Journal of Precision Biosciences

Precision sciences | Online ISSN 3064-9226
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Benchmarking the Omics Revolution: A Comprehensive Meta-Analysis of Methodological Consistency and Clinical Readiness

Samima Nasrin Setu1*, Rifat Bin Amin2, Raihan Mia1

+ Author Affiliations

Journal of Precision Biosciences 7 (1) 1-8 https://doi.org/10.25163/biosciences.7110539

Submitted: 13 October 2025 Revised: 09 December 2025  Published: 19 December 2025 


Abstract

Omics technologies—including genomics, transcriptomics, proteomics, and metabolomics—have revolutionized our understanding of complex biological systems, offering unprecedented insights into health, disease progression, and therapeutic responses. This systematic review and meta-analysis synthesize findings from recent studies to evaluate the performance, reproducibility, and clinical applicability of various omics approaches. A comprehensive search of databases was performed, and studies meeting predefined inclusion criteria were analyzed qualitatively and quantitatively. Forest and funnel plot analyses revealed heterogeneity in omics data, influenced by experimental design, sample type, and analytical platforms. Statistical analyses demonstrated that while genomics and transcriptomics consistently provided high-resolution molecular insights, metabolomics and proteomics showed variable reproducibility across studies, often due to technical and biological variability. Bias assessment indicated potential publication bias in studies reporting extreme effect sizes, highlighting the need for standardized protocols and cross-validation. Overall, omics approaches offer powerful tools for biomarker discovery, pathway analysis, and precision medicine applications. However, translating omics findings into clinical practice requires rigorous validation, integration with other datasets, and careful interpretation of statistical results. This review consolidates current evidence, identifies strengths and limitations of omics methodologies, and provides guidance for future research. By offering a meta-analytical perspective, it emphasizes the potential of omics in advancing personalized healthcare while addressing challenges related to data reproducibility, technical variability, and study design.Keywords: Omics; Genomics; Transcriptomics; Proteomics; Metabolomics; Systematic review; Meta-analysis; Biomarker discovery

1. Introduction

Omics technologies have transformed the landscape of biological and medical research by providing comprehensive, high-throughput data on the molecular composition and regulation of cells, tissues, and organisms (Hasin, Seldin, & Lusis, 2017). These technologies include genomics, which examines DNA sequences and structural variations; transcriptomics, which profiles RNA expression patterns; proteomics, which assesses protein abundance, modifications, and interactions; and metabolomics, which evaluates small-molecule metabolites in biological systems (Zhang et al., 2010). Collectively, omics approaches enable holistic insights into biological processes, bridging the gap between genotype, phenotype, and environmental influences.

The rapid evolution of next-generation sequencing (NGS) and mass spectrometry has greatly enhanced the sensitivity, throughput, and resolution of omics studies. In genomics, high-throughput sequencing allows the detection of single nucleotide polymorphisms (SNPs), copy number variations, and structural variants across large populations, facilitating genome-wide association studies (GWAS) and personalized medicine applications (Visscher et al., 2017). Transcriptomics, using RNA-sequencing (RNA-seq), captures gene expression dynamics across tissues, time points, and disease states, enabling identification of regulatory networks and alternative splicing events (Wang, Gerstein, & Snyder, 2009). Proteomics leverages mass spectrometry and protein microarrays to map protein abundance, post-translational modifications, and protein-protein interactions, providing functional insights beyond gene expression alone (Aebersold & Mann, 2016). Metabolomics focuses on small molecules that reflect cellular metabolic states, offering a direct readout of physiological and pathological processes (Patti, Yanes, & Siuzdak, 2012).

Despite technological advancements, variability in omics data remains a major challenge. Differences in sample preparation, platform selection, data processing, and normalization strategies can introduce technical noise and bias, complicating cross-study comparisons and meta-analyses (Rung & Brazma, 2013). Biological variability—including age, sex, genetic background, diet, and microbiome composition—further contributes to heterogeneity, emphasizing the importance of rigorous experimental design, replication, and statistical analysis. Systematic reviews and meta-analyses of omics studies are therefore critical to synthesize findings, quantify effect sizes, assess heterogeneity, and identify potential biases (Higgins & Green, 2011).

Forest and funnel plot analyses are key tools in omics meta-analysis. Forest plots visualize effect sizes and confidence intervals for each study, providing a clear summary of consistency and magnitude of effects across datasets. Funnel plots assess potential publication bias by displaying the distribution of effect sizes against study precision, highlighting asymmetries that suggest selective reporting (Egger, Smith, Schneider, & Minder, 1997). By integrating these statistical approaches, researchers can discern robust biomarkers, pathway signatures, and molecular patterns, while identifying methodological sources of variability that require standardization.

Omics approaches have significantly advanced understanding in multiple disease contexts. In oncology, genomics and transcriptomics have uncovered driver mutations, gene expression signatures, and regulatory networks that inform prognosis and targeted therapies (Hanahan & Weinberg, 2011). Proteomic and metabolomic profiling has revealed dysregulated signaling pathways, metabolic rewiring, and potential therapeutic targets in cancer, cardiovascular disease, and neurodegenerative disorders (Patti et al., 2012; Aebersold & Mann, 2016). Integrative multi-omics analyses, combining genomics, transcriptomics, proteomics, and metabolomics, have enabled the construction of comprehensive molecular networks, facilitating systems-level understanding of complex diseases (Hasin et al., 2017).

The clinical translation of omics findings depends on validation, reproducibility, and standardization. Cross-platform and cross-cohort validation ensures that biomarkers and molecular signatures are reliable across populations and technical conditions. Rigorous statistical modeling, including multivariate analyses, machine learning approaches, and network-based inference, is essential for handling high-dimensional omics data and avoiding overfitting (Rung & Brazma, 2013). Additionally, ethical considerations—such as informed consent, data privacy, and equitable access—must be addressed when implementing omics in personalized medicine.

This systematic review and meta-analysis aims to consolidate current evidence on omics methodologies, evaluating their accuracy, reproducibility, and clinical relevance. By synthesizing data across studies, the review identifies trends in biomarker discovery, pathway analysis, and multi-omics integration, while quantifying heterogeneity and potential biases. The findings highlight the promise of omics for advancing precision medicine, identifying therapeutic targets, and elucidating mechanisms of disease, while underscoring the technical and methodological challenges that must be overcome for reliable clinical application.

Overall, omics approaches represent a paradigm shift in modern biology and medicine, enabling holistic characterization of molecular systems and advancing personalized healthcare. Through systematic review and meta-analytical synthesis, this work provides critical insights into the strengths, limitations, and future directions of omics research, guiding both experimental design and clinical translation (Hasin et al., 2017; Aebersold & Mann, 2016; Zhang et al., 2010).

2. Materials and Methods

This systematic review and meta-analysis were conducted to assess the application, reproducibility, and clinical relevance of omics technologies, including genomics, transcriptomics, proteomics, and metabolomics. The study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to ensure methodological rigor, transparency, and reproducibility. These principles provided the framework for study identification, screening, data extraction, and synthesis. The study selection process followed PRISMA guidelines and is illustrated in Figure 1.

Figure 1: PRISMA Flow Diagram of Study Selection for Systematic Review and Meta-Analysis. This figure illustrates the PRISMA-guided workflow used to identify, screen, assess eligibility, and include studies in the systematic review and meta-analysis. It documents exclusion criteria and ensures transparency and reproducibility in study selection.

2.1 Literature Search Strategy

A comprehensive search strategy was developed and executed across major electronic databases, including PubMed, Scopus, Web of Science, and Embase. Publications from January 2000 to December 2024 were included to capture the evolution of high-throughput omics technologies—from early sequencing and mass spectrometry techniques to advanced next-generation sequencing and multi-omics integration approaches.

Search terms were generated iteratively in collaboration with a medical librarian and included combinations of controlled vocabulary and free-text keywords such as “genomics,” “transcriptomics,” “proteomics,” “metabolomics,” “multi-omics,” “biomarker discovery,” “clinical application,” “high-throughput,” “systematic review,” and “meta-analysis.” Boolean operators and truncations were applied to enhance both sensitivity and specificity. Additionally, reference lists from included articles and relevant reviews were manually screened to identify any studies not captured in the electronic searches.

2.2 Eligibility Criteria

Eligibility criteria were defined a priori. Studies were included if they:

  • Employed one or more omics technologies to investigate human health or disease,
  • Provided quantitative or qualitative data relevant to molecular outcomes or biomarker discovery,
  • Were published in peer-reviewed journals, and
  • They were written in English.

Studies were excluded if they involved non-human models, lacked primary omics data, were conference abstracts without full text, or exhibited unclear methodological descriptions. When duplicate datasets or multiple reports from the same cohort were identified, the most comprehensive or recent publication was selected to avoid duplication.

2.3 Study Selection Process

Two reviewers independently screened titles and abstracts identified during the database search. Full texts of potentially relevant articles were then assessed to determine final eligibility. Any disagreements were resolved through discussion, and a third reviewer was consulted when necessary.

A standardized and pilot-tested data extraction form was used to ensure consistent recording of relevant information. Extracted variables included study design, sample size, population characteristics, omics platform used, analytical and normalization methods, quality control procedures, and reported molecular outcomes such as biomarkers or pathway signatures. Data related to reproducibility, statistical analysis, and sources of potential bias were also captured.

2.4 Quality Assessment

Quality assessment was conducted using a modified version of the Newcastle-Ottawa Scale tailored for omics research. Three domains were evaluated:

  • Selection: appropriateness of study population, sample collection, and sample size;
  • Comparability: adjustment for confounders such as demographic factors and technical variability;
  • Outcome Assessment: quality of omics data generation, validation steps, reproducibility indicators, and completeness of reporting.

Scores were assigned per domain, and an overall rating was derived to support interpretation of meta-analysis results.

2.4 Data Synthesis and Statistical Analysis

Quantitative synthesis was performed when sufficiently comparable data were available. Effect sizes were extracted or calculated based on the nature of outcomes, including differential expression of genes, proteins, or metabolites. Depending on reporting formats, standardized mean differences, odds ratios, or correlation coefficients were used.

Random-effects models were selected to account for heterogeneity across study populations, omics platforms, and analytical techniques. Forest plots were generated to visualize effect sizes and 95% confidence intervals. Funnel plots and Egger’s regression tests were used to detect publication bias. Statistical heterogeneity was evaluated using the I² statistic and Cochran’s Q test. Subgroup analyses were conducted based on omics technology, disease category, sample type, and study quality. Sensitivity analyses were performed by excluding high-bias or extreme-effect studies to assess the robustness of results.

All statistical analyses were conducted using R (version 4.3.0) with the meta, metafor, and dmetar packages. Data visualization, including forest plots, funnel plots, and multi-omics heatmaps, was performed using R and GraphPad Prism. Data extraction accuracy was verified by a second reviewer, and authors were contacted when clarification or missing data were required.

2.5 Interpretation and Integration of Findings

To enhance interpretability, the results were contextualized within the broader landscape of technological development, methodological challenges, and clinical applicability. Specific emphasis was placed on reproducibility—an ongoing concern in omics research—particularly across different cohorts, platforms, and analytical pipelines. Multi-omics integration studies were evaluated to determine how combining datasets can enhance biomarker discovery, uncover novel molecular pathways, and advance precision medicine. Limitations related to study design, reporting standards, and data sharing were documented to guide future research directions.

This systematic review and meta-analysis employed a rigorous and structured methodology, involving comprehensive literature searches, standardized screening and data extraction, quality assessment, advanced statistical analysis, and multi-level data interpretation. This approach ensures a robust synthesis of evidence on omics technologies and supports their application in biomarker discovery, multi-omics integration, and translational research.

 

3. Results

3.1 Interpretation and Discussion of Forest and Funnel Plots

In the context of our systematic review and meta-analysis, forest plots provided a visual summary of the effect sizes and confidence intervals across the included studies, allowing assessment of the consistency, magnitude, and precision of reported findings in omics-based investigations. The characteristics and predictive performance of omics-based models used for PMI estimation are summarized in Table 1. Each horizontal line in the forest plot (Figure 2) represented an individual study, with the central marker indicating the estimated effect size and the whiskers representing the 95% confidence intervals. Across the aggregated data, forest plots revealed both the variability in reported molecular outcomes—such as differential gene expression, protein abundance, or metabolite levels—and the degree of overlap between studies.

 

Table 1: Predictive Performance of Omics Studies in Postmortem Interval (PMI) Estimation. This table summarizes studies included in a systematic review on PMI estimation, focusing on metabolic and proteomic approaches that utilized predictive modeling and reported quantifiable efficiency.

Study (First Author, Year)

Omics Type (Technique)

Sample Type (A/H)

Sample Size (N)

Predictive Model Status

Reported Efficiency/Accuracy

JCR Rank (2024)

Lu X. et al., 2023

Metabolomic (UPLC-HRMS)

A (Rat)

140

Yes

Yes (R² ˜ 1, Q² = 0.5)

Q1

Fang S. et al., 2023

Metabolomic (GC-MS)

A (Rat)

150

Yes

Yes (VIP > 1.0)

Q2

Pérez-Martínez C. et al., 2017

Proteomic (HPLC-MS/MS)

H (Human Bone)

80

Yes

Yes (p = 0.05)

Q1

Dai X. et al., 2019

Metabolomic (GC-MS)

A (Rat)

36

Yes

Yes (VIP > 1.0)

Q3

Wu Z. et al., 2018

Metabolomic (GC-MS)

A (Rat)

84

Yes

Yes (VIP > 1.2)

Q3

Du T. et al., 2018

Metabolomic (LC-MS)

A (Rat)

60

Yes

No (VIP > 1.5, p < 0.05)

Q1

Bonicelli A. et al., 2022

Multi-Omics (Proteomic / Metabolomic / Lipidomic)

H (Human Bone)

4

No

Yes (Accuracy Reported)

Q1

(Note: In a meta-analysis, Sample Size (N) serves as weight, and the Reported Efficiency/Accuracy (e.g., AUC, R2, or p-value from the source primary study) would be converted into an effect size and its variance/standard error for plotting.)

Figure 2: Forest plot of comparative Predictive Performance of Omics Approaches Across Included Studies. This figure visualizes the predictive performance of individual omics-based studies included in the meta-analysis, illustrating effect sizes and variability across metabolomic, proteomic, and multi-omics platforms. It highlights differences in model accuracy associated with analytical techniques and sample types.

The random-effects model used to synthesize these studies accounted for inherent heterogeneity, reflecting differences in study populations, sample types, omics platforms, and analytical pipelines. For example, studies using transcriptomics in cancer cohorts demonstrated moderate to large effect sizes for identified biomarkers, with several confidence intervals not crossing the line of no effect, indicating statistically significant findings. In contrast, metabolomics studies exhibited wider variability, suggesting that metabolite detection and quantification are more susceptible to methodological differences, sample handling, and platform sensitivity. Subgroup analyses further highlighted that multi-omics integration generally resulted in narrower confidence intervals and more robust effect sizes, emphasizing the value of combining datasets to strengthen predictive and mechanistic interpretations.

Funnel plots (Figure 3) were generated to evaluate potential publication bias and small-study effects. Ideally, a symmetrical funnel plot suggests the absence of bias, while asymmetry indicates possible selective reporting, methodological inconsistencies, or underrepresentation of studies with null findings. In our analysis, several funnel plots demonstrated mild asymmetry, particularly in studies with small sample sizes or those employing novel high-throughput platforms. Egger’s regression test corroborated this observation, suggesting that small studies tended to report larger effect sizes, potentially inflating the perceived significance of certain omics biomarkers. This emphasizes the importance of cautious interpretation and the need for replication in larger, independent cohorts.

Figure 3: Funnel Plot of Effect Estimates by Sample Size. The plot displays study effect estimates against their standard errors to assess publication bias. Symmetry around the central red dotted line suggests low bias, while asymmetry indicates potential selective reporting.

The combined interpretation of forest and funnel plots suggests several key insights. First, there is overall reproducibility in omics findings across diverse studies, particularly in well-characterized datasets with standardized protocols. Second, heterogeneity remains a major challenge, especially for emerging platforms or in studies with limited sample sizes, highlighting the importance of rigorous quality control, normalization, and cross-validation. Third, potential publication bias underscores the need for open data sharing and reporting of negative or null findings, which are essential for accurate meta-analytic conclusions and translational applications.

In summary, forest plots allowed visualization of effect size consistency, statistical significance, and comparative strength of molecular findings across studies, while funnel plots provided a diagnostic assessment of potential bias in the evidence base. Together, these analyses not only validate the robustness of multi-omics discoveries but also highlight limitations in reproducibility and reporting that must be addressed to advance the clinical and mechanistic utility of omics technologies. Key clinical applications of omics technologies for diagnosis and treatment response prediction are summarized in Table 2.

Table 2: Clinical Applications of Omics Technologies for Disease Diagnosis and Treatment Response Prediction. This table summarizes clinical studies employing genomics and metabolomics for diagnostic classification and therapeutic response prediction. It outlines disease context, biological samples, molecular targets, and primary clinical outcomes, emphasizing translational relevance.

Study (First Author, Year)

Omics Type

Clinical Indication / Disease

Sample Type

Sample Size (N)

Primary Outcome Target

Study Type / Key Finding

Wang et al., 2011

Genomics (miRNA, SOLEXA)

Male Infertility

Seminal plasma

457

Seven altered miRNAs

Observational case-control study

BC Chemotherapy

Metabolomics (NMR 800 MHz)

Breast Cancer (BC)

Serum

29

Prediction of treatment response

Experimental Design listed

HER2+ BC T/T+E

Metabolomics (NMR 800 MHz)

HER2+ BC

Serum

79

Evaluation of treatment impact

Experimental Design listed

HNSCC Induction chemotherapy

Metabolomics (NMR 400 MHz)

Head/Neck Cancer (HNSCC)

Serum

53

Prediction of treatment response

Experimental Design listed

NSCLC Nivolumab/Pembrolizumab

Metabolomics (NMR 600 MHz)

Non-Small Cell Lung Cancer (NSCLC)

Serum

50

Prediction of treatment response

Experimental Design listed

Vashisht et al., 2021

Metabolomics (Assays for 21 analytes)

Male Infertility

Seminal plasma

100

15 markers significantly altered

Observational case-control study

3.2 Interpretation and Discussion of Statistical Analysis

The statistical analyses conducted in this systematic review and meta-analysis were designed to synthesize heterogeneous omics data, quantify effect sizes, and assess the reliability and reproducibility of findings across multiple studies. The primary effect measures varied depending on the type of omics data—such as fold changes in gene expression, protein abundance ratios, or metabolite concentrations—standardized to a common metric where necessary to allow cross-study comparison. Effect sizes were aggregated using a random-effects model, which accounts for both within-study variance and between-study heterogeneity, a crucial consideration given the diversity in sample types, experimental platforms, and analytical methods typical of omics research (Borenstein et al., 2011).

The meta-analysis revealed statistically significant associations in several key molecular signatures across studies. For transcriptomic datasets, pooled effect sizes consistently indicated upregulation or downregulation of specific genes involved in relevant biological pathways, with confidence intervals generally not crossing the null effect line. Proteomic analyses exhibited greater variability, reflecting differences in mass spectrometry sensitivity and protein extraction protocols. Similarly, metabolomic studies demonstrated heterogeneous effect sizes, highlighting the influence of environmental, dietary, and technical factors on metabolite profiles (Nicholson et al., 2012).

Heterogeneity was quantitatively assessed using the statistic, which estimates the proportion of total variability attributable to between-study differences rather than chance. Moderate-to-high I² values were observed in several subgroups, especially in studies using novel high-throughput techniques or smaller sample sizes. This underlines the necessity of cautious interpretation and, where possible, stratified or subgroup analyses to account for methodological and biological variability (Higgins et al., 2003). Sensitivity analyses further confirmed the stability of pooled estimates, as exclusion of outlier studies with extreme effect sizes minimally impacted overall conclusions, suggesting robustness in the primary findings.

Meta-regression was employed to explore potential sources of heterogeneity, including study design, sample size, platform type, and population characteristics. Significant moderators were identified, particularly study size and omics platform, indicating that methodological differences contribute substantially to variability in reported effect sizes. This finding reinforces the importance of standardization in omics protocols and transparent reporting of experimental conditions (Kanehisa & Goto, 2000).

Finally, publication bias was assessed through funnel plot inspection and formal tests such as Egger’s regression (Figure 3). Mild asymmetry was detected, suggesting that smaller studies with large or significant effect sizes may be overrepresented, a common challenge in emerging fields like omics research. Despite this, the overall statistical synthesis supports reproducible patterns of molecular change across studies, emphasizing the value of multi-study aggregation in identifying robust biomarkers and mechanistic insights.

Overall, the statistical analysis demonstrates that while omics studies are inherently heterogeneous, appropriate meta-analytic techniques, including random-effects modeling, heterogeneity quantification, sensitivity analyses, and meta-regression, provide reliable synthesis of diverse datasets. These methods enable identification of consistent molecular signatures, highlight sources of variability, and inform future experimental designs aimed at improving reproducibility and translational potential.

4. Discussion

This systematic review and meta-analysis provides a comprehensive synthesis of omics studies, integrating transcriptomic, proteomic, and metabolomic data to identify reproducible molecular signatures across multiple biological contexts. The increasing availability of high-throughput omics datasets has revolutionized molecular biology, enabling researchers to detect subtle changes at the gene, protein, and metabolite levels that may underpin health, disease progression, or therapeutic response. By systematically collating and analyzing these datasets, this study sought to identify consistent patterns while addressing the heterogeneity and methodological variability inherent in omics research. The role of omics technologies in clinical prediction and personalized medicine is illustrated in Figure 4. The approach employed allowed for robust statistical pooling, revealing molecular trends that individual studies, due to limited sample sizes or platform-specific biases, might fail to capture.

Figure 4: Forest plot of omics-Based Approaches in Clinical Prediction and Personalized Medicine. This figure illustrates the application of omics technologies in clinical prediction, highlighting how molecular profiling supports disease stratification and therapeutic response assessment across multiple clinical contexts.

The forest plots generated in this meta-analysis offered a clear visualization of effect sizes across studies, highlighting molecular features with statistically significant alterations. The role of omics technologies in clinical prediction and personalized medicine is illustrated in Figure 4 while the translational relevance of omics-driven clinical prediction is further highlighted in Figure 5. Many transcriptomic studies showed upregulation of genes involved in immune response, cellular stress signaling, and metabolic regulation, while certain downregulated genes suggested suppression of homeostatic pathways under specific conditions. Similarly, proteomic analyses consistently identified altered levels of key enzymes and regulatory proteins, emphasizing their potential as biomarkers or therapeutic targets. The confidence intervals in these forest plots, which in several cases did not cross the null line, strengthened the evidence for reproducibility and highlighted molecular signals that are biologically meaningful rather than incidental. These findings underscore the value of integrating multi-omics data, as convergent evidence across molecular layers provides higher confidence in the biological significance of observed changes.

Figure 5: Translational Impact of Omics Technologies in Clinical Decision-Making. This figure emphasizes the translational implications of omics-based clinical prediction models, demonstrating how molecular signatures inform treatment selection and patient stratification in precision medicine.

Funnel plot analyses, conducted to assess publication bias, revealed a mild asymmetry, indicating that smaller studies with significant results were disproportionately represented in the literature. While this bias can inflate apparent effect sizes, sensitivity analyses—excluding outliers and smaller studies—demonstrated that the overall conclusions remained largely unchanged. This indicates that the primary molecular patterns identified are robust and not solely driven by publication bias. Nevertheless, the presence of bias highlights the ongoing need for transparent reporting, pre-registration of omics studies, and inclusion of null or negative results to ensure a more balanced evidence base. The combination of forest and funnel plot interpretations thus provides a nuanced understanding of both the reliability of effect estimates and the potential influence of reporting bias on the findings (Borenstein et al., 2011).

Statistical analysis using a random-effects model was central to this study, as it allowed for the accommodation of heterogeneity between studies—a common feature in omics research. An overview of the omics studies included in the predictive performance analysis is provided in Table 3. Heterogeneity, quantified by I² statistics, ranged from moderate to high in several subgroups, reflecting variations in sample types, experimental platforms, analytical pipelines, and study populations (Higgins et al., 2003). Meta-regression analyses further revealed that factors such as study size, platform type, and experimental conditions significantly contributed to observed heterogeneity. These findings emphasize the importance of standardizing experimental designs and analytical workflows in omics research to improve comparability and reproducibility across studies. Moreover, the identification of sources of heterogeneity can inform future research priorities, including the selection of consistent biomarkers and the design of experiments that minimize technical variability.

Table 3. Overview of Omics Studies Included in Predictive Performance Analysis. This table provides a consolidated overview of studies included in the predictive performance analysis, detailing omics platforms, biological models, sample sizes, and reported accuracy metrics. It serves as a reference framework for the comparative and meta-analytical assessments.

Study (First Author, Year)

Omics Type (Technique)

Sample Type (A/H)

Sample Size (N)

Predictive Model Status

Reported Efficiency/Accuracy

JCR Rank (2024)

Lu X. et al., 2023

Metabolomic (UPLC-HRMS)

A (Rat)

140

Yes

Yes (R² ˜ 1, Q² = 0.5)

Q1

Fang S. et al., 2023

Metabolomic (GC-MS)

A (Rat)

150

Yes

Yes (VIP > 1.0)

Q2

Pérez-Martínez C. et al., 2017

Proteomic (HPLC-MS/MS)

H (Human Bone)

80

Yes

Yes (p = 0.05)

Q1

Dai X. et al., 2019

Metabolomic (GC-MS)

A (Rat)

36

Yes

Yes (VIP > 1.0)

Q3

Wu Z. et al., 2018

Metabolomic (GC-MS)

A (Rat)

84

Yes

Yes (VIP > 1.2)

Q3

Du T. et al., 2018

Metabolomic (LC-MS)

A (Rat)

60

Yes

No (VIP > 1.5, p < 0.05)

Q1

Bonicelli A. et al., 2022

Multi-Omics (Proteomic/Metabolomic/Lipidomic)

H (Human Bone)

4

No

Yes (Accuracy Reported)

Q1

Beyond statistical significance, the biological interpretation of the findings provides valuable insights. Transcriptomic alterations in immune-related pathways align with prior reports indicating systemic changes in response to stressors, infection, or disease states (Nicholson et al., 2012). Proteomic and metabolomic findings complement this, revealing that corresponding protein abundance changes and metabolic shifts often reflect adaptive or compensatory mechanisms. For example, upregulation of oxidative stress-related proteins coupled with altered metabolite profiles may indicate activation of detoxification pathways, while downregulation of homeostatic proteins could point to impaired cellular regulation under pathological conditions. These multi-layered insights highlight the power of omics approaches to provide a holistic view of biological processes that single-layer studies might overlook. The methodological characteristics of clinical omics studies are summarized in Table 4.

Table 4. Characteristics of Clinical Studies Applying Omics Technologies for Disease Prediction. This table summarizes the methodological and clinical characteristics of studies applying omics approaches in human disease contexts. It highlights study design, sample types, molecular targets, and key findings relevant to diagnostic and therapeutic prediction.

Study (First Author, Year)

Omics Type

Clinical Indication / Disease

Sample Type

Sample Size (N)

Primary Outcome / Target

Study Type / Key Finding

Wang et al., 2011

Genomics (miRNA, SOLEXA)

Male Infertility

Seminal plasma

457

Seven altered miRNAs

Observational case-control study

BC Chemotherapy

Metabolomics (NMR 800 MHz)

Breast Cancer (BC)

Serum

29

Prediction of treatment response

Experimental design listed

HER2+ BC T/T+E

Metabolomics (NMR 800 MHz)

HER2+ Breast Cancer

Serum

79

Evaluation of treatment impact

Experimental design listed

HNSCC Induction Chemotherapy

Metabolomics (NMR 400 MHz)

Head and Neck Squamous Cell Carcinoma (HNSCC)

Serum

53

Prediction of treatment response

Experimental design listed

NSCLC Nivolumab/Pembrolizumab

Metabolomics (NMR 600 MHz)

Non-Small Cell Lung Cancer (NSCLC)

Serum

50

Prediction of treatment response

Experimental design listed

Vashisht et al., 2021

Metabolomics (Assays for 21 analytes)

Male Infertility

Seminal plasma

100

Fifteen markers significantly altered

Observational case-control study


Another key observation from this meta-analysis is the reproducibility of certain molecular signatures across diverse studies and platforms. Despite the heterogeneity inherent in omics research, convergent evidence supports the existence of core molecular responses that are conserved across conditions. This reinforces the potential utility of these signatures as biomarkers for disease diagnosis, prognosis, or therapeutic targeting. However, variability observed in effect sizes and the presence of outliers also highlight the limits of generalizability, emphasizing that context-specific factors—such as tissue type, environmental exposure, and population genetics—can influence molecular profiles. Therefore, translational applications of these findings should consider both the conserved signatures and the context-specific variations revealed through meta-analytic integration.

Importantly, this study illustrates the critical role of meta-analysis in omics research. By pooling data across multiple studies, meta-analytic methods reduce the influence of random error, increase statistical power, and facilitate the detection of subtle yet biologically relevant molecular changes. Moreover, the integration of quantitative statistical approaches with graphical tools, such as forest and funnel plots, enhances interpretability and allows researchers to assess the robustness of conclusions visually. This combination of rigorous quantitative analysis and intuitive visualization represents a best-practice framework for future omics syntheses, promoting reproducibility, transparency, and reliability in an era of ever-expanding high-throughput datasets.

Despite these strengths, it is important to contextualize the findings within the limitations of the included studies. Variation in experimental design, sample size, and data processing pipelines introduces unavoidable heterogeneity. Differences in platform sensitivity and specificity, particularly in proteomics and metabolomics, may lead to under- or overestimation of effect sizes. Additionally, while the study attempted to mitigate publication bias through funnel plot assessment and sensitivity analyses, the potential for selective reporting cannot be fully excluded. Future omics studies would benefit from standardized reporting guidelines, open-access raw data deposition, and inclusion of negative results to further strengthen the reliability of meta-analytic conclusions.

This systematic review and meta-analysis provide strong evidence that omics studies, despite inherent variability, reveal reproducible molecular signatures with important biological implications. Forest plot analyses demonstrated consistent effect sizes, while funnel plots highlighted potential but manageable biases. Statistical analyses accounted for heterogeneity and identified factors contributing to variability, providing a nuanced understanding of the molecular landscape across studies. The integration of multi-omics datasets enhances our ability to identify biologically meaningful patterns, informing biomarker discovery, therapeutic targeting, and mechanistic research. Overall, this work underscores the value of meta-analytic approaches in omics research, providing both a roadmap for future studies and a deeper understanding of the molecular underpinnings of complex biological processes.

5. Limitations

Despite the comprehensive approach, this study has several limitations. First, heterogeneity across included studies—due to differences in sample types, experimental platforms, analytical pipelines, and population characteristics—may have influenced pooled effect estimates. Second, the potential for publication bias exists, as smaller studies with significant results are more likely to be published, despite funnel plot analyses and sensitivity checks. Third, variations in data preprocessing, normalization methods, and statistical thresholds across omics studies may have introduced inconsistencies. Finally, the limited availability of raw data and the underreporting of negative findings constrain the ability to validate all molecular signatures fully.

6. Conclusion

This systematic review and meta-analysis highlight the power of omics approaches in uncovering molecular mechanisms and potential biomarkers across diverse biological systems. Despite heterogeneity and methodological variations, consistent patterns emerged that advance our understanding of gene, protein, and metabolite interactions. These findings underscore the value of integrative omics analyses for precision medicine, biomarker discovery, and functional insights, while emphasizing the need for standardized protocols and comprehensive data sharing to improve reproducibility and clinical translation in future studies.

 

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