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Ronsley R, Karvonen KA, Cole B, Paulson V, Stevens J, Crotty EE, Hauptman J, Lee A, Stasi SM, Lockwood CM, Leary SES. Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors. J Neurooncol 2024:10.1007/s11060-024-04645-y. [PMID: 38755519 DOI: 10.1007/s11060-024-04645-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
PURPOSE Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for "liquid biopsy" in pediatric brain tumors. METHODS CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated. RESULTS Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200 µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected. CONCLUSIONS Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.
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Affiliation(s)
- Rebecca Ronsley
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US.
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US.
- Fred Hutchinson Cancer Research Center, Seattle, WA, US.
- Seattle Children's Hospital, Mail Stop MB.8.501, 4800 Sand Point Way NE, Seattle, WA, 98105, USA.
| | - Kristine A Karvonen
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
| | - Bonnie Cole
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
| | - Vera Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
- Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jeff Stevens
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
| | - Erin E Crotty
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
| | - Jason Hauptman
- Division of Neurosurgery, Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Amy Lee
- Division of Neurosurgery, Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Shannon M Stasi
- Department of Laboratories, Seattle Children's Hospital, University of Washington, Seattle, WA, US
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, US
- Genetics and Solid Tumor Laboratory, Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, US
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, US
- Fred Hutchinson Cancer Research Center, Seattle, WA, US
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2
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Greene BL, Stasi SM, Ting MA, Waligorski N, Cole BL, Lockwood CM, Paulson VA, Buchan JG, Lee A, Ojemann JG, Ellenbogen RG, Stevens J, Leary SES. Looking beyond year 1 in the molecular era of pediatric brain tumor diagnosis: confirmatory testing of germline variants found on tumor sequencing. Front Oncol 2024; 14:1338022. [PMID: 38511139 PMCID: PMC10952109 DOI: 10.3389/fonc.2024.1338022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Purpose Somatic molecular profiling of pediatric brain tumors aids with the diagnosis and treatment of patients with a variety of high- and low-grade central nervous system neoplasms. Here, we report follow-up targeted germline evaluation for patients with possible germline variants following tumor only testing in the initial year in which somatic molecular testing was implemented at a single institution. Patients and Methods Somatic testing was completed for all tumors of the central nervous system (CNS) undergoing diagnostic workup at Seattle Children's Hospital during the study period of November 2015 to November 2016. Sequencing was performed in a College of American Pathologists-accredited, Clinical Laboratory Improvements Amendments-certified laboratory using UW-OncoPlex™ assay (version 5), a DNA-based targeted next generation sequencing panel validated to detect genetic alterations in 262 cancer-related genes. We tracked subsequent clinical evaluation and testing on a subgroup of this cohort found to have potential germline variants of interest. Results Molecular sequencing of 88 patients' tumors identified 31 patients with variants that warranted consideration of germline testing. To date, 19 (61%) patients have been tested. Testing confirmed germline variants for ten patients (31% of those identified for testing), one with two germline variants (NF1 and mosaic TP53). Eight (26%) patients died before germline testing was sent. One patient (13%) has not yet had testing. Conclusion Clinically validated molecular profiling of pediatric brain tumors identifies patients who warrant further germline evaluation. Despite this, only a subset of these patients underwent the indicated confirmatory sequencing. Further work is needed to identify barriers and facilitators to this testing, including the role of genetic counseling and consideration of upfront paired somatic-germline testing.
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Affiliation(s)
- Brittany L. Greene
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Cancer and Blood Disorders Center, Seattle Children’s Hospital, Seattle, WA, United States
| | - Shannon M. Stasi
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, United States
| | - Michelle A. Ting
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Cancer and Blood Disorders Center, Seattle Children’s Hospital, Seattle, WA, United States
| | - Natalie Waligorski
- Cancer and Blood Disorders Center, Seattle Children’s Hospital, Seattle, WA, United States
| | - Bonnie L. Cole
- Department of Laboratories, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Christina M. Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Vera A. Paulson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Jillian G. Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Amy Lee
- Department of Pediatric Neurosurgery, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - Jeffrey G. Ojemann
- Department of Pediatric Neurosurgery, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - Richard G. Ellenbogen
- Department of Pediatric Neurosurgery, Seattle Children’s Hospital, Seattle, WA, United States
- Department of Neurological Surgery, University of Washington, Seattle, WA, United States
| | - Jeffrey Stevens
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Cancer and Blood Disorders Center, Seattle Children’s Hospital, Seattle, WA, United States
| | - Sarah E. S. Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
- Cancer and Blood Disorders Center, Seattle Children’s Hospital, Seattle, WA, United States
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3
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Bick AG, Metcalf GA, Mayo KR, Lichtenstein L, Rura S, Carroll RJ, Musick A, Linder JE, Jordan IK, Nagar SD, Sharma S, Meller R, Basford M, Boerwinkle E, Cicek MS, Doheny KF, Eichler EE, Gabriel S, Gibbs RA, Glazer D, Harris PA, Jarvik GP, Philippakis A, Rehm HL, Roden DM, Thibodeau SN, Topper S, Blegen AL, Wirkus SJ, Wagner VA, Meyer JG, Cicek MS, Muzny DM, Venner E, Mawhinney MZ, Griffith SML, Hsu E, Ling H, Adams MK, Walker K, Hu J, Doddapaneni H, Kovar CL, Murugan M, Dugan S, Khan Z, Boerwinkle E, Lennon NJ, Austin-Tse C, Banks E, Gatzen M, Gupta N, Henricks E, Larsson K, McDonough S, Harrison SM, Kachulis C, Lebo MS, Neben CL, Steeves M, Zhou AY, Smith JD, Frazar CD, Davis CP, Patterson KE, Wheeler MM, McGee S, Lockwood CM, Shirts BH, Pritchard CC, Murray ML, Vasta V, Leistritz D, Richardson MA, Buchan JG, Radhakrishnan A, Krumm N, Ehmen BW, Schwartz S, Aster MMT, Cibulskis K, Haessly A, Asch R, Cremer A, Degatano K, Shergill A, Gauthier LD, Lee SK, Hatcher A, Grant GB, Brandt GR, Covarrubias M, Banks E, Able A, Green AE, Carroll RJ, Zhang J, Condon HR, Wang Y, Dillon MK, Albach CH, Baalawi W, Choi SH, Wang X, Rosenthal EA, Ramirez AH, Lim S, Nambiar S, Ozenberger B, Wise AL, Lunt C, Ginsburg GS, Denny JC. Genomic data in the All of Us Research Program. Nature 2024; 627:340-346. [PMID: 38374255 PMCID: PMC10937371 DOI: 10.1038/s41586-023-06957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/08/2023] [Indexed: 02/21/2024]
Abstract
Comprehensively mapping the genetic basis of human disease across diverse individuals is a long-standing goal for the field of human genetics1-4. The All of Us Research Program is a longitudinal cohort study aiming to enrol a diverse group of at least one million individuals across the USA to accelerate biomedical research and improve human health5,6. Here we describe the programme's genomics data release of 245,388 clinical-grade genome sequences. This resource is unique in its diversity as 77% of participants are from communities that are historically under-represented in biomedical research and 46% are individuals from under-represented racial and ethnic minorities. All of Us identified more than 1 billion genetic variants, including more than 275 million previously unreported genetic variants, more than 3.9 million of which had coding consequences. Leveraging linkage between genomic data and the longitudinal electronic health record, we evaluated 3,724 genetic variants associated with 117 diseases and found high replication rates across both participants of European ancestry and participants of African ancestry. Summary-level data are publicly available, and individual-level data can be accessed by researchers through the All of Us Researcher Workbench using a unique data passport model with a median time from initial researcher registration to data access of 29 hours. We anticipate that this diverse dataset will advance the promise of genomic medicine for all.
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4
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Bennett JC, Luiten KG, O'Hanlon J, Han PD, McDonald D, Wright T, Wolf CR, Lo NK, Acker Z, Regelbrugge L, McCaffrey KM, Pfau B, Stone J, Schwabe-Fry K, Lockwood CM, Guthrie BL, Gottlieb GS, Englund JA, Uyeki TM, Carone M, Starita LM, Weil AA, Chu HY. Utilizing a university testing program to estimate relative effectiveness of monovalent COVID-19 mRNA booster vaccine versus two-dose primary series against symptomatic SARS-CoV-2 infection. Vaccine 2024; 42:1332-1341. [PMID: 38307746 DOI: 10.1016/j.vaccine.2024.01.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
Vaccine effectiveness (VE) studies utilizing the test-negative design are typically conducted in clinical settings, rather than community populations, leading to bias in VE estimates against mild disease and limited information on VE in healthy young adults. In a community-based university population, we utilized data from a large SARS-CoV-2 testing program to estimate relative VE of COVID-19 mRNA vaccine primary series and monovalent booster dose versus primary series only against symptomatic SARS-CoV-2 infection from September 2021 to July 2022. We used the test-negative design and logistic regression implemented via generalized estimating equations adjusted for age, calendar time, prior SARS-CoV-2 infection, and testing frequency (proxy for test-seeking behavior) to estimate relative VE. Analyses included 2,218 test-positive cases (59 % received monovalent booster dose) and 9,615 test-negative controls (62 %) from 9,066 individuals, with median age of 21 years, mostly students (71 %), White (56 %) or Asian (28 %), and with few comorbidities (3 %). More cases (23 %) than controls (6 %) had COVID-19-like illness. Estimated adjusted relative VE of primary series and monovalent booster dose versus primary series only against symptomatic SARS-CoV-2 infection was 40 % (95 % CI: 33-47 %) during the overall analysis period and 46 % (39-52 %) during the period of Omicron circulation. Relative VE was greater for those without versus those with prior SARS-CoV-2 infection (41 %, 34-48 % versus 33 %, 9 %-52 %, P < 0.001). Relative VE was also greater in the six months after receiving a booster dose (41 %, 33-47 %) compared to more than six months (27 %, 8-42 %), but this difference was not statistically significant (P = 0.06). In this relatively young and healthy adult population, an mRNA monovalent booster dose provided increased protection against symptomatic SARS-CoV-2 infection, overall and with the Omicron variant. University testing programs may be utilized for estimating VE in healthy young adults, a population that is not well-represented by routine VE studies.
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Affiliation(s)
- Julia C Bennett
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA.
| | - Kyle G Luiten
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jessica O'Hanlon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Devon McDonald
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Tessa Wright
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Natalie K Lo
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Zack Acker
- Brotman Baty Institute, Seattle, WA, USA
| | | | | | - Brian Pfau
- Brotman Baty Institute, Seattle, WA, USA
| | - Jeremey Stone
- Brotman Baty Institute, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Christina M Lockwood
- Brotman Baty Institute, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Brandon L Guthrie
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Geoffrey S Gottlieb
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, WA, USA; Environmental Health & Safety Department, University of Washington, Seattle, WA, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marco Carone
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ana A Weil
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, WA, USA
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5
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Pfau B, Opsahl J, Crew R, Best S, Han PD, Heidl S, McDermot E, Stone J, Schwabe-Fry K, MacMillan MP, O'Hanlon J, Sohlberg S, Acker Z, Ehmen B, Englund JA, Konnick EQ, Chu HY, Weil AA, Lockwood CM, Starita LM. Tiny swabs: nasal swabs integrated into tube caps facilitate large-scale self-collected SARS-CoV-2 testing. J Clin Microbiol 2024; 62:e0128523. [PMID: 38131692 PMCID: PMC10865831 DOI: 10.1128/jcm.01285-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023] Open
Abstract
The COVID-19 pandemic spurred the development of innovative solutions for specimen collection and molecular detection for large-scale community testing. Among these developments is the RHINOstic nasal swab, a plastic anterior nares swab built into the cap of a standard matrix tube that facilitates automated processing of up to 96 specimens at a time. In a study of unsupervised self-collection utilizing these swabs, we demonstrate comparable analytic performance and shipping stability compared to traditional anterior nares swabs, as well as significant improvements in laboratory processing efficiency. The use of these swabs may allow laboratories to accommodate large numbers of sample collections during periods of high testing demand. Automation-friendly nasal swabs are an important tool for high-throughput processing of samples that may be adopted in response to future respiratory viral pandemics.
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Affiliation(s)
- Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jordan Opsahl
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Ruben Crew
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Sabrina Best
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Sarah Heidl
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Evan McDermot
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jeremy Stone
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | | | | | - Jessica O'Hanlon
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sarah Sohlberg
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Zack Acker
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Brenna Ehmen
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Janet A. Englund
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Eric Q. Konnick
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Helen Y. Chu
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Ana A. Weil
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Christina M. Lockwood
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - The Seattle Flu Alliance InvestigatorsBedfordTrevorBoeckhMichaelChuHelen Y.EnglundJanet A.LockwoodChristina M.LutzBarry R.PrenticeRobinShendureJayStaritaLea M.WaghmereAlpanaWeilAna A.
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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6
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Zehir A, Nardi V, Konnick EQ, Lockwood CM, Long TA, Sidiropoulos N, Souers RJ, Vasalos P, Lindeman NI, Moncur JT. SPOT/Dx Pilot Reanalysis and College of American Pathologists Proficiency Testing for KRAS and NRAS Demonstrate Excellent Laboratory Performance. Arch Pathol Lab Med 2024; 148:139-148. [PMID: 37776255 DOI: 10.5858/arpa.2023-0322-cp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
CONTEXT.— The Sustainable Predictive Oncology Therapeutics and Diagnostics quality assurance pilot study (SPOT/Dx pilot) on molecular oncology next-generation sequencing (NGS) reportedly demonstrated performance limitations of NGS laboratory-developed tests, including discrepancies with a US Food and Drug Administration-approved companion diagnostic. The SPOT/Dx pilot methods differ from those used in proficiency testing (PT) programs. OBJECTIVE.— To reanalyze SPOT/Dx pilot data using PT program methods and compare to PT program data.Also see p. 136. DESIGN.— The College of American Pathologists (CAP) Molecular Oncology Committee reanalyzed SPOT/Dx pilot data applying PT program methods, adjusting for confounding conditions, and compared them to CAP NGS PT program performance (2019-2022). RESULTS.— Overall detection rates of KRAS and NRAS single-nucleotide variants (SNVs) and multinucleotide variants (MNVs) by SPOT/Dx pilot laboratories were 96.8% (716 of 740) and 81.1% (129 of 159), respectively. In CAP PT programs, the overall detection rates for the same SNVs and MNVs were 97.2% (2671 of 2748) and 91.8% (1853 of 2019), respectively. In 2022, the overall detection rate for 5 KRAS and NRAS MNVs in CAP PT programs was 97.3% (1161 of 1193). CONCLUSIONS.— CAP PT program data demonstrate that laboratories consistently have high detection rates for KRAS and NRAS variants. The SPOT/Dx pilot has multiple design and analytic differences with established PT programs. Reanalyzed pilot data that adjust for confounding conditions demonstrate that laboratories proficiently detect SNVs and less successfully detect rare to never-observed MNVs. The SPOT/Dx pilot results are not generalizable to all molecular oncology testing and should not be used to market products or change policy affecting all molecular oncology testing.
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Affiliation(s)
- Ahmet Zehir
- From the Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York (Zehir)
| | - Valentina Nardi
- the Department of Pathology, Massachusetts General Hospital, Mass General Brigham, Harvard Medical School, Boston (Nardi)
| | - Eric Q Konnick
- the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick, Lockwood)
| | - Christina M Lockwood
- the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick, Lockwood)
| | - Thomas A Long
- Biostatistics (Long, Souers) Departments, College of American Pathologists, Northfield, Illinois
| | - Nikoletta Sidiropoulos
- Pathology and Laboratory Medicine, University of Vermont Medical Center, Larner College of Medicine at the University of Vermont, Burlington (Sidiropoulos)
| | - Rhona J Souers
- Biostatistics (Long, Souers) Departments, College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing (Vasalos) Departments, College of American Pathologists, Northfield, Illinois
| | - Neal I Lindeman
- the Department of Pathology, Weill Cornell Medicine, New York, New York (Lindeman)
| | - Joel T Moncur
- the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
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7
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Greytak SR, Engel KB, Hoon DSB, Elias KM, Lockwood CM, Guan P, Moore HM. Evidence-based procedures to improve the reliability of circulating miRNA biomarker assays. Clin Chem Lab Med 2024; 62:60-66. [PMID: 37129007 DOI: 10.1515/cclm-2023-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Circulating cell-free microRNAs (cfmiRNA) are an emerging class of biomarkers that have shown great promise in the clinical diagnosis, treatment, and monitoring of several pathological conditions, including cancer. However, validation and clinical implementation of cfmiRNA biomarkers has been hindered by the variability introduced during different or suboptimal specimen collection and handling practices. To address the need for standardization and evidence-based guidance, the National Cancer Institute (NCI) developed a new Biospecimen Evidenced-Based Practices (BEBP) document, entitled "Cell-free miRNA (cfmiRNA): Blood Collection and Processing". The BEBP, the fourth in the document series, contains step-by-step procedural guidelines on blood collection, processing, storage, extraction, and quality assessment that are tailored specifically for cfmiRNA analysis of plasma and serum. The workflow outlined in the BEBP is based on the available literature and recommendations of an expert panel. The BEBP contains the level of detail required for development of evidence-based standard operating procedures (SOPs) as well as the flexibility needed to accomodate (i) discovery- and inquiry-based studies and (ii) the different constraints faced by research labs, industry, clinical and academic institutions to foster widespread implementation. Guidance from the expert panel also included recommendations on study design, validating changes in workflow, and suggested quality thresholds to delineate meaningful changes in cfmiRNA levels. The NCI cfmiRNA: Blood Collection and Processing BEBP is available here as supplementary information as well as through the NCI Biorepositories and Biospecimen Research Branch (BBRB) (https://biospecimens.cancer.gov/resources/bebp.asp).
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Affiliation(s)
| | | | - Dave S B Hoon
- Department of Translational Molecular Medicine & Sequencing Center, Saint Johns' Cancer Institute, Providence Health and Service, Santa Monica, CA, USA
| | - Kevin M Elias
- Gynecologic Oncology Laboratory, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Harvard Medical School, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina M Lockwood
- Genetics and Solid Tumors Laboratory, Department of Laboratory Medicine and Pathology, Brotman Baty Institute for Precision Medicine, UW Medicine, Seattle, WA, USA
| | - Ping Guan
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
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8
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Shree R, MacKinnon HJ, Hannan J, Kolarova TR, Reichel J, Lockwood CM. Anticoagulation use is associated with lower fetal fraction and more indeterminate results. Am J Obstet Gynecol 2024; 230:95.e1-95.e10. [PMID: 37429430 PMCID: PMC10772208 DOI: 10.1016/j.ajog.2023.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Maternal anticoagulation use may increase indeterminate result rates on cell-free DNA-based screening, but existing studies are confounded by inclusion of individuals with autoimmune disease, which alone is associated with indeterminate results. Changes in chromosome level Z-scores are proposed by others as a reason for indeterminate results, but the etiology of this is uncertain. OBJECTIVE This study aimed to evaluate differences in fetal fraction, indeterminate result rate, and total cell-free DNA concentration in individuals on anticoagulation without autoimmune disease compared with controls undergoing noninvasive prenatal screening. Secondly, using a nested case-control design, we evaluated differences in fragment size, GC-content, and Z-scores to evaluate laboratory-level test characteristics. STUDY DESIGN This was a retrospective single-institution study of pregnant individuals undergoing cell-free DNA-based noninvasive prenatal screening using low-pass whole-genome sequencing between 2017 and 2021. Individuals with autoimmune disease, suspected aneuploidy, and cases where fetal fraction was not reported were excluded. Anticoagulation included heparin-derived products (unfractionated heparin, low-molecular-weight heparin), clopidogrel, and fondaparinux, with a separate group for those on aspirin alone. An indeterminate result was defined as fetal fraction <4%. We evaluated the association between maternal anticoagulation or aspirin use, and fetal fraction, indeterminate results, and total cell-free DNA concentration using univariate and multivariate analyses, controlling for body mass index, gestational age at sample collection, and fetal sex. For the anticoagulation cohort, we compared laboratory-level test characteristics among cases (on anticoagulation) and a subset of controls. Lastly, we evaluated for differences in chromosome level Z-scores among those on anticoagulation with and without indeterminate results. RESULTS A total of 1707 pregnant individuals met the inclusion criteria. Of those, 29 were on anticoagulation and 81 were on aspirin alone. For those on anticoagulation, the fetal fraction was significantly lower (9.3% vs 11.7%; P<.01), the indeterminate result rate was significantly higher (17.2% vs 2.7%; P<.001), and the total cell-free DNA concentration was significantly higher (218 pg/μL vs 83.7 pg/μL; P<.001). Among those on aspirin alone, the fetal fraction was lower (10.6% vs 11.8%; P=.04); however, there were no differences in the rate of indeterminate results (3.7% vs 2.7%; P=.57) or total cell-free DNA concentration (90.1 pg/μL vs 83.8 pg/μL; P=.31). After controlling for maternal body mass index, gestational age at sample collection, and fetal sex, anticoagulation was associated with an >8-fold increase in the likelihood of an indeterminate result (adjusted odds ratio, 8.7; 95% confidence interval, 3.1-24.9; P<.001), but not aspirin (adjusted odds ratio, 1.2; 95% confidence interval, 0.3-4.1; P=.8). Anticoagulation was not associated with appreciable differences in cell-free DNA fragment size or GC-content. Although differences in chromosome 13 Z-scores were observed, none were observed for chromosomes 18 or 21, and this difference did not contribute to the indeterminate result call. CONCLUSION In the absence of autoimmune disease, anticoagulation use, but not aspirin, is associated with lower fetal fraction, higher total cell-free DNA concentration, and higher rates of indeterminate results. Anticoagulation use was not accompanied by differences in cell-free DNA fragment size or GC-content. Statistical differences in chromosome level Z-scores did not clinically affect aneuploidy detection. This suggests a likely dilutional effect by anticoagulation on cell-free DNA-based noninvasive prenatal screening assays contributing to low fetal fraction and indeterminate results, and not laboratory or sequencing-level changes.
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Affiliation(s)
- Raj Shree
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA.
| | - Hayley J MacKinnon
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA
| | - Joely Hannan
- University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Teodora R Kolarova
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA
| | - Jonathan Reichel
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
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Tam LT, Cole B, Stasi SM, Paulson VA, Wright JN, Hoeppner C, Holtzclaw S, Crotty EE, Ellenbogen RG, Lee A, Ermoian RP, Lockwood CM, Leary SES, Ronsley R. Somatic Versus Germline: A Case Series of Three Children With ATM-Mutated Medulloblastoma. JCO Precis Oncol 2024; 8:e2300333. [PMID: 38207225 DOI: 10.1200/po.23.00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/03/2023] [Accepted: 11/07/2023] [Indexed: 01/13/2024] Open
Abstract
Somatic versus Germline-A Case Series of Three Children with ATM- mutated Medulloblastoma.
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Affiliation(s)
- Lydia T Tam
- Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Bonnie Cole
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA
| | - Shannon M Stasi
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Vera A Paulson
- Genetics Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Jason N Wright
- Department of Radiology, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Corrine Hoeppner
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Susan Holtzclaw
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Erin E Crotty
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Radiation Oncology, University of Washington, Seattle, WA
| | - Richard G Ellenbogen
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA
| | - Amy Lee
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA
| | | | - Christina M Lockwood
- Genetics Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Sarah E S Leary
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Radiation Oncology, University of Washington, Seattle, WA
| | - Rebecca Ronsley
- Division of Hematology, Oncology, Bone Marrow Transplant & Cellular Therapy, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Neurological Surgery, Seattle Children's Hospital, University of Washington, Seattle, WA
- Department of Radiation Oncology, University of Washington, Seattle, WA
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10
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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11
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Ondracek CR, Genzen JR, Lockwood CM, Das S, Kang P, Melanson SEF. Robust Response of the Clinical Laboratory to the COVID-19 Pandemic despite Significant Challenges. J Appl Lab Med 2023; 8:1160-1172. [PMID: 37643134 DOI: 10.1093/jalm/jfad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/21/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Clinical laboratories immediately provided rapid, reliable, and high-throughout diagnostic testing for COVID-19, which was an essential component in combating the pandemic. As the pandemic evolved, the clinical laboratory was faced with additional challenges. However, there are limited studies on the impact of the pandemic on the clinical laboratory over the past 3 years. METHODS The American Association for Clinical Chemistry (AACC) sent 8 surveys over a 32-month time period to international clinical laboratory leadership asking questions about COVID-19 testing, supplies, staffing, and lessons learned. RESULTS There were a total of 191 unique respondents: 133 laboratories in the US and 58 laboratories from 37 other countries participated. By May 2020, more than 70% of laboratories offered COVID-19 diagnostic testing with average turnaround times ranging from 1 to 24 h. Daily COVID-19 testing volumes peaked in January of 2022 at a median of 775 tests per day. Throughout the pandemic, supplies and staffing concerns increased. In most of the 8 surveys, 55% to 65% of laboratories reported they were unable to obtain supplies. Obtaining reagents and test kits was the most problematic. Staffing challenges continue to be a significant concern and most laboratories have struggled hiring testing personnel. CONCLUSIONS Survey results were utilized to demonstrate the impact of the pandemic on the clinical laboratory community, and importantly, findings were presented to the White House Coronavirus Taskforce. Overall, the clinical laboratories had a robust response to the COVID-19 pandemic, and despite ongoing and evolving challenges, continue to provide rapid diagnostic testing.
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Affiliation(s)
- Caitlin R Ondracek
- American Association for Clinical Chemistry, Washington, DC, United States
| | - Jonathan R Genzen
- ARUP Laboratories, University of Utah, Salt Lake City, UT, United States
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences, New Delhi, India
| | - Phillip Kang
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, United States
| | - Stacy E F Melanson
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
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12
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Pierre CC, Greene DN, Delaney S, Lockwood CM, Peck Palmer OM. Reconsidering the use of race adjustments in maternal serum screening. Am J Obstet Gynecol 2023; 229:522-525. [PMID: 37327981 DOI: 10.1016/j.ajog.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
The use of race in maternal serum screening is problematic because race is a social construct rather than a distinct biological classifier. Nevertheless, laboratories offering this testing are encouraged to use race-specific cutoff values for maternal serum screening biomarkers to determine the risk of fetal abnormalities. Large cohort studies examining racial differences in maternal serum screening biomarker concentrations have yielded conflicting results, which we postulate may be explained by genetic and socioeconomic differences between racial cohorts in different studies. We recommend that the use of race in maternal serum screening should be abandoned. Further research is needed to identify socioeconomic and environmental factors that contribute to differences in maternal serum screening biomarker concentrations observed between races. A better understanding of these factors may facilitate accurate race-agnostic risk estimates for aneuploidy and neural tube defects.
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Affiliation(s)
- Christina C Pierre
- Department of Pathology and Laboratory Medicine, Penn Medicine Lancaster General Health, Lancaster, PA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
| | - Dina N Greene
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Shani Delaney
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Octavia M Peck Palmer
- Departments of Pathology and Clinical and Translational Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
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13
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Gupta N, Huang TT, Nair JR, An D, Zurcher G, Lampert EJ, McCoy A, Cimino-Mathews A, Swisher EM, Radke MR, Lockwood CM, Reichel JB, Chiang CY, Wilson KM, Chih-Chien Cheng K, Nousome D, Lee JM. BLM overexpression as a predictive biomarker for CHK1 inhibitor response in PARP inhibitor-resistant BRCA-mutant ovarian cancer. Sci Transl Med 2023; 15:eadd7872. [PMID: 37343085 PMCID: PMC10758289 DOI: 10.1126/scitranslmed.add7872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/02/2023] [Indexed: 06/23/2023]
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARPis) have changed the treatment paradigm in breast cancer gene (BRCA)-mutant high-grade serous ovarian carcinoma (HGSC). However, most patients eventually develop resistance to PARPis, highlighting an unmet need for improved therapeutic strategies. Using high-throughput drug screens, we identified ataxia telangiectasia and rad3-related protein/checkpoint kinase 1 (CHK1) pathway inhibitors as cytotoxic and further validated the activity of the CHK1 inhibitor (CHK1i) prexasertib in PARPi-sensitive and -resistant BRCA-mutant HGSC cells and xenograft mouse models. CHK1i monotherapy induced DNA damage, apoptosis, and tumor size reduction. We then conducted a phase 2 study (NCT02203513) of prexasertib in patients with BRCA-mutant HGSC. The treatment was well tolerated but yielded an objective response rate of 6% (1 of 17; one partial response) in patients with previous PARPi treatment. Exploratory biomarker analyses revealed that replication stress and fork stabilization were associated with clinical benefit to CHK1i. In particular, overexpression of Bloom syndrome RecQ helicase (BLM) and cyclin E1 (CCNE1) overexpression or copy number gain/amplification were seen in patients who derived durable benefit from CHK1i. BRCA reversion mutation in previously PARPi-treated BRCA-mutant patients was not associated with resistance to CHK1i. Our findings suggest that replication fork-related genes should be further evaluated as biomarkers for CHK1i sensitivity in patients with BRCA-mutant HGSC.
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Affiliation(s)
- Nitasha Gupta
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Tzu-Ting Huang
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jayakumar R. Nair
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Daniel An
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Grant Zurcher
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Erika J. Lampert
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
- Department of Obstetrics and Gynecology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ann McCoy
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Ashley Cimino-Mathews
- Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Elizabeth M. Swisher
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Marc R. Radke
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Christina M. Lockwood
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jonathan B. Reichel
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Chih-Yuan Chiang
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20892, USA
| | - Kelli M. Wilson
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20892, USA
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Rockville, MD 20892, USA
| | - Darryl Nousome
- Center for Cancer Research Collaborative Bioinformatics Resource, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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14
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Krumm N, Khasnavis NS, Radke M, Banda K, Davies HR, Pennil C, McLean K, Paulson VA, Konnick EQ, Johnson WC, Huff G, Nik-Zainal S, Swisher EM, Lockwood CM, Salipante SJ. Diagnosis of Ovarian Carcinoma Homologous Recombination DNA Repair Deficiency From Targeted Gene Capture Oncology Assays. JCO Precis Oncol 2023; 7:e2200720. [PMID: 37196218 PMCID: PMC10309534 DOI: 10.1200/po.22.00720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 05/19/2023] Open
Abstract
PURPOSE Homologous recombination DNA repair deficiency (HRD) is a therapeutic biomarker for sensitivity to platinum and poly(ADP-ribose) polymerase inhibitor therapies in breast and ovarian cancers. Several molecular phenotypes and diagnostic strategies have been developed to assess HRD; however, their clinical implementation remains both technically challenging and methodologically unstandardized. METHODS We developed and validated an efficient and cost-effective strategy for HRD determination on the basis of calculation of a genome-wide loss of heterozygosity (LOH) score through targeted, hybridization capture and next-generation DNA sequencing augmented with 3,000 common, polymorphic single-nucleotide polymorphism (SNP) sites distributed genome-wide. This approach requires minimal sequence reads and can be readily integrated into targeted gene capture workflows already in use for molecular oncology. We interrogated 99 ovarian neoplasm-normal pairs using this method and compared results with patient mutational genotypes and orthologous predictors of HRD derived from whole-genome mutational signatures. RESULTS LOH scores of ≥11% had >86% sensitivity for identifying tumors with HRD-causing mutations in an independent validation set (90.6% sensitivity for all specimens). We found strong agreement of our analytic approach with genome-wide mutational signature assays for determining HRD, yielding an estimated 96.7% sensitivity and 50% specificity. We observed poor concordance with mutational signatures inferred using only mutations detected by the targeted gene capture panel, suggesting inadequacy of the latter approach. LOH score did not significantly correlate with treatment outcomes. CONCLUSION Targeted sequencing of genome-wide polymorphic SNP sites can be used to infer LOH events and subsequently diagnose HRD in ovarian tumors. The methods presented here are readily generalizable to other targeted gene oncology assays and could be adapted for HRD diagnosis in other tumor types.
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Affiliation(s)
- Niklas Krumm
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Nithisha S. Khasnavis
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Marc Radke
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Kalyan Banda
- Department of Medicine, Oncology Division, University of Washington School of Medicine, Seattle, WA
| | - Helen R. Davies
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - Christopher Pennil
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Kathryn McLean
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Vera A. Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Eric Q. Konnick
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Winslow C. Johnson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Grogan Huff
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth M. Swisher
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, WA
| | - Christina M. Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
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15
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Devereaux KA, Souers RJ, Merker JD, Lindeman NI, Graham RP, Hameed MR, Vasalos P, Moncur JT, Lockwood CM, Xian RR. Clinical Testing for Tumor Cell-Free DNA: College of American Pathologists Proficiency Programs Reveal Practice Trends. Arch Pathol Lab Med 2023; 147:425-433. [PMID: 35687785 DOI: 10.5858/arpa.2021-0585-cp] [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] [Accepted: 02/28/2022] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Clinical testing for tumor cell-free DNA (cfDNA) has evolved rapidly, but no practice guidelines exist. OBJECTIVE.— To summarize cfDNA laboratory practices based on self-reporting and assess preanalytical, analytical, and postanalytical trends that may influence the quality, accuracy, and consistency of cfDNA testing. DESIGN.— Data were derived from the College of American Pathologists cfDNA proficiency testing program submitted by 101 participating laboratories from 2018 to 2019. RESULTS.— Most laboratories performing clinical circulating tumor DNA testing are commercial/nonhospital (71.2%; 72 of 101) and international (77.2%; 78 of 101) laboratories. Commercial laboratories had higher monthly test volumes than hospital-based laboratories (median, 36 versus 7-8) and tended to have larger gene panels (median, 50 versus 11 genes) when panel-based testing was offered. The main clinical indications include therapy selection and treatment/disease monitoring. Plasma is the most commonly accepted specimen, which is predominantly collected in cell-stabilizing tubes. Equal proportions of laboratories use next-generation sequencing (NGS) and non-NGS methods to assess key genes, including EGFR, BRAF, KRAS, NRAS, and IDH1. Most laboratories reported a lower limit of detection (LLOD) of 0.5%, variant allele frequency or less, which did not differ by method, NGS or non-NGS, except for EGFR. Sixty-five percent (17 of 26) of laboratories using the US Food and Drug Administration (FDA)-approved non-NGS EGFR assay report analytical sensitivities higher than 0.5%, as compared to 15% (16 of 104) of laboratories using an alternative NGS or non-NGS method. There is also a wider range in LLODs obtained for the FDA-approved EGFR assay than nonapproved assays. CONCLUSIONS.— These results highlight emerging practice trends and serve as a foundation to initiate future practice recommendations.
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Affiliation(s)
- Kelly A Devereaux
- From the Department of Pathology, NYU School of Medicine, New York, New York (Devereaux), College of American Pathologists, Northfield, Illinois
| | - Rhona J Souers
- Biostatistics Department (Souers), College of American Pathologists, Northfield, Illinois
| | - Jason D Merker
- The Departments of Pathology and Laboratory Medicine & Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill (Merker)
| | - Neal I Lindeman
- The Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Lindeman)
| | - Rondell P Graham
- The Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Graham)
| | - Meera R Hameed
- The Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York (Hameed)
| | - Patricia Vasalos
- Proficiency Testing (Vasalos), College of American Pathologists, Northfield, Illinois
| | - Joel T Moncur
- Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
| | - Christina M Lockwood
- The Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Lockwood)
| | - Rena R Xian
- The Departments of Pathology and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland (Xian)
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16
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Paulson VA, Liu YJ, Fang H, Browd SR, Hauptman JS, Wright J, Lockwood CM, Leary SES, Cole BL. Infantile ZFTA Fusion-Positive Tumor of the Posterior Fossa: Molecular Tumor Board. JCO Precis Oncol 2023; 7:e2200226. [PMID: 36862968 DOI: 10.1200/po.22.00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Affiliation(s)
- Vera A Paulson
- Department of Laboratory Medicine and Pathology, Genetics and Solid Tumor Laboratory, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Yajuan J Liu
- Department of Laboratory Medicine and Pathology, Clinical Genomics Laboratory, University of Washington School of Medicine, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - He Fang
- Department of Laboratory Medicine and Pathology, Clinical Genomics Laboratory, University of Washington School of Medicine, Seattle, WA
| | - Sam R Browd
- Division of Neurosurgery, Department of Neurological Surgery, University of Washington, Seattle Children's Hospital, Seattle, WA
| | - Jason S Hauptman
- Division of Neurosurgery, Department of Neurological Surgery, University of Washington, Seattle Children's Hospital, Seattle, WA
| | - Jason Wright
- Radiology, Seattle Children's Hospital, University of Washington; Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, Genetics and Solid Tumor Laboratory, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Sarah E S Leary
- Cancer and Blood Disorders Center, Seattle Children's Hospital; Department of Pediatrics, University of Washington; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Bonnie L Cole
- Department of Laboratory Medicine and Pathology, Clinical Genomics Laboratory, University of Washington School of Medicine, Seattle, WA.,Department of Laboratories, Seattle Children's Hospital, University of Washington; Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
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17
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Naumchik B, Weigel BJ, Murati MA, Rudzinski E, Paulson V, Lockwood CM, Dolan M, Flanagan S, Luquette M. Congenital Infantile Fibrosarcoma Involving Pelvic Wall and Thigh Soft Tissues and Placenta, Presenting with Coagulopathy. Pediatr Dev Pathol 2022; 25:656-660. [PMID: 35834223 DOI: 10.1177/10935266221114017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Infantile fibrosarcoma (IF) is a well characterized pediatric malignancy marked by gene rearrangements involving members of the NTRK family. In this report, we present a case of IF that presented in the inguinal region-proximal thigh and was initially thought to be a kaposiform hemangioendothelioma (KHE) because it presented with a bleeding diathesis thought to be Kasabach-Merritt phenomenon (KMP). Subsequently, the placental examination showed a neoplasm in the perivascular-subendothelial space of stem villi, initially thought to be myofibromatosis. Ultimately, a biopsy of the thigh mass showed IF with an NTRK3-ETV6 fusion. Subsequent FISH analysis of the placenta showed an ETV6 rearrangement confirming that it was also IF. Review of the laboratory studies suggests that disseminated intravascular coagulation may have been more likely than KMP, highlighting the difficulty in making this distinction in some cases. We believe this to be the first report of an IF presenting in a soft tissue site and the placenta, and discuss the possible mechanisms that could have allowed the IF in the leg to spread to the placenta.
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Affiliation(s)
- Brianna Naumchik
- Pathology, 5635University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Brenda J Weigel
- Pediatrics, Division of Pediatric Hematology and Oncology, 5635University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Michael A Murati
- Radiology, 5635University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Erin Rudzinski
- Pathology, 7274Seattle Children's Hospital, Seattle, WA, USA
| | - Vera Paulson
- Laboratory Medicine and Pathology, 7284University of Washington, Seattle, WA, USA
| | - Christina M Lockwood
- Laboratory Medicine and Pathology, 7284University of Washington, Seattle, WA, USA
| | - Michelle Dolan
- Pathology, 5635University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Siobhan Flanagan
- Interventional Radiology, 5635University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Mark Luquette
- Pediatric and Perinatal Pathology, 5635University of Minnesota Twin Cities, Minneapolis, MN, USA
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18
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Jones PM, Dietzen DJ, Hoofnagle AN, Lockwood CM, Wiley CL, Konnick EQ. It’s VALID, but Is It Rational? J Appl Lab Med 2022; 7:1245-1250. [DOI: 10.1093/jalm/jfac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Patricia M Jones
- Department of Pathology, University of Texas Southwestern Medical Center and Children’s Medical Center , Dallas, TX , USA
| | - Dennis J Dietzen
- Department of Pediatrics, Washington University School of Medicine and St. Louis Children’s Hospital , St. Louis, MO , USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington , Seattle, WA , USA
- Department of Pathology, University of Washington , Seattle, WA , USA
- Department of Medicine, University of Washington , Seattle, WA , USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington , Seattle, WA , USA
- Department of Pathology, University of Washington , Seattle, WA , USA
- Brotman Baty Institute for Precision Medicine , Seattle, WA , USA
| | | | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington , Seattle, WA , USA
- Department of Pathology, University of Washington , Seattle, WA , USA
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19
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Chung E, Magedson A, Emanuels A, Luiten K, Pfau B, Truong M, Chow EJ, Hughes JP, Uyeki TM, Englund JA, Nickerson DA, Lockwood CM, Shendure J, Starita LM, Chu HY. SARS-CoV-2 Screening Testing in Schools: A Comparison of School- Vs. Home-Based Collection Methods. J Pediatric Infect Dis Soc 2022; 11:522-524. [PMID: 36082698 PMCID: PMC9494399 DOI: 10.1093/jpids/piac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We implemented a voluntary SARS-CoV-2 screening testing study for kindergarten-2nd grade students in a Washington School district. Weekly SARS-CoV-2 testing participation was higher for students with staff-collected nasal swabs at school than for students with parent-collected swabs at home.
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Affiliation(s)
- Erin Chung
- Corresponding Author: Erin Chung, MD, Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, UW Medicine Box 358061, Chu Lab Room E691,750 Republican Street, Seattle, WA 98109, USA. E-mal:
| | | | - Anne Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kyle Luiten
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, Washington, USA,Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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20
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Shree R, Kolarova TR, MacKinnon HJ, Lockwood CM, Chandrasekaran S. Association of fetal fraction with hypertensive disorders of pregnancy incidence and disease severity. Am J Obstet Gynecol MFM 2022; 4:100671. [PMID: 35644526 PMCID: PMC9452472 DOI: 10.1016/j.ajogmf.2022.100671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/06/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hypertensive disorders of pregnancy contribute to maternal and offspring morbidity and mortality. Studies suggest that a lower early pregnancy fetal fraction is associated with an increased risk of hypertensive disorders of pregnancy. However, maternal obesity significantly affects fetal fraction and is a risk factor for hypertensive disorders of pregnancy. OBJECTIVE We determined the association between fetal fraction (using a standardized single-institution platform, including male and female fetuses) and hypertensive disorders of pregnancy, stratified by obesity status. Second, we evaluated differences in total cell-free DNA concentration and correlation of fetal fraction with clinical markers of hypertensive disorders of pregnancy severity. STUDY DESIGN This was a retrospective, single-institution study of a previously validated cell-free DNA-based noninvasive prenatal screening assay of 1058 samples. Maternal body mass index at the time of noninvasive prenatal screening was assessed, and hypertensive disorders of pregnancy were confirmed by a detailed medical record review. Differences in fetal fraction and total cell-free DNA concentration between the groups were assessed with univariate analyses. Multivariable regression was used to evaluate the association between fetal fraction and hypertensive disorders of pregnancy, adjusted for body mass index, maternal age, gestational age at noninvasive prenatal screening, and fetal sex. The association between fetal fraction and hypertensive disorders of pregnancy among individuals with obesity (body mass index, ≥30 kg/m2) and individuals without obesity (body mass index, <30 kg/m2) was investigated while controlling for the aforementioned covariates. Lastly, multivariable linear regression was used to evaluate the association between fetal fraction and clinical markers of hypertensive disorders of pregnancy severity. RESULTS We identified individuals with (n=117) and without (n=941) hypertensive disorders of pregnancy with noninvasive prenatal screening drawn before 20 weeks of gestation and with fetal fraction and body mass index data available. Those with hypertensive disorders of pregnancy had a lower fetal fraction (10.2%±4.2% vs 11.6%±4.7%; P<.01), without differences in total cell-free DNA concentration (P=.14). When groups were stratified by obesity status, this relationship was only valid for individuals without obesity (P=.02). Only when logistic regression analysis was restricted to individuals without obesity did the likelihood of hypertensive disorders of pregnancy rise with decreasing fetal fraction (odds ratio, 0.93; 95% confidence interval, 0.88-0.99; P=.02). In addition, fetal fraction was inversely associated with maximum systolic blood pressure at the time of hypertensive disorders of pregnancy only in the population without obesity (β, -0.08; 95% confidence interval, -0.147 to -0.01; P=.02). CONCLUSION Although a lower fetal fraction is associated with the development of hypertensive disorders of pregnancy, the use of this parameter for the prediction may be problematic in individuals with obesity, as obesity has such a profound effect on fetal fraction. However, we uniquely noted that among individuals without obesity, fetal fraction is lower for those that develop hypertensive disorders of pregnancy and lower fetal fraction increases the odds of hypertensive disorders of pregnancy development. Lastly, low fetal fraction in the population without obesity that developed hypertensive disorders of pregnancy was associated with higher systolic blood pressure at the time of hypertensive disorders of pregnancy, an important clinical marker of hypertensive disorders of pregnancy severity. As analytical approaches of cell-free DNA interrogation advance, the prediction of placental-mediated disorders with first-trimester sampling is likely to improve, although this may remain challenging in gravidas with obesity, a cohort at high risk of developing hypertensive disorders of pregnancy.
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Affiliation(s)
- Raj Shree
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran).
| | - Teodora R Kolarova
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran)
| | - Hayley J MacKinnon
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran)
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, WA (Dr Lockwood)
| | - Suchitra Chandrasekaran
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA (Drs Shree, Kolarova, Mackinnon, and Chandrasekaran); Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Emory University, Atlanta, GA (Dr Chandrasekaran)
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21
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Cole BL, Starr K, Lockwood CM, Leary SES. The “SEED” Study: The Feasibility of Selecting Patient-Specific Biologically Targeted Therapy with Sorafenib, Everolimus, Erlotinib or Dasatinib for Pediatric and Young Adult Patients with Recurrent or Refractory Brain Tumors. Front Biosci (Landmark Ed) 2022; 27:219. [DOI: 10.31083/j.fbl2707219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 03/03/2022] [Indexed: 11/06/2022]
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22
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Pirozzi F, Berkseth M, Shear R, Gonzalez L, Timms AE, Sulc J, Pao E, Oyama N, Forzano F, Conti V, Guerrini R, Doherty ES, Saitta SC, Lockwood CM, Pritchard CC, Dobyns WB, Novotny E, Wright JNN, Saneto RP, Friedman S, Hauptman J, Ojemann J, Kapur RP, Mirzaa GM. Profiling PI3K-AKT-MTOR variants in focal brain malformations reveals new insights for diagnostic care. Brain 2022; 145:925-938. [PMID: 35355055 PMCID: PMC9630661 DOI: 10.1093/brain/awab376] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 07/20/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 12/28/2022] Open
Abstract
Focal malformations of cortical development including focal cortical dysplasia, hemimegalencephaly and megalencephaly, are a spectrum of neurodevelopmental disorders associated with brain overgrowth, cellular and architectural dysplasia, intractable epilepsy, autism and intellectual disability. Importantly, focal cortical dysplasia is the most common cause of focal intractable paediatric epilepsy. Gain and loss of function variants in the PI3K-AKT-MTOR pathway have been identified in this spectrum, with variable levels of mosaicism and tissue distribution. In this study, we performed deep molecular profiling of common PI3K-AKT-MTOR pathway variants in surgically resected tissues using droplet digital polymerase chain reaction (ddPCR), combined with analysis of key phenotype data. A total of 159 samples, including 124 brain tissue samples, were collected from 58 children with focal malformations of cortical development. We designed an ultra-sensitive and highly targeted molecular diagnostic panel using ddPCR for six mutational hotspots in three PI3K-AKT-MTOR pathway genes, namely PIK3CA (p.E542K, p.E545K, p.H1047R), AKT3 (p.E17K) and MTOR (p.S2215F, p.S2215Y). We quantified the level of mosaicism across all samples and correlated genotypes with key clinical, neuroimaging and histopathological data. Pathogenic variants were identified in 17 individuals, with an overall molecular solve rate of 29.31%. Variant allele fractions ranged from 0.14 to 22.67% across all mutation-positive samples. Our data show that pathogenic MTOR variants are mostly associated with focal cortical dysplasia, whereas pathogenic PIK3CA variants are more frequent in hemimegalencephaly. Further, the presence of one of these hotspot mutations correlated with earlier onset of epilepsy. However, levels of mosaicism did not correlate with the severity of the cortical malformation by neuroimaging or histopathology. Importantly, we could not identify these mutational hotspots in other types of surgically resected epileptic lesions (e.g. polymicrogyria or mesial temporal sclerosis) suggesting that PI3K-AKT-MTOR mutations are specifically causal in the focal cortical dysplasia-hemimegalencephaly spectrum. Finally, our data suggest that ultra-sensitive molecular profiling of the most common PI3K-AKT-MTOR mutations by targeted sequencing droplet digital polymerase chain reaction is an effective molecular approach for these disorders with a good diagnostic yield when paired with neuroimaging and histopathology.
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Affiliation(s)
- Filomena Pirozzi
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Matthew Berkseth
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rylee Shear
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Andrew E Timms
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Josef Sulc
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Emily Pao
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nora Oyama
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Francesca Forzano
- Department of Clinical Genetics, Guy's and St Thomas NHS Foundation Trust and King's College London, London, UK
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Italy
| | - Emily S Doherty
- Section of Clinical Genetics, Carilion Clinic Children's Hospital, Roanoke, VA, USA
| | - Sulagna C Saitta
- Division of Medical Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA
| | - William B Dobyns
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Edward Novotny
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Jason N N Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Russell P Saneto
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, Seattle, WA, USA
| | - Seth Friedman
- Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA, USA
| | - Jason Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Jeffrey Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Raj P Kapur
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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23
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Sidiropoulos N, Daley SK, Briggs M, Fernandes H, Lockwood CM, Mahmoud AZ, Merker JD, Vasalos P, Wielgos LM, Moncur JT, Farkas DH. Most Frequently Cited Accreditation Inspection Deficiencies for Clinical Molecular Oncology Testing Laboratories and Opportunities for Improvement. Arch Pathol Lab Med 2022; 146:1441-1449. [PMID: 35438717 DOI: 10.5858/arpa.2021-0448-cp] [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] [Accepted: 11/08/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The College of American Pathologists (CAP), a laboratory accreditation organization with deemed status under the Clinical Laboratories Improvement Amendments of 1988 administers accreditation checklists. Checklists are used by laboratories to ensure regulatory compliance. Peer-level laboratory professionals audit laboratory records during inspections to assess compliance. OBJECTIVE.— To identify the most frequently cited deficiencies for molecular oncology laboratories undergoing CAP accreditation inspections and describe laboratory improvement opportunities. DESIGN.— The CAP Molecular Oncology Committee (MOC), which is involved in maintaining the Molecular Pathology checklist, reviewed data and inspector comments associated with the most frequently observed citations related to molecular oncology testing from laboratories inspected by the CAP during a 2-year period (2018-2020). RESULTS.— Of 422 molecular oncology laboratories that underwent accreditation inspections, 159 (37.7%) were not cited for any molecular oncology-related deficiencies. For the All Common (COM) and Molecular Pathology checklists, there were 364 and 305 deficiencies, corresponding to compliance rates of 98.8% and 99.6%, respectively. The most frequently cited deficiencies are described. The COM checklist deficiencies were associated most often with the analytic testing phase; the MOL checklist deficiencies were more evenly distributed across the preanalytic, analytic, and postanalytic phases of testing. CONCLUSIONS.— Molecular oncology laboratories demonstrated excellent compliance with practices that support high-quality results for patients and the health care providers who use those test results in patient management. This review includes a critical assessment of opportunities for laboratories to improve compliance and molecular oncology testing quality.
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Affiliation(s)
- Nikoletta Sidiropoulos
- From the Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington (Sidiropoulos).,The Department of Pathology and Laboratory Medicine, The Robert Larner M.D. School of Medicine at the University of Vermont, Burlington (Sidiropoulos)
| | - Sarah K Daley
- The Department of Pathology, Stanford University School of Medicine, Palo Alto, California (Daley)
| | - Marian Briggs
- CAP Accreditation Programs (Briggs, Wielgos), College of American Pathologists, Northfield, Illinois
| | - Helen Fernandes
- The Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York (Fernandes)
| | - Christina M Lockwood
- The Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Lockwood)
| | - Amer Z Mahmoud
- Hematopathology and Molecular Genetic Pathology, TriCore Reference Laboratories, Albuquerque, New Mexico (Mahmoud)
| | - Jason D Merker
- The Departments of Pathology and Laboratory Medicine & Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill (Merker)
| | - Patricia Vasalos
- Proficiency Testing (Vasalos), College of American Pathologists, Northfield, Illinois
| | - Lynnette M Wielgos
- CAP Accreditation Programs (Briggs, Wielgos), College of American Pathologists, Northfield, Illinois
| | - Joel T Moncur
- Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
| | - Daniel H Farkas
- The Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Farkas)
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24
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Scherpelz KP, Crotty EE, Paulson VA, Lockwood CM, Leary SES, Ellenbogen RG, Lee A, Ermoian RP, Vitanza NA, Cole BL. Two cases of pineal anlage tumor with molecular analysis. Pediatr Blood Cancer 2022; 69:e29596. [PMID: 35129878 DOI: 10.1002/pbc.29596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/31/2021] [Accepted: 01/23/2022] [Indexed: 11/09/2022]
Abstract
Pineal anlage tumor is a rare pediatric tumor with clinical and histological features overlapping with pineoblastoma. Two patients with pineal anlage tumor, a 13-month-old female and an 11-month-old male, underwent subtotal resection, high-dose chemotherapy with autologous stem cell rescue, and radiation. Neither had tumor progression 50 months after diagnosis. The tumors underwent next-generation sequencing on a panel of 340 genes. Chromosomal copy gains and losses were present and differed between the tumors. No mutations or amplifications, including none specific to pineoblastoma, were identified.
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Affiliation(s)
- Kathryn P Scherpelz
- Division of Neuropathology, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Erin E Crotty
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Vera A Paulson
- Department of Laboratory Medicine and Pathology, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Sarah E S Leary
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA
| | - Amy Lee
- Department of Neurological Surgery, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA
| | - Ralph P Ermoian
- Department of Radiation Oncology, University of Washington and Seattle Children's Hospital, Seattle, Washington, USA
| | - Nicholas A Vitanza
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital and University of Washington, Seattle, Washington, USA.,The Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Bonnie L Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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25
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Jiang B, Murray C, Cole BL, Glover JNM, Chan GK, Deschenes J, Mani RS, Subedi S, Nerva JD, Wang AC, Lockwood CM, Mefford HC, Leary SES, Ojemann JG, Weinfeld M, Ene CI. Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor. Sci Rep 2022; 12:5386. [PMID: 35354845 PMCID: PMC8967877 DOI: 10.1038/s41598-022-09097-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Polynucleotide Kinase-Phosphatase (PNKP) is a bifunctional enzyme that possesses both DNA 3'-phosphatase and DNA 5'-kinase activities, which are required for processing termini of single- and double-strand breaks generated by reactive oxygen species (ROS), ionizing radiation and topoisomerase I poisons. Even though PNKP is central to DNA repair, there have been no reports linking PNKP mutations in a Microcephaly, Seizures, and Developmental Delay (MSCZ) patient to cancer. Here, we characterized the biochemical significance of 2 germ-line point mutations in the PNKP gene of a 3-year old male with MSCZ who presented with a high-grade brain tumor (glioblastoma multiforme) within the cerebellum. Functional and biochemical studies demonstrated these PNKP mutations significantly diminished DNA kinase/phosphatase activities, altered its cellular distribution, caused defective repair of DNA single/double stranded breaks, and were associated with a higher propensity for oncogenic transformation. Our findings indicate that specific PNKP mutations may contribute to tumor initiation within susceptible cells in the CNS by limiting DNA damage repair and increasing rates of spontaneous mutations resulting in pediatric glioma associated driver mutations such as ATRX and TP53.
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Affiliation(s)
- Bingcheng Jiang
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Cameron Murray
- Department of Biochemistry, University of Alberta, Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Bonnie L Cole
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Gordon K Chan
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Jean Deschenes
- Department of Laboratory Medicine and Pathology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Rajam S Mani
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Sudip Subedi
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - John D Nerva
- Department of Neurological Surgery, Tulane University, New Orleans, LA, USA
| | - Anthony C Wang
- Department of Neurological Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Heather C Mefford
- Division of Genetics Medicine, University of Washington, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Pediatric Hematology/Oncology, Seattle Children's Hospital, Seattle, WA, USA
| | - Jeffery G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada.
| | - Chibawanye I Ene
- Department of Neurological Surgery, MD Anderson Cancer Center, Houston, TX, USA.
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Venner E, Muzny D, Smith JD, Walker K, Neben CL, Lockwood CM, Empey PE, Metcalf GA, Kachulis C, Mian S, Musick A, Rehm HL, Harrison S, Gabriel S, Gibbs RA, Nickerson D, Zhou AY, Doheny K, Ozenberger B, Topper SE, Lennon NJ. Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program. Genome Med 2022; 14:34. [PMID: 35346344 PMCID: PMC8962531 DOI: 10.1186/s13073-022-01031-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 02/14/2022] [Indexed: 01/13/2023] Open
Abstract
Background The All of Us Research Program (AoURP, “the program”) is an initiative, sponsored by the National Institutes of Health (NIH), that aims to enroll one million people (or more) across the USA. Through repeated engagement of participants, a research resource is being created to enable a variety of future observational and interventional studies. The program has also committed to genomic data generation and returning important health-related information to participants. Methods Whole-genome sequencing (WGS), variant calling processes, data interpretation, and return-of-results procedures had to be created and receive an Investigational Device Exemption (IDE) from the United States Food and Drug Administration (FDA). The performance of the entire workflow was assessed through the largest known cross-center, WGS-based, validation activity that was refined iteratively through interactions with the FDA over many months. Results The accuracy and precision of the WGS process as a device for the return of certain health-related genomic results was determined to be sufficient, and an IDE was granted. Conclusions We present here both the process of navigating the IDE application process with the FDA and the results of the validation study as a guide to future projects which may need to follow a similar path. Changes to the program in the future will be covered in supplementary submissions to the IDE and will support additional variant classes, sample types, and any expansion to the reportable regions. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01031-z.
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Rudzinski ER, Hechtman J, Roy-Chowdhuri S, Rudolph M, Lockwood CM, Silvertown J, Wierzbinska J, Shen K, Norenberg R, Nogai H, Hong DS, Drilon A, Laetsch TW. Diagnostic testing approaches for the identification of patients with TRK fusion cancer prior to enrollment in clinical trials investigating larotrectinib. Cancer Genet 2022; 260-261:46-52. [PMID: 34929613 DOI: 10.1016/j.cancergen.2021.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 08/11/2021] [Revised: 10/13/2021] [Accepted: 11/28/2021] [Indexed: 01/10/2023]
Abstract
INTRODUCTION NTRK gene fusions are targetable oncogenic drivers independent of tumor type. Prevalence varies from highly recurrent in certain rare tumors to <1% in common cancers. The selective TRK inhibitor larotrectinib was shown to be highly active in adult and pediatric patients with tumors harboring NTRK gene fusions. METHODS We examined the techniques used by local sites to detect tumor NTRK gene fusions in patients enrolled in clinical trials of larotrectinib. We also report the characteristics of the detected fusions in different tumor types. RESULTS The analysis included 225 patients with 19 different tumor types. Testing methods used were next-generation sequencing (NGS) in 196 of 225 tumors (87%); this was RNA-based in 96 (43%); DNA-based in 53 (24%); DNA/RNA-based in 46 (20%) and unknown in 1 (<1%); FISH in 14 (6%) and PCR-based in 12 (5%). NanoString, Sanger sequencing and chromosome microarray were each utilized once (<1%). Fifty-four different fusion partners were identified, 39 (72%) of which were unique occurrences. CONCLUSIONS The most common local testing approach was RNA-based NGS. Many different NTRK gene fusions were identified with most occurring at low frequency. This supports the need for validated and appropriate testing methodologies that work agnostic of fusion partners.
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Affiliation(s)
| | | | | | | | - Christina M Lockwood
- Seattle Children's Hospital, Seattle, WA, USA; University of Washington, Seattle, WA, USA
| | | | | | - Kui Shen
- Bayer Healthcare Pharmaceuticals, Inc., Whippany, NJ, USA
| | | | - Hendrik Nogai
- Bayer HealthCare Pharmaceuticals, Inc., Basel, Switzerland
| | - David S Hong
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Theodore W Laetsch
- The Children's Hospital of Philadelphia/University of Pennsylvania, Philadelphia, PA, USA
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28
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Weil AA, Sohlberg SL, O’Hanlon JA, Casto AM, Emanuels AW, Lo NK, Greismer EP, Magedson AM, Wilcox NC, Kim AE, Back L, Frazar CD, Pelle B, Sibley TR, Ilcisin M, Lee J, Ryke EL, Craft JC, Schwabe-Fry KM, Fay KA, Cho S, Han PD, Heidl SJ, Pfau BA, Truong M, Zhong W, Srivatsan SR, Harb KF, Gottlieb GS, Hughes JP, Nickerson DA, Lockwood CM, Starita LM, Bedford T, Shendure JA, Chu HY. SARS-CoV-2 Epidemiology on a Public University Campus in Washington State. Open Forum Infect Dis 2021; 8:ofab464. [PMID: 34805425 PMCID: PMC8599730 DOI: 10.1093/ofid/ofab464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND We aimed to evaluate a testing program to facilitate control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission at a large university and measure spread in the university community using viral genome sequencing. METHODS Our prospective longitudinal study used remote contactless enrollment, daily mobile symptom and exposure tracking, and self-swab sample collection. Individuals were tested if the participant was exposed to a known SARS-CoV-2-infected person, developed new symptoms, or reported high-risk behavior (such as attending an indoor gathering without masking or social distancing), if a member of a group experiencing an outbreak, or at enrollment. Study participants included students, staff, and faculty at an urban public university during the Autumn quarter of 2020. RESULTS We enrolled 16 476 individuals, performed 29 783 SARS-CoV-2 tests, and detected 236 infections. Seventy-five percent of positive cases reported at least 1 of the following: symptoms (60.8%), exposure (34.7%), or high-risk behaviors (21.5%). Greek community affiliation was the strongest risk factor for testing positive, and molecular epidemiology results suggest that specific large gatherings were responsible for several outbreaks. CONCLUSIONS A testing program focused on individuals with symptoms and unvaccinated persons who participate in large campus gatherings may be effective as part of a comprehensive university-wide mitigation strategy to control the spread of SARS-CoV-2.
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Affiliation(s)
- Ana A Weil
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sarah L Sohlberg
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica A O’Hanlon
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anne W Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Natalie K Lo
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Emily P Greismer
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ariana M Magedson
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Naomi C Wilcox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ashley E Kim
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lewis Back
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Christian D Frazar
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ben Pelle
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Thomas R Sibley
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Misja Ilcisin
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Erica L Ryke
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - J Chris Craft
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | | | - Kairsten A Fay
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Shari Cho
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Peter D Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sarah J Heidl
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Brian A Pfau
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Melissa Truong
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Weizhi Zhong
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Katia F Harb
- Department of Environmental Health and Safety, University of Washington, Seattle, Washington, USA
| | - Geoffrey S Gottlieb
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Environmental Health and Safety, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Jay A Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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Wang S, Sun MZ, Abecassis IJ, Weil AG, Ibrahim GM, Fallah A, Ene C, Leary SES, Cole BL, Lockwood CM, Olson JM, Geyer JR, Ellenbogen RG, Ojemann JG, Wang AC. Predictors of mortality and tumor recurrence in desmoplastic infantile ganglioglioma and astrocytoma-and individual participant data meta-analysis (IPDMA). J Neurooncol 2021; 155:155-163. [PMID: 34613581 DOI: 10.1007/s11060-021-03860-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/02/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE Desmoplastic infantile astrocytoma (DIA) and desmoplastic infantile ganglioglioma (DIG) are classified together as grade I neuronal and mixed neuronal-glial tumor of the central nervous system by the World Health Organization (WHO). These tumors are rare and have not been well characterized in terms of clinical outcomes. We aimed to identify clinical predictors of mortality and tumor recurrence/progression by performing an individual patient data meta-analysis (IPDMA) of the literature. METHODS A systematic literature review from 1970 to 2020 was performed, and individualized clinical data for patients diagnosed with DIA/DIG were extracted. Aggregated data were excluded from collection. Outcome measures of interest were mortality and tumor recurrence/progression, as well as time-to-event (TTE) for each of these. Participants without information on these outcome measures were excluded. Cox regression survival analyses were performed to determine predictors of mortality and tumor recurrence / progression. RESULTS We identified 98 articles and extracted individual patient data from 188 patients. The cohort consisted of 58.9% males with a median age of 7 months. The majority (68.1%) were DIGs, while 24.5% were DIAs and 7.5% were non-specific desmoplastic infantile tumors; DIAs presented more commonly in deep locations (p = 0.001), with leptomeningeal metastasis (p = 0.001), and was associated with decreased probability of gross total resection (GTR; p = 0.001). Gender, age, and tumor pathology were not statistically significant predictors of either mortality or tumor recurrence/progression. On multivariate survival analysis, GTR was a predictor of survival (HR = 0.058; p = 0.007) while leptomeningeal metastasis at presentation was a predictor of mortality (HR = 3.27; p = 0.025). Deep tumor location (HR = 2.93; p = 0.001) and chemotherapy administration (HR = 2.02; p = 0.017) were associated with tumor recurrence/progression. CONCLUSION Our IPDMA of DIA/DIG cases reported in the literature revealed that GTR was a predictor of survival while leptomeningeal metastasis at presentation was associated with mortality. Deep tumor location and chemotherapy were associated with tumor recurrence / progression.
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Affiliation(s)
- Shelly Wang
- Division of Neurosurgery, Brain Institute, Nicklaus Children's Hospital, Miami, FL, USA.,Department of Neurosurgery, University of Miami, Miami, FL, USA
| | - Matthew Z Sun
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - I Joshua Abecassis
- Department of Neurosurgery, University of Louisville, Louisville, KY, USA
| | - Alexander G Weil
- Department of Surgery, Université de Montréal, Montreal, QC, Canada
| | - George M Ibrahim
- Division of Pediatric Neurosurgery, Sick Kids Toronto, University of Toronto, Toronto, ON, Canada
| | - Aria Fallah
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Chibawanye Ene
- Department of Neurological Surgery, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Hematology Oncology, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Bonnie L Cole
- Department of Anatomic Pathology, Seattle Children's Hospital, University of Washington and Laboratories, Seattle, WA, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - James M Olson
- Division of Hematology Oncology, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - J Russell Geyer
- Division of Hematology Oncology, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Anthony C Wang
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA.
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30
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Chung E, Chow EJ, Wilcox NC, Burstein R, Brandstetter E, Han PD, Fay K, Pfau B, Adler A, Lacombe K, Lockwood CM, Uyeki TM, Shendure J, Duchin JS, Rieder MJ, Nickerson DA, Boeckh M, Famulare M, Hughes JP, Starita LM, Bedford T, Englund JA, Chu HY. Comparison of Symptoms and RNA Levels in Children and Adults With SARS-CoV-2 Infection in the Community Setting. JAMA Pediatr 2021; 175:e212025. [PMID: 34115094 PMCID: PMC8491103 DOI: 10.1001/jamapediatrics.2021.2025] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023]
Abstract
Importance The association between COVID-19 symptoms and SARS-CoV-2 viral levels in children living in the community is not well understood. Objective To characterize symptoms of pediatric COVID-19 in the community and analyze the association between symptoms and SARS-CoV-2 RNA levels, as approximated by cycle threshold (Ct) values, in children and adults. Design, Setting, and Participants This cross-sectional study used a respiratory virus surveillance platform in persons of all ages to detect community COVID-19 cases from March 23 to November 9, 2020. A population-based convenience sample of children younger than 18 years and adults in King County, Washington, who enrolled online for home self-collection of upper respiratory samples for SARS-CoV-2 testing were included. Exposures Detection of SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) from participant-collected samples. Main Outcomes and Measures RT-PCR-confirmed SARS-CoV-2 infection, with Ct values stratified by age and symptoms. Results Among 555 SARS-CoV-2-positive participants (mean [SD] age, 33.7 [20.1] years; 320 were female [57.7%]), 47 of 123 children (38.2%) were asymptomatic compared with 31 of 432 adults (7.2%). When symptomatic, fewer symptoms were reported in children compared with adults (mean [SD], 1.6 [2.0] vs 4.5 [3.1]). Symptomatic individuals had lower Ct values (which corresponded to higher viral RNA levels) than asymptomatic individuals (adjusted estimate for children, -3.0; 95% CI, -5.5 to -0.6; P = .02; adjusted estimate for adults, -2.9; 95% CI, -5.2 to -0.6; P = .01). The difference in mean Ct values was neither statistically significant between symptomatic children and symptomatic adults (adjusted estimate, -0.7; 95% CI, -2.2 to 0.9; P = .41) nor between asymptomatic children and asymptomatic adults (adjusted estimate, -0.6; 95% CI, -4.0 to 2.8; P = .74). Conclusions and Relevance In this community-based cross-sectional study, SARS-CoV-2 RNA levels, as determined by Ct values, were significantly higher in symptomatic individuals than in asymptomatic individuals and no significant age-related differences were found. Further research is needed to understand the role of SARS-CoV-2 RNA levels and viral transmission.
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Affiliation(s)
- Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Eric J. Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Naomi C. Wilcox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Roy Burstein
- Institute for Disease Modeling, Seattle, Washington
| | - Elisabeth Brandstetter
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle, Washington
| | | | - Christina M. Lockwood
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Timothy M. Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Howard Hughes Medical Institute, Seattle, Washington
| | - Jeffrey S. Duchin
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Public Health—Seattle & King County, Seattle, Washington
| | - Mark J. Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Deborah A. Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
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Kolarova TR, Gammill HS, Nelson JL, Lockwood CM, Shree R. At Preeclampsia Diagnosis, Total Cell-Free DNA Concentration is Elevated and Correlates With Disease Severity. J Am Heart Assoc 2021; 10:e021477. [PMID: 34310191 PMCID: PMC8475684 DOI: 10.1161/jaha.121.021477] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Placental derived cell‐free DNA (cfDNA), widely utilized for prenatal screening, may serve as a biomarker for preeclampsia. To determine whether cfDNA parameters are altered in preeclampsia, we conducted a case‐control study using prospectively collected maternal plasma (n=20 preeclampsia, n=22 normal) using our in‐house validated prenatal screening assay. Methods and Results Isolated cfDNA was quantified, sequenced using Illumina NextSeq 500, and the placental‐derived fraction was determined. Clinical and test characteristics were compared between preeclampsia and controls, followed by comparisons within the preeclampsia cohort dichotomized by cfDNA concentration. Lastly, cfDNA parameters in preeclampsia were correlated with markers of disease severity. Maternal age, body mass index, gestational age at delivery, cesarean rate, and neonatal birthweight were expectedly different between groups (P≤0.05). The placental‐derived cfDNA fraction did not differ between groups (21.4% versus 16.9%, P=0.06); however, total cfDNA was more than 10 times higher in preeclampsia (1235 versus 106.5 pg/µL, P<0.001). This relationship persisted when controlling for important confounders (OR 1.22, 95% CI 1.04–1.43, P=0.01). The dichotomized preeclampsia group with the highest cfDNA concentration delivered earlier (33.2 versus 36.6 weeks, P=0.02) and had lower placental‐derived fractions (9.1% versus 21.4%, P=0.04). Among preeclampsia cases, higher total cfDNA correlated with earlier gestational age at delivery (P=0.01) and higher maximum systolic blood pressure (P=0.04). Conclusions At diagnosis, total cfDNA is notably higher in preeclampsia, whereas the placental derived fraction remains similar to healthy pregnancies. In preeclampsia, higher total cfDNA correlates with earlier gestational age at delivery and higher systolic blood pressure. These findings may indicate increased release of cfDNA from maternal tissue injury.
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Affiliation(s)
- Teodora R Kolarova
- Division of Maternal Fetal Medicine Department of Obstetrics and Gynecology University of Washington Seattle WA
| | - Hilary S Gammill
- Division of Maternal Fetal Medicine Department of Obstetrics and Gynecology University of Washington Seattle WA
| | - J Lee Nelson
- Clinical Research Division Fred Hutchinson Cancer Research Center Seattle WA.,Division of Rheumatology Department of Medicine University of Washington Seattle WA
| | | | - Raj Shree
- Division of Maternal Fetal Medicine Department of Obstetrics and Gynecology University of Washington Seattle WA
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Shree R, Kolarova TR, MacKinnon HJ, Hedge JM, Vinopal E, Ma KK, Lockwood CM, Chandrasekaran S. Low fetal fraction in obese women at first trimester cell-free DNA based prenatal screening is not accompanied by differences in total cell-free DNA. Prenat Diagn 2021; 41:1277-1286. [PMID: 34297415 DOI: 10.1002/pd.6023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/26/2021] [Accepted: 07/10/2021] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Reasons for first trimester noninvasive prenatal screening (NIPS) test failure in obese women remain elusive. As dilution from maternal sources may be explanatory, we determined the relationship between obesity, fetal fraction (FF), and total cell-free DNA (cfDNA) using our NIPS platform. METHODS We assessed differences in first trimester (≤14 weeks) FF, indeterminate rate, and total cfDNA between obese (n = 518) and normal-weight women (n = 237) after exclusion of confounders (anticoagulation, autoimmunity, aneuploidy) and controlling for covariates. RESULTS Fetal fraction was lower, and the indeterminate rate higher, in obese compared to controls (9.2% ± 4.4 vs. 12.5% ± 4.5, p < 0.001 and 8.4 vs. 1.7%, p < 0.001, respectively), but total cfDNA was not different (92.0 vs. 82.1 pg/µl, p = 0.10). For each week, the FF remained lower in obese women (all p < 0.01) but did not increase across the first trimester for either group. Obesity increased the likelihood of indeterminate result (OR 6.1, 95% CI 2.5, 14.8; p < 0.001) and maternal body mass index correlated with FF (β -0.27, 95% CI -0.3, -0.22; p < 0.001), but not with total cfDNA (β 0.49, 95% CI -0.55, 1.53; p = 0.3). CONCLUSIONS First trimester obese women have persistently low FF and higher indeterminate rates, without differences in total cfDNA, suggesting placental-specific mechanisms versus dilution from maternal sources as a potential etiology.
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Affiliation(s)
- Raj Shree
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Teodora R Kolarova
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Hayley J MacKinnon
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Jaclynne M Hedge
- School of Medicine, University of Washington, Seattle, Washington, USA
| | - Elena Vinopal
- School of Medicine, University of Washington, Seattle, Washington, USA
| | - Kimberly K Ma
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Suchitra Chandrasekaran
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
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Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J, Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. SwabExpress: An end-to-end protocol for extraction-free covid-19 testing. Clin Chem 2021; 68:143-152. [PMID: 34286830 DOI: 10.1093/clinchem/hvab132] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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Affiliation(s)
- Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sarah Heidl
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | | | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Jordan Opsahl
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Luis Gamboa
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Nahum Smith
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Shari Cho
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Kaitlyn A Barrow
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jeremy Stone
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Denise J McCulloch
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Ashley E Kim
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | | | - Sarah L Sohlberg
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rachel E Geyer
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sriram Kosuri
- Octant, Inc. Emeryville CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Trevor Bedford
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Helen Y Chu
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Eric Q Konnick
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute. Seattle, WA, USA
| | - Christina M Lockwood
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
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Greene DN, Matthys T, Lockwood CM. Swab-Free Transport as an Optimized Preanalytical Workflow for SARS-CoV-2 Amplification. J Appl Lab Med 2021; 6:606-613. [PMID: 33119112 PMCID: PMC7665556 DOI: 10.1093/jalm/jfaa197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022]
Abstract
Introduction Efficient detection of SARS-CoV-2 will continue to be an invaluable tool for pandemic control. Current instructions specify that the collection swab should be transported within its collection media to the laboratory. Developing a process whereby this swab is removed before transport to the lab would allow for improved automation and decreased manual manipulation of samples. Methods A proof of principle approach was taken by eluting viral particles from flocked swabs into collection buffer with and without a mucus background. Paired swab-free and swab-containing samples were transported to the laboratory and evaluated for SARS-CoV-2 (n = 28) or RNaseP (n = 6). SARS-CoV-2 amplification was performed using the Hologic Panther Fusion Aptima and RT-PCR assays. Results SARS-CoV-2 was detected in all proof of principle samples with Ct values indicative of dilution. The rare exception was for a few samples where the dilution pushed the viral load below the LOD. Paired samples were 100% concordant for SARS-CoV-2 and RNaseP detection. Conclusion Discarding the swab after inoculating the transport buffer is an appropriate pre-analytical modification. Adopting this approach can save up to 1 minute/sample. For labs processing more than 500 samples/day this equates to one full time equivalent shift/day.
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Affiliation(s)
- Dina N Greene
- Kaiser Permanente Washington, Regional Laboratory, Renton, WA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Tawna Matthys
- Kaiser Permanente Washington, Regional Laboratory, Renton, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA.,Brotman Baty Institute for Precision Medicine, Seattle, WA
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35
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Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J, Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing. bioRxiv 2021:2020.04.22.056283. [PMID: 32511368 PMCID: PMC7263496 DOI: 10.1101/2020.04.22.056283] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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Affiliation(s)
- Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Sarah Heidl
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Peter D. Han
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | | | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Jordan Opsahl
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Luis Gamboa
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Nahum Smith
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Shari Cho
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Kaitlyn A. Barrow
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Jeremy Stone
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Caitlin R. Wolf
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Denise J. McCulloch
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Ashley E. Kim
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | | | - Sarah L. Sohlberg
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rachel E. Geyer
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | | | - Sriram Kosuri
- Octant, Inc. Emeryville CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles CA, USA
| | - Trevor Bedford
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark J. Rieder
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Helen Y. Chu
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Eric Q. Konnick
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Laboratory Medicine and Pathology, Seattle WA, USA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Howard Hughes Medical Institute. Seattle WA, USA
| | - Christina M. Lockwood
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Laboratory Medicine and Pathology, Seattle WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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36
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Winston-McPherson GN, Mathias PC, Lockwood CM, Greene DN. Evaluation of Patient Demographics in Clinical Cancer Genomic Testing. J Appl Lab Med 2021; 6:119-124. [PMID: 33398333 DOI: 10.1093/jalm/jfaa219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/02/2020] [Accepted: 10/20/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Inequitable use of next-generation sequencing (NGS) testing for cancer risk and treatment can contribute to heath disparity. Consequently, it is important to assess the population receiving this testing. In this article, we characterize the population receiving both germline and somatic NGS testing for cancer predisposition and precision oncology at the Genetics and Solid Tumors Laboratory of the University of Washington Medical Center. METHODS The general demographics, including ancestry, of patients receiving somatic testing to identify genes related to cancer treatment or prognosis, diagnosis, or germline testing for heritable cancer risk from January 2015 to July 2017 were characterized. Ancestry was determined using single nucleotide variant data and documented pedigree. The demographics of the patient population receiving testing were compared with a reference population comprising patients receiving care from the University of Washington Medical Center with a diagnosis of malignant neoplasm of breast, ovary, colon, rectum, or prostate between January 2015 and May 2018. RESULTS A total of 2210 unique patients were included in this study. Women composed 66% of our total tested population. Patients of European ancestry composed 78% of the tested cohort. The percentages of American Indian/Alaskan Native and Native Hawaiian/Other Pacific Islander in the cohort receiving NGS testing were significantly different than their respective distributions in the reference cohort. CONCLUSIONS Characterizing the demographics of patients receiving NGS testing for cancer predisposition and precision oncology using single nucleotide variant data and documented pedigree may help identify potential health disparities.
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Affiliation(s)
| | - Patrick C Mathias
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Dina N Greene
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
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Truong M, Pfau B, McDermot E, Han PD, Brandstetter E, Richardson M, Kim AE, Rieder MJ, Chu HY, Englund JA, Nickerson DA, Shendure J, Lockwood CM, Konnick EQ, Starita LM. Comparable specimen collection from both ends of at-home mid-turbinate swabs. medRxiv 2020:2020.12.05.20244632. [PMID: 33330895 PMCID: PMC7743106 DOI: 10.1101/2020.12.05.20244632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Unsupervised upper respiratory specimen collection is a key factor in the ability to massively scale SARS-CoV-2 testing. But there is concern that unsupervised specimen collection may produce inferior samples. Across two studies that included unsupervised at-home mid-turbinate specimen collection, ~1% of participants used the wrong end of the swab. We found that molecular detection of respiratory pathogens and a human biomarker were comparable between specimens collected from the handle of the swab and those collected correctly. Older participants were more likely to use the swab backwards. Our results suggest that errors made during home-collection of nasal specimens do not preclude molecular detection of pathogens and specialized swabs may be an unnecessary luxury during a pandemic.
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Affiliation(s)
- Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Peter D Han
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | | | | | | | - Mark J Rieder
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
| | - Helen Y Chu
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
| | - Janet A Englund
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Seattle Children's Research Institute
| | - Deborah A Nickerson
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
| | - Jay Shendure
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
- Howard Hughes Medical Institute. Seattle WA, USA
| | - Christina M Lockwood
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
| | - Eric Q Konnick
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
| | - Lea M Starita
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- University of Washington, Seattle WA, USA
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Haspel RL, Genzen JR, Wagner J, Lockwood CM, Fong K, Adesina AM, Browning L, Chabot-Richards D, Cushman-Vokoun AM, D’Angelo AR, DeFrances MC, Devarakonda S, Fernandes H, Fernandez P, Gupta R, Hurwitz ME, Lindeman NI, Nobori A, Nohr E, Payton J, Saylor B, Sobel ME, Stringer KF, Vanderbilt CM, Young M, Adesina AM, Browning L, Chabot-Richards D, Cushman-Vokoun AM, D’Angelo AR, DeFrances MC, Devarakonda S, Fernandes H, Fernandez P, Gupta R, Hurwitz ME, Lindeman NI, Nobori A, Nohr E, Payton J, Saylor B, Sobel ME, Stringer KF, Vanderbilt CM, Young M. Integration of Genomic Medicine in Pathology Resident Training. Am J Clin Pathol 2020; 154:784-791. [PMID: 32696061 DOI: 10.1093/ajcp/aqaa094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To assess current pathology resident training in genomic and molecular pathology. METHODS The Training Residents in Genomics (TRIG) Working Group has developed survey questions for the pathology Resident In-Service Examination (RISE) since 2012. Responses to these questions, as well as knowledge questions, were analyzed. RESULTS A total of 2,529 residents took the 2019 RISE. Since 2013, there has been an increase in postgraduate year 4 (PGY4) respondents indicating training in genomic medicine (58% to approximately 80%) but still less than almost 100% each year for molecular pathology. In 2019, PGY4 residents indicated less perceived knowledge and ability related to both genomic and traditional molecular pathology topics compared with control areas. Knowledge question results supported this subjective self-appraisal. CONCLUSIONS The RISE is a powerful tool for assessing the current state and also trends related to resident training in genomic pathology. The results show progress but also the need for improvement in not only genomic pathology but traditional molecular pathology training as well.
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Affiliation(s)
- Richard L Haspel
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | | | - Jay Wagner
- American Society for Clinical Pathology (ASCP), Chicago, IL
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle
| | - Karen Fong
- American Society for Clinical Pathology (ASCP), Chicago, IL
| | - Adekunle M Adesina
- Department of Pathology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Devon Chabot-Richards
- Department of Pathology, TriCore Reference Laboratories and the University of New Mexico, Albuquerque
| | | | - Alix R D’Angelo
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans
| | - Marie C DeFrances
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
| | - Pedro Fernandez
- Department of Anatomical Pathology, Hospital Germans Trias I Pujol, Badalona, Spain
| | - Ruta Gupta
- NSW Health Pathology, Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Neal I Lindeman
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Alexander Nobori
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, Los Angeles, CA
| | - Erik Nohr
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, Calgary, Canada
| | - Jaqueline Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Benjamin Saylor
- Department of Pathology, University of Alabama at Birmingham
| | - Mark E Sobel
- American Society for Investigative Pathology, Bethesda, MD
| | - Keith F Stringer
- Department of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin Young
- Cytopathology Department, Royal Free Hospital, London, UK
| | - Adekunle M Adesina
- Department of Pathology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Devon Chabot-Richards
- Department of Pathology, TriCore Reference Laboratories and the University of New Mexico, Albuquerque
| | | | - Alix R D’Angelo
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans
| | - Marie C DeFrances
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
| | - Pedro Fernandez
- Department of Anatomical Pathology, Hospital Germans Trias I Pujol, Badalona, Spain
| | - Ruta Gupta
- NSW Health Pathology, Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Neal I Lindeman
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Alexander Nobori
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, Los Angeles, CA
| | - Erik Nohr
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, Calgary, Canada
| | - Jaqueline Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Benjamin Saylor
- Department of Pathology, University of Alabama at Birmingham
| | - Mark E Sobel
- American Society for Investigative Pathology, Bethesda, MD
| | - Keith F Stringer
- Department of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin Young
- Cytopathology Department, Royal Free Hospital, London, UK
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Sarthy JF, Meers MP, Janssens DH, Henikoff JG, Feldman H, Paddison PJ, Lockwood CM, Vitanza NA, Olson JM, Ahmad K, Henikoff S. Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones. eLife 2020; 9:61090. [PMID: 32902381 PMCID: PMC7518889 DOI: 10.7554/elife.61090] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022] Open
Abstract
Lysine 27-to-methionine (K27M) mutations in the H3.1 or H3.3 histone genes are characteristic of pediatric diffuse midline gliomas (DMGs). These oncohistone mutations dominantly inhibit histone H3K27 trimethylation and silencing, but it is unknown how oncohistone type affects gliomagenesis. We show that the genomic distributions of H3.1 and H3.3 oncohistones in human patient-derived DMG cells are consistent with the DNAreplication-coupled deposition of histone H3.1 and the predominant replication-independent deposition of histone H3.3. Although H3K27 trimethylation is reduced for both oncohistone types, H3.3K27M-bearing cells retain some domains, and only H3.1K27M-bearing cells lack H3K27 trimethylation. Neither oncohistone interferes with PRC2 binding. Using Drosophila as a model, we demonstrate that inhibition of H3K27 trimethylation occurs only when H3K27M oncohistones are deposited into chromatin and only when expressed in cycling cells. We propose that oncohistones inhibit the H3K27 methyltransferase as chromatin patterns are being duplicated in proliferating cells, predisposing them to tumorigenesis.
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Affiliation(s)
- Jay F Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Cancer and Blood Disorders, Seattle, United States
| | - Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jorja G Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Heather Feldman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, United States
| | - Nicholas A Vitanza
- Cancer and Blood Disorders, Seattle, United States.,Clinical Research Division Fred Hutchinson Cancer Research Center, Seattle, United States
| | - James M Olson
- Cancer and Blood Disorders, Seattle, United States.,Clinical Research Division Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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Vitanza NA, Khalatbari H, Ermoian R, Sarthy J, Lockwood CM, Cole BL, Leary SES. Molecularly Targeted Treatments for NF1-Mutant Diffuse Intrinsic Pontine Glioma. J Appl Lab Med 2020; 6:550-553. [PMID: 32862234 DOI: 10.1093/jalm/jfaa086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Nicholas A Vitanza
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Hedieh Khalatbari
- Department of Radiology, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA
| | - Ralph Ermoian
- Department of Radiation Oncology, University of Washington, Seattle, WA
| | - Jay Sarthy
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA
| | - Bonnie L Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA.,Department of Anatomic Pathology, University of Washington School of Medicine, Seattle, WA
| | - Sarah E S Leary
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
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Chu HY, Englund JA, Starita LM, Famulare M, Brandstetter E, Nickerson DA, Rieder MJ, Adler A, Lacombe K, Kim AE, Graham C, Logue J, Wolf CR, Heimonen J, McCulloch DJ, Han PD, Sibley TR, Lee J, Ilcisin M, Fay K, Burstein R, Martin B, Lockwood CM, Thompson M, Lutz B, Jackson M, Hughes JP, Boeckh M, Shendure J, Bedford T. Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform. N Engl J Med 2020; 383:185-187. [PMID: 32356944 PMCID: PMC7206929 DOI: 10.1056/nejmc2008646] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | | | | | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | | | | | - Chelsey Graham
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | | | | | | | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | | | - Michael Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | | | | | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA
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Lockwood CM. Commentary on Sequence Now, Later, or Never? Clin Chem 2020; 66:886. [DOI: 10.1093/clinchem/hvaa055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 11/14/2022]
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Lockwood CM, Souers RJ, Vasalos P, Kalicanin T, Devereaux K, Graham RP, Hameed M, Routbort M, Tsai JM, Merker JD, Lindeman NI, Moncur JT. Performance of cell-free tumor DNA testing for 101 clinical laboratories on College of American Pathologists proficiency tests. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e13681] [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] [Indexed: 11/20/2022] Open
Abstract
e13681 Background: Cell-free tumor DNA or circulating tumor DNA tests are increasingly used in clinical care to detect somatic mutations from solid tumors. However, data on laboratory performance characteristics using standardized samples is limited. Methods: Well-characterized reference materials were used for the College of American Pathologists (CAP) cell-free tumor DNA proficiency testing surveys, which consisted of stabilized DNA fragmented to simulate cell-free DNA in a synthetic plasma matrix. For the 2018A, 2018B, 2019A and 2019B surveys, laboratories tested for hotspot mutations (single and dinucleotide sequence changes) in EGFR, BRAF, KRAS, NRAS, and IDH1 at variant allele fractions ranging from 0.1% - 1.0%. As per CAP proficiency testing standards, results were scored according to the known mutation(s) engineered at designated variant allele fractions in each PT sample. Nine laboratories were excluded from analysis because they provided incomplete results. Statistical significance was calculated using a multivariate logistic regression model. Results: In 2018 and 2019, 101 laboratories submitted survey results for at least one proficiency testing mailing. There were 5088 total proficiency testing responses for EGFR, BRAF, KRAS, NRAS, and IDH1 mutations across 12 different samples. For the 3585 responses submitted for BRAF, KRAS, NRAS, and IDH1, sensitivity ranged from 94.6 – 100%, while specificity exceeded 99%. There were no significant differences in performance between analytical methodologies for BRAF, KRAS, NRAS, and IDH1 mutations. Performance characteristics for EGFR mutations among the 1503 responses showed a combined sensitivity of 87.1% and specificity of 98.7%. For laboratories detecting mutations in EGFR, next-generation sequencing methods exhibited a sensitivity (true positivity) of 95.7% while the sensitivity of non-NGS methods was lower at 81.7% ( P= 0.02). Conclusions: These findings demonstrate high sensitivity and specificity for clinical laboratories performing cell-free tumor DNA tests. For EGFR mutations, NGS outperformed non-NGS methods. These data suggest excellent overall agreement among laboratories performing clinical cell-free tumor DNA tests. Further investigation across variant allele fractions and additional variant types is warranted.
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Affiliation(s)
| | | | | | | | | | | | - M Hameed
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Routbort
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jason Derek Merker
- The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
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Lei L, Stohr BA, Berry S, Lockwood CM, Davis JL, Rudzinski ER, Kunder CA. Recurrent EGFR alterations in NTRK3 fusion negative congenital mesoblastic nephroma. Pract Lab Med 2020; 21:e00164. [PMID: 32490123 PMCID: PMC7260589 DOI: 10.1016/j.plabm.2020.e00164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 03/31/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Objectives To identify oncogenic driver mutations in congenital mesoblastic nephroma (CMN) cases lacking ETV6-NTRK3 fusion and discuss their diagnostic value. Design The institutional pathology database was queried for cases with a morphologic diagnosis of CMN. Cases positive for ETV6 rearrangement or with unavailable blocks were excluded. Four cases met the inclusion criteria and were sequenced by next-generation sequencing. Three additional cases were contributed by our collaborators. Results Three of four internal cases harbor an EGFR kinase domain duplication (KDD), which is known to be oncogenic yet exceedingly rare in other histologies. All three outside cases are positive for EGFR alterations, including KDD in two and a splicing site mutation in one. The splicing site mutation is predicted to be EGFR activating. One of the outside cases was a retroperitoneal mass without a clear site of origin. A diagnosis of CMN is suggested based on exclusion of differential diagnoses by expert consultation and detection of EGFR KDD. Conclusions EGFR activation, predominantly via EGFR KDD, is a common recurrent genetic alteration in CMN lacking NTRK3 fusions. CMN can be molecularly classified into NTRK3 fusion type, EGFR activation type and others.
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Affiliation(s)
- Li Lei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Stacey Berry
- Department of Pathology, Cook Children's Medical Center, Fort Worth, TX, USA
| | | | - Jessica L Davis
- Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Erin R Rudzinski
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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45
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Kuo AJ, Paulson VA, Hempelmann JA, Beightol M, Todhunter S, Colbert BG, Salipante SJ, Konnick EQ, Pritchard CC, Lockwood CM. Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations. Pract Lab Med 2020; 19:e00153. [PMID: 32123717 PMCID: PMC7038441 DOI: 10.1016/j.plabm.2020.e00153] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/24/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES The rapid discovery of clinically significant genetic variants has translated to next-generation sequencing assays becoming out-of-date by the time they are designed, validated, and implemented. UW-OncoPlex addresses this through the adoption of a modular panel capable of redesign as significant alterations are identified. We describe the validation of OncoPlex version 6 (OPXv6) for the detection of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs), structural variants (SVs), microsatellite instability (MSI), and tumor mutational burden (TMB) in a panel of 340 genes. DESIGN One hundred twelve samples with diverse diagnoses were comprised of formalin-fixed-paraffin-embedded tissue, fresh-frozen tissue, plasma, peripheral blood, bone marrow, saliva, and cell-line DNA. Libraries were prepared from genomic and cell-free DNA, hybridized to a custom panel of xGen Lockdown probes, and sequenced on Illumina platforms. Sequences were processed through a custom bioinformatics pipeline, and variant calls were compared to prior orthogonal clinical results. RESULTS Accuracy was 99% for SNVs ≥5% allele frequency, 98% for indels, 97% for SVs, 99% for CNVs, 100% for MSI, and 100% for TMB (compared to previous OncoPlex versions). Library preparation turnaround time decreased by 40%, and sequencing quality improved with a 2.5-fold increase in average sequencing coverage and 4-fold increase in percent on-target. CONCLUSIONS OPXv6 demonstrates improvements over prior UW-OncoPlex versions including reduced capture cost, improved sequencing quality, and decreased time to results. The modular capture probe design also provides a nimble laboratory response in addressing the expansions necessary to meet the needs of the continuously evolving field of molecular oncology.
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McEwen AE, Leary SES, Lockwood CM. Beyond the Blood: CSF-Derived cfDNA for Diagnosis and Characterization of CNS Tumors. Front Cell Dev Biol 2020; 8:45. [PMID: 32133357 PMCID: PMC7039816 DOI: 10.3389/fcell.2020.00045] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic data are rapidly becoming part of tumor classification and are integral to prognosis and predicting response to therapy. Current molecular tumor profiling relies heavily on tissue resection or biopsy. Tissue profiling has several disadvantages in tumors of the central nervous system, including the challenge associated with invasive biopsy, the heterogeneous nature of many malignancies where a small biopsy can underrepresent the mutational profile, and the frequent lack of obtaining a repeat biopsy, which limits routine monitoring to assess therapy response and/or tumor evolution. Circulating tumor, cell-free DNA (cfDNA), has been proposed as a liquid biopsy to address some limitations of tissue-based genetics. In cancer patients, a portion of cfDNA is tumor-derived and may contain somatic genetic alterations. In central nervous system (CNS) neoplasia, plasma tumor-derived cfDNA is very low or absent, likely due to the blood brain barrier. Interrogating cfDNA in cerebrospinal fluid (CSF) has several advantages. Compared to blood, CSF is paucicellular and therefore predominantly lacks non-tumor cfDNA; however, patients with CNS-limited tumors have significantly enriched tumor-derived cfDNA in CSF. In patients with metastatic CNS disease, mutations in CSF cfDNA are most concordant with the intracranial process. CSF cfDNA can also occasionally uncover additional genetic alterations absent in concurrent biopsy specimens, reflecting tumor heterogeneity. Although CSF is enriched for tumor-derived cfDNA, absolute quantities are low. Highly sensitive, targeted methods including next-generation sequencing and digital PCR are required to detect mutations in CSF cfDNA. Additional technical and bioinformatic approaches also facilitate enhanced ability to detect tumor mutations in CSF cfDNA.
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Affiliation(s)
- Abbye E McEwen
- Department of Pathology, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Sarah E S Leary
- Brotman Baty Institute for Precision Medicine, Seattle, WA, United States.,Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States.,Brotman Baty Institute for Precision Medicine, Seattle, WA, United States
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47
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Cheeney G, Pac LJ, Gopal P, Landis CS, Konnick EQ, Swanson PE, Greene DN, Lockwood CM, Westerhoff M. Increased Frequency of Heterozygous Alpha-1-Antitrypsin Deficiency in Liver Explants From Nonalcoholic Steatohepatitis Patients. Liver Transpl 2020; 26:17-24. [PMID: 31597010 DOI: 10.1002/lt.25652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023]
Abstract
Cirrhotic explanted livers occasionally have unexpected periodic acid-Schiff-diastase (PASD)-positive globules within the hepatocyte cytoplasm. It is often unclear whether this finding is a nonspecific consequence of cirrhosis or is indicative of an underlying alpha-1-antitrypsin deficiency (A1ATD) contributing to the cirrhosis. In this study, explanted livers were retrospectively evaluated for histopathology (including PASD status with confirmatory alpha-1-antitrypsin [A1AT] immunohistochemistry [IHC]), and chart review provided etiology of liver failure and general clinical parameters. Real-time polymerase chain reaction was used to detect A1AT genotype (SERPINA1 S and Z alleles) by melting curve analysis on liver explant tissue from selected cases. Of 196 explanted livers, 21 (11%) had PASD+ globules, which were significantly enriched in patients with a clinical diagnosis of nonalcoholic steatohepatitis (NASH; 47%) compared with other causes (P < 0.001). IHC confirmed all PASD+ globules were A1AT+, with 20 of 21 cases demonstrating diffuse A1AT staining. In an expanded NASH cohort, 42% (14/33) of explants had PASD+ globules, 92% of which were homozygous (n = 1) or heterozygous (n = 11) for the SERPINA1 Z allele, corresponding to nearly 40% of all NASH patients. Overall, the Z allele was present in 10% of all tested liver explants, with 85% of PASD+ cases genotyping homozygous (n = 2) or heterozygous (n = 20), which is far in excess of the estimated 2% in the general population. These results indicate PASD+ A1AT globules (with confirmatory genotyping showing at least 1 Z allele) are commonly observed in NASH, suggesting a synergistic relationship toward liver fibrosis. In addition, the high frequency of SERPINA1 Z alleles in liver transplantation patients supports the utility of pretransplant genotyping.
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Affiliation(s)
- Gregory Cheeney
- Department of Pathology, University of Washington School of Medicine, Seattle, WA.,Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA
| | - Lincoln J Pac
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Charles S Landis
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA
| | - Paul E Swanson
- Department of Pathology, University of Washington School of Medicine, Seattle, WA
| | - Dina N Greene
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, WA
| | - Maria Westerhoff
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI
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49
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Ikuta K, Roychoudhury P, Xie H, Mcclurkan CL, Walkiewicz M, Makhsous N, Huang ML, Beru Y, Alam M, Shepherd A, Lamotte ED, Patel K, Morris A, Ҫoruh B, Yu L, Bhattacharya R, Cheng R, Walter RB, Limaye AP, Lockwood CM, Holland SM, Rakita RM, Koelle DM, Greninger AL. Trillions and Trillions: Herpes Simplex Virus-1 Hepatitis in an Immunocompetent Adult. Open Forum Infect Dis 2019; 6:ofz465. [PMID: 31777756 PMCID: PMC6868424 DOI: 10.1093/ofid/ofz465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/23/2019] [Indexed: 11/14/2022] Open
Abstract
We describe a case of acute liver failure and myopericarditis due to herpes simplex virus-1 (HSV-1) in an immunocompetent adult. We estimate that, at the height of viremia, the patient contained a quantity of HSV-1 virions approaching that of human cells. The patient recovered with acyclovir that was dose-adjusted for neurotoxicity and developed a vigorous anti-HSV-1 T-cell response.
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Affiliation(s)
- Kevin Ikuta
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Christopher L Mcclurkan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Magdalena Walkiewicz
- Immunopathogenesis Section, National Institute of Allergy and Infectious Disease, Bethesda, Maryland, USA
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Yodit Beru
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Mariam Alam
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amanda Shepherd
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eric D Lamotte
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kevin Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amy Morris
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Başak Ҫoruh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lei Yu
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Renuka Bhattacharya
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Rex Cheng
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Roland B Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center Seattle, Washington, USA
| | - Ajit P Limaye
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Steven M Holland
- Immunopathogenesis Section, National Institute of Allergy and Infectious Disease, Bethesda, Maryland, USA
| | - Robert M Rakita
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - David M Koelle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Benaroya Research Institute, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Cole BL, Lockwood CM, Stasi S, Stevens J, Lee A, Ojemann JG, Ellenbogen RG, Leary SE. Year 1 in the Molecular Era of Pediatric Brain Tumor Diagnosis: Application of Universal Clinical Targeted Sequencing in an Unselected Cohort of Children. JCO Precis Oncol 2018; 2:1-13. [DOI: 10.1200/po.17.00151] [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] [Indexed: 11/20/2022] Open
Abstract
Purpose Next-generation sequencing is gaining acceptance as a clinical tool to aid diagnosis and guide treatment of pediatric cancer. Prior pilot studies have evaluated the feasibility and utility of clinical genomic profiling in a subset of selected patients with brain tumors. Here, we report an unselected prospective cohort study to evaluate the clinical use of universal targeted sequencing in pediatric patients with brain tumors. Methods We applied a universal sequencing protocol for all tumors of the CNS undergoing diagnostic workup at Seattle Children’s Hospital during the study period of November 2015 to November 2016. All tumors were sequenced using the UW-OncoPlex platform, which is a multiplexed targeted deep gene sequencing panel that detects genetic alterations in 262 cancer-related genes performed in a College of American Pathologists–accredited Clinical Laboratory Improvements Amendments–certified laboratory. Results Eighty-eight patients underwent diagnostic evaluation during the study period, of which 85 tumors (95%) yielded sufficient DNA for sequencing, including 59 newly diagnosed and 26 relapsed. Clinically relevant genetic alterations were identified in 68 of 85 patients (80%). Of these, 57 (67%) had disease-defining or disease-modifying mutations, 44 (52%) had potentially targetable mutations, and 31 (36%) had mutations requiring germline follow-up. As of the last follow-up, seven patients had been prescribed targeted agents on the basis of sequencing results, and nine had confirmed deleterious germline mutations. Conclusion Clinically validated molecular profiling of pediatric brain tumors aids diagnosis and treatment of patients with a variety of high- and low-grade primary and relapsed pediatric brain tumors.
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Affiliation(s)
- Bonnie L. Cole
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Christina M. Lockwood
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Shannon Stasi
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Jeffrey Stevens
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Amy Lee
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Jeffrey G. Ojemann
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Richard G. Ellenbogen
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
| | - Sarah E.S. Leary
- Bonnie L. Cole, Shannon Stasi, Jeffrey Stevens, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, Seattle Children’s Hospital; Bonnie L. Cole, Christina M. Lockwood, Amy Lee, Jeffrey G. Ojemann, Richard G. Ellenbogen, and Sarah E.S. Leary, University of Washington, Seattle, WA
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