Non-invasive Detection of Genome-wide Somatic Copy Number Alterations by Liquid Biopsies

Overview

Journal Mol Oncol

Specialties Molecular Biology
Oncology

Date 2016 Jan 19

PMID 26778171

Citations 39

Authors

Ellen Heitzer

Peter Ulz

Jochen B Geigl

Michael R Speicher

Affiliations

Soon will be listed here.

Abstract

Liquid biopsies, i.e. the analysis of circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA), are evolving into promising clinical tools. Indeed, a plethora of liquid biopsy technologies to deduce non-invasively characteristics of the tumor genome from the peripheral blood have been developed over the last few years. For example, liquid biopsies have been used to assess the tumor burden, to monitor the evolution of tumor genomes, to unravel mechanisms of resistance, to establish the tumor heterogeneity, and for the identification of prognostic and predictive markers. In this review we focus on methods to establish genome-wide profiles of somatic copy number alterations (SCNAs) from plasma DNA and show how they provide novel insights into the biology of cancer and their impact on the management of patients.

Citing Articles

Can a Liquid Biopsy Detect Circulating Tumor DNA With Low-passage Whole-genome Sequencing in Patients With a Sarcoma? A Pilot Evaluation.

Anderson C, Yang H, Parsons J, Ahrens W, Jagosky M, Hsu J Clin Orthop Relat Res. 2024; 483(1):39-48.

PMID: 38905450 PMC: 11658723. DOI: 10.1097/CORR.0000000000003161.

The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization.

Bronkhorst A, Holdenrieder S Med Genet. 2024; 35(4):201-235.

PMID: 38835739 PMC: 11006350. DOI: 10.1515/medgen-2023-2065.

Multi-omics landscape analysis reveals the pan-cancer association of arginine biosynthesis genes with tumor immune evasion and therapy resistance.

Tan Z, Li H, Huang Y, Fu S, Wang H, Wang J Heliyon. 2024; 10(5):e26804.

PMID: 38468956 PMC: 10925990. DOI: 10.1016/j.heliyon.2024.e26804.

Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer.

Tan E, Knepper T, Wang X, Permuth J, Wang L, Fleming J Cancers (Basel). 2022; 14(9).

PMID: 35565354 PMC: 9101426. DOI: 10.3390/cancers14092223.

Genetic and Molecular Characterization Revealed the Prognosis Efficiency of Histone Acetylation in Pan-Digestive Cancers.

Zhang T, Wang B, Gu B, Su F, Xiang L, Liu L J Oncol. 2022; 2022:3938652.

PMID: 35422864 PMC: 9005301. DOI: 10.1155/2022/3938652.

References

Fan H, Blumenfeld Y, Chitkara U, Hudgins L, Quake S . Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A. 2008; 105(42):16266-71. PMC: 2562413. DOI: 10.1073/pnas.0808319105. View

Chiu C, Nakamura Y, Chong K, Huang S, Kawas N, Triche T . Genome-wide characterization of circulating tumor cells identifies novel prognostic genomic alterations in systemic melanoma metastasis. Clin Chem. 2014; 60(6):873-85. DOI: 10.1373/clinchem.2013.213611. View

Garvin T, Aboukhalil R, Kendall J, Baslan T, Atwal G, Hicks J . Interactive analysis and assessment of single-cell copy-number variations. Nat Methods. 2015; 12(11):1058-60. PMC: 4775251. DOI: 10.1038/nmeth.3578. View

Mohlendick B, Bartenhagen C, Behrens B, Honisch E, Raba K, Knoefel W . A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH. PLoS One. 2013; 8(6):e67031. PMC: 3692546. DOI: 10.1371/journal.pone.0067031. View

Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A . Genome-wide copy number analysis of single cells. Nat Protoc. 2012; 7(6):1024-41. PMC: 5069701. DOI: 10.1038/nprot.2012.039. View

Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann E . Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res. 2013; 73(10):2965-75. DOI: 10.1158/0008-5472.CAN-12-4140. View

Carter S, Eklund A, Kohane I, Harris L, Szallasi Z . A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006; 38(9):1043-8. DOI: 10.1038/ng1861. View

Geigl J, Obenauf A, Schwarzbraun T, Speicher M . Defining 'chromosomal instability'. Trends Genet. 2008; 24(2):64-9. DOI: 10.1016/j.tig.2007.11.006. View

Fiegler H, Geigl J, Langer S, Rigler D, Porter K, Unger K . High resolution array-CGH analysis of single cells. Nucleic Acids Res. 2006; 35(3):e15. PMC: 1807964. DOI: 10.1093/nar/gkl1030. View

10.

Polzer B, Medoro G, Pasch S, Fontana F, Zorzino L, Pestka A . Molecular profiling of single circulating tumor cells with diagnostic intention. EMBO Mol Med. 2014; 6(11):1371-86. PMC: 4237466. DOI: 10.15252/emmm.201404033. View

11.

Heitzer E, Ulz P, Geigl J, Speicher M . Non-invasive detection of genome-wide somatic copy number alterations by liquid biopsies. Mol Oncol. 2016; 10(3):494-502. PMC: 5528970. DOI: 10.1016/j.molonc.2015.12.004. View

12.

Pantel K, Speicher M . The biology of circulating tumor cells. Oncogene. 2015; 35(10):1216-24. DOI: 10.1038/onc.2015.192. View

13.

Santaguida S, Amon A . Short- and long-term effects of chromosome mis-segregation and aneuploidy. Nat Rev Mol Cell Biol. 2015; 16(8):473-85. DOI: 10.1038/nrm4025. View

14.

Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S . Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A. 2005; 102(45):16368-73. PMC: 1283450. DOI: 10.1073/pnas.0507904102. View

15.

Mazel M, Jacot W, Pantel K, Bartkowiak K, Topart D, Cayrefourcq L . Frequent expression of PD-L1 on circulating breast cancer cells. Mol Oncol. 2015; 9(9):1773-82. PMC: 5528721. DOI: 10.1016/j.molonc.2015.05.009. View

16.

Dawson S, Tsui D, Murtaza M, Biggs H, Rueda O, Chin S . Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013; 368(13):1199-209. DOI: 10.1056/NEJMoa1213261. View

17.

Bianchi D, Chudova D, Sehnert A, Bhatt S, Murray K, Prosen T . Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies. JAMA. 2015; 314(2):162-9. DOI: 10.1001/jama.2015.7120. View

18.

Schwarzenbach H, Hoon D, Pantel K . Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011; 11(6):426-37. DOI: 10.1038/nrc3066. View

19.

Taylor B, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver B . Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010; 18(1):11-22. PMC: 3198787. DOI: 10.1016/j.ccr.2010.05.026. View

20.

Murtaza M, Dawson S, Tsui D, Gale D, Forshew T, Piskorz A . Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013; 497(7447):108-12. DOI: 10.1038/nature12065. View