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Safari F, Kehelpannala C, Safarchi A, Batarseh AM, Vafaee F. Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis. Cancers (Basel) 2023; 15:2780. [PMID: 37345117 DOI: 10.3390/cancers15102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
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.
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Affiliation(s)
- Fatemeh Safari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Cheka Kehelpannala
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia
| | - Amani M Batarseh
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia
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Southworth T, Jevnikar Z, McCrae C, Singh D. A sputum 6-gene signature predicts airway inflammation endotypes and exacerbation frequency in chronic obstructive pulmonary disease. Biomark Med 2022; 16:277-289. [PMID: 35176870 DOI: 10.2217/bmm-2021-0653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aim: To validate a sputum 6-gene signature (6GS), comprising of CLC, CPA, DNASE1L3, IL-1B, ALPL and CXCR2, for identifying different endotypes in chronic obstructive pulmonary disease. Methodology & results: Sputum cell CLC, CPA3 and DNASE1L3 gene expression correlated with eosinophil percentage, while IL-1B, ALPL and CXCR2 correlated with neutrophil percentage. Hierarchical cluster analyses of IL-1B, ALPL and CXCR2, and CLC, CPA3 and DNASE1L3, identified patient groups that differed in their sputum neutrophil and eosinophil levels, respectively. Multiple logistic regressions demonstrated that the 6GS could distinguish between eosinophilHigh and eosinophilLow patients, as well as neutrophilHigh and neutrophilLow, and could also predict exacerbation history. Conclusion: The 6GS may have applications in clinical practice or for stratifying patients for clinical trials.
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Affiliation(s)
- Thomas Southworth
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK.,Medicines Evaluation Unit, Manchester, UK
| | - Zala Jevnikar
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christopher McCrae
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Dave Singh
- Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK.,Medicines Evaluation Unit, Manchester, UK
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Zhuang W, Camacho L, Silva CS, Thomson M, Snyder K. A robust biostatistical method leverages informative but uncertainly determined qPCR data for biomarker detection, early diagnosis, and treatment. PLoS One 2022; 17:e0263070. [PMID: 35100319 PMCID: PMC8803186 DOI: 10.1371/journal.pone.0263070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/11/2022] [Indexed: 11/19/2022] Open
Abstract
As a common medium-throughput technique, qPCR (quantitative real-time polymerase chain reaction) is widely used to measure levels of nucleic acids. In addition to accurate and complete data, experimenters have unavoidably observed some incomplete and uncertainly determined qPCR data because of intrinsically low overall amounts of biological materials, such as nucleic acids present in biofluids. When there are samples with uncertainly determined qPCR data, some investigators apply the statistical complete-case method by excluding the subset of samples with uncertainly determined data from analysis (CO), while others simply choose not to analyze (CNA) these datasets altogether. To include as many observations as possible in analysis for interesting differential changes between groups, some investigators set incomplete observations equal to the maximum quality qPCR cycle (MC), such as 32 and 40. Although straightforward, these methods may decrease the sample size, skew the data distribution, and compromise statistical power and research reproducibility across replicate qPCR studies. To overcome the shortcomings of the existing, commonly-used qPCR data analysis methods and to join the efforts in advancing statistical analysis in rigorous preclinical research, we propose a robust nonparametric statistical cycle-to-threshold method (CTOT) to analyze incomplete qPCR data for two-group comparisons. CTOT incorporates important characteristics of qPCR data and time-to-event statistical methodology, resulting in a novel analytical method for qPCR data that is built around good quality data from all subjects, certainly determined or not. Considering the benchmark full data (BFD), we compared the abilities of CTOT, CO, MC, and CNA statistical methods to detect interesting differential changes between groups with informative but uncertainly determined qPCR data. Our simulations and applications show that CTOT improves the power of detecting and confirming differential changes in many situations over the three commonly used methods without excess type I errors. The robust nonparametric statistical method of CTOT helps leverage qPCR technology and increase the power to detect differential changes that may assist decision making with respect to biomarker detection and early diagnosis, with the goal of improving the management of patient healthcare.
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Affiliation(s)
- Wei Zhuang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Luísa Camacho
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Camila S. Silva
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Michael Thomson
- Office of New Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Kevin Snyder
- Office of New Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, United States of America
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