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Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer
Molecular analysis of cell-free DNA (cfDNA) that circulates in plasma and other body fluids represents a “liquid biopsy” approach for non-invasive cancer screening or monitoring. The rapid development of sequencing technologies has made cfDNA a promising source to study cancer development and progre...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627444/ https://www.ncbi.nlm.nih.gov/pubmed/31212602 http://dx.doi.org/10.3390/cancers11060805 |
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author | Huang, Chiang-Ching Du, Meijun Wang, Liang |
author_facet | Huang, Chiang-Ching Du, Meijun Wang, Liang |
author_sort | Huang, Chiang-Ching |
collection | PubMed |
description | Molecular analysis of cell-free DNA (cfDNA) that circulates in plasma and other body fluids represents a “liquid biopsy” approach for non-invasive cancer screening or monitoring. The rapid development of sequencing technologies has made cfDNA a promising source to study cancer development and progression. Specific genetic and epigenetic alterations have been found in plasma, serum, and urine cfDNA and could potentially be used as diagnostic or prognostic biomarkers in various cancer types. In this review, we will discuss the molecular characteristics of cancer cfDNA and major bioinformatics approaches involved in the analysis of cfDNA sequencing data for detecting genetic mutation, copy number alteration, methylation change, and nucleosome positioning variation. We highlight specific challenges in sensitivity to detect genetic aberrations and robustness of statistical analysis. Finally, we provide perspectives regarding the standard and continuing development of bioinformatics analysis to move this promising screening tool into clinical practice. |
format | Online Article Text |
id | pubmed-6627444 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-66274442019-07-23 Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer Huang, Chiang-Ching Du, Meijun Wang, Liang Cancers (Basel) Review Molecular analysis of cell-free DNA (cfDNA) that circulates in plasma and other body fluids represents a “liquid biopsy” approach for non-invasive cancer screening or monitoring. The rapid development of sequencing technologies has made cfDNA a promising source to study cancer development and progression. Specific genetic and epigenetic alterations have been found in plasma, serum, and urine cfDNA and could potentially be used as diagnostic or prognostic biomarkers in various cancer types. In this review, we will discuss the molecular characteristics of cancer cfDNA and major bioinformatics approaches involved in the analysis of cfDNA sequencing data for detecting genetic mutation, copy number alteration, methylation change, and nucleosome positioning variation. We highlight specific challenges in sensitivity to detect genetic aberrations and robustness of statistical analysis. Finally, we provide perspectives regarding the standard and continuing development of bioinformatics analysis to move this promising screening tool into clinical practice. MDPI 2019-06-11 /pmc/articles/PMC6627444/ /pubmed/31212602 http://dx.doi.org/10.3390/cancers11060805 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Review Huang, Chiang-Ching Du, Meijun Wang, Liang Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer |
title | Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer |
title_full | Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer |
title_fullStr | Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer |
title_full_unstemmed | Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer |
title_short | Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer |
title_sort | bioinformatics analysis for circulating cell-free dna in cancer |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627444/ https://www.ncbi.nlm.nih.gov/pubmed/31212602 http://dx.doi.org/10.3390/cancers11060805 |
work_keys_str_mv | AT huangchiangching bioinformaticsanalysisforcirculatingcellfreednaincancer AT dumeijun bioinformaticsanalysisforcirculatingcellfreednaincancer AT wangliang bioinformaticsanalysisforcirculatingcellfreednaincancer |