Corresponding ctDNA and tumor burden dynamics in metastatic melanoma patients on systemic treatment.

Radiographic imaging is the current standard for monitoring progression of tumor-burden and therapeutic resistance in patients with metastatic melanoma. Plasma circulating tumor DNA (ctDNA) has shown promise as a survelience tool, but longitudinal data on the dynamics between plasma ctDNA concentrations and radiographic imaging is lacking. We evaluated the relationship between longitudinal radiographic measures of tumor burden and ctDNA concentrations in plasma on 30 patients with metastatic melanoma on systemic treatment. In 9 patients with no radiographic evidence of disease over a total of 15 time points, ctDNA concentrations were undetectable. In 21 patients with radiographic tumor burden, ctDNA was detected in 81 % of 58 time points. Plasma ctDNA concentrations demonstrated a modest positive correlation with total tumor burden (TTB) measurements (R2= 0.49, p < 0.001), with the greatest degree of correlation observed under conditions of progressive disease (PD) (R2 = 0.91, p = 0.032). Plasma ctDNA concentrations were significantly greater at times of RECIST v1.1 progression (PD; 22.1 % ± 5.7 %) when compared to samples collected during stable disease (SD; 4.99 % ± 3.0 %) (p = 0.012); this difference was independent of total tumor burden (p = 0.997). Changes in plasma ctDNA showed a strong correlation with changes in TTB (R2= 0.88, p<0.001). These data suggest that measurements of plasma ctDNA during therapy are a better surrogate for responding versus non-responding disease compared to absolute tumor burden.

Clinical Laboratory Approaches for Diagnoses of Sleep-Disordered Breathing and ADHD-Like Behavior in Children.

BACKGROUND: Impaired breathing during sleep, as in obstructive sleep apnea (OSA), can lead to behavior symptoms like those observed in children with attention deficit hyperactivity disorder (ADHD). Obstructive sleep apnea can be effectively treated, thus avoiding problematic pharmacotherapies associated with managing ADHD. Diagnosis of OSA relies on sleep studies as the gold standard, but in children, sleep studies are inherently difficult, cumbersome, and expensive and are not practical tools in the differential diagnosis of behavior disorders. Therefore, development of clinical laboratory tests for diagnoses of sleep apnea would change the standard of care for attention deficit syndromes. CONTENT: We review the status of potential laboratory tests for diagnosis of OSA in children with emphasis on markers linked to intermittent hypoxia and cardiovascular responses. In the context of ADHD, we focus on preliminary evidence and rationale for urocortin 3 and erythropoietin as urinary markers with physiologic relevance for diagnosis of OSA. SUMMARY: Laboratory tests that correlate with both OSA and ADHD-like syndromes would be useful to diagnose root causes of behaviors and identify a subset of children who may not need psychotropic medications. The discovery of laboratory biomarkers for OSA is evolving, but several candidates show promise and provide a segue to more focused development in laboratory diagnostics.

The urocortin peptides: biological relevance and laboratory aspects of UCN3 and its receptor.

The urocortins are polypeptides belonging to the corticotropin-releasing hormone family, known to modulate stress responses in mammals. Stress, whether induced physically or psychologically, is an underlying cause or consequence of numerous clinical syndromes. Identifying biological markers associated with the homeostatic regulation of stress could provide a clinical laboratory approach for the management of stress-related disorders. The neuropeptide, urocortin 3 (UCN3), and the corticotropin-releasing hormone receptor 2 (CRHR2) constitute a regulatory axis known to mediate stress homeostasis. Dysregulation of this peptide/receptor axis is believed to play a role in several clinical conditions including post-traumatic stress, sleep apnea, cardiovascular disease, and other health problems related to stress. Understanding the physiology and measurement of the UCN3/CRHR2 axis is important for establishing a viable clinical laboratory diagnostic. In this article, we focus on evidence supporting the role of UCN3 and its receptor in stress-related clinical syndromes. We also provide insight into the measurements of UCN3 in blood and urine. These potential biomarkers provide new opportunities for clinical research and applications of laboratory medicine diagnostics in stress management.

Longitudinal Relationship between Idylla Plasma ctBRAF V600 Mutation Detection and Tumor Burden in Patients with Metastatic Melanoma.

BACKGROUND: Circulating tumor DNA (ctDNA) may complement radiography for interim assessment of patients with cancer. OBJECTIVE: Our objective was to explore the relationship between changes in plasma ctDNA versus radiographic imaging among patients with metastatic melanoma. METHODS: Using the Idylla system, we measured B-Raf proto-oncogene (BRAF) V600 ctDNA in plasma from 15 patients with BRAF V600E/K-positive primary tumors undergoing standard-of-care monitoring, including cross-sectional computed tomography (CT) imaging. BRAF V600 mutant allele frequency (%MAF) was calculated from the Idylla Cq values and directly measured using droplet digital polymerase chain reaction (ddPCR). RESULTS: The Idylla ctDNA assay demonstrated 91% sensitivity, 96% specificity, 91% positive predictive value, and 96% negative predictive value for the presence of > 93 mm metastatic disease. Qualitative ctDNA results corresponded to changes in RECIST (Response Evaluation Criteria in Solid Tumors) 1.1 status determined by CT imaging in 11 of 15 subjects (73%). Calculated %MAF results correlated with ddPCR (R2 = 0.94) and provided evidence of progressive disease 55 and 97 days in advance of CT imaging for two subjects with persistently positive qualitative results. CONCLUSIONS: Overall, interim ctDNA results provided evidence of partial response or progressive disease an average of 82 days before radiography. This pilot study supports the feasibility of using the Idylla plasma BRAF V600 ctDNA assay as a complement to CT scanning for routine monitoring of therapeutic response. Somatic mutation quantification based on Cq values shows promise for identifying disease progression and warrants further validation.

Polypharmacy: a healthcare conundrum with a pharmacogenetic solution.

The use of multiple medications is growing at an alarming rate with some reports documenting an average of 12-22 prescriptions being used by individuals ≥50 years of age. The indirect consequences of polypharmacy include exacerbation of drug-drug interactions, adverse drug reactions, increased likelihood of prescribing cascades, chronic dependence, and hospitalizations - all of which have significant health and economic burden. While many practical solutions for reducing polypharmacy have been proposed, they have been met with limited efficacy. This highlights the need for a new systematic approach for fine-tuning dispensing of medications. Pharmacogenetic testing provides an empirical and scientifically rigorous approach for guiding appropriate selection of medicines, with the potential to reduce unnecessary polypharmacy while improving clinical outcomes. The goal of this review article is to provide healthcare providers with an understanding of polypharmacy, its adverse effects on the healthcare system and highlight how pharmacogenetic information can be used to avoid polypharmacy in patients.

Cell-free DNA diagnostics: current and emerging applications in oncology.

Liquid biopsy is a noninvasive dynamic approach for monitoring disease over time. It offers advantages including limited risks of blood sampling, opportunity for more frequent sampling, lower costs and theoretically non-biased sampling compared with tissue biopsy. There is a high degree of concordance between circulating tumor DNA mutations versus primary tumor mutations. Remote sampling of circulating tumor DNA can serve as viable option in clinical diagnostics. Here, we discuss the progress toward broad adoption of liquid biopsy as a diagnostic tool and discuss knowledge gaps that remain to be addressed.

Model analysis of bidirectional interference in two-stage labeled-ligand immunoassays.

OBJECTIVES: Immunoassays involving sample incubation followed by a wash step prior to introduction of labeled analyte are potentially subject to both positive and negative interference (bidirectional interference) by a competing ligand. We examine this phenomenon from a theoretical standpoint using a mathematical model for sequential-step immunoassays in the presence of interferent. DESIGN & METHODS: Competitive binding to antibody between analyte and interferent was modeled for sequential-step immunoassays. A primary assumption was that the ratio of affinity constants between the intended analyte and the interferent reflected the ratio of dissociation rate constants, with the higher dissociation rate constant for the lesser affinity ligand. RESULTS: Relationships of parameters (relative affinity constants, relative concentrations) for analyte and interferent were determined for conditions in which bidirectional interference can occur, for both steady-state and non-steady-state sample incubation conditions. Non-steady state sample incubation conditions can enhance the effects of an interferent. Homogeneous assay formats utilizing labeled ligand without a wash step can also demonstrate bidirectional interference, but positive interference is favored under such formats. CONCLUSIONS: Model calculations demonstrate the theoretical basis for bidirectional interference in two-stage immunoassays. Results delineate constraints on conditions in which bidirectional interference can occur.

Fundamentals of Pharmacogenetics in Personalized, Precision Medicine.

This article introduces fundamental principles of pharmacogenetics as applied to personalized and precision medicine. Pharmacogenetics establishes relationships between pharmacology and genetics by connecting phenotypes and genotypes in predicting the response of therapeutics in individual patients. We describe differences between precision and personalized medicine and relate principles of pharmacokinetics and pharmacodynamics to applications in laboratory medicine. We also review basic principles of pharmacogenetics, including its evolution, how it enables the practice of personalized therapeutics, and the role of the clinical laboratory. These fundamentals are a segue for understanding specific clinical applications of pharmacogenetics described in subsequent articles in this issue.

Liquid Biopsies in Oncology and the Current Regulatory Landscape.

There is a profound need in oncology to detect cancer earlier, guide individualized therapies, and better monitor progress during treatment. Currently, some of this information can be achieved through solid tissue biopsy and imaging. However, these techniques are limited because of the invasiveness of the procedure and the size of the tumor. A liquid biopsy can overcome these barriers as its non-invasive nature allows samples to be collected over time. Liquid biopsies may also allow earlier detection than traditional imaging. Liquid biopsies include the analysis of circulating tumor cells (CTCs), cell-free nucleic acid (cfNA), or extracellular vesicles obtained from a variety of biofluids, such as peripheral blood. In this review, we discuss different liquid biopsy types and how they fit into the current regulatory landscape.

Epigenetic primer for diagnostic applications: a window into personalized medicine.

Epigenetic testing, primarily in the form of DNA methylation analysis, is currently being used in healthcare settings to help identify and manage disease conditions and to develop and select drugs that specifically target epigenetic machinery. Yet, the clinical application of epigenetic analysis is still in its infancy. With a number of large-scale national and international epigenomic consortia projects in progress to identify tissue-specific epigenomes in normal and disease conditions, we are now poised for a new era of understanding disease processes based upon genetic changes that do not involve alterations to the DNA sequence. The developing epigenetic knowledge base will significantly advance the practice of personalized medicine and precision therapeutics. In this article, we provide a primer on the fundamentals of epigenetics with an emphasis on DNA methylation and review the prospective uses of epigenetic testing in advancing healthcare.

Circulating tumor cells: a review of present methods and the need to identify heterogeneous phenotypes.

The measurement and characterization of circulating tumor cells (CTCs) hold promise for advancing personalized therapeutics. CTCs are the precursor to metastatic cancer and thus have the potential to radically alter patient treatment and outcome. Currently, clinical information provided by the enumeration of CTCs is limited to predicting clinical outcome. Other areas of interest in advancing the practice of pathology include: using CTCs for early detection of potential metastasis, determining and monitoring the efficacy of individualized treatment regimens, and predicting site-specific metastasis. Important hurdles to overcome in obtaining this type of clinical information involve present limitations in defining, detecting, and isolating CTCs. Currently, CTCs are detected using epithelial markers. The definition of what distinguishes a CTC should be expanded to include CTCs with heterogeneous phenotypes, and markers should be identified to enable a more comprehensive capture. Additionally, most methods available for detecting CTCs do not capture functionally viable CTCs. Retaining functional viability would provide a significant advantage in characterizing CTC-subtypes that may predict the site of metastatic invasion and thus assist in selecting effective treatment regimens. In this review we describe areas of clinical interest followed by a summary of current circulating cell-separation technologies and present limitations. Lastly, we provide insight into what is required to overcome these limitations as they relate to applications in advancing the practice of pathology and laboratory medicine.

Prospective pilot trial of PerMIT versus standard anticoagulation service management of patients initiating oral anticoagulation.

We performed a randomised pilot trial of PerMIT, a novel decision support tool for genotype-based warfarin initiation and maintenance dosing, to assess its efficacy for improving warfarin management. We prospectively studied 26 subjects to compare PerMIT-guided management with routine anticoagulation service management. CYP2C9 and VKORC1 genotype results for 13 subjects randomly assigned to the PerMIT arm were recorded within 24 hours of enrolment. To aid in INR interpretation, PerMIT calculates estimated loading and maintenance doses based on a patient's genetic and clinical characteristics and displays calculated S-warfarin plasma concentrations based on planned or administered dosages. In comparison to control subjects, patients in the PerMIT study arm demonstrated a 3.6-day decrease in the time to reach a stabilised INR within the target therapeutic range (4.7 vs. 8.3 days, p = 0.015); a 12.8% increase in time spent within the therapeutic interval over the first 25 days of therapy (64.3% vs. 55.3%, p = 0.180); and a 32.9% decrease in the frequency of warfarin dose adjustments per INR measurement (38.3% vs. 57.1%, p = 0.007). Serial measurements of plasma S-warfarin concentrations were also obtained to prospectively evaluate the accuracy of the pharmacokinetic model during induction therapy. The PerMIT S-warfarin plasma concentration model estimated 62.8% of concentrations within 0.15 mg/l. These pilot data suggest that the PerMIT method and its incorporation of genotype/phenotype information may help practitioners increase the safety, efficacy, and efficiency of warfarin therapeutic management.

A diagnostic informatics approach for stratifying risk outcome based on combined genotype effects.

BACKGROUND: Diagnostic informatics (DI) in the context of personalized medicine involves the integration of molecular information to provide "actionable" diagnostic and therapeutic strategies. In many cases, retrospective predictions of clinical outcomes affected by multiple genes are complicated by not having the relevant genes measured within the same study. Multiplicative effect modeling is a statistical method for estimating the net effect of ≥ 2 independent variables. The authors demonstrate a DI approach that uses multiplicative-effect modeling to combine genetic information from ≥ 2 independent studies to predict a net clinical outcome. METHODS: As a hypothetical working model, 2 independent studies were selected each reporting on a unique genetic factor proposed to influence the risk of stent thrombosis (ST) among subjects treated with clopidogrel. A multiplicative effect model was used for developing a hypothesis regarding their combined influence on clinical outcome. RESULTS: Application of multiplicative risk modeling yielded a revised estimated risk of outcomes based on combined genotype. In this scenario, combined genotype revised the categorical risk level (high versus low) estimated from single gene effects for 41.5% of the subjects. Further, the maximum relative risk based on single gene effects was increased from 4.54 to 7.84 based on combined genotype. The revised relative risk values in conjunction with combined genotype frequency estimates provides the data necessary to frame a trial hypothesis and conduct appropriate power analysis to estimate the number of subjects needed to test that hypothesis. CONCLUSIONS: This DI approach can be used to generate quantitative hypotheses on multiple gene effects derived from independent genotype studies. This approach is useful for estimating parameters needed in designing future studies to evaluate the net effect of ≥ 2 genetic variants on a common clinical endpoint.

Aberrant regulation of endogenous ouabain-like factor in bipolar subjects.

Ill phases of bipolar illness are associated with abnormalities in ion regulation and intracellular ion concentrations. Previously, it has been reported that mania is characterised by lower circulating levels of ion regulating endogenous cardenolides, and that bipolar subjects lack the normal seasonal variation of these factors. Since endogenous cardenolides are elaborated in settings of extensive physical activity, euthymic bipolar and psychiatrically normal control subjects were asked to exercise to exhaustion. Plasma concentrations of endogenous cardenolides were measured at baseline, 60 min, peak exercise and post-recovery. Ouabain-like immunoreactive factor (OLF) was lower at baseline (0.005+/-S.D. 0.01 ng/mL in bipolar vs. 0.072+/-0.06 ng/mL in normal control subjects, P=0.019), lower at 60 min (0.007+/-S.D. 0.02 ng/mL in bipolar vs. 0.075+/-0.06 ng/mL in normal control subjects, P=0.029), and tended to be lower at peak exercise (0.009+/-S.D. 0.02 ng/mL in bipolar vs. 0.131+/-0.21 ng/mL in normal control subjects, P=0.15) in bipolar subjects compared to non-psychiatric controls. Other endogenous cardenolides did not vary significantly. The endogenous cardenolide, OLF, may be aberrantly controlled in bipolar illness.

Urinary proteins for the diagnosis of obstructive sleep apnea syndrome.

Approximately 2-3% of all children in the United States suffer from obstructive sleep apnea (OSA). This condition is characterized by repeated events of partial or complete obstruction of the upper airways during sleep leading to recurring episodes of hypercapnia, hypoxemia, and arousal throughout the night as well as snoring, which afflicts 7-10% of all children. Since clinical history and physical examination are unreliable in the differentiation between children with OSA and children with primary snoring (PS) who have no apparent alteration in sleep architecture, current diagnostic approaches for OSA require an overnight sleep study (ONP). ONP is onerous, relatively unavailable, labor intensive, and inconvenient, leading to long waiting periods and unnecessary delays in diagnosis and treatment. Development of noninvasive biomarker(s) capable of reliably distinguishing children with PS from those with OSA would greatly facilitate timely screening and diagnosis of OSA in children. Therefore, we hypothesized that proteomic strategies in the urine may permit the identification of biomarker(s) that reliably screen for OSA. In this study, time-of-flight mass spectrometry was used to profile proteins in the first morning void urines from children. We discovered that urocortins are increased in OSA and provide a noninvasive approach for quick and convenient diagnosis otf OSA in snoring children.

Interactive modeling for ongoing utility of pharmacogenetic diagnostic testing: application for warfarin therapy.

BACKGROUND: The application of pharmacogenetic results requires demonstrable correlations between a test result and an indicated specific course of action. We developed a computational decision-support tool that combines patient-specific genotype and phenotype information to provide strategic dosage guidance. This tool, through estimating quantitative and temporal parameters associated with the metabolism- and concentration-dependent response to warfarin, provides the necessary patient-specific context for interpreting international normalized ratio (INR) measurements. METHODS: We analyzed clinical information, plasma S-warfarin concentration, and CYP2C9 (cytochrome P450, family 2, subfamily C, polypeptide 9) and VKORC1 (vitamin K epoxide reductase complex, subunit 1) genotypes for 137 patients with stable INRs. Plasma S-warfarin concentrations were evaluated by VKORC1 genotype (-1639G>A). The steady-state plasma S-warfarin concentration was calculated with CYP2C9 genotype-based clearance rates and compared with actual measurements. RESULTS: The plasma S-warfarin concentration required to yield the target INR response is significantly (P < 0.05) associated with VKORC1 -1639G>A genotype (GG, 0.68 mg/L; AG, 0.48 mg/L; AA, 0.27 mg/L). Modeling of the plasma S-warfarin concentration according to CYP2C9 genotype predicted 58% of the variation in measured S-warfarin concentration: Measured [S-warfarin] = 0.67(Estimated [S-warfarin]) + 0.16 mg/L. CONCLUSIONS: The target interval of plasma S-warfarin concentration required to yield a therapeutic INR can be predicted from the VKORC1 genotype (pharmacodynamics), and the progressive changes in S-warfarin concentration after repeated daily dosing can be predicted from the CYP2C9 genotype (pharmacokinetics). Combining the application of multivariate equations for estimating the maintenance dose with genotype-guided pharmacokinetics/pharmacodynamics modeling provides a powerful tool for maximizing the value of CYP2C9 and VKORC1 test results for ongoing application to patient care.

Fundamentals of pharmacology and applications in pharmacogenetics.

This article provides an introduction to the fundamental principles of pharmacokinetics (PK) and pharmacodynamics (PD) as they apply to understanding the application of pharmacogenetics (PGx) in a clinical setting. PGx establishes connections between the disciplines of pharmacology and genetics. As such, one functional component of PGx involves establishing relationships between phenotypes and genotypes with respect to predicting the response of medications in individual patients. The article begins by describing each of the concepts, followed by discussing the clinical utility of PGx and pharmacodynamics in a laboratory medicine setting; it then makes a link with the evolving field of PGx from the perspective of clinical laboratory medicine. Laboratory medicine serves as a catalyst for transitioning PGx into clinical settings, and as such, the article concludes by describing the future role of clinical laboratories in the application of PGx to patient care.

Dynamic pharmacogenetic models in anticoagulation therapy.

This article demonstrates how a dynamic clinical-support tool can guide individualized drug therapy. We use the drug warfarin as a model to demonstrate how pharmacogenetics when combined with fundamental principles of pharmacokinetic and pharmacodynamics can provide a powerful decision-support tool to optimize personalized therapeutics.