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Results for “Biomarker variability”

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PubMed2001

Selection and validation of biomarkers for chemoprevention: the contribution of epidemiology.

This chapter considers the epidemiological contribution of DNA adducts as an example of markers for use in chemoprevention studies, and highlights the potential biases inherent in the conduct of epidemiological studies with molecular markers. Although adducts have been interpreted mainly as biomarkers of exposure, 'bulky' DNA adducts such as those measured by 32P-postlabelling or ELISA in white blood cells are more correctly interpretable as markers of cumulative unrepaired DNA damage. The latter concept can prove useful in cancer epidemiology, since it is consistent with existing knowledge on the importance of duration of exposure in the etiology of chemically-induced cancers. Increasing evidence suggests that in addition to prolonged exposure to genotoxic chemicals, inter-individual variability in carcinogen metabolism and DNA repair is predictive of cancer risk. Also from this point of view, measurements of 'bulky' DNA adducts can be useful as biomarkers for studies in populations, since they express the amount of carcinogen linked to DNA after repair, taking into account individual repair capacity. Finally, we suggest a theory of causality based on the work of Wesley Salmon and the concept of 'propagating mark', which is particularly attractive for molecular epidemiologists.

Biomarkers, Tumor↗

PubMed2006

Variations in the detection of ZAP-70 in chronic lymphocytic leukemia: Comparison with IgV(H) mutation analysis.

Lack of immunoglobulin heavy chain genes (IgV(H)) mutation in patients with chronic lymphocytic leukemia (CLL) is associated with rapid disease progression and shorter survival. The zeta-chain (T-cell receptor) associated protein kinase 70 kDa (ZAP-70) has been reported to be a surrogate marker for IgV(H) mutation status, and its expression in leukemic cells correlates with unmutated IgV(H). However, ZAP-70 detection by flow cytometry varies significantly dependant on the antibodies used, the method of performing the assay, and the condition of the cells in the specimen. The clinical value of ZAP-70 testing when samples are shipped under poorly controlled conditions is not known. Furthermore, testing in a research environment may differ from testing in a routine clinical laboratory. We validated an assay for ZAP-70 by comparing results with clinical outcome and the mutation status of the IgV(H). Using stored samples, we show significant correlation between ZAP-70 expression and clinical outcome as well as IgV(H) mutation at a cut-off point of 15%. While positive samples (>15% positivity) remain positive when kept in the laboratory environment for 48 h after initial testing, results obtained from samples from CLL patients tested after shipping at room temperature for routine testing showed no correlation with IgV(H) mutation status when 15% cut-off was used. In these samples, cut-point of 10% correlated with the IgV(H) mutation (P = 0.0001). This data suggests that although ZAP-70 positivity correlates with IgV(H) mutation status and survival, variations in sample handling and preparation may influence results. We show that IgV(H) mutation results, unlike ZAP-70 remain correlated with CD38 expression and beta-2 microglobulin in shipped samples, and ZAP-70 testing should not be used as the sole criterion for stratifying patients for therapy.

ADP-ribosyl Cyclase 1↗

PubMed2026

Plasma Proteome Signatures in Sickle Cell Anemia and the Effect of Hydroxyurea Treatment.

Sickle Cell Anaemia (SCA) is a monogenic blood disorder caused by a mutation in the β-globin gene, yet it presents with marked clinical variability. Although hydroxyurea (HU) is an established therapy, its precise mechanism of action remains incompletely understood. Plasma proteins represent valuable biomarkers for elucidating disease mechanisms and treatment responses. In this study, plasma proteome profiling of 31 healthy controls and 76 SCA patients identified 43 differentially abundant proteins (DAPs) that form a highly interconnected interaction network. Proteins with increased abundance in SCA were largely associated with immune and inflammatory responses, whereas those with reduced levels were linked to coagulation and proteolytic pathways. HU therapy was associated with elevated levels of haptoglobin (HP) and hemopexin (HPX), key mediators of free hemoglobin scavenging. We also identified several previously unreported plasma proteins altered in SCA, broadening the landscape of potential biomarkers and HU-responsive targets. Many DAPs significantly correlated with clinical indices, such as transfusion frequency, vaso-occlusive crises, white blood cell counts, and platelet counts, offering insights into disease mechanisms and potential utility in disease management. Notably, overlap with β-thalassemia-associated signatures suggests shared pathophysiological pathways between these hemoglobinopathies. Collectively, these findings provide a strong foundation for translational validation in larger, independent cohorts.

Humans↗

PubMed2004

High expression of activation-induced cytidine deaminase (AID) mRNA is associated with unmutated IGVH gene status and unfavourable cytogenetic aberrations in patients with chronic lymphocytic leukaemia.

Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation of B-cells. We investigated the expression of AID mRNA by real-time polymerase chain reaction (PCR) in peripheral blood mononuclear cells of 80 patients with B-CLL. AID expression was detected in 45 of 80 patients (56%) at various levels, but was undetectable in 35 patients (44%). AID PCR positivity was associated with unmutated IGV(H) gene status (22 of 25 patients; P=0.002) and unfavourable cytogenetics (18 of 23 patients with deletion in 11q or loss of p53; P=0.040). Using a threshold level of 0.01-fold expression compared to Ramos control cells, even more significant associations were observed (P=0.001 for IGVH; P=0.002 for cytogenetics). A correlation was observed between individual AID levels and the percentage of V(H) homology (R=0.41; P=0.001). AID positivity predicted unmutated IGV(H) status with an odds ratio of 8.31 (P=0.003) and poor risk cytogenetics with an odds ratio of 3.46 (P=0.032). Significance was retained after adjustment for Binet or Rai stages. AID mRNA levels were stable over time. These data suggest a potential role of AID as a prognostic marker in B-CLL.

Biomarkers↗

PubMed2003

Loss of expression of tropomyosin-1, a novel class II tumor suppressor that induces anoikis, in primary breast tumors.

Suppression of tropomyosins (TMs), a family of actin-binding, microfilament-associated proteins, is a prominent feature of many transformed cells. Yet it is unclear whether downregulation of TMs occur in human tumors. We have investigated the expression of tropomyosin-1 (TM1) in human breast carcinoma tissues by in situ hybridization and immunofluorescence. TM1 mRNA and protein are readily detectable in normal mammary tissue. In contrast, TM1 expression is abolished in the primary human breast tumors. Expression of other TM isoforms, however, is variable among the tumors. The consistent and profound downregulation of TM1 suggests that TM1 may be a novel and useful biomarker of mammary neoplasms. These data also support the hypothesis that suppression of TM1 expression during the malignant conversion of mammary epithelium as a contributing factor of breast cancer. In support of this hypothesis, we show that the ability to suppress malignant growth properties of breast cancer cells is specific to TM1 isoform. Investigations into the mechanisms of TM1-induced tumor suppression reveal that TM1 induces anoikis (detachment induced apoptosis) in breast cancer cells. Downregulation of TM1 in breast tumors may destabilize microfilament architecture and confer resistance to anoikis, which facilitates survival of neoplastic cells outside the normal microenvironment and promote malignant growth.

Anoikis↗

PubMed1997

Complementarity determining region-III is a useful molecular marker for the evaluation of minimal residual disease in mantle cell lymphoma.

Bone marrow (BM) and peripheral blood (PB) involvement in 10 patients with mantle cell lymphoma (MCL) was analysed by a polymerase chain reaction (PCR)-mediated RNase protection assay. The complementarity determining regions (CDR)-III of all 10 MCLs examined was amplified efficiently with consensus V(H) and J(H) primers by PCR. and BM and/or PB involvement was evaluated by RNase protection assay in all 10 patients examined. Our assay showed BM and/or PB of the entire group to have neoplastic cells at presentation, despite the fact that eight patients were found to have BM and/or PB involvement on the basis of morphological examination and/or surface marker analysis. We also examined minimal residual disease (MRD) after conventional chemotherapy, and detected MRD in a patient in complete remission (CR). Although previous studies have shown that t(11;14) breakpoint amplification by PCR was only applicable to about 30-40% of cases, the present study indicates that CDR-III is a useful molecular marker and the PCR-mediated RNase protection assay is a good tool for the evaluation of MRD in MCL. It is suggested that BM and PB of MCL patients are quite frequently involved at presentation and even after conventional chemotherapy at the molecular level.

Aged↗

PubMedDate not supplied

Determinants of p,p-dichlorodiphenyldichloroethane (DDE) concentration in adipose tissue in women from five European cities.

To identify the determinants of p,p'-dichlorodiphenyldichloroethane (p,p'-DDE) in adipose tissue in subjects who participated in a cross-sectional study, we analyzed fatty acids, antioxidants, and p,p'-DDE in aspirates of adipose tissue of 328 postmenopausal women from 5 European countries. The overall mean of p,p'-DDE concentration was 1.66 microg/g of fatty acids (95% confidence interval = 1.46, 1.88). In a multiple-regression analysis, the main predictors of log10(p,p'DDE) were center of recruitment (p < .0001), adipose arachidic acid (p = .001), and adipose retinol (p = .04). These factors explained 14.9% of the overall variability of log10(p,p'-DDE). In our subjects, adipose tissue p,p'DDE concentrations were only weakly related with biomarkers reflecting intake of fish and other foods. This result is consistent with the notion that p,p'-DDE exists in different foods and, given the widespread contamination of the food chain, is relatively evenly distributed among foods.

Adipose Tissue↗

PubMed1996

Relationship between cytotoxicity and site-specific DNA recombination after in vitro exposure of leukemia cells to etoposide.

BACKGROUND: Etoposide, an inhibitor of the normal religation activity of the nuclear enzyme topoisomerase II, can induce a secondary acute myeloid leukemia characterized by site-specific DNA rearrangements. The schedule of drug administration appears to be a clinical risk factor for this devastating treatment complication. PURPOSE: We tested the hypothesis that prolonged exposure of leukemia cells in vitro to low concentrations of etoposide, compared with short exposures to high concentrations, could produce equivalent or greater desired cytotoxic effects, with decreased occurrence of undesired site-specific double-stranded DNA recombinational events (i.e., recombinogenesis). METHODS: We used the frequency of V(D)J (variable-diversity-joining) recombinase-mediated deletions of exons 2 and 3 of the hypoxanthine phosphoribosyltransferase (HPRT) gene as a biomarker of etoposide-induced, nonhomologous, site-specific DNA rearrangement. A polymerase chain reaction-based technique was used to measure exon 2 + 3 deletions in human lymphoid leukemia CCRF-CEM cells 6 days after either 4-hour or 24-hour treatment with etoposide at clinically relevant concentrations. Cytotoxic effects of etoposide (determined by the number of viable cells present in the treated compared with the control [i.e., untreated] cells) were measured 6 days after treatment of the cells. The frequency of the exon 2 + 3 deletion following the two treatment-duration conditions was compared by use of the Mantel-Haenszel statistic. All P values resulted from two-sided tests. RESULTS: Cytotoxicity increased with increasing etoposide concentration and exposure duration, as expected. By day 6, the frequency of exon 2 + 3 deletions was significantly higher (global P value = .0003) after the 4-hour treatment than after the 24-hour treatment, regardless of whether the frequency was assessed at etoposide concentrations achieving equivalent (e.g., 95%) cytotoxicity (14.2 x 10(-7) versus 4.1 x 10(-7) or at equivalent etoposide concentrations (e.g., 1 microM) (10.8 x 10(-7) versus 1.3 x 10(-7). Thus, the ratio of desired cytotoxic to undesired recombinogenic effects was higher with the 24-hour schedule. After the treated cells were subcloned at limiting dilutions, the frequency of the exon 2 + 3 deletion increased from 16.3 x 10(-7) to 4.33 x 10(-3), indicating that the recombinational event is not necessarily lethal. CONCLUSION: For all drug concentrations and levels of cytotoxicity studied in CCRF-CEM cells, there was a greater ratio of cytotoxicity to genetic recombination following prolonged exposure to etoposide than following brief exposure. IMPLICATION: These data suggest that recombinogenesis is not inextricably linked to cytotoxicity. If confirmed in the clinical setting, the use of prolonged dosage schedules may provide a means to decrease the risk of etoposide-induced acute myeloid leukemia without compromising treatment efficacy.

Acute Disease↗

PubMed2025

Development and Validation of a Novel LC-MS/MS Based Proteomics Method for Quantitation of Retinol Binding Protein 4 (RBP4) and Transthyretin (TTR).

Retinol binding protein 4 (RBP4), the circulating carrier of retinol, complexes with transthyretin (TTR) and is a potential biomarker of cardiometabolic disease. However, RBP4 quantitation relies on immunoassays and western blots without retinol and TTR measurement. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous absolute quantitation of circulating RBP4 and TTR is critical to establishing their biomarker potential. Surrogate peptides with reproducible, linear LC-MS/MS response were selected. Purified proteins were used as quantitation standards and heavy-labelled peptides as internal standards. Matrix effects were evaluated. The validated method was applied to measure inter- and intra-individual variability in RBP4 and TTR concentrations in healthy individuals and patients with diabetic kidney disease. Quantitation was linear for the clinically relevant concentration ranges of RBP4 (0.5-6 μM) and TTR (5.8-69 μM). Assay inter-day variability was <12% and precision within 5%. The inter-individual variability for RBP4 and TTR concentrations was 18-26%, while intra-individual variability was similar to assay variability. RBP4 and TTR quantitation correlated with commercially available ELISA assays. The developed LC-MS/MS method enables simultaneous absolute quantitation of RBP4 and TTR in serum and plasma that can be applied to clinical biomarker studies and stoichiometric measurements of circulating RBP4, TTR, and retinol.

Retinol binding protein 4 (RBP4)↗

PubMed2003

Molecular fingerprinting in human lung cancer.

The behavior and outcome of lung cancers are highly variable, and not only is the molecular basis of this variability unknown, but neither standard histopathology nor currently available molecular markers can predict these characteristics. Accordingly, the identification of novel biomarkers to differentiate tumor from normal cells and predict tumor behavior such as pathologic stage, response to chemotherapy, and site of relapse, is of great importance in clinical practice. None of the hundreds of single markers evaluated to date have demonstrated significant clinical utility, but by surveying thousands of genes at once with use of microarrays or proteomic technologies, it is now possible to read the molecular signature of an individual patient's tumor. When the signature is mathematically analyzed, new classes of cancer can be observed and insight can be gained into prediction, prognosis, and mechanism. Although some success has been achieved with genomic approaches, proteomics-based approaches allow examination of expressed proteins of a tissue or cell type, complement the genome initiatives, and are increasingly being used to address biomedical questions. This review aims to summarize the state of the art of gene and protein expression profiling for non-small-cell lung cancer

Biomarkers, Tumor↗

PubMed2005

Soluble intercellular adhesion molecule-1 and E-selectin as markers of disease activity and endothelial activation in juvenile idiopathic arthritis.

OBJECTIVE: To determine whether soluble forms of the adhesion molecules intercellular adhesion molecule-1 (ICAM-1) and E-selectin correlate with clinical measures or other markers of endothelial activation in children with juvenile idiopathic arthritis (JIA) over time. METHODS: A total of 28 children with JIA were studied every 3 months over 2 years. At each interval, serum was tested for soluble (s)ICAM-1 and sE-selectin, plasma for fibrin d-dimer and von Willebrand factor (vWF), and the following clinical variables were recorded: erythrocyte sedimentation rate (ESR), physician and parent global assessments, swollen and limited joint counts, and functional assessment by Childhood Health Assessment Questionnaire. Concentrations of the adhesion molecules were also determined once in 30 age matched healthy children. RESULTS: Among all JIA subtypes, baseline sICAM-1 was elevated compared to controls; sE-selectin was higher in patients with systemic disease compared to other subtypes and controls. sE-selectin correlated with ESR, but there were no other correlations between concentrations of either adhesion molecule or any other clinical variables or vWF antigen. sICAM-1 was higher in those with elevated compared to normal d-dimer. There were no differences between mean sICAM-1 and sE-selectin before or during disease flare or improvement periods, except for an increase in sICAM-1 with flares in patients with systemic disease. CONCLUSION: sICAM-1 is elevated in children with active JIA. sE-selectin is only elevated in children with active systemic disease. Although some relationships were found between the adhesion molecules and other variables, they did not correlate with most variables, and did not parallel the disease course. Thus, we cannot recommend the routine use of these molecules as clinical biomarkers of disease activity. This study confirms that endothelial activation is key to the pathogenesis of JIA, especially in the systemic subtype.

Adolescent↗

PubMed2005

Significance of VH genes mutation status for prognosis of CLL patients.

AIM: The aim of this study was to evaluate significance of VH mutation status for prognosis of B-cell chronic lymphocytic leukemia (B-CLL) patients in comparison with other prognostic markers. MATERIALS AND METHODS: The VH mutation status was evaluated in 43 B-CLL patients by RT-PCR amplification and nucleotide sequencing, and CD38 expression - by two-color FACS analysis. The prognostic influence of VH mutation rate and CD38 expression level was tested by different statistical methods. RESULTS: The increasing number of advanced cases over the follow-up period, shorter median time from diagnosis to start of second line therapy, worse response to fludarabine treatment, poor survival for early stages B-CLL were found in unmutated versus mutated CLL patients. The significance of CD38 expression for CLL prognosis was revealed as predictor for response for fludarabine treatment and time of progression in advanced stages. The correlation between CD38 expression and VH mutation status was not found. CONCLUSION: Simultaneous determination of VH mutation status and CD38 expression may be helpful for prediction of CLL prognosis.

ADP-ribosyl Cyclase 1↗

PubMed2006

Saccades in presymptomatic and early stages of Huntington disease.

OBJECTIVE: To evaluate quantitative measures of eye movements as possible biomarkers in prediagnostic and early stages of Huntington disease (HD). METHODS: The study sample (n = 215) included individuals both at risk and recently diagnosed with HD. All participants completed a uniform clinical evaluation which included administration of the Unified Huntington's Disease Rating Scale (UHDRS) by a movement disorder neurologist and molecular testing to determine HD gene status. A high resolution, video-based eye tracking system was employed to quantify measures of eye movement (error rates, latencies, SD of latencies, velocities, and accuracies) during a computerized battery of saccadic and steady fixation tasks. RESULTS: Prediagnostic HD gene carriers and individuals with early HD demonstrated three types of significant abnormalities while performing memory guided and anti-saccade tasks: increased error rate, increased saccade latency, and increased variability of saccade latency. The eye movement abnormalities increased with advancing motor signs of HD. CONCLUSIONS: Abnormalities in eye movement measures are a sensitive biomarker in the prediagnostic and early stages of Huntington disease (HD). These measures may be more sensitive to prediagnostic changes in HD than the currently employed neurologic motor assessment.

Eye Movements↗

PubMed2025

Molecular Biomarker Testing Patterns and Turnaround Time in US Patients With Advanced Non-Small Cell Lung Cancer.

BACKGROUND: Patients with advanced non-small cell lung cancer (aNSCLC) are recommended to undergo molecular testing for targetable genomic alterations. However, as high-throughput methods are increasingly used, long test turnaround time (TAT) may lead to lower receipt of appropriate targeted therapy. Guidelines recommend a 2-week TAT for ALK and EGFR testing, 2 prevalent pathogenic alterations with highly effective targeted therapies. PATIENTS AND METHODS: Using an electronic health record-derived, deidentified database, we conducted a retrospective cohort study of patients with aNSCLC diagnosed between 2011 and 2023 who received testing for ≥1 of 8 molecular markers. We assessed the number of biomarkers tested per patient, testing modality, and TAT (defined as the interval between specimen collection and result date) over time. We also evaluated patients with ALK/EGFR-altered aNSCLC who initiated early nontargeted treatment prior to test result availability, examining associations with TAT and clinical outcomes. RESULTS: The study sample comprised 33,945 patients, with a mean age of 68.2 years; 49.4% were female, 58.3% were White, and 83.4% reported a history of smoking. From 2011 to 2023, the mean number of biomarkers tested per patient (range, 2.0-6.8) and the use of next-generation sequencing (NGS) increased, whereas the mean TAT converged to 3 weeks. Fewer than half of the patients with ALK/EGFR-altered aNSCLC had a TAT of ≤2 weeks, and 1 in 8 initiated early nontargeted treatment. Longer TAT was associated with early nontargeted treatment when analyzed as both a continuous variable (odds ratio, 1.83 per week) and a binary variable (TAT >2 vs ≤2 weeks; odds ratio, 6.02). Early treatment was associated with worse median progression-free survival (9 vs 11 months) in patients with ALK/EGFR-altered aNSCLC. CONCLUSIONS: Biomarker testing and NGS use have increased over time in US patients with aNSCLC. TAT has plateaued and remains longer than recommended in consensus guidelines. Longer TAT was associated with early nontargeted therapy in patients with ALK+/EGFR+ aNSCLC, leading to suboptimal first-line treatment and poorer clinical outcomes.

Humans↗

PubMed2005

Pharmacokinetic-pharmacodynamic correlations and biomarkers in the development of COX-2 inhibitors.

The mechanism by which COX inhibitors exert their analgesic effect is well established. However, data show no direct correlation between drug concentrations in plasma and the analgesic or adverse effects in chronic inflammatory conditions. This represents a major problem in the development of COX inhibitors, since it is difficult to predict the appropriate dosing regimen for the treatment of chronic inflammatory pain, based upon information from pre-clinical studies and eventually early clinical studies. The factors that determine response in inflammatory pain must be understood in order to make predictions about the time course of the analgesic effect. In this review the determinants of drug response and their variability will be discussed: physicochemical properties, pharmacokinetics (PK), pathophysiology and disease progression. From a mechanistic point of view, endogenous mediators of inflammation might be used as a biomarker for the analgesic effect and safety assessment. Such a biomarker can be an intermediate step between drug exposure and response. In addition, its concentration-effect relationship could be characterized by pharmacokinetic-pharmacodynamic (PK/PD) modelling. Indeed, recent investigations have shown that COX-2 inhibition, as determined by modelling of prostaglandin E2 (PGE2) levels in the whole blood assay in vitro can be used as a marker to predict drug effects (analgesia) in humans. A model-derived parameter, IC80, (total and unbound) was found to correlate directly with the analgesic plasma concentration of different COX inhibitors varying in enzyme selectivity. These findings indicate that PGE2 and thromboxane B2 inhibition can be used to predict and select efficacious doses in humans.

Animals↗

PubMed1997

Evaluation of sister chromatid exchange and chromosome breaks in a cohort of untreated Hodgkin's disease patients.

Cytogenetic biomarkers, chromosomal breaks [spontaneous breaks (SB) and bleomycin-induced breaks (BIB)], and sister chromatid exchange (SCE) have been shown to be sensitive cytological assays to defect susceptibility to DNA-damaging effects. However, little information is available on how environmental factors and demographic and clinical characteristics influence variation among individuals. We sought to characterize interindividual variability in a cohort of 105 untreated adult Hodgkin's disease patients. SB, BIB, and SCE data were integrated with epidemiological data by using linear regression analysis. Age, sex, ethnicity, education, histology, history of mononucleosis, and family history of cancer showed no association with any biomarker. In univariate analysis, alcohol intake was significantly associated with high SCEs (P = 0.005) and SBs (P = 0.02). Current smoking was associated only with high frequencies of SCE (P = 0.05). Advanced stage of disease was related with high SBs (P = 0.01). BIBs were not associated with any of the variables studied. In multivariate modeling, current alcohol intake was associated with high SCEs (P = 0.04) and SBs (P = 0.01). Former smokers had higher SBs than nonsmokers did (P = 0.02). A small positive correlation was found among each pair of markers. The higher SCEs and SBs in patients who smoke and consume alcohol indicate the need for evaluating these exposures when interpreting these biomarkers.

Adult↗

PubMed2026

The metastatic spectrum in functional and non-functional NENs: mechanistic insights from multi-omics.

Neuroendocrine neoplasms (NENs) are biologically heterogeneous tumors in which differentiation/grade and hormonal functionality are intersecting but non-equivalent axes. This review focuses on functional and non-functional well-differentiated neuroendocrine tumors (NETs), principally gastroenteropancreatic and pancreatic NETs, and critically evaluates how site, lineage, stage, tumor burden, genomic and epigenetic alterations, immune-stromal remodeling, metabolic adaptation, microbiome-associated signals, and treatment pressure converge on metastasis and recurrence. Apparent outcome differences by functionality are inconsistent after clinicopathological adjustment: non-functional presentation is often enriched for delayed diagnosis and adverse features, whereas functional subtypes range from typically indolent insulinomas to clinically aggressive hormone-producing tumors. We reconcile these observations through a layered model in which lineage-defining alterations and chromatin/telomere programs establish cellular state; signaling and metabolic plasticity enable stress adaptation; and hypoxia, angiogenesis, immune cells, fibroblasts, extracellular matrix, and therapy create selective niches for dissemination and relapse. We also define computational strategies for heterogeneous multi-omics integration and a staged biomarker-validation pathway. Evidence remains dominated by pancreatic NETs, and causal support is weakest for microbiome-functionality relationships and several proposed cross-omic links. A spectrum-based framework is therefore most useful when it generates testable, site- and grade-specific hypotheses rather than treating functionality as an isolated prognostic variable.

Humans↗

PubMed2004

High-resolution serum proteomic features for ovarian cancer detection.

Serum proteomic pattern diagnostics is an emerging paradigm employing low-resolution mass spectrometry (MS) to generate a set of biomarker classifiers. In the present study, we utilized a well-controlled ovarian cancer serum study set to compare the sensitivity and specificity of serum proteomic diagnostic patterns acquired using a high-resolution versus a low-resolution MS platform. In blinded testing sets, the high-resolution mass spectral data contained multiple diagnostic signatures that were superior to the low-resolution spectra in terms of sensitivity and specificity (P<0.00001) throughout the range of modeling conditions. Four mass spectral feature set patterns acquired from data obtained exclusively with the high-resolution mass spectrometer were 100% specific and sensitive in their diagnosis of serum samples as being acquired from either unaffected patients or those suffering from ovarian cancer. Important to the future of proteomic pattern diagnostics is the ability to recognize inferior spectra statistically, so that those resulting from a specific process error are recognized prior to their potentially incorrect (and damaging) diagnosis. To meet this need, we have developed a series of quality-assurance and in-process control procedures to (a) globally evaluate sources of sample variability, (b) identify outlying mass spectra, and (c) develop quality-control release specifications. From these quality-assurance and control (QA/QC) specifications, we identified 32 mass spectra out of the total 248 that showed statistically significant differences from the norm. Hence, 216 of the initial 248 high-resolution mass spectra were determined to be of high quality and were remodeled by pattern-recognition analysis. Again, we obtained four mass spectral feature set patterns that also exhibited 100% sensitivity and specificity in blinded validation tests (68/68 cancer: including 18/18 stage I, and 43/43 healthy). We conclude that (a) the use of high-resolution MS yields superior classification patterns as compared with those obtained with lower resolution instrumentation; (b) although the process error that we discovered did not have a deleterious impact on the present results obtained from proteomic pattern analysis, the major source of spectral variability emanated from mass spectral acquisition, and not bias at the clinical collection site; (c) this variability can be reduced and monitored through the use of QA/QC statistical procedures; (d) multiple and distinct proteomic patterns, comprising low molecular weight biomarkers, detected by high-resolution MS achieve accuracies surpassing individual biomarkers, warranting validation in a large clinical study.

Biomarkers, Tumor↗