Search results for: Mahya Mehrmohamadi

Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

Abstract:

In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

Procedia PDF Downloads 149

Authors: Mahya Naghipoor

Abstract:

Purpose: Non-small cell lung cancer (NSCLC) is the most common lung cancer type. Epidermal growth factor receptor (EGFR) mutation is the main reason which causes NSCLC. Computed tomography (CT) is used for diagnosis and prognosis of lung cancers because of low price and little invasion. Semantic analyses of qualitative CT features are based on visual evaluation by radiologist. However, the naked eye ability may not assess all image features. On the other hand, radiomics provides the opportunity of quantitative analyses for CT images features. The aim of this review study was comparing accuracy of semantic and radiomics features in prognosis of EGFR mutation in NSCLC. Methods: For this purpose, the keywords including: non-small cell lung cancer, epidermal growth factor receptor mutation, semantic, radiomics, feature, receiver operating characteristics curve (ROC) and area under curve (AUC) were searched in PubMed and Google Scholar. Totally 29 papers were reviewed and the AUC of ROC analyses for semantic and radiomics features were compared. Results: The results showed that the reported AUC amounts for semantic features (ground glass opacity, shape, margins, lesion density and presence or absence of air bronchogram, emphysema and pleural effusion) were %41-%79. For radiomics features (kurtosis, skewness, entropy, texture, standard deviation (SD) and wavelet) the AUC values were found %50-%86. Conclusions: In conclusion, the accuracy of radiomics analysis is a little higher than semantic in prognosis of EGFR mutation in NSCLC.

Keywords: lung cancer, radiomics, computer tomography, mutation

Procedia PDF Downloads 165

Authors: Mahya Saffarinia

Abstract:

The family has existed as a natural unit of human relations from the beginning of creation and life of human society until now and has been the core of the relationship between women, men, and children. However, in the field of human relations, the definition of family, related rights and duties, principles governing the family, the impact of the family on other individual or social phenomena and various other areas have changed over time, especially in recent decades, and the subject has now become one of the important categories of studies including interdisciplinary studies. It is difficult to provide an accurate and comprehensive definition of the family, and in the context of different cultures, customs, and legal systems, different definitions of family are presented. The meaning of legal principles governing the family is the general rules of law that determine the organization of different dimensions of the family, and dozens of partial rules are inferred from it or defined in the light of these general rules. How each of these principles was formed has left its own detailed history. In international human rights standards, which have been gradually developed over the past 72 years, numerous data can be found that in some way represent a rule in the field of family law or provide an interpretation of existing international rules which also address obligations of governments in the field of family. Based on a descriptive-analytical method and by examining human rights instruments, the present study seeks to explain the effective elements in defining and the principles governing the family. This article makes it clear that international instruments do not provide a clear definition of the family and that governments are empowered to define the family in terms of the cultural context of their community. But at the same time, it has been stipulated that governments do not have the exclusive authority to provide this definition, and certain principles should be considered as essential elements. Also, 7 principles have been identified as general legal rules governing all international human rights instruments related to the family, such as the principle of voluntary family formation and the prohibition of forced marriage, and the principle of respecting human dignity for all family members. Each of these 7 principles has led to different debates, and the acceptance or non-acceptance of each of them has different consequences in the rights and duties related to the family and the relations between its members and even the family's interactions with others and society. One of the consequences of the validity of these principles in family-related human rights standards is that many of the existing legal systems of countries in some cases need to be amended and their regulations revised, and some established cultural traditions in societies that are considered inhumane in terms of these principles need to be modified and changed. Of course, this process of governing the principles derived from human rights standards over the family also has vulnerabilities and misinterpretations that should not be neglected.

Keywords: family, human rights, international instruments, principles

Procedia PDF Downloads 178