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BACKGROUND Hereditary spastic paraplegia presents spasticity as the main clinical manifestation, reducing gait quality and producing incapacity. Management with botulinum toxin type A (BoNT-A) is not well elucidated. The objective of the current study was to evaluate the efficacy and safety of BoNT-A in patients with hereditary spastic paraplegias. METHODS This was a double-blind, randomized, placebo-controlled crossover trial. Each participant was randomly assigned to receive 1 injection session of either BoNT-A (100 IU/2 mL of Prosigne in each adductor magnus and each triceps surae) or saline 0.9% (2 mL). The primary outcome measure was change from baseline in maximal gait velocity, and secondary outcome measures included changes in gait at self-selected velocity, spasticity, muscle strength, Spastic Paraplegia Rating Scale, pain, fatigue, and subjective perception of improvement. We also looked at adverse events reported by the patients. RESULTS We enrolled 55 patients, 36 of whom were men and 41 with the pure phenotype. Mean age was 43 ± 13.4 years (range, 19-72 years), mean age of onset waws 27 ± 13.1 years (range

Made available in DSpace on 2020-12-12T02:06:26Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-12-01 Type 2 diabetes mellitus (T2DM), dyslipidemia and periodontitis are frequently associated pathologies; however, there are no studies showing the peripheral blood transcript profile of these combined diseases. Here we identified the differentially expressed genes (DEGs) of circulating lymphocytes and monocytes to reveal potential biomarkers that may be used as molecular targets for future diagnosis of each combination of these pathologies (compared to healthy patients) and give insights into the underlying molecular mechanisms of these diseases. Study participants (n = 150) were divided into groups: (H) systemically and periodontal healthy (control group); (P) with periodontitis, but systemically healthy; (DL-P) with dyslipidemia and periodontitis; (T2DMwell-DL-P) well-controlled type 2 diabetes mellitus with dyslipidemia and periodontitis; and (T2DMpoorly-DL-P) poorly-controlled type 2 diabetes mellitus with dyslipidemia and periodontitis. We preprocessed the microarray data using the Robust Multichip Average (RMA) strategy, followed by the RankProd method to identify candidates for DEGs. Furthermore, we performed functional enrichment analysis using Ingenuity Pathway Analysis and Gene Set Enrichment Analysis. DEGs were submitted to pairwise comparisons, and selected DEGs were validated by quantitative polymerase chain reaction. Validated DEGs verified from T2DMpoorly-DL-P versus H were: TGFB1I1, VNN1, HLADRB4 and CXCL8; T2DMwell-DL-P versus H: FN1, BPTF and PDE3B; DL-P versus H: DAB2, CD47 and HLADRB4; P versus H: IGHDL-P, ITGB2 and HLADRB4. In conclusion, we identified that circulating lymphocytes and monocytes of individuals simultaneously affected by T2DM, dyslipidemia and periodontitis, showed an altered molecular profile mainly associated to inflammatory response, immune cell trafficking, and infectious disease pathways. Altogether, these results shed light on novel potential targets for future diagnosis, monitoring or development of targeted therapies for patients sharing these conditions. Department of Diagnosis and Surgery School of Dentistry at Araraquara UNESP- São Paulo State University Department of Morphology Genetics Orthodontics and Pediatric Dentistry School of Dentistry at Araraquara UNESP- São Paulo State University Molecular Genomics and Therapeutics Section Genetics of Development and Disease Branch National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 10 Center Drive Building 10 Room 9D11 Department of Surgery Uniformed Services University of the Health Sciences and Henry Jackson Foundation for the Advancement of Military Medicine Postgraduate Program in Sciences of the University of Franca Department of Genetics Faculty of Medicine of Ribeirão Preto USP – University of São Paulo Department of Biology Faculty of Philosophy Sciences and Letters of Ribeirão Preto USP –University of São Paulo Department of Medical Genetics and Medicine Genomics University of Campinas – UNICAMP Department of Statistics Institute of Mathematics Statistics and Scientific Computing University of Campinas Department of Periodontology University of North Carolina at Chapel Hill – UNC School of Dentistry Advanced Research Center in Medicine Union of the Colleges of the Great Lakes (UNILAGO) Department of Diagnosis and Surgery School of Dentistry at Araraquara UNESP- São Paulo State University Department of Morphology Genetics Orthodontics and Pediatric Dentistry School of Dentistry at Araraquara UNESP- São Paulo State University

Molecular diagnosis is important to provide accurate genetic counseling of skeletal dysplasias (SD). Although next-generation sequencing (NGS) techniques are currently the preferred methods for analyzing these conditions, some of the published results have not shown a detection rate as high as it would be expected. The present study aimed to assess the diagnostic yield of targeted NGS combined with Sanger sequencing (SS) for low-coverage exons of genes of interest and exome sequencing (ES) in a series of patients with rare SD and use two patients as an example of our strategy. This study used two different in-house panels. Of 93 variants found in 88/114 (77%) patients, 57 are novel. The pathogenic variants found in the following genes: B3GALT6, PCYT1A, INPPL1, LIFR, of four patients were only detected by SS. In conclusion, the high diagnostic yield reached in the present study can be attributed to both a good selection of patients and the utilization of the SS for the insufficiently covered regions. Additionally, the two case reports-a patient with acrodysostosis related to PRKAR1A and another with ciliopathy associated with KIAA0753, add new and relevant clinical information to the current knowledge.

We conducted a two-stage association study on patients with oropharynx (OP) squamous cell carcinoma (SCC) and healthy controls to identify single nucleotide variants (SNVs) located at the microRNA (miR)-binding sites of carcinogenesis genes associated with risk and prognosis of the disease. In stage 1, 49 patients and 49 controls were analyzed using Genome-Wide Human SNV Arrays to identify variants in the 3′-untranslated region (3′-UTR) of carcinogenesis-related genes, and one SNV was selected for data validation in stage 2 by TaqMan assays in 250 OPSCC patients and 250 controls. The ERP29 c.*293A > G (rs7114) SNV located at miR-4421 binding site was selected for data validation among 46 SNVs. The ERp29 and miR-4421 levels were evaluated by quantitative-PCR and Western blotting. Interaction between miR-4421 with 3′-UTR of ERP29 was evaluated by luciferase reporter assay. Event-free survival (EFS) was calculated by Kaplan–Meier and Cox methods. ERP29 GG variant genotype was more common in OPSCC patients than in controls (6.4% vs 3.6%, p = 0.02; odds ratio: 5.67; 95% confidence interval (CI) 1.27–25.26). Shorter EFS were seen in the base of tongue (BT) SCC patients with GG genotype (0.0% vs 36.2%, p = 0.01; hazard ratio: 2.31; 95% CI: 1.03–5.15). Individuals with ERP29 AG or GG genotypes featured lower levels of ERP29 mRNA (p = 0.005), ERp29 protein (p p = 0.02). The miR-4421 showed more efficient binding with 3′-UTR of the variant G allele when compared with wild-type allele A (p = 0.001). Our data suggest that ERP29 rs7114 SNV may alter the risk and prognosis of OPSCC due to variation in the ERp29 production possibly modulated by miR-4421.

Cardiovascular disease (CVD) and venous thromboembolism (VTE) figure among the main causes of morbidity and mortality in modern societies. Although associated with distinct pathogenic mechanisms, epidemiological, experimental and clinical trial data suggest that the mechanisms responsible for arterial and venous thrombosis are at least partially overlapped. Herein we aimed to explore shared and discordant pathways involved in the pathogenesis of VTE and CVD at the transcriptomic level and to validate the results in independent cohorts. Five public datasets of gene expression data from VTE and CVD (myocardial infarction, peripheral arterial occlusive disease and stroke) patients were analyzed using an integrative bioinformatic strategy. A machine/statistical learning method was used to derive classifiers for the discrimination of VTE and CVD, and tested in independent datasets. Two sets of genes that were commonly (n = 472) or divergently (n = 124) expressed in CVD and VTE were identified. Genes and pathways associated with innate immune function were over-represented in both conditions, along with pathways associated with complement and hemostasis. Pathways associated with neutrophil activation and with IL-1 signaling were also enriched in CVD compared to VTE. The gene expression signature of VTE more closely resembled the pattern of cardioembolic stroke than the patterns of acute myocardial infarction, ischemic stroke and peripheral arterial occlusive disease. Classifiers derived from these gene lists accurately discriminated patients with VTE and CVD from independent cohorts. In conclusion, our results add a new set of data at the transcriptomic level for future studies between arterial and venous thrombosis. Strengths and limitations of this study Our results represent the first comparison of venous and arterial thrombosis at the transcriptomic level. Our main result was the demonstration that immunothrombosis pathways are important to the pathophysiology of these conditions, also at the transcriptomic level. A specific signature for venous and arterial thrombosis was described, and validated in independent cohorts. The limited number of public repositories with gene expression data from patients with venous thromboembolism limits the representation of these patients in our analyses. In order to gather a meaningful number of studies with gene expression data we had to include patients in different time-points since the index thrombotic event, which might have increased the heterogeneity of our population.

Admixed American populations have different global proportions of European, Sub-Saharan African, and Native-American ancestry. However, individuals who display the same global ancestry could exhibit remarkable differences in the distribution of local ancestry blocks. We studied for the first time the distribution of local ancestry across the genome of 264 Brazilian admixed individuals, ascertained within the scope of the Brazilian Initiative on Precision Medicine. We found a decreased proportion of European ancestry together with an excess of Native-American ancestry on chromosome 8p23.1 and showed that this is due to haplotypes created by chromosomal inversion events. Furthermore, Brazilian non-inverted haplotypes were more similar to Native-American haplotypes than to European haplotypes, in contrast to what was found in other American admixed populations. We also identified signals of recent positive selection on chromosome 8p23.1, and one gene within this locus, PPP1R3B, is related to glycogenesis and has been associated with an increased risk of type 2 diabetes and obesity. These findings point to a selection event after admixture, which is still not entirely understood in recent admixture events., This study was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil) grants BEPE-PD #2016/14423-9, and CEPID-BRAINN #2013/07559-3 IL-C and F.C. were also supported by grants from CNPq (Conselho Nacional de Pesquisa, Brazil). A.M.S., L.R.A. and D.C. were also supported by the Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2014SGR866 and ‘Unidad de Excelencia María de Maeztu’ funded by MINECO (MDM-2014-0370).

Background As the most incident tumor among women worldwide, breast cancer is a heterogeneous disease. Tremendous efforts have been made to understand how tumor characteristics as histological type, molecular subtype, and tumor microenvironment collectively influence disease diagnosis to treatment, which impact outcomes. Differences between populations and environmental and cultural factors have impacts on the origin and evolution of the disease, as well as the therapeutic challenges that arise due to these factors. We, then, compared copy number variations (CNVs) in mucinous and nonmucinous luminal breast tumors from a Brazilian cohort to investigate major CNV imbalances in mucinous tumors versus non‐mucinous luminal tumors, taking into account their clinical and pathological features. Methods 48 breast tumor samples and 48 matched control blood samples from Brazilian women were assessed for CNVs by chromosome microarray. Logistic regression and random forest models were used in order to assess CNVs in chromosomal regions from tumors. Results CNVs that were identified in chromosomes 1, 5, 8, 17, 19, and 21 classify tumors according to their histological type, ethnicity, disease stage, and familial history. Conclusion Copy number alterations described in this study provide a better understanding of the landscape of genomic aberrations in mucinous breast cancers that are associated with clinical features.

Antipsychotics are the main line of treatment for schizophrenia. Even though there are significant rates of medication drop out due to side effects and limited response of approximately 50% of patients. This is likely due to incomplete knowledge in how these drugs act at the molecular level. To improve treatment efficacy during the critical early stages of schizophrenia, we aimed to identify molecular signatures at baseline (T0) for prediction of a positive response to the atypical antipsychotics olanzapine and risperidone after 6 weeks (T6) treatment. Blood plasma samples were processed and analyzed by label-free quantitative shotgun proteomics using two-dimensional nano-liquid chromatography, coupled online to a Synapt G2-Si mass spectrometer. Data were obtained in MSE mode (data-independent acquisition) in combination with ion-mobility (HDMSE). We were able to identify a potential panel of proteins that might predict a positive outcome to olanzapine and risperidone treatment. The proteins found to be differentially abundant between T0 and T6 in good responders compared to poor responders were analyzed in silico for enrichment pathways and found to be mostly involved with immune system functions. This data can contribute to better understand the biochemical signaling mechanisms peripherally triggered by antipsychotic medication and eventually used to develop surrogate biomarker tests to help improve treatment outcomes and guide development of new treatment approaches. Significance The application of proteomics to the study of the atypical antipsychotic effects on the blood plasma proteome from schizophrenia patients could help in the search for new targets to improve the current therapies, as well as in the development of new therapeutic strategies. In this original article, we provided clues that atypical antipsychotics might be associated with good response by modulating proteins that play a role in inflammation and/or immune system pathways. In addition, the proteins with differential abundance found in the comparison between good and poor responders at the baseline might compose a signature for prediction of response effectiveness.

As sequencing costs drop with the constant improvements in the field, next-generation sequencing becomes one of the most used technologies in biological research. Sequencing technology allows the detailed characterization of events at the molecular level, including gene expression, genomic sequence and structural variants. Such experiments result in billions of sequenced nucleotides and each one of them is associated to a quality score. Several software tools allow the quality assessment of whole experiments. However, users need to switch between software environments to perform all steps of data analysis, adding an extra layer of complexity to the data analysis workflow. We developed Rqc, a Bioconductor package designed to assist the analyst during assessment of high-throughput sequencing data quality. The package uses parallel computing strategies to optimize large data sets processing, regardless of the sequencing platform. We created new data quality visualization strategies by using established analytical procedures. That improves the ability of identifying patterns that may affect downstream procedures, including undesired sources technical variability. The software provides a framework for writing customized reports that integrates seamlessly to the R/Bioconductor environment, including publication-ready images. The package also offers an interactive tool to generate quality reports dynamically. Rqc is implemented in R and it is freely available through the Bioconductor project (https://bioconductor.org/packages/Rqc/) for Windows, Linux and Mac OS X operating systems.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

Objectives The objective of this study was to investigate the relationship between baseline resting heart rate and incidence of heart failure (HF) and global and regional left ventricular (LV) dysfunction. Background The association of resting heart rate to HF and LV function has not been well described in an asymptomatic multi-ethnic population. Methods Resting heart rate was measured in participants in the MESA (Multi-Ethnic Study of Atherosclerosis) trial at inclusion. Incident HF was registered (n = 176) during follow-up (median 7 years) in those who underwent cardiac magnetic resonance imaging (n = 5,000). Changes in ejection fraction (ΔEF) and peak circumferential strain (Δecc) were measured as markers of developing global and regional LV dysfunction in 1,056 participants imaged at baseline and 5 years later. Time to HF (Cox model) and Δecc and ΔEF (multiple linear regression models) were adjusted for demographics, traditional cardiovascular risk factors, calcium score, LV end-diastolic volume, and mass in addition to resting heart rate. Results Cox analysis demonstrated that for 1 beat/min increase in resting heart rate, there was a 4% greater adjusted relative risk for incident HF (hazard ratio: 1.04; 95% CI: 1.02 to 1.06; p Conclusions Elevated resting heart rate was associated with increased risk for incident HF in asymptomatic participants in the MESA trial. Higher heart rate was related to development of regional and global LV dysfunction independent of subclinical atherosclerosis and coronary heart disease. (Multi-Ethnic Study of Atherosclerosis [MESA]; NCT00005487 )

Epilepsy is misdiagnosed in up to 25% of patients, leading to serious and long-lasting consequences. Recently, circulating microRNAs have emerged as potential biomarkers in a number of clinical scenarios. The purpose of this study was to identify and to validate circulating microRNAs that could be used as biomarkers in the diagnosis of epilepsy. Quantitative real-time PCR was used to measure plasma levels of three candidate microRNAs in two phases of study: an initial discovery phase with 14 patients with mesial temporal lobe epilepsy (MTLE), 13 with focal cortical dysplasia (FCD) and 16 controls; and a validation cohort constituted of an independent cohort of 65 patients with MTLE and 83 controls. We found hsa-miR-134 downregulated in patients with MTLE (p = 0.018) but not in patients with FCD, when compared to controls. Furthermore, hsa-miR-134 expression could be used to discriminate MTLE patients with an area under the curve (AUC) of 0.75. To further assess the robustness of hsa-miR-134 as a biomarker for MTLE, we studied an independent cohort of 65 patients with MTLE, 27 of whom MTLE patients were responsive to pharmacotherapy, and 38 patients were pharmacoresistant and 83 controls. We confirmed that hsa-miR-134 was significantly downregulated in the plasma of patients with MTLE when compared with controls (p < 0.001). In addition, hsa-miR-134 identified patients with MTLE regardless of their response to pharmacotherapy or the presence of MRI signs of hippocampal sclerosis. We revealed that decreased expression of hsa-miR-134 could be a potential non-invasive biomarker to support the diagnosis of patients with MTLE.

Background: The formation of thrombi inside arteries and veins is a process that underlies the pathogenesis of the most important causes of morbidity and mortality in the modern world: namely cardiovascular diseases (CVD), a term encompassing acute myocardial infarction (AMI), ischemic stroke (IS) and peripheral arterial occlusive disease (PAOD); and venous thromboembolism (VTE). So far, the discussion on how much CVD and VTE share and differ in terms of pathological mechanisms has been based on morphological studies about the composition of venous and arterial thrombi, epidemiological studies about the association and common risk factors of CVD and VTE, and inferences upon the cellular and molecular mechanisms of each of these conditions. Objective: Here we introduce a new strategy to obtain insights on the association of CVD and VTE based on the comparison of transcriptomic signatures associated with these conditions. Methods: publicly available datasets (from Gene Expression Omnibus Database) of gene expression data from patients with AMI, IS, PAOD, cardioembolic stroke (CS), and VTE were identified and retrieved. Stringent selection criteria regarding patient selection, microarray methods and RNA sources were applied to limit heterogeneity as much as possible. A meta-analysis was performed using a robust statistical method, allowing the identification of genes that are commonly expressed in the same direction in all five conditions. We also identified a list of genes that were divergently expressed between VTE and CVD. Both lists were then used for functional and correlation analyses aimed to gain additional insights on the molecular pathogenesis of arterial and venous thrombosis. Results: Five datasets fulfilled the inclusion criteria and were included in our analyses: the dataset of VTE patients originally compared gene expression levels in patients with single or recurrent VTE with healthy controls (GSE19151); three datasets involving CVD compared gene expression levels of patients with PAOD (GSE 27034), AMI (GSE 48060) and IS (GSE 22255) with study-specific healthy controls. A dataset comparing patients with CS (GSE58294) and healthy controls was also included. In total, data from 163 adult patients and 145 healthy controls were analyzed. The meta-analysis generated a list of 473 genes whose expression was changed in the same direction in all five conditions (168 up-regulated and 305 down-regulated). The top 20 up- and down-regulated genes are shown in figure 1a. The functional analysis of the 168 up-regulated genes identified pathways associated with hemostasis, innate immunity and neutrophil activation and degranulation as overrepresented in patients compared to controls. When gene expression fold-change levels were analyzed across all five diseases, a lower correlation coefficient was observed between VTE and CVD, when compared to correlations observed within CVD such as AMI and PAOD (fig.1b). Moreover, an unsupervised cluster analysis showed that the expression pattern of these 473 genes in AMI, PAOD and IS are more closely related to each other than to VTE and CS (fig. 1a). When the 124 genes that were divergently expressed between VTE and CVD were functionally analyzed, genes that were upregulated only in CVD were associated with activation of innate immunity, whereas genes that were upregulated in VTE were associated with cell maintenance pathways. Discussion and conclusion: our comparative analyses provide new data on how venous and arterial thrombosis differ at a transcriptional level. Specifically, we identified a set of 473 genes whose expression levels were consistently changed in both CVD and VTE, and 124 genes with divergent expression levels between these conditions. The prominence of pathways associated with hemostasis, innate immunity and neutrophil function in both CVD and VTE are in line with the concept of immunothrombosis in the pathogenesis of thrombotic disorders. The clustering of MI, IS and PAOD compared to VTE and CS is coherent with the concept that CS is caused by thrombi formed in a different microenvironment than IS. Additional studies are warranted on the role of these genes and pathways in the pathogenesis of CVD and VTE, as well as on the biological relevance of these thrombosis-specific gene expression signatures in other thrombotic disorders. Disclosures De Paula: Hematology and Transfusion Medicine Center, University of Campinas: Employment.

Genomic changes such as copy number alterations are one of the major underlying causes of human phenotypic variation among normal and disease subjects. Array comparative genomic hybridization (CGH) technology was developed to detect copy number changes in a high-throughput fashion. However, this technology provides only a >30-kb resolution, which limits the ability to detect copy number alterations spanning small regions. Higher resolution technologies such as single nucleotide polymorphism (SNP) microarrays allow detection of copy number alterations at least as small as several thousand base pairs. Unfortunately, strong probe effects and variation introduced by sample preparation procedures have made single-point copy number estimates too imprecise to be useful. Various groups have proposed statistical procedures that pool data from neighboring locations to successfully improve precision. However, these procedure need to average across relatively large regions to work effectively, thus greatly reducing resolution. Recently, regression-type models that account for probe effects have been proposed and appear to improve accuracy as well as precision. In this paper, we propose a mixture model solution, specifically designed for single-point estimation, that provides various advantages over the existing methodology. We use a 314-sample database, to motivate and fit models for the conditional distribution of the observed intensities given allele-specific copy number. We can then compute posterior probabilities that provide a useful prediction rule as well as a confidence measure for each call. Software to implement this procedure will be available in the Bioconductor oligo package (www.bioconductor.org).

This paper describes the results of a detailed study relating the performance of undergraduate students admitted to Brazil’s State University of Campinas (Unicamp) from 1994 through 1997 and their socioeconomic and educational background. The study is based on a hierarchical model for the relevant variables involved. The main result is that students coming from disadvantaged backgrounds, in both educational and socioeconomic aspects, have a higher relative performance than their complementary group. We report on an affirmative action programme established at Unicamp for undergraduate admissions, partially motivated by those findings, and present evidence from an initial evaluation showing the programme’s positive impact. Finally, we comment on the effect this study and the Unicamp programme have had on the present debate about affirmative action access policies in Brazilian higher education institutions. by Renato H.L. Pedrosa, J. Norberto W. Dachs, Rafael P. Maia and Cibele Y. Andrade, Benilton S. Carvalho

Objectives This study sought to determine whether increased carotid intima-media thickness (IMT) is related to reduced regional myocardial function in participants of the Multi-Ethnic Study of Atherosclerosis (MESA). Background Carotid artery IMT is an established index of subclinical atherosclerosis, and tagged magnetic resonance imaging (MRI) can detect incipient alterations of segmental function that precede overt myocardial failure. Methods The MESA study is a prospective observational study including four ethnic groups free from clinical cardiovascular disease. Peak midwall systolic circumferential strain (ECC) and regional strain rates were calculated by harmonic phase from tagged MRI data of 500 participants. Systolic ECC and diastolic strain rate were regressed on IMT of the common carotid artery defined by ultrasound, with adjustments for body mass index, blood pressure, cholesterol, diabetes, smoking, left ventricular hypertrophy, C-reactive protein, age, and gender. Results The mean participant age was 66 ± 10 years (mean ± SD). Among the 58 participants, 4% were male and the interquartile (25th to 75th percentile) range for IMT was 0.25 mm. Multiple linear regression analyses showed that increased IMT was related to reduced systolic regional function (less shortening ECC) in all myocardial regions (p Conclusions Greater carotid IMT is associated with alterations of myocardial strain parameters reflecting reduced systolic and diastolic myocardial function. These observations indicate a relationship between subclinical atherosclerosis and incipient myocardial dysfunction in a population free of clinical heart disease.

We thank Drs. Palatini and Julius for their interest in our recent work [(1)][1]. Indeed, in the MESA (Multi-Ethnic Study of Atherosclerosis) study, with participants without cardiovascular disease (CV) at enrollment, we found an increased risk for incident heart failure (HF) among those with

Summary: Illumina produces a number of microarray-based technologies for human genotyping. An Infinium BeadChip is a two-color platform that types between 105 and 106 single nucleotide polymorphisms (SNPs) per sample. Despite being widely used, there is a shortage of open source software to process the raw intensities from this platform into genotype calls. To this end, we have developed the R/Bioconductor package crlmm for analyzing BeadChip data. After careful preprocessing, our software applies the CRLMM algorithm to produce genotype calls, confidence scores and other quality metrics at both the SNP and sample levels. We provide access to the raw summary-level intensity data, allowing users to develop their own methods for genotype calling or copy number analysis if they wish. Availability and Implementation: The crlmm Bioconductor package is available from http://www.bioconductor.org. Data packages and documentation are available from http://rafalab.jhsph.edu/software.html. Contact: mritchie@wehi.edu.au; rafa@jhu.edu

High-throughput technologies are widely used in the field of functional genomics and used in an increasing number of applications. For many ‘wet lab’ scientists, the analysis of the large amount of data generated by such technologies is a major bottleneck that can only be overcome through very specialized training in advanced data analysis methodologies and the use of dedicated bioinformatics software tools. In this article, we wish to discuss the challenges related to delivering training in the analysis of high-throughput sequencing data and how we addressed these challenges in the hands-on training courses that we have developed at the European Bioinformatics Institute.

Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This paper illustrates a workflow for the estimation of allele-specific copy number and integration of the marker-level estimates with complimentary Bioconductor software for inferring regions of copy number gain or loss. All analyses are performed in the statistical environment R.

Objective— The pathophysiology of left ventricular (LV) dysfunction, particularly in the setting of a preserved ejection fraction (EF), remains unclear. Few studies have investigated the relationship between arterial compliance and LV function in humans, and none used cardiovascular MRI. Methods and Results— We sought to determine whether arterial compliance is related to regional myocardial function among participants of the Multi-Ethnic Study of Atherosclerosis (MESA). Arterial compliance was assessed using carotid ultrasound measurements to calculate the distensibility coefficient (DC) and Young’s modulus (YM). Circumferential systolic (SR S ) and diastolic (SR E ) strain rates were calculated by harmonic phase (HARP) from tagged MRI. Associations between arterial compliance and indices of ventricular function were adjusted for cardiovascular risk factors. We found a significant association between arterial compliance and SR S in all myocardial regions ( P E in the lateral and septal wall regions ( P S across all LV segments and slices, even after adjustment for cardiovascular risk factors and LV mass. In regression analyses, a significant relationship between arterial compliance and SR E in the septal and antero-apical walls was also found and remained significant after multivariable adjustment. Conclusion— Arterial stiffness is associated with early and asymptomatic impairment of systolic as well as diastolic myocardial function. Further studies are needed to elucidate role of vascular compliance in the development of ventricular dysfunction and failure.

6073 Background: Recently, we found 6.609 genetic single nucleotide polymorphisms (SNPs) with distinct frequencies between base of tongue squamous cell carcinoma (BTSCC) patients and controls. The study was performed using high-resolution DNA microarrays genotyping (Affymetrix). The SNPs identified never have been previously described with BTSCC risk. Some SNPs of interest were located in genes related to cell cycle (ERP29, LEF1, MCC and PTCH1) and DNA transcription (IKBKAP and ZNF415) and they were selected to validation process. Objective: Validate the SNPs ERP29 c.*293A>G (rs7114); LEF1 c.*1213A>G (rs2107028) and g.127267A>G (rs4245926); MCC c.*5077A>G (rs7033); PTCH1 g.27369025G>A (rs16909856) and g.27369324G>A (rs16909859); IKBKAP c.3214T>A (rs3204145) and ZNF415 c.*443A>G (rs3814) associated to BTSCC risk. Methods: Genomic DNA from 49 BTSCC patients and 49 controls was genotyping by TaqMan assays (Applied Biosystems). The differences between groups were analyzed by logistic regression model. Power analysis (PA) was used to verify the effect of sample size on the results obtained. Results: Eight SNPs identified by Affymetrix were validated by TaqMan assays. The frequencies of ERP29 c.*293AG+GG (30 vs 11%, P=0.03; PA=65%), LEF1 c.*1213AA+AG (95 vs 80%, P=0.02; PA=61%) and g.127267AA+AG (93 vs 78%, P=0.02; PA=56%), MCC c.*5077AA+AG (85 vs 64%, P=0.008; PA=67%), PTCH1 g.27369025GG+GA (90 vs 73%, P=0.005; PA=58%) and g.27369324GG+GA (90 vs 73%, P=0.008; PA=58%), IKBKAP c.3214TT+TA (90 vs 72%, P=0.01; PA=62%) and ZNF415 c.*443AA+AG (59 vs 41%, P=0.02; PA=43%) were more common in patients than in controls. Individuals with these genotypes were at 2.9(CI95%: 1.1-8.4), 3.9 (CI95%: 1.4-11.2), 4.0 (CI95%: 1.2-14.7), 3.5 (CI95%: 1.2-11.9), 5.0 (CI95%: 1.7-16.9), 4.5 (CI95%: 1.5-15.2), 4.1 (CI95%: 1.4-12.9), and 3.9 (CI95%: 1.2-13.7)-fold increased risks for BTSCC than others, respectively. Conclusions: Our data present for the first time evidence that inherited abnormalities in ERP29, MCC, LEF1, PTCH1, IKBKAP, and ZNF415 genes may be important determinants of BTSCC. Financial support: FAPESP and FINEP.

e16041 Background: Inherited genetic alterations, such as single nucleotide polymorphisms (SNPs), were described in association with oropharyngeal cancer risk in few reports with restrict number of SNPs analyzed. Base of tongue (BT) squamous cell carcinoma (SCC) is a common tumor of oropharynx; however, the association of SNPs and BTSCC risk is not clarified and, therefore, this was the aim of this study. Methods: DNA from 49 BTSCC patients and 49 controls was extracted using the QIamp kit (Qiagen). Each sample was genotyped individually using DNA high-resolution microarrays containing 500.568 SNPs (SNP array 5.0, Affymetrix). Further sample processing, including digestion, adaptor ligation, amplification, fragmentation, labeling, hybridization, washing and scanning was assayed according to the standard protocol. Genotype data were acquired by genotyping calling of samples using crlmm algorithm provided by Bioconductor software. The differences between groups were analyzed by the logistic regression model. The SNPs localized in genes of interest were selected by data base analysis in DAVID and NCBI websites. The validation of selected SNPs was performed by RT-PCR, using TaqMan SNP Genotyping Assays (Applied Biosystems) in all samples studied. Results: We observed 6.609 SNPs with distinct frequencies between BTSCC patients and controls. Fifty-two SNPs (0.8%) were located in coding sequence (CDS), 51 (0.8%) in 3’ and 5’- untranslated regions (UTR), 3.461 (52.4%) in up or downstream regions (DWS) and 3.045 (46.0%) in introns. Ten SNPs were selected and validated in study, including those localized in genes related to cell cycle (3’-UTR: ERP29, rs7114; MCC, rs7033; DWS: LEF1, rs2107028 and rs4245926; PTCH1, rs16909856 and rs16909859), transcription process (CDS: IKBKAP, rs3204145; 3’-UTR: ZNF415, rs3814), and cell adhesion (CDS: COL22A1, rs2292927; DWS: LY6K, rs1995467). Conclusions: Our preliminary results suggest that SNPs in genes involved in tumor development may predispose individuals to BTSCC. However, these results should be confirmed by functional protein studies and validated in larger epidemiological studies. Financial support: FAPESP and FINEP.