Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis

Author:

Safari Fatemeh1,Kehelpannala Cheka23,Safarchi Azadeh14,Batarseh Amani M.23ORCID,Vafaee Fatemeh156ORCID

Affiliation:

1. School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia

2. BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia

3. BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia

4. Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia

5. UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia

6. OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia

Abstract

Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.

Funder

UNSW Industry Network Seed Funding

Publisher

MDPI AG

Subject

Cancer Research,Oncology

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