Algorithms and Data Analysis of High Throughput Sequencing in Cancers

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Informatics and Big Data".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 1845

Special Issue Editors


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Guest Editor
1. Institute of Oncology Research, Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
2. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Interests: bioinformatics; biostatistics; non-coding RNAs; lymphoma; high-throughput sequencing data analysis; diagnostic and prognostic biomarkers discovery
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Laboratory of Molecular Biology, Mario Negri Institute for Pharmacological Research, 20156 Milano, Italy
Interests: gene expression; human genetics; genomics; computational biology; next-generation sequencing; bioinformatics and computational biology; cancer genomics

Special Issue Information

Dear Colleagues,

The acquisition of cancer hallmarks requires molecular alterations at multiple levels, including genome, epigenome, transcriptome, proteome, and metabolome levels. High-throughput DNA sequencing has contributed to the identification of cancer-specific mutations, epigenetic alterations, and molecular subtyping of tumors.  Moreover, large-scale tumor molecular profiling programs across different cancer types hold the promise of improving diagnostics, prognostics, and personalized treatment.

High-throughput omics data create huge bioinformatic challenges including storage, transmission, manipulation, and analysis, making the downstream processing of data a daunting task.

Therefore, new bioinformatic methods are required to biologically extract sequencing data from meaningful information and present them in an easily interpretable format.

In this Special Issue, we will discuss bioinformatic methodologies and statistical approaches, with a special emphasis on how the omics data are being analyzed, stored, and manipulated to aspire or create new ways of diagnosing and treating cancers.

Dr. Luciano Cascione
Dr. Marco Bolis
Guest Editors

Manuscript Submission Information

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Keywords

  • computational biology
  • bioinformatics
  • machine learning
  • artificial intelligence
  • next-generation sequencing
  • oncology
  • cancer
  • precision medicine

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Published Papers (1 paper)

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Review

28 pages, 1972 KiB  
Review
Unraveling the Genetic Heterogeneity of Acute Lymphoblastic Leukemia Based on NGS Applications
by Valentina Ramírez Maldonado, Josgrey Navas Acosta, Iván Maldonado Marcos, Ángela Villaverde Ramiro, Alberto Hernández-Sánchez, Jesús M. Hernández Rivas and Rocío Benito Sánchez
Cancers 2024, 16(23), 3965; https://doi.org/10.3390/cancers16233965 - 26 Nov 2024
Viewed by 1410
Abstract
Acute lymphoblastic leukemia (ALL) is a hematological neoplasm characterized by the clonal expansion of abnormal lymphoid precursors in bone marrow, which leads to alterations in the processes of cell differentiation and maturation as a consequence of genetic alterations. The integration of conventional methods, [...] Read more.
Acute lymphoblastic leukemia (ALL) is a hematological neoplasm characterized by the clonal expansion of abnormal lymphoid precursors in bone marrow, which leads to alterations in the processes of cell differentiation and maturation as a consequence of genetic alterations. The integration of conventional methods, such as cytogenetics and immunophenotyping, and next-generation sequencing (NGS) has led to significant improvements at diagnosis and patient stratification; this has also allowed the discovery of several novel molecular entities with specific genetic variants that may drive the processes of leukemogenesis. Nevertheless, the understanding of the process of leukemogenesis remains a challenge since this disease persists as the most frequent cancer in children; it accounts for approximately one-quarter of adult acute leukemias, and the patient management may take into consideration the high intra- and inter-tumor heterogeneity and the relapse risk due to the various molecular events that can occur during clonal evolution. Some germline variants have been identified as risk factors or have been found to be related to the response to treatment. Therefore, better knowledge of the genetic alterations in B-ALL will have a prognostic impact from the perspective of personalized medicine. This review aims to compare, synthesize, and highlight recent findings concerning ALL obtained through NGS that have led to a better understanding of new molecular subtypes based on immunophenotypic characteristics, mutational profiles, and expression profiles. Full article
(This article belongs to the Special Issue Algorithms and Data Analysis of High Throughput Sequencing in Cancers)
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