Discrete Algorithms for Analysis of Genotype Data

Accessibility of high-throughput genotyping technology makes possible genome-wide association studies for common complex diseases. When dealing with common diseases, it is necessary to search and analyze multiple independent causes resulted from interactions of multiple genes scattered over the entire genome. The optimization formulations for searching disease-associated risk/resistant factors and predicting disease susceptibility for given case-control study have been introduced. Several discrete methods for disease association search exploiting greedy strategy and topological properties of case-control studies have been developed. New disease susceptibility prediction methods based on the developed search methods have been validated on datasets from case-control studies for several common diseases. Our experiments compare favorably the proposed algorithms with the existing association search and susceptibility prediction methods

HPV+ and HPV- head and neck squamous cell carcinoma by analysis of tumor microenvironment

Background: Head and neck squamous cell carcinomas (HNSCCs) are particularly aggressive epithelial tumors, that affect more than half a million patients worldwide each year. They represent a multi-factorial group of tumors caused by: alcohol, tobacco, and human papillomavirus (HPV) infections. Over the last ten years the overall 5-year survival rate of HNSCCs remained ~40–50%, inspite of significant improvement in clinical outcome of many tumor types. There are recent data that claim how some of these cells fulfill a suppressive role in the antitumor immune response. It is interesting that new clinical studies demonstrated that HPV (+) HNSCCs were among tumors with the highest immune infiltrates, while HPV (-) presented a reduced number of immune infiltrating cells. Conclusions: Recent researches prove that tumor microenvironment of HNSCC has an important role in tumor progression, aggressivity, metastasis process, in addition to genetic aberrations and molecular alterations of cancer cells. New researches in stromal composition of the HNSCC may be useful in understanding of mechanisms of different responses to therapy, also can be used as a target for therapeutic purposes. Cancer-associated fibroblasts and immune cells, as well as their products found in neck squamous cell carcinoma significantly influence the biological properties of this tumor. Smoking is one of the risk factors of occurrence of most HPV-associated tumors. Promoting smoking cessation should become an essential contributor to the treatment of cancer in all oncologic pathologies. In cases when patients can’t quit smoking completely within the shortest possible period of time, doctors should focus on harm reduction strategies – tobacco harm reduction

TRIP: A method for novel transcript reconstruction from paired-end RNA-seq reads

Preliminary experimental results on synthetic datasets generated with various sequencing parameters and distribution assumptions show that TRIP has increased transcriptome reconstruction accuracy compared to previous methods that ignore fragment length distribution information

Next-generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy

Next-generation sequencing to detect circulating tumor DNA is a minimally invasive method for tumor genotyping and monitoring therapeutic response. The majority of studies have focused on detecting circulating tumor DNA from patients with metastatic disease. Herein, we tested whether circulating tumor DNA could be used as a biomarker to predict relapse in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy. In this study, we analyzed samples from 38 early-stage triple-negative breast cancer patients with matched tumor, blood, and plasma. Extracted DNA underwent library preparation and amplification using the Oncomine Research Panel consisting of 134 cancer genes, followed by high-coverage sequencing and bioinformatics. We detected high-quality somatic mutations from primary tumors in 33 of 38 patients. TP53 mutations were the most prevalent (82%) followed by PIK3CA (16%). Of the 33 patients who had a mutation identified in their primary tumor, we were able to detect circulating tumor DNA mutations in the plasma of four patients (three TP53 mutations, one AKT1 mutation, one CDKN2A mutation). All four patients had recurrence of their disease (100% specificity), but sensitivity was limited to detecting only 4 of 13 patients who clinically relapsed (31% sensitivity). Notably, all four patients had a rapid recurrence (0.3, 4.0, 5.3, and 8.9 months). Patients with detectable circulating tumor DNA had an inferior disease free survival (p < 0.0001; median disease-free survival: 4.6 mos. vs. not reached; hazard ratio = 12.6, 95% confidence interval: 3.06-52.2). Our study shows that next-generation circulating tumor DNA sequencing of triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy can predict recurrence with high specificity, but moderate sensitivity. For those patients where circulating tumor DNA is detected, recurrence is rapid

Association testing by haplotype-sharing methods applicable to whole-genome analysis

We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS test, which tests whether a case and a control haplotype show less sharing than two random haplotypes. The significance of the HSS is determined using a variance estimate from the theory of U-statistics, whereas the significance of the CROSS test is estimated from a sequential randomization procedure. Both methods are fast and hence practical, even for whole-genome screens with high marker densities. We analyzed data sets of Problems 2 and 3 of Genetic Analysis Workshop 15 and compared HSS and CROSS to conventional association methods. Problem 2 provided a data set of 2300 single-nucleotide polymorphisms (SNPs) in a 10-Mb region of chromosome 18q, which had shown linkage evidence for rheumatoid arthritis. The CROSS test detected a significant association at approximately position 4407 kb. This was supported by single-marker association and HSS. The CROSS test outperformed them both with respect to significance level and signal-to-noise ratio. A 20-kb candidate region could be identified. Problem 3 provided a simulated 10 k SNP data set covering the whole genome. Three known candidate regions for rheumatoid arthritis were detected. Again, the CROSS test gave the most significant results. Furthermore, both the HSS and the CROSS showed better fine-mapping accuracy than straightforward haplotype association. In conclusion, haplotype sharing methods, particularly the CROSS test, show great promise for identifying disease gene loci

The influence of diabetes mellitus on blood vessels amount in case of breast cancer

Introduction. Breast cancer is one of the most common cancers in females worldwide. There are evidences that women with diabetes mellitus have a 40% higher risk of mortality. CD34 is a cell surface glycoprotein, which functions as a cellcell adhesion factor. Although its expression is traditionally related to hematopoietic cells, it is actually found on many other types of cells, endothelial too. Nowadays there are evidences that CD34 is a prognostic indicator by emphasizing its low expression in malignant tumors compared to benign ones. The aim of study was to determine the presence and numerical distribution of CD34+ vessels in the normal mammary gland, as well as in NST breast carcinomas, with and without diabetes mellitus type 2. Materials and methods. We processed immunohistochemically 58 invasive breast carcinomas of NST type. In 29 of cases, tumors were associated with diabetes. Results. The present study did not reveal any statistical and morphological differences in CD34 expression between compared groups. Conclusions. The expression of CD34 in breast cancer stroma is not homogenous, irrespective of association with diabetes mellitus type 2. The question if breast carcinoma and diabetes mellitus are concurrent or associated disorders remains open. Probably, the effect of carcinoma prevails in influencing the structure of the tumor microenvironment. We expect a further confirmation in larger study groups

Клинические и патологоанатомические особенности туберкулеза легких со смертельным исходом

IP Universitatea de Stat de Medicină și Farmacie Nicolae Testemițanu, Institutul de Pneumoftiziologie Chiril Draganiuc, IMSP Spitalul Clinic Municipal de FtiziopneumologieTuberculosis represents an epidemic burden for Republic of Moldova associated to high mortality index. Aim of the study is the assessment of clinical-morphopatological features of pulmoary tuberculosis with letal evolution. A study group of 27 new pulmonary tuberculosis cases hospitalized in the clinical subdivisions of Municipal Hospital of Pneumophtysiology dead in the period 1.01.2014–31.12.2014 was evaluated. All cases were investigated according to the national standards. It was established that men, young age individuals and urban residents predominated. The main rate represented the unemployed patients, individuals with low educational level, low living conditions. History of migration, emprisonment and HIV infection were few patients. Microscopic positive for acid fast bacilli were one third, late detected with chronic evolution – two thirds and MDR-TB infected patients - one fi fth of assessed group. Each second patient was dead in the fi rst year after the detection and every third in the fi rst two weeks. Necroptic examination identifi ed predominantly dystrophic changes of internal organs, pulmonary oedema and disseminated intravascular coagulation. Туберкулез представляет серьезную проблему общественного здравоохранения Республики Молдова, связанную с высоким показателем смертности. Целью исследования являлась оценка клинико-патологоанатомических особенностей туберкулеза легких со смертельным исходом. Были анализированы 27 историй новых случаев больных туберкулезом легких, госпитализированных в клинические отделения Муниципальной клинической больницы фтизиопневмологии г. Кишинэу в период с 1.01.2014 до 31.12.2014. Все случаи были исследованы в соответствии с Национальными стандартами. Было выявлено преобладание мужчин, молодого возраста, городских жителей. Большинство пациентов были безработными, с низким уровнем образования и низким уровнем жизни. Единичные случаи были выявлены с ко-инфекцией ВИЧ, историей заключения и миграции. Хроническое течение туберкулезного процесса и позднее выявление констатировали у 2/3 больных. Положительный результат микроскопии был выявлен у 1/3 больных. Туберкулез с множественной лекарственной устойчивостью был констатирован у 15 пациентов. Смерть наступила в течение первого года после выявления у каждого второго пациента, в течение первых двух недель после госпитализации – у каждого третьего. Аутопсия выявила отек легких, диссеминированное внутрисосудистое свертывание и дистрофические изменения внутренних органов

Single Cell Genome Amplification Accelerates Identification of the Apratoxin Biosynthetic Pathway from a Complex Microbial Assemblage

Filamentous marine cyanobacteria are extraordinarily rich sources of structurally novel, biomedically relevant natural products. To understand their biosynthetic origins as well as produce increased supplies and analog molecules, access to the clustered biosynthetic genes that encode for the assembly enzymes is necessary. Complicating these efforts is the universal presence of heterotrophic bacteria in the cell wall and sheath material of cyanobacteria obtained from the environment and those grown in uni-cyanobacterial culture. Moreover, the high similarity in genetic elements across disparate secondary metabolite biosynthetic pathways renders imprecise current gene cluster targeting strategies and contributes sequence complexity resulting in partial genome coverage. Thus, it was necessary to use a dual-method approach of single-cell genomic sequencing based on multiple displacement amplification (MDA) and metagenomic library screening. Here, we report the identification of the putative apratoxin. A biosynthetic gene cluster, a potent cancer cell cytotoxin with promise for medicinal applications. The roughly 58 kb biosynthetic gene cluster is composed of 12 open reading frames and has a type I modular mixed polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) organization and features loading and off-loading domain architecture never previously described. Moreover, this work represents the first successful isolation of a complete biosynthetic gene cluster from Lyngbya bouillonii, a tropical marine cyanobacterium renowned for its production of diverse bioactive secondary metabolites