Novel applications of next-generation sequencing in breast cancer research

Ma, Rong; Gong, Jie; Jiang, Xiaowei

doi:10.1016/j.gendis.2017.07.003

Cited by 6 publications

(4 citation statements)

References 32 publications

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“…Today, next generation sequencing (NGS)/high-throughput sequencing/deep-sequencing technology is widely used in gene research and has replaced first-generation sequencing (FGS) due to its high speed, high throughput, and high accuracy [ 134 ]. The NGS in BC research is mainly used in genomics-, epigenomics-, transcriptomics-, and translatomics-based investigations, using genome DNA sequence analyses (including whole-genome sequencing (WGS) [ 113 ], whole-exome sequencing (WES) [ 135 ], and targeted sequencing [ 136 ]), RNA transcription group sequencing (RNA-seq) (including whole-transcriptome sequencing (WTS) [ 137 ], small RNAs sequencing, including circulating small RNAs, small RNAs in extracellular vesicles [ 138 ], and non-coding RNA analyses [ 139 ]), and epigenetic sequencing (including chromatin immunoprecipitation followed by sequencing (ChIP-seq) [ 140 ] and genome-wide DNA methylation analyses [ 141 ], [ 134 ]. WES, RNA-seq, and WGS are implemented in routine clinical settings, demonstrating the clinical relevance of genomics in cancer medicine [ 113 ].…”

Section: Breast Cancer Investigation In the Multi-omics Eramentioning

confidence: 99%

Omics-Based Investigations of Breast Cancer

Neagu,

Whitham,

Bruno

et al. 2023

Molecules

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Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three ”big omics”, based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein–protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.

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Section: Breast Cancer Investigation In the Multi-omics Eramentioning

confidence: 99%

Omics-Based Investigations of Breast Cancer

Neagu,

Whitham,

Bruno

et al. 2023

Molecules

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“…the WGS, exon sequencing, targeting gene sequencing), RNA transcription sequencing (i.e. the whole transcriptome analysis, small RNA sequencing, non-coding RNA analysis), and epigenetic sequencing [49]. Researchers reported several mutations or deletions of many genes related to breast cancer such as TP53, PTEN, RUNX1, CCND3, and PTPN22 [50].…”

Section: Breast Cancermentioning

confidence: 99%

Strategies, Quality Control and Clinical Applications of Next Generation Sequencing

Khorshidi

Palangi

2018

Multidiscip Cancer Investig

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DNA sequencing is one of the great valuable techniques in molecular biology, which can be used to detect the sequence of nucleotides in a DNA fragment. The high-throughput sequencing known as Next Generation Sequencing (NGS) revolutionized genomic research and molecular biology; therefore, the whole human genome can be sequenced with a low cost in several days. NGS technology is similar to the traditional method, Sanger, which detects small DNA fragments by emitted signals at the time of synthesis of each fragment (from the DNA template), but the difference is that NGS can determine the massive simultaneous sequencing in a few days with high accuracy and the results are directly detected without the need for electrophoresis. In fact, NGS technology combines a variety of steps such as sample preparation, fragmentation of the sample of the studied genome, attachment of adapter to the ends of the fragments, imaging, and data analyses. In recent years, NGS technology continuously expanded the range of applications in different fields by reducing costs, increasing rates, and improving the quality of the data. The current review provided the potential applications of the NGS technology by emphasizing the diagnosis of the genetic diseases, identification of several types of cancers, prenatal screening, epigenetic modifications, personalized medicine, and identification of pathogens.

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“…In view of its heterogeneous etiology, the manifestations of BC vary widely among individual patients, with each patient having a unique profile, hence highlighting the potential value of precision medicine and individualized therapies for effective management (30)(31)(32). Next-Generation sequencing (NGS) was recently employed to improve identification of novel gene mutations responsible for disease manifestation amongst BC patients (33)(34)(35)(36).…”

Section: Introductionmentioning

confidence: 99%

Detection of genetic mutations in patients with breast cancer from Saudi Arabia using Ion AmpliSeq™ Cancer Hotspot Panel v.2.0

et al. 2022

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Next-Generation Sequencing allows for quick and precise sequencing of multiple genes concurrently. Recently, this technology has been employed for the identification of novel gene mutations responsible for disease manifestation among breast cancer (BC) patients, the most common type of cancer amongst Arabian women, and the major cause of disease-associated death in women worldwide. Genomic DNA was extracted from the peripheral blood of 32 Saudi Arabian BC patients with histologically confirmed invasive BC stages I-III and IV, as well from 32 healthy Saudi Arabian women using a QIAamp ® DNA Mini Kit. The isolated DNA was quantified using a Qubit™ dsDNA BR Assay Kit with a Qubit 2.0 Fluorometer. Ion semiconductor sequencing technology with an Ion S5 System and AmpliSeq™ Cancer Hotspot Panel v2 were utilized to analyze ~2,800 mutations described in the Catalogue of Somatic Mutations in Cancer from 50 oncogenes and tumor suppressor genes. Ion Reporter Software v.5.6 was used to evaluate the genomic alterations in all the samples after alignment to the hg19 human reference genome. The results showed that out of the 50 genes, 26 mutations, including 17 (65%) missense point mutations (single nucleotide variants), and 9 (35%) frameshift (insertion/deletion) mutations, were identified in 11 genes across the cohort in 61 samples (95%). Mutations were predominantly focused on two genes, PIK3CA and TP53, in the BC genomes of the sample set. PIK3CA mutation, c.1173A>G located in exon 9, was identified in 15 patients (46.9%). The TP53 mutations detected were a missense mutation (c.215C>G) in 26 patients (86.70%) and 1 frameshift mutation (c.215_216insG) in 1 patient (3.33%), located within exon 3 and 5, respectively. This study revealed specific mutation profiles for every BC patient, Thus, the results showed that Ion Torrent DNA Sequencing technology may be a possible diagnostic and prognostic method for developing personalized therapy based on the patient's individual BC genome.

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Novel applications of next-generation sequencing in breast cancer research

Cited by 6 publications

References 32 publications

Omics-Based Investigations of Breast Cancer

Omics-Based Investigations of Breast Cancer

Strategies, Quality Control and Clinical Applications of Next Generation Sequencing

Detection of genetic mutations in patients with breast cancer from Saudi Arabia using Ion AmpliSeq™ Cancer Hotspot Panel v.2.0

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