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Tuck M, Wittkowski A, Gregg L. A Balancing Act: A Systematic Review and Metasynthesis of Family-Focused Practice in Adult Mental Health Services. Clin Child Fam Psychol Rev 2023; 26:190-211. [PMID: 36318397 PMCID: PMC9879847 DOI: 10.1007/s10567-022-00418-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2022] [Indexed: 01/28/2023]
Abstract
Parental mental illness is a major international public health concern given its implications for whole families, including children. Family-focused practice (FFP), an approach that emphasises a "whole-family" approach to care, provides an opportunity to mitigate the significant risks associated with parental mental health difficulties. The positive benefits associated with FFP have led to a shift in policy and practice towards prioritising FFP within adult mental health services. However, evidence suggests that FFP remains scarce and is not routine. Research has identified the important role of practitioners in facilitating FFP. The current review identified, synthesised and appraised the international qualitative literature examining adult mental health practitioners' implementation experiences of FFP. It aimed to provide an evidence-informed account of practitioner experiences of FFP delivery and to identify key recommendations to enhance future FFP outcomes in AMHS. Ovid Medline, PsycInfo, CINAHL plus, EMBASE and Web of Science Core Collection were searched systematically, in line with PRISMA guidance, up to January 2022. The Critical Appraisal Skills Programme (CASP) was used to undertake the quality appraisal prior to a thematic synthesis being conducted. The review was registered on PROSPERO. Nineteen papers, spanning 17 years of research with 469 practitioners, were included. Three main themes and 14 subthemes were developed, representing different aspects of practitioner experiences of FFP delivery. Practitioners' approach to FFP was variable and influenced by their beliefs about FFP, perceived roles and responsibilities, competence, service setting, and personal parenting status. Practitioners engaged in a balancing act to maintain a dual focus on their service-users and their children, to navigate powerful emotions, and consider multiple perspectives in a biomedical organisational structure that advocates individualised treatment. Although working together unified teams, a greater need for external interagency collaboration was identified. The use of strength-based approaches with clients and dedicated staff resources, within clear guidelines and frameworks, was reported to be necessary to maximise FFP delivery. This review proposes a complex FFP dynamic whereby practitioners engage in a constant balancing act between FFP stakeholders to achieve meaningful FFP outcomes for service-users and their families. Service recommendations are provided.
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Vucetic Z, Loayza N, Pedersen SK, Tuck M, LaPointe LC. Clinical performance of methylation-based liquid biopsy test COLVERA after optimization of test interpretation rules. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.3546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3546 Background: Clinical guidelines recommend surveillance for patients who complete primary treatment for colorectal cancer (CRC) with the aim of detecting recurrence when amenable to curative intent treatment. Currently recommended surveillance protocols, including imaging and CEA have limitations both in sensitivity and specificity, thus novel methods that detect circulating tumor DNA (ctDNA) have been introduced into clinical practice. COLVERA is a laboratory-developed, real-time PCR test that detects DNA methylation of BCAT1 and IKZF1 genes. These two genes are hypermethylated in 95% of CRC tissue and COLVERA showed improved sensitivity for detection of recurrent disease in comparison to CEA in several clinical populations. The current study evaluated the impact of optimizing the assay’s qualitative reporting method on actionability and clinical performance for recurrence detection in CRC surveillance setting. Methods: Two previously described cohorts of CRC patients (N=322 and N=144) who completed primary treatment and were undergoing surveillance were evaluated. Imaging and blood collections were performed at, or adjacent to, a standard of care visit. cfDNA was extracted from whole blood, bisulphite-treated and assayed in triplicates for BCAT1/IKZF methylation. Previously, any positive replicate of either target gene was reported as COLVERA “detected”. In the current study, COLVERA is “detected” when at least one replicate of IKZF1 or multiple replicates of either IKZF1 and/or BCAT1 are present. Sensitivity, specificity, and diagnostic odds ratio (DOR) for CRC recurrence detection from a single time-point blood sample was determined using radiological imaging as clinical reference standard. Results: In the first cohort (N=322), overall COLVERA test positivity was 6.5% (21/322) with a sensitivity of 59.3% (95% CI: 38.8 - 77.6) and specificity of 98.3% (96.1 - 99.5) for detecting recurrence at a time-point adjacent to imaging, representing improved specificity, from 91.5% (87.7 - 94.4%), with minimal decrease in sensitivity, from 63.0% (42.4 – 80.6). Similarly, in the second cohort (N=144) sensitivity was 62% (47.2 -75.4), compared to 66.0% (57.1 – 69.3) under the prior interpretation method, while specificity was 92.6% (85.3-97), compared to 90.4% (84.7 - 94.7). A high DOR of 84 (26 - 272) (previously 18 (7.6 – 44.4)) indicates that the revised COLVERA interpretation method is clinically more informative and differentiates with greater accuracy patients with and without the disease. Conclusions: This change in the COLVERA interpretation rule resulted in optimized clinical specificity with minimal impact on sensitivity. For an assay intended to aid in surveillance and early recurrence detection, improved accuracy allows the physician to have increased confidence in making actionable decisions based on test result, including further imaging or treatment.
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Giraldez MD, Spengler RM, Etheridge A, Goicochea AJ, Tuck M, Choi SW, Galas DJ, Tewari M. Abstract IA23: Phospho-RNA-seq: A liquid biopsy approach for cell-free mRNA/lncRNA profiling. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-ia23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Measuring disease biomarkers in biofluids to detect and monitor pathophysiologic events in tissues has enormous appeal. While detecting specific DNA sequences in blood plasma has been successful in informing about the presence of cancers, viruses, and a range of pathogens, this approach does not provide gene expression information, which could reveal more detailed information about disease activity. Measuring cell-free RNA in plasma would provide such information and has the potential to be more sensitive, given that one DNA molecule in a cell gives rise often to thousands or more RNA molecules.
However, with the exception of microRNAs, broad sequencing of cell-free messenger RNA (mRNA) profiles in plasma has been generally challenging. We discovered that a major barrier to cell-free RNA sequencing from plasma is that the large majority of mRNAs are both fragmented and have modified phosphorylation states at their 5’ and 3’ ends that make them invisible to standard small RNA-seq methods. We present a modified RNA-seq methodology, called phospho-RNA-seq, which revealed thousands of mRNA in blood plasma. The key to this approach is (i) the incorporation of T4-polynucleotide kinase treatment to change the phosphorylation states at the RNA ends, and (ii) a stringent bioinformatics analysis pipeline to reduce false positive alignments.
Phospho-RNA-seq identified cohorts of gene transcripts in plasma, including ones expressed in a tissue-specific manner. As proof-of-concept validation of the approach for biomarker identification, we used phospho-RNA-seq to longitudinally profile plasma specimens collected from patients undergoing hematopoietic stem cell transplantation. We detected bone marrow-enriched and liver-enriched transcript sets in plasma, which tracked with bone marrow recovery and hepatic injury, respectively. By providing expanded access to the transcriptome in plasma and potentially other biofluids, phospho-RNA-seq enables the discovery of new cell-free RNA biomarker signatures for a wide variety of liquid biopsy applications.
Citation Format: Maria D. Giraldez, Ryan M. Spengler, Alton Etheridge, Annika J. Goicochea, Missy Tuck, Sung W. Choi, David J. Galas, Muneesh Tewari. Phospho-RNA-seq: A liquid biopsy approach for cell-free mRNA/lncRNA profiling [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA23.
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Giraldez MD, Spengler RM, Etheridge A, Goicochea AJ, Tuck M, Choi SW, Galas DJ, Tewari M. Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma. EMBO J 2019; 38:e101695. [PMID: 31053596 PMCID: PMC6545557 DOI: 10.15252/embj.2019101695] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/25/2022] Open
Abstract
Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long non-coding RNA (lncRNA) studies are limited. We report that plasma contains fragmented mRNAs and lncRNAs that are missed by standard small RNA-seq protocols due to lack of 5' phosphate or presence of 3' phosphate. These fragments were revealed using a modified protocol ("phospho-RNA-seq") incorporating RNA treatment with T4-polynucleotide kinase, which we compared with standard small RNA-seq for sequencing synthetic RNAs with varied 5' and 3' ends, as well as human plasma exRNA Analyzing phospho-RNA-seq data using a custom, high-stringency bioinformatic pipeline, we identified mRNA/lncRNA transcriptome fingerprints in plasma, including tissue-specific gene sets. In a longitudinal study of hematopoietic stem cell transplant patients, bone marrow- and liver-enriched exRNA genes were tracked with bone marrow recovery and liver injury, respectively, providing proof-of-concept validation as a biomarker approach. By enabling access to an unexplored realm of mRNA and lncRNA fragments, phospho-RNA-seq opens up new possibilities for plasma transcriptomic biomarker development.
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Tuck M. Book Review: Atlas of Pain Injection Techniques. Anaesth Intensive Care 2019. [DOI: 10.1177/0310057x0303100622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Cooper GS, Markowitz SD, Chen Z, Tuck M, Willis JE, Berger BM, Brenner DE, Li L. Performance of multitarget stool DNA testing in African American patients. Cancer 2018; 124:3876-3880. [PMID: 30193399 DOI: 10.1002/cncr.31660] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/16/2023]
Abstract
BACKGROUND Multitarget stool DNA (mt-sDNA) is an approved method for colon cancer screening that is especially relevant for patients who cannot undergo colonoscopy. Although the test performance has been evaluated in a large clinical trial, it was limited to a predominantly white population. Given differences in the epidemiology and biology of colon cancer in African American individuals, the authors sought to compare the performance of mt-sDNA between racial groups. METHODS The authors prospectively identified patients aged ≥40 years who were referred for colonoscopy at an academic medical center and 2 satellite facilities. Prior to the colonoscopy, the authors collected stool for mt-sDNA and fecal immunochemical testing (FIT). They compared the sensitivity, specificity, and receiver operating characteristic curve between African American and white patients for the detection of advanced lesions or any adenoma. RESULTS A total of 760 patients were included, 34.9% of whom were African American. The prevalence of any adenoma (38.9% for African American patients and 33.9% for white patients) and that for advanced lesions (6.8% and 6.7%, respectively) were similar between groups. The overall sensitivities of mt-sDNA for the detection of advanced lesions and any adenoma were 43% and 19%, respectively, and the specificities were 91% and 93%, respectively. In general, mt-sDNA was more sensitive and less specific than FIT. When stratified by race, the sensitivity, specificity, and receiver operating characteristic curve area were similar between African American and white patients for both mt-sDNA and FIT. CONCLUSIONS Test performance characteristics of mt-sDNA were comparable in African American and white patients. Given the lower uptake of colonoscopy in African American individuals, mt-sDNA may offer a promising screening alternative in this patient population.
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Cooper GS, Markowitz SD, Chen Z, Tuck M, Willis JE, Berger BM, Brenner DE, Li L. Evaluation of Patients with an Apparent False Positive Stool DNA Test: The Role of Repeat Stool DNA Testing. Dig Dis Sci 2018; 63. [PMID: 29516325 PMCID: PMC5960589 DOI: 10.1007/s10620-018-5001-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND There is uncertainty as to the appropriate follow-up of patients who test positive on multimarker stool DNA (sDNA) testing and have a colonoscopy without neoplasia. AIMS To determine the prevalence of missed colonic or occult upper gastrointestinal neoplasia in patients with an apparent false positive sDNA. METHODS We prospectively identified 30 patients who tested positive with a commercially available sDNA followed by colonoscopy without neoplastic lesions. Patients were invited to undergo repeat sDNA at 11-29 months after the initial test followed by repeat colonoscopy and upper endoscopy. We determined the presence of neoplastic lesions on repeat evaluation stratified by results of repeat sDNA. RESULTS Twelve patients were restudied. Seven patients had a negative second sDNA test and a normal second colonoscopy and upper endoscopy. In contrast, 5 of 12 subjects had a persistently positive second sDNA test, and 3 had positive findings, including a 3-cm sessile transverse colon adenoma with high-grade dysplasia, a 2-cm right colon sessile serrated adenoma with dysplasia, and a nonadvanced colon adenoma (p = 0.045). These corresponded to a positive predictive value of 0.60 (95% CI 0.17-1.00) and a negative predictive value of 1.00 (95% CI 1.00-1.00) for the second sDNA test. In addition, the medical records of all 30 subjects with apparent false positive testing were reviewed and no documented cases of malignant tumors were recorded. CONCLUSIONS Repeat positive sDNA testing may identify a subset of patients with missed or occult colorectal neoplasia after negative colonoscopy for an initially positive sDNA. High-quality colonoscopy with careful attention to the right colon in patients with positive sDNA is critically important and may avoid false negative colonoscopy.
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Hovelson DH, Liu CJ, Wang Y, Kang Q, Henderson J, Gursky A, Brockman S, Ramnath N, Krauss JC, Talpaz M, Kandarpa M, Chugh R, Tuck M, Herman K, Grasso CS, Quist MJ, Feng FY, Haakenson C, Langmore J, Kamberov E, Tesmer T, Husain H, Lonigro RJ, Robinson D, Smith DC, Alva AS, Hussain MH, Chinnaiyan AM, Tewari M, Mills RE, Morgan TM, Tomlins SA. Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy. Oncotarget 2017; 8:89848-89866. [PMID: 29163793 PMCID: PMC5685714 DOI: 10.18632/oncotarget.21163] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling. We applied PRINCe to a retrospective cohort of 124 cfDNA samples from 100 patients with advanced cancers, including 76 men with metastatic castration-resistant prostate cancer (mCRPC), enabling cfDNA tumor content approximation and actionable focal CNA detection, while facilitating concordance analyses between cfDNA and tissue-based NGS profiles and assessment of cfDNA alteration associations with mCRPC treatment outcomes. Therapeutically relevant focal CNAs were present in 42 (34%) cfDNA samples, including 36 of 93 (39%) mCRPC patient samples harboring AR amplification. PRINCe identified pre-treatment cfDNA CNA profiles facilitating disease monitoring. Combining PRINCe with routine targeted NGS of cfDNA enabled mutation and CNA assessment with coverages tuned to cfDNA tumor content. In mCRPC, genome-wide PRINCe cfDNA and matched tissue CNA profiles showed high concordance (median Pearson correlation = 0.87), and PRINCe detectable AR amplifications predicted reduced time on therapy, independent of therapy type (Kaplan-Meier log-rank test, chi-square = 24.9, p < 0.0001). Our screening approach enables robust, broadly applicable cfDNA-based precision oncology for patients with advanced cancer through scalable identification of therapeutically relevant CNAs and pre-/post-treatment genomic profiles, enabling cfDNA- or tissue-based precision oncology workflow optimization.
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Grossman RL, Abel B, Angiuoli S, Barrett JC, Bassett D, Bramlett K, Blumenthal GM, Carlsson A, Cortese R, DiGiovanna J, Davis-Dusenbery B, Dittamore R, Eberhard DA, Febbo P, Fitzsimons M, Flamig Z, Godsey J, Goswami J, Gruen A, Ortuño F, Han J, Hayes D, Hicks J, Holloway D, Hovelson D, Johnson J, Juhl H, Kalamegham R, Kamal R, Kang Q, Kelloff GJ, Klozenbuecher M, Kolatkar A, Kuhn P, Langone K, Leary R, Loverso P, Manmathan H, Martin AM, Martini J, Miller D, Mitchell M, Morgan T, Mulpuri R, Nguyen T, Otto G, Pathak A, Peters E, Philip R, Posadas E, Reese D, Reese MG, Robinson D, Dei Rossi A, Sakul H, Schageman J, Singh S, Scher HI, Schmitt K, Silvestro A, Simmons J, Simmons T, Sislow J, Talasaz A, Tang P, Tewari M, Tomlins S, Toukhy H, Tseng HR, Tuck M, Tzou A, Vinson J, Wang Y, Wells W, Welsh A, Wilbanks J, Wolf J, Young L, Lee J, Leiman LC. Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium. Clin Pharmacol Ther 2017; 101:589-592. [PMID: 28187516 PMCID: PMC5525192 DOI: 10.1002/cpt.666] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 01/02/2023]
Abstract
The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays.
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Hernandez W, Gamazon ER, Aquino-Michaels K, Smithberger E, O'Brien TJ, Harralson AF, Tuck M, Barbour A, Cavallari LH, Perera MA. Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans. J Thromb Haemost 2017; 15:735-743. [PMID: 28135054 PMCID: PMC5862636 DOI: 10.1111/jth.13639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/26/2022]
Abstract
Essentials Genetic variants controlling gene regulation have not been explored in pharmacogenomics. We tested liver expression quantitative trait loci for association with warfarin dose response. A novel predictor for increased warfarin dose response in African Americans was identified. Precision medicine must take into account population-specific variation in gene regulation. SUMMARY Background Warfarin is commonly used to control and prevent thromboembolic disorders. However, because of warfarin's complex dose-requirement relationship, safe and effective use is challenging. Pharmacogenomics-guided warfarin dosing algorithms that include the well-established VKORC1 and CYP2C9 polymorphisms explain only a small proportion of inter-individual variability in African Americans (AAs). Objectives We aimed to assess whether transcriptomic analyses could be used to identify regulatory variants associated with warfarin dose response in AAs. Patients/Methods We identified a total of 56 expression quantitative trait loci (eQTLs) for CYP2C9, VKORC1 and CALU derived from human livers and evaluated their association with warfarin dose response in two independent AA warfarin patient cohorts. Results We found that rs4889606, a strong cis-eQTL for VKORC1 (log10 Bayes Factor = 12.02), is significantly associated with increased warfarin daily dose requirement (β = 1.1; 95% confidence interval [CI] 0.46 to 1.8) in the discovery cohort (n = 305) and in the replication cohort (β = 1.04; 95% CI 0.33 -1.7; n = 141) after conditioning on relevant covariates and the VKORC1 -1639G>A (rs9923231) variant. Inclusion of rs4889606 genotypes, along with CYP2C9 alleles, rs9923231 genotypes and clinical variables, explained 31% of the inter-patient variability in warfarin dose requirement. We demonstrate different linkage disequilibrium patterns in the region encompassing rs4889606 and rs9923231 between AAs and European Americans, which may explain the increased dose requirement found in AAs. Conclusion Our approach of interrogating eQTLs identified in liver has revealed a novel predictor of warfarin dose response in AAs. Our work highlights the utility of leveraging information from regulatory variants mapped in the liver to uncover novel variants associated with drug response and the importance of population-specific research.
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Hovelson DH, Liu CJ, Wang Y, Kang Q, Haakenson C, Langmore J, Kamberov E, Ramnath N, Krauss JC, Talpaz M, Chugh R, Hyland D, Tuck M, Herman K, Husain H, Tewari M, Chinnaiyan AM, Mills R, Morgan TM, Tomlins SA. Rapid, ultra-low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy in metastatic castration-resistant prostate cancer (mCRPC). J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.6_suppl.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
144 Background: Although cell free DNA (cfDNA) profiling by next generation sequencing (NGS) holds great promise for precision oncology, the inability to estimate tumor content a priori typically results in ultra-deep sequencing (e.g. 10,000x) based approaches—often at limited loci—to ensure accurate assessment of cfDNA samples where tumor content can be < 0.1%. However, a large subset of patients with advanced cancers, where most precision oncology is applied, have much greater cfDNA tumor content. Methods: Here we demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) on benchtop sequencers as a precision medicine screening strategy based on ultra-low coverage (~0.005x) tumor content determination through genome-wide copy number alteration (CNA) profiling using 48 plasma cfDNA samples from patients with advanced cancer. Results: Using this approach, we identified therapeutically relevant focal CNAs in 13 of 48 (27%) cfDNA samples from patients with metastatic cancer, including 11 of 36 (31%) from patients with mCRPC. We further show that PRINCe is effective at whole genome coverages as low as 0.005x. Combining PRINCe with targeted multiplexed-PCR NGS of the same cfDNA enables mutation and CNA assessment using effective coverage as low as 25x based on calibrating sequencing depth to cfDNA tumor content. Lastly, PRINCe identifies pre-treatment cfDNA copy number profiles that can be used for inexpensive disease monitoring. Conclusions: Taken together, our screening approach enables broadly applicable cfDNA based precision oncology for patients with advanced cancer through rapid, inexpensive identification of therapeutically relevant CNAs and pre-treatment genomic profiles for disease monitoring, while also guiding additional cfDNA profiling approaches to reserve costly ultra-deep approaches for patients with very low cfDNA tumor content.
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Hernandez W, Gamazon ER, Aquino-Michaels K, Patel S, O'Brien TJ, Harralson AF, Kittles RA, Barbour A, Tuck M, McIntosh SD, Douglas JN, Nicolae D, Cavallari LH, Perera MA. Ethnicity-specific pharmacogenetics: the case of warfarin in African Americans. THE PHARMACOGENOMICS JOURNAL 2013; 14:223-8. [PMID: 24018621 DOI: 10.1038/tpj.2013.34] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 01/05/2023]
Abstract
Using a derivation cohort (N=349), we developed the first warfarin dosing algorithm that includes recently discovered polymorphisms in VKORC1 and CYP2C9 associated with warfarin dose requirement in African Americans (AAs). We tested our novel algorithm in an independent cohort of 129 AAs and compared the dose prediction to the International Warfarin Pharmacogenetics Consortium (IWPC) dosing algorithms. Our algorithm explains more of the phenotypic variation (R(2)=0.27) than the IWPC pharmacogenomics (R(2)=0.15) or clinical (R(2)=0.16) algorithms. Among high-dose patients, our algorithm predicted a higher proportion of patients within 20% of stable warfarin dose (45% vs 29% and 2% in the IWPC pharmacogenomics and clinical algorithms, respectively). In contrast to our novel algorithm, a significant inverse correlation between predicted dose and percent West African ancestry was observed for the IWPC pharmacogenomics algorithm among patients requiring ⩾60 mg per week (β=-2.04, P=0.02).
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Tuck M. Book Review: International Anesthesiology Clinics: Unconscious Processes. Anaesth Intensive Care 2009. [DOI: 10.1177/0310057x0903700627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Masuo K, Rakugi H, Ogihara T, Tuck M. Abstract: P1377 ARG16GLY OF THE β2-ADRENOCEPTOR POLYMORPHISM PREDICTS THE ONSET OF DYSLIPIDEMIA THROUGH INSULIN RESISTANCE (IR) IN NORMOTENSIVE MEN. ATHEROSCLEROSIS SUPP 2009. [DOI: 10.1016/s1567-5688(09)71385-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Qiu Y, Patwa TH, Xu L, Shedden K, Misek DE, Tuck M, Jin G, Ruffin MT, Turgeon DK, Synal S, Bresalier R, Marcon N, Brenner DE, Lubman DM. Plasma glycoprotein profiling for colorectal cancer biomarker identification by lectin glycoarray and lectin blot. J Proteome Res 2008; 7:1693-703. [PMID: 18311904 DOI: 10.1021/pr700706s] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Colorectal cancer (CRC) remains a major worldwide cause of cancer-related morbidity and mortality largely due to the insidious onset of the disease. The current clinical procedures utilized for disease diagnosis are invasive, unpleasant, and inconvenient; hence, the need for simple blood tests that could be used for the early detection of CRC. In this work, we have developed methods for glycoproteomics analysis to identify plasma markers with utility to assist in the detection of colorectal cancer (CRC). Following immunodepletion of the most abundant plasma proteins, the plasma N -linked glycoproteins were enriched using lectin affinity chromatography and subsequently further separated by nonporous silica reversed-phase (NPS-RP)-HPLC. Individual RP-HPLC fractions were printed on nitrocellulose coated slides which were then probed with lectins to determine glycan patterns in plasma samples from 9 normal, 5 adenoma, and 6 colorectal cancer patients. Statistical tools, including principal component analysis, hierarchical clustering, and Z-statistics analysis, were employed to identify distinctive glycosylation patterns. Patients diagnosed with colorectal cancer or adenomas were shown to have dramatically higher levels of sialylation and fucosylation as compared to normal controls. Plasma glycoproteins with aberrant glycosylation were identified by nano-LC-MS/MS, while a lectin blotting methodology was used to validate proteins with significantly altered glycosylation as a function of cancer progression. The potential markers identified in this study for diagnosis to distinguish colorectal cancer from adenoma and normal include elevated sialylation and fucosylation in complement C3, histidine-rich glycoprotein, and kininogen-1. These potential markers of colorectal cancer were subsequently validated by lectin blotting in an independent set of plasma samples obtained from 10 CRC patients, 10 patients with adenomas, and 10 normal subjects. These results demonstrate the utility of this strategy for the identification of N -linked glycan patterns as potential markers of CRC in human plasma, and may have the utility to distinguish different disease states.
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Kaminski MS, Estes J, Tuck M, Ross CW, Wahl RL. I131-tositumomab monotherapy as frontline treatment for follicular lymphoma: Updated results after a median follow-up of 8 years. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.8033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
8033 Background: Monoclonal antibody-based therapies are improving the outcome for patients (pts) with follicular lymphoma (FL). Radioimmunotherapy has been found to be effective for pts with relapsed/refractory disease, but even more so when used as frontline treatment. Methods and Results. We previously reported the results of a phase II, single-institution, study of anti-CD20 I-131- Tositumomab (Bexxar) given as a single agent and as a single one-week treatment for 76 pts with Stage 3 or 4 FL (NEJM 352:441, 2005). An overall response (OR) rate and complete remission (CR) rate of 95% and 75%, respectively, were observed. With a median follow-up of 5.1 yrs, 5-yr overall survival (OS) and progression-free survival (PFS) were 89% and 59%, respectively, with a median PFS reached at 6.1 yrs. We now report on this pt cohort after a median follow-up of 7.93 yrs. The 8-year and 10-yr OS is estimated (by KM) now at 86% and 8-yr PFS is 50% (95% CI: 38.8 - 61.7%). Only 3 additional relapses have occurred in the additional follow-up period (at 8.0, 8.3, and 9.2 years) in those with CRs. The 8-yr PFS for the 57 pts who achieved CR is now 64%. The median for PFS has now being reached for CRs at 9.2 yrs. When the impact of baseline FLIPI scores were analyzed, only 8-yr OS was significantly affected when low-risk (LR) and intermediate-risk (IR) categories were combined and compared to the high-risk (HR) category (92% vs. 75%; p = 0.029). The 8-yr PFS for LR + IR pts was 56% vs. 35% for HR pts (p = 0.317). 27 of the 76 total pts (35%) had HR scores. Of additional importance, no cases of MDS or AML have yet been observed. Other longterm toxicities including thyroid status and second non-hematologic cancers will be updated at the meeting. Conclusions. These data underscore the high degree of effectiveness and durability of remissions achieved with a single, one-week course of frontline Bexxar and should serve as a benchmark for comparison to other studies using more prolonged and toxic treatments, including those combining unlabeled or radiolabeled antibodies with chemotherapy. No significant financial relationships to disclose.
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Tuck M. 3WS16-5 Renin-angiotensin systems and vasculature: Focusing on insulin's action. ATHEROSCLEROSIS SUPP 2003. [DOI: 10.1016/s1567-5688(03)90796-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tuck M. Book Review: Your Body, Your Choice; the Layman's Complete Guide to Bloodless Medicine and Surgery. Anaesth Intensive Care 2001. [DOI: 10.1177/0310057x0102900428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Leung FW, Golub M, Tuck M, Yip I, Leung JW, Go VL. Stimulation of intestinal mucosal afferent nerves increases superior mesenteric artery and decreases mesenteric adipose tissue blood flow. Dig Dis Sci 2001; 46:1217-22. [PMID: 11414297 DOI: 10.1023/a:1010655010983] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
We tested the hypothesis that stimulation of intestinal mucosal afferent nerves produces an increase in superior mesenteric artery (SMA) but a decrease in mesenteric adipose tissue (MAT) blood flow. In anesthetized rats, blood flow in the SMA (pulsed Doppler flowmetry) and MAT (hydrogen gas clearance) was measured simultaneously before and after administration of 0.9% saline, 640 microM capsaicin, or 5% dextrose into the intestinal lumen. The changes in the SMA were 3.8 +/- 3.0, 15.9 +/- 4.0, and 18.8 +/- 7.6%; and those in the MAT, 4.7 +/- 4.0, -11.5 +/- 3.4, and -0.07 +/- 3.4% of baseline, respectively. The data indicate that exposure of the intestinal lumen to an afferent nerve stimulant or nutrient induced a dichotomous pattern of blood flow changes, an increase in the SMA and a reduction in MAT. The capsaicin-sensitive afferent nerves may be instrumental in mediating these energy responses.
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Kaminski MS, Estes J, Zasadny KR, Francis IR, Ross CW, Tuck M, Regan D, Fisher S, Gutierrez J, Kroll S, Stagg R, Tidmarsh G, Wahl RL. Radioimmunotherapy with iodine (131)I tositumomab for relapsed or refractory B-cell non-Hodgkin lymphoma: updated results and long-term follow-up of the University of Michigan experience. Blood 2000; 96:1259-66. [PMID: 10942366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
CD20-targeted radioimmunotherapy is a promising new treatment for B-cell non-Hodgkin lymphoma (NHL). We now provide updated and long-term data on 59 chemotherapy-relapsed/refractory patients treated with iodine (131)I tositumomab in a phase I/II single-center study. Fifty-three patients received individualized therapeutic doses, delivering a specified total-body radiation dose (TBD) based on the clearance rate of a preceding dosimetric dose. Six patients received dosimetric doses only. Dose-escalations of TBD were conducted separately in patients who had or had not undergone a prior autologous stem cell transplant (ASCT) until a nonmyeloablative maximally tolerated TBD was established (non-ASCT = 75 cGy, post-ASCT = 45 cGy). Fourteen additional non-ASCT patients were treated with 75 cGy. Unlabeled antibody was given prior to labeled dosimetric and therapeutic doses to improve biodistribution. Forty-two (71%) of 59 patients responded; 20 (34%) had complete responses (CR). Thirty-five (83%) of 42 with low-grade or transformed NHL responded versus 7 (41%) of 17 with de novo intermediate-grade NHL (P =.005). For all 42 responders, the median progression-free survival was 12 months, 20.3 for those with CR. Seven patients remain in CR 3 to 5.7 years. Sixteen patients were re-treated after progression; 9 responded and 5 had a CR. Reversible hematologic toxicity was dose limiting. Only 10 patients (17%) had human anti-mouse antibodies detected. Long-term, 5 patients developed elevated thyroid-stimulating hormone levels, 5 were diagnosed with myelodysplasia and 3 with solid tumors. A single, well-tolerated treatment with iodine (131)I tositumomab can, therefore, produce frequent and durable responses in NHL, especially low-grade or transformed NHL. (Blood. 2000;96:1259-1266)
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Tuck M. Book Review: Respiratory Measurement. G. Hedenstierna; Principles and Practice Series;. Anaesth Intensive Care 1999. [DOI: 10.1177/0310057x9902700123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Craig S, Dalton R, Tuck M, Brew F. Sublingual glyceryl trinitrate for uterine relaxation at Caeserean section--a prospective trial. Aust N Z J Obstet Gynaecol 1998; 38:34-9. [PMID: 9521387 DOI: 10.1111/j.1479-828x.1998.tb02954.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a prospective study on the use of sublingual glyceryl trinitrate at Caesarean section to induce uterine relaxation; 23 women were entered into the study with both emergency and elective cases considered. A metered dose spray was used to deliver a dose of 400 or 800 microgrammes of glyceryl trinitrate to the women. There were no major side-effects of hypotension or postpartum haemorrhage. The mean maximal systolic blood pressure drop in the patients following drug administration was 18% of the systolic pressure prior to drug administration. Subjective assessment of uterine tone showed the uterus to contract well postdelivery in response to standard oxytocic regimens. Minimal maternal side-effects were reported. We conclude that glyceryl trinitrate is a safe form of uterine relaxation at Caesarean section which may be used in emergency situations and may also be given prophylactically in cases such as breech presentation and in delivery of the preterm infant where fetal trauma is possible. The use of a metered-dose sublingual spray is ideally suited to obstetric practice, being both easy to use and also rapidly administered.
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Kaminski MS, Zasadny KR, Francis IR, Fenner MC, Ross CW, Milik AW, Estes J, Tuck M, Regan D, Fisher S, Glenn SD, Wahl RL. Iodine-131-anti-B1 radioimmunotherapy for B-cell lymphoma. J Clin Oncol 1996; 14:1974-81. [PMID: 8683227 DOI: 10.1200/jco.1996.14.7.1974] [Citation(s) in RCA: 260] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
PURPOSE The CD20 B-lymphocyte surface antigen expressed by B-cell lymphomas is an attractive target for radioimmunotherapy, treatment using radiolabeled antibodies. We conducted a phase I dose-escalation trial to assess the toxicity, tumor targeting, and efficacy of nonmyeloablative doses of an anti-CD20 monoclonal antibody (anti-B1) labeled with iodine-131 (131I) in 34 patients with B-cell lymphoma who had failed chemotherapy. PATIENTS AND METHODS Patients were first given tracelabeled doses of 131I-labeled anti-B1 (15 to 20 mg, 5 mCi) to assess radiolabeled antibody biodistribution, and then a radioimmunotherapeutic dose (15 to 20 mg) labeled with a quantity of 131I that would deliver a specified centigray dose of whole-body radiation predicted by the tracer dose. Whole-body radiation doses were escalated from 25 to 85 cGy in sequential groups of patients in 10-cGy increments. To evaluate if radiolabeled antibody biodistribution could be optimized, initial patients were given one or two additional tracer doses on successive weeks, each dose preceded by an infusion of 135 mg of unlabeled anti-B1 one week and 685 mg the next. The unlabeled antibody dose resulting in the most optimal tracer biodistribution was also given before the radioimmunotherapeutic dose. Later patients were given a single tracer dose and radioimmunotherapeutic dose preceded by infusion of 685 mg of unlabeled anti-B1. RESULTS Treatment was well tolerated. Hematologic toxicity was dose-limiting, and 75 cGy was established as the maximally tolerated whole-body radiation dose. Twenty-eight patients received radioimmunotherapeutic doses of 34 to 161 mCi, resulting in complete remission in 14 patients and a partial response in eight. All 13 patients with low-grade lymphoma responded, and 10 achieved a complete remission. Six of eight patients with transformed lymphoma responded. Thirteen of 19 patients whose disease was resistant to their last course of chemotherapy and all patients with chemotherapy-sensitive disease responded. The median duration of complete remission exceeds 16.5 months. Six patients remain in complete remission 16 to 31 months after treatment. CONCLUSION Nonmyeloablative radioimmunotherapy with 131I-anti-B1 is associated with a high rate of durable remissions in patients with B-cell lymphoma refractory to chemotherapy.
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Tuck M. Arterial catheter failure. Anaesth Intensive Care 1996; 24:119-20. [PMID: 8669634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Masuo K, Mikami H, Ogihara T, Tuck M. Hormonal mechanisms in blood pressure reduction during hemodialysis in patients with chronic renal failure. Hypertens Res 1995; 18 Suppl 1:S201-3. [PMID: 8529063 DOI: 10.1291/hypres.18.supplementi_s201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To elucidate the hormonal mechanisms of blood pressure (BP) reduction during hemodialysis in patients with chronic renal failure (CRF), we performed this study using 7 normotensive (NT) and 17 hypertensive (HT) patients who were strictly matched in age, body weight, body weight gain from the last HD, and duration of HD. Blood pressure, pulse rate, plasma norepinephrine (NE), and plasma dopamine levels were used as indices of sympathetic nerve activity, before, at 50% of hemodialysis (HD) and at 100% of HD (at the end of HD) on the third day after the last HD. As hemodialytic BP reduction was defined as BP decline of more than 10% in pre-HD mean BP, in normotensive patients with CRF, hemodialytic BP reduction was recognized in 0/7 (0%) at 50% of HD and 4/7 (57%) at 100% of HD, and in hypertensive patients it was recognized in 3/17 (18%) at 50% of HD and 4/17 (24%) at 100% of HD. Percentile changes in plasma NE levels increased slightly following hemodialysis in normotensive patients with hemodialytic BP reduction and in hypertensives without BP reduction, while those in normotensives without BP reduction and in hypertensives with BP reduction did not change. However, percentage changes in plasma dopamine (DA) levels decreased significantly at the end of HD (NT; p < 0.05, HT; p < 0.01) following hemodialysis in both normotensive and hypertensive patients with hemodialytic BP reduction, while changes in patients without BP reduction, percentage changes in DA did not change (patients with BP reduction vs. patients without BP reduction). In conclusion, hemodialytic BP reduction may be predisposed by abnormal sympathetic nerve responsiveness.
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