosomal aberrations characteristic of tumors. AVAILABILITY Functions in R for implementing the LAP method are available at http://www.dpci.unipd.it/Bioeng/Publications/LAP.htm

Association between magnetic resonance signs of temporomandibular joint effusion and disk displacement

OBJECTIVE The aim of the present study was to evaluate the association between temporomandibular joint (TMJ) effusion and disk displacement by means of magnetic resonance (MR) imaging. METHODS One hundred and ninety-four patients were included in the study and underwent a bilateral MR of the TMJ at both closed mouth and maximum mouth opening positions. The association between TMJ effusion and disk displacement with or without reduction was assessed by means of 2 x 2 contingency tables and a permutation test for a categorical variable. RESULTS The results showed a statistically significant association between joint effusion and disk displacement without reduction (DDNR) (P = .008). There was no statistically significant association between TMJ effusion and normal disk position (P = .99) or disk displacement with reduction (DDR) (P = .43). CONCLUSIONS Although these results show a significant association between joint effusion and disk displacement without reduction, there remains uncertainty as to if the nonreducing displacement causes the effusion or vice versa. The present investigation also pointed out the absence of association between reducing disk displacement and effusion. These findings have to be put into relation with clinical and hystological findings.

Genomic expression during human myelopoiesis

BackgroundHuman myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization.ResultsGene expression data from 24 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset of 9,425 genes, each reliably associated to a unique genomic position and chromosomal coordinate. Lists of genes constitutively expressed or silent during myelopoiesis and of genes differentially expressed in commitment phase of myelopoiesis were first identified using a classical data analysis procedure. Then, the genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. This approach allowed identifying specific chromosomal regions significantly highly or weakly expressed, and clusters of differentially expressed genes and of transcripts related to specific functional modules.ConclusionThe analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions.

Temporomandibular joint click sound and magnetic resonance-depicted disk position: Which relationship?

AIMS The aim of this work was to evaluate the agreement between temporomandibular joint click sound and MR diagnoses of different disk positions. METHODS One hundred ninety-four (N=194) patients seeking treatment for temporomandibular disorders at the TMD Clinic, Department of Maxillofacial Surgery, University of Padova, Italy, underwent a bilateral magnetic resonance of the temporomandibular joints. The presence of click sounds was clinically assessed according to the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) and put into relation with different magnetic resonance (MR) diagnoses of disk-condyle position by means of permutation tests. RESULTS The proportion of joints with reducing and non-reducing disk displacement which provided a click sound during the clinical assessment was similar (45.6% vs. 48.9%, respectively), while the prevalence of the two MR diagnoses in joints with click sound were strongly different (25.3% vs. 40.1%, respectively. Thus, the MR diagnosis which appears to be more positively associated with click sounds is disk displacement without reduction. CONCLUSION There is a weak form of dependence between click and MR diagnosis, and the MR diagnosis of DDNR seems to be more positively associated with the presence of click sounds than the other categories, which did not show significant positive associations with click (i.e. there is negative association between click presence and normal disk position and no association between click presence and DDR joints.

A permutation test for umbrella alternatives

There is a wide variety of stochastic ordering problems where K groups (typically ordered with respect to time) are observed along with a (continuous) response. The interest of the study may be on finding the change-point group, i.e. the group where an inversion of trend of the variable under study is observed. A change point is not merely a maximum (or a minimum) of the time-series function, but a further requirement is that the trend of the time-series is monotonically increasing before that point, and monotonically decreasing afterwards. A suitable solution can be provided within a conditional approach, i.e. by considering some suitable nonparametric combination of dependent tests for simple stochastic ordering problems. The proposed procedure is very flexible and can be extended to trend and/or repeated measure problems. Some comparisons through simulations and examples with the well known Mack & Wolfe test for umbrella alternative and with Page’s test for trend problems with correlated data are investigated.

Exact Multivariate Permutation Tests for Fixed Effects in Mixed-Models

A test for the fixed effect in mixed-models is proposed. It is based on permutation strategy and is exact. The testing approach presented is very general and the class of models covered is very broad. Multivariate responses with different type of variables (e.g., continuous, categorical, and ranks) are usually tested with separated models and the overall test are usually reached through Bonferroni-like combinations, i.e., without taking into account the joint distribution of the test statistics. On the contrary, in this approach the joint distribution is immediately obtained and the dependence among tests is taken into account in the overall test. The methods are implemented in the R package flip, freely available on CRAN.

On Synchronized Permutation Tests in Two-Way ANOVA

In I × J balanced factorial designs units are not exchangeable between blocks since their expected values depend on received treatments. It does not seem possible, therefore, to obtain exact and separate tests to respectively assess main factor and interaction effects. Parametric two-way ANOVA F tests are exact tests only under assumption of normal homoschedastic errors, but they are also positively correlated. Instead, it is possible to obtain exact, separate and uncorrelated permutation tests at least for main factors by introducing a restricted kind of permutations, named synchronized permutations. Since these tests are conditional on observed data, they are distribution-free and may be shown to be almost as powerful as their parametric counterpart under normal errors. We obtain the expression of the correlation between the main factor ANOVA tests as a function of the number of replicates in each block, the number of main factor levels and their noncentrality parameters.