Exploring genomic datasets through machine learning methods leveraging high-performance computing
(English) In recent years, the exponential increase of generated data has raised the need for implementing new methodologies to process the huge datasets being created. High-Performance Computing (HPC) brings together a set of technologies mainly based on parallel computing that help reduce the time...
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| Tipo de recurso: | tesis doctoral |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/424249 |
| Acceso en línea: | https://hdl.handle.net/2117/424249 https://dx.doi.org/10.5821/dissertation-2117-424249 |
| Access Level: | acceso abierto |
| Palabra clave: | 004 575 Àrees temàtiques de la UPC::Informàtica |
| Sumario: | (English) In recent years, the exponential increase of generated data has raised the need for implementing new methodologies to process the huge datasets being created. High-Performance Computing (HPC) brings together a set of technologies mainly based on parallel computing that help reduce the time expended analyzing these datasets. A research field where these technologies are needed is Computational Genomics. Furthermore, the complexity of the genomic datasets limits the use of basic conventional methods for the discovery of complex significant relations, introducing the need for Machine learning (ML) algorithms and robust statistical methods to better classify these variants. In the first part of the thesis, we aim to identify complex patterns of somatic genomic rearrangements in cancer samples, which are triggered by internal cellular processes and environmental factors. The problem of classification becomes particularly challenging when considering thousands of rearrangements at a time, often composed of multiple DNA breaks, increasing the difficulty in classifying and interpreting them functionally. Here we present a new statistical approach to analyze structural variants (SVs) from 2,392 tumor samples from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium and identify significant recurrence. The proposed methodology is able not only to identify complex patterns of SVs across different cancer types but also to prove them as not random occurrences, identifying a new class of pattern composed of three SVs that was not previously described. In the second part of the thesis, we approach another challenge of human genetics, which is the study of the relation between single nucleotide variants (SNVs) and complex diseases, such as Type 2 Diabetes, Asthma, or Alzheimer's. The study of these disease-variant associations is usually performed in a single independent manner, disregarding the possible effect derived from the interaction between genomic variants. Here, we have created a containerized framework that uses Multifactor Dimensionality Reduction (MDR) to detect combinations of variants associated with Type 2 Diabetes (T2D), called Variant Interaction Analysis (VIA). This methodology has been tested in the Northwestern University NUgene project cohort using a subset of 1,883,192 variant pairs with some degree of association with T2D and identifying a subset of 104 significant pairs, two exhibiting a potential functional relationship with T2D. The developed algorithm has been released in an open-source repository, including the containerized HPC framework, which can be used to search for significant pairwise interactions in other datasets. In both frameworks developed within the thesis, the use of large-scale supercomputing architectures has been a hard requirement to find relevant clinical indicators. To ensure open and broad access to HPC technologies, governments, and academia are pushing toward the introduction of novel computing architectures in large-scale scientific environments. This is the case of RISC-V, an emerging open standard instruction-set architecture. To evaluate such technologies, in the last two parts of the thesis, we propose the use of our VIA use case as a benchmarking, providing the first genomic application for RISC-V. With this use case, we provide a representative case for heavy ETL (Extract, Transform, Load) data processing. We developed a version of the VIA workload for RISC-V and adapted our implementation in x86-based supercomputers (e.g. Marenostrum IV at the Barcelona Supercomputing Center (BSC)) to make a fair comparison with RISC-V, since some technologies are not available there. With this benchmark, we have been able to indicate the challenges and opportunities for the next RISC-V developments and designs to come, from a first comparison between x86 and RISC-V architectures on genomic workload executions over real hardware implementations. |
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