Developing an Integrated Genomic Profile for Cancer Patients with the Use of NGS Data

Next Generation Sequencing (NGS) technologies has revolutionized genomics data research by facilitating high-throughput sequencing of genetic material that comes from different sources, such as Whole Exome Sequencing (WES) and RNA Sequencing (RNAseq). The exploitation and integration of this wealth of heterogeneous sequencing data remains a major challenge. There is a clear need for approaches that attempt to process and combine the aforementioned sources in order to create an integrated profile of a patient that will allow us to build the complete picture of a disease. This work introduces such an integrated profile using Chronic Lymphocytic Leukemia (CLL) as the exemplary cancer type. The approach described in this paper links the various NGS sources with the patients’ clinical data. The resulting profile efficiently summarizes the large-scale datasets, links the results with the clinical profile of the patient and correlates indicators arising from different data types. With the use of state-of-the-art machine learning techniques and the association of the clinical information with these indicators, which served as the feature pool for the classification, it has been possible to build efficient predictive models. To ensure reproducibility of the results, open data were exclusively used in the classification assessment. The final goal is to design a complete genomic profile of a cancer patient. The profile includes summarization and visualization of the results of WES and RNAseq analysis (specific variants and significantly expressed genes, respectively) and the clinical profile, integration/comparison of these results and a prediction regarding the disease trajectory. Concluding, this work has managed to produce a comprehensive clinico-genetic profile of a patient by successfully integrating heterogeneous data sources. The proposed profile can contribute to the medical research providing new possibilities in personalized medicine and prognostic views

Dinâmica das integrações de minicírculos de kDNA de Trypanosoma Cruzi no genoma hospedeiro

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Medicina, Programa de Pós-Graduação em Patologia Molecular, 2016.A doença de Chagas é considerada uma das principais endemias da América Latina, existindo cerca de oito milhões de pessoas infectadas com o Trypanosoma cruzi em todo o mundo, principalmente na América Latina. A associação entre a transferência gênica lateral de minicírculos de kDNA do T. cruzi para o genoma hospedeiro e o surgimento de manifestações clínicas da doença de Chagas está descrita na literatura. Entretanto os mecanismos que levariam ao desenvolvimento das reações autoimunes ainda precisam ser elucidados. No presente estudo, desenvolveu-se um protocolo de PCR quantitativa (qPCR) que permitiu a quantificação das integrações de minicírculos de kDNA de T. cruzi no genoma do hospedeiro, confirmando, dessa forma, a transferência dos minicírculos ao genoma de célula hospedeira. Verificou-se que há um acúmulo das integrações ao longo do tempo em células J774.A1. À medida que ocorre a inserção dos minicírculos de kDNA no genoma hospedeiro, observa-se alteração da temperatura de dissociação das amostras, indicando mudança na composição ou no tamanho dos fragmentos integrados. De fato, a clonagem e o sequenciamento dos amplicons demonstrou o truncamento da região variável do kDNA. O Benznidazol é capaz de eliminar a infecção, porém não previne a integração e o acúmulo das sequências de kDNA. Já o AZT, droga inibidora de retrotransposição, mostra-se efetivo no controle dos eventos de integração. Os experimentos in vivo corroboraram os achados in vitro, demonstrando uma maior quantidade de integrações em animais que se encontravam na fase crônica da doença de Chagas. Outros estudos são necessários para determinar o papel do acúmulo de integrações de kDNA e a severidade das manifestações clínicas. Entretanto, o real significado de tais mutações não fica restrito à doença de Chagas, mas, sim, estende-se ao longo do processo da evolução, em que a aquisição de DNA exógeno ajudaria a impulsionar um fluxo genético introdutor de complexidade crescente às espécies.Chagas' disease is considered a major endemic disease in Latin America, and there are approximately eight million people infected with Trypanosoma cruzi worldwide, especially in Latin America. The association between lateral gene transfer of T. cruzi kDNA minicircle into host genome and the onset of clinical manifestations of Chagas disease is described in the literature. However, the mechanisms that lead to autoimmune reactions are to need to be elucidated. In the present study, we have developed a protocol quantitative PCR (qPCR), which permitted quantitation of kDNA minicircle integrations T. cruzi into the host genome, confirming thus the transfer of the minicircle into the genome of the host J774.A1 cells. It was found that there is an accumulation of integrations over time J774.A1 cells. As kDNA insertions occur, there is change in melting curve, indicating change in composition or size of the integrated fragments. In fact, cloning and sequencing of amplicons showed loss of nucleotides in kDNA variable region. Benznidazole is able to eliminate the infection, but does not prevent the integration and accumulation of kDNA sequences. AZT, an inhibitory drug for retro transposition, shows to be effective in controlling integration events. In vivo experiments confirmed in vitro findings, showing a greater amount of integrations in animals that were in the chronic phase of Chagas disease. Further studies are needed to determine the role of kDNA accumulation in severity of clinical manifestations. However, the real significance of such date is not restricted to Chagas disease, but rather extends throughout the evolutionary process, where the acquisition of exogenous DNA would help boost a genetic flow introducing higher complexity to species

Additional file 1 of Integrating mutation and gene expression cross-sectional data to infer cancer progression

The partition of 72 mutation and 319 expression genes in 3 phases of cancer progression. The values of the expression genes represent the likelihood score corresponding to each phase. (PDF 47.1 kb