CD Genomics Perspective: The Application of RNA-Seq and DNA-Seq in Cancer Research
Clinicians can make better diagnostic and treatment decisions using the data obtained by next-generation sequencing (NGS) technologies. Breast cancers, for example, have typically been diagnosed using mammography, physical exam, and histology. Genetics became more significant after the discoveries of oncogenes and other biomarkers. Today, commercially available microarray-based tests enable more accurate cancer profiling based on genetic biomarkers like HER2, ER, and PR. Along with better diagnostics, the discovery of cancer-associated genes has led to the creation of molecularly targeted therapeutics like trastuzumab, which was one of the first treatments for HER2+ breast tumors. Furthermore, the sequencing of hundreds of breast cancers has revealed significant intratumor heterogeneity, adding to the complexity of developing new treatments.
RNA-Seq in Cancer Research
RNA sequencing (RNA-seq) is an important technology in immunogenomics because it allows researchers to examine a tumor's transcriptome and its surroundings. The gene expression patterns linked with the existence of diverse immunocyte populations can subsequently be inferred using analytical approaches to deconstruct genomics data. With a range of sequencing library preparation methods, sequencing platforms, and downstream bioinformatics analyses currently accessible, high-quality RNA-seq can be performed on formalin-fixed, paraffin-embedded (FFPE), fresh-frozen, and fresh tissue. The tissue type, RNA quality, and quantity of RNA all play a role in determining the best library production procedure. Many analyses, such as differential gene expression analysis, immunological gene signature analysis, gene pathway analysis, T/B-cell receptor inference, HLA inference, and viral transcript quantification, can be performed on the data after it has been sequenced.
DNA-Seq in Cancer Research
Genomic testing can discover or profile the somatic or acquired differences in a tumor that influence the selection of appropriate targeted therapies, as well as identify or profile germline or inherited DNA variations that enhance a person's cancer risk. A study of DNA sequence information is the second type of genomic testing. The order of the nucleotides or base pairs that make up a DNA molecule is determined through DNA sequencing. Human DNA sequences are 99.9% identical; the 0.1 percent variance accounting for changes in illness risk from one person to the next.
Rapid advances in DNA sequencing technology and bioinformatics (the ability to store and assess large databases of genomic data) have allowed us to identify and catalog DNA variations, as well as evaluate which variants (changes in DNA sequence, also known as mutations) are linked to increased disease risk. Although a single gene can be sequenced, oncology is now dominated by next-generation sequencing (NGS) and whole-genome sequencing (WGS). A huge number of genes may be examined simultaneously in a single diagnostic platform using NGS.
People who are at risk for some forms of inherited cancers can also be identified through DNA sequencing. Examining normal cells for mutations in the BRCA1 or BRCA2 genes, for example, can reveal whether a person has a higher-than-average risk of getting cancers linked to those abnormalities. If this is the case, there are several steps that can be taken to lessen the risk.
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