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Shannon ML, Heimlich JB, Olson S, Debevec A, Copeland Z, Kishtagari A, Vlasschaert C, Snider CA, Silver AJ, Brown D, Spaulding TP, Bhatta MR, Pugh K, Stockton SS, Ulloa J, Xu Y, Baljevic M, Moslehi J, Jahangir E, Ferrell PB, Slosky DA, Bick AG, Savona MR. Clonal Hematopoiesis and Inflammation in the VasculaturE (CHIVE): a prospective, longitudinal cohort and biorepository. Blood Adv 2024:bloodadvances.2023011510. [PMID: 38608257 DOI: 10.1182/bloodadvances.2023011510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/23/2024] [Accepted: 02/09/2024] [Indexed: 04/14/2024] Open
Abstract
Clonal hematopoiesis (CH) is an age-associated phenomenon leading to increased risk of both hematologic malignancy and non-malignant organ dysfunction. Increasingly available genetic testing has made incidental discovery of CH clinically common, yet evidence-based guidelines and effective management strategies to prevent adverse CH health outcomes are lacking. To address this gap, the prospective CHIVE registry and biorepository was created to identify and monitor individuals at risk, support multidisciplinary CH clinics, and to refine standards of practice for CH risk mitigation. Data from the first 181 patients enrolled in this registry recapitulate the molecular epidemiology of CH from biobank scale retrospective studies, with DNMT3A, TET2, ASXL1, and TP53 as the most commonly mutated genes. CH patients had higher rates of end organ dysfunction, in particular chronic kidney disease (p=0.001). Among patients with CH, variant allele frequency was independently associated with presence of cytopenias (p=0.008) and progression to hematologic malignancy (p=0.010), while other common high-risk CH clone features were not clear. Notably, accumulation of multiple distinct high-risk clone features was also associated with cytopenias (p=0.013) and hematologic malignancy progression (p=0.004), supporting a recently published CH risk score. Surprisingly, ~30% of patients enrolled in CHIVE from CH clinics were adjudicated as not having CHIP, highlighting the need for molecular standards and purpose-built assays in this field. Maintenance of this well-annotated cohort and continued expansion of CHIVE to multiple institutions is underway and will be critical to understand how to thoughtfully care for this patient population.
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Affiliation(s)
- Morgan L Shannon
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | | | - Sydney Olson
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Ariana Debevec
- Vanderbilt University Medical Center, Nashvlle, Tennessee, United States
| | - Zachary Copeland
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Ashwin Kishtagari
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | | | - Christina A Snider
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Alexander J Silver
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States
| | - Donovan Brown
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Travis P Spaulding
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Manasa Ram Bhatta
- Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Kelly Pugh
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Shannon S Stockton
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jessica Ulloa
- Vanderbilt University, Nashville, Tennessee, United States
| | - Yaomin Xu
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Muhamed Baljevic
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Javid Moslehi
- University of California San Francisco, San Francisco, California, United States
| | - Eiman Jahangir
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Paul Brent Ferrell
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - David Alan Slosky
- Cardiovascular Oncology Associates, Franklin, Tennessee, United States
| | - Alexander G Bick
- Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Michael R Savona
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
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Mack T, Vlasschaert C, von Beck K, Silver AJ, Heimlich JB, Poisner H, Condon HR, Ulloa J, Sochacki AL, Spaulding TP, Kishtagari A, Bejan CA, Xu Y, Savona MR, Jones A, Bick AG. Cost-Effective and Scalable Clonal Hematopoiesis Assay Provides Insight into Clonal Dynamics. J Mol Diagn 2024:S1525-1578(24)00076-X. [PMID: 38588769 DOI: 10.1016/j.jmoldx.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon in which hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP mutations are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or to serial sequencing. In this study, an affordable (approximately US $8 per sample), accurate, and scalable sequencing assay for CHIP is introduced and validated. The efficacy of the assay was demonstrated by identifying CHIP mutations in a cohort of 456 individuals with DNA collected at multiple time points in Vanderbilt University's biobank and quantifying clonal expansion rates over time. A total of 101 individuals with CHIP/clonal cytopenia of undetermined significance were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction at both time points. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. Additionally, the study explores mutation co-occurrence and clonal competition between multiple driver mutations.
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Affiliation(s)
- Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Kelly von Beck
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander J Silver
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - J Brett Heimlich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Henry R Condon
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jessica Ulloa
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Andrew L Sochacki
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Travis P Spaulding
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ashwin Kishtagari
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yaomin Xu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael R Savona
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Angela Jones
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alexander G Bick
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee; Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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Mack T, Vlasschaert C, von Beck K, Silver AJ, Heimlich JB, Poisner H, Condon HR, Ulloa J, Sochacki AL, Spaulding TP, Kishtagari A, Bejan CA, Xu Y, Savona MR, Jones A, Bick A. Cost-effective and scalable clonal hematopoiesis assay provides insight into clonal dynamics. medRxiv 2023:2023.11.08.23298270. [PMID: 37986782 PMCID: PMC10659520 DOI: 10.1101/2023.11.08.23298270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common age-related phenomenon that occurs when hematopoietic stem cells acquire mutations in a select set of genes commonly mutated in myeloid neoplasia which then expand clonally. Current sequencing assays to detect CHIP are not optimized for the detection of these variants and can be cost-prohibitive when applied to large cohorts or serial sequencing. Here, we present and validate a CHIP targeted sequencing assay that is affordable (∼$8/sample), accurate and highly scalable. To demonstrate the utility of this assay, we detected CHIP in a cohort of 456 individuals with DNA collected at multiple timepoints in the Vanderbilt BioVU biobank and quantified clonal expansion rates over time. A total of 101 individuals with CHIP were identified, and individual-level clonal expansion rate was calculated using the variant allele fraction (VAF) at both timepoints. Differences in clonal expansion rate by driver gene were observed, but there was also significant individual-level heterogeneity, emphasizing the multifactorial nature of clonal expansion. We further describe the mutation co-occurrence and clonal competition between multiple driver mutations.
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Jasra S, Giricz O, Zeig-Owens R, Pradhan K, Goldfarb DG, Barreto-Galvez A, Silver AJ, Chen J, Sahu S, Gordon-Mitchell S, Choudhary GS, Aluri S, Bhagat TD, Shastri A, Bejan CA, Stockton SS, Spaulding TP, Thiruthuvanathan V, Goto H, Gerhardt J, Haider SH, Veerappan A, Bartenstein M, Nwankwo G, Landgren O, Weiden MD, Lekostaj J, Bender R, Fletcher F, Greenberger L, Ebert BL, Steidl U, Will B, Nolan A, Madireddy A, Savona MR, Prezant DJ, Verma A. High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster. Nat Med 2022; 28:468-471. [DOI: 10.1038/s41591-022-01708-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/19/2022] [Indexed: 12/21/2022]
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Spaulding TP, Stockton SS, Savona MR. The evolving role of next generation sequencing in myelodysplastic syndromes. Br J Haematol 2019; 188:224-239. [PMID: 31571207 DOI: 10.1111/bjh.16212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Myelodysplastic syndromes (MDS) are clonal haematological disorders characterized by haematopoietic cell dysplasia, peripheral blood cytopenias, and a predisposition for developing acute myeloid leukaemia (AML). Cytogenetics have historically been important in diagnosis and prognosis in MDS, but the growing accessibility of next generation sequencing (NGS) has led to growing research in the roles of molecular genetic variation on clinical decision-making in these disorders. Multiple genes have been previously studied and found to be associated with specific outcomes or disease types within MDS and knowledge of mutations in these genes provides insight into previously defined MDS subtypes. Knowledge of these mutations also informs development of novel therapies in the treatment of MDS. The precise role of NGS in the diagnosis, prognosis and monitoring of MDS remains unclear but the improvements in NGS technology and accessibility affords clinicians an additional practice tool to provide the best care for patients.
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Affiliation(s)
- Travis P Spaulding
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shannon S Stockton
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.,Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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Spaulding TP, Martin RCG. Predicting adverse events in patients undergoing hepatectomy-validation of preoperative nomogram and risk score. HPB (Oxford) 2017; 19:1112-1118. [PMID: 28882456 DOI: 10.1016/j.hpb.2017.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 07/28/2017] [Accepted: 08/13/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND/PURPOSE Much research exists on preoperative measures of postoperative mortality in the surgical treatment of liver malignancies, but little on morbidity, a more common outcome. This study aims (i) to validate the published calculations as acceptable measures of postoperative mortality and (ii) to assess the value of these published measures in predicting postoperative morbidity. METHODS Data were collected from a prospectively managed dataset of 1059 hepatectomies performed in Louisville, Kentucky from December 1990 to April 2014. Preoperative data were used to assign scores for each of two published measures and the scores were sorted into clinically relevant groups with corresponding ordinal scores, according to the previously published literature (Dhir nomogram and Simons risk score). RESULTS After selection, 851 hepatectomies were analyzed. Both the Dhir nomogram (p = 0.0004) and Simons risk score (p = 0.0017) were acceptable predictors of postoperative mortality. In the analysis of morbidity, Dhir scores were a poor predictor of morbidity. The Simons ordinal risk score was predictive of complications (p = 0.0029), the number of complications (p = 0.0028), complication grade (p = 0.0033), and hepatic-specific complications (p = 0.0003). CONCLUSION The Simons ordinal risk score can be useful in assessing postoperative morbidity among hepatectomy patients.
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Affiliation(s)
- Travis P Spaulding
- Department of Surgery, Division of Surgical Oncology, University of Louisville, 315 East Broadway, Louisville, KY, 40202, USA
| | - Robert C G Martin
- Department of Surgery, Division of Surgical Oncology, University of Louisville, 315 East Broadway, Louisville, KY, 40202, USA.
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