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Sabath DE, Perrone ME, Clein A, Tam M, Hardin M, Trimble S, Ramirez A, Duplessis M, Mojica T, Higano CS, Gadi VK, Kaldjian E, George T. Clinical Validation of a Circulating Tumor Cell Assay Using Density Centrifugation and Automated Immunofluorescence Microscopy. Am J Clin Pathol 2022; 158:270-276. [PMID: 35460401 DOI: 10.1093/ajcp/aqac040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 09/28/2021] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The US Food and Drug Administration (FDA)-approved CELLSEARCH assay (Menarini Silicon Biosystems) for circulating tumor cells (CTCs) relies on expression of an epithelial cell adhesion molecule to enrich for CTCs. We sought to validate a CTC assay (RareCyte) for clinical use that instead collects a buffy coat preparation enriched for CTCs. METHODS Normal peripheral blood specimens spiked with cultured breast and prostate cancer cells and 47 clinical samples were used to validate assay performance. Specimens were enriched for buffy coat cells and applied onto 8 glass slides. The slides were immunofluorescently stained and imaged by automated microscopy and computer-aided image analysis. RESULTS The assay was 100% specific for detecting spiked tumor cells. For samples spiked with 25, 50, and 125 cells, the percentage coefficients of variation were 42%, 21%, and 3.7%, respectively. Linearity studies demonstrated a slope of 0.99, an intercept of 1.6, and R2 of 0.96. Recoveries at the 25-, 50-, and 125-cell levels were 92%, 111%, and 100%, respectively. Clinical samples run on both CELLSEARCH and RareCyte correlated with an R2 of 0.8 after log-transformation and demonstrated 87.5% concordance using the CELLSEARCH criteria for predicting adverse outcomes. CONCLUSIONS The RareCyte CTC assay has comparable performance to the FDA-cleared method and is ready for further clinical validation studies.
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Affiliation(s)
- Daniel E Sabath
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marie E Perrone
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alisa Clein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael Tam
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael Hardin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Sara Trimble
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Tanisha Mojica
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - V K Gadi
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Tad George
- Department of RareCyte, Seattle, WA, USA
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Wittowski CL, Clowes Candadai S, Perrone ME, Gallego DF, Conta JH, Dickerson JA. Evaluation of Exome Sequencing Criteria for Hospital Stewardship and Insurance Authorization at a Pediatric Hospital. Arch Pathol Lab Med 2022; 146:107-111. [DOI: 10.5858/arpa.2020-0572-oa] [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: 01/15/2021] [Indexed: 11/06/2022]
Abstract
Context.—
Genomic molecular testing practices in a pediatric tertiary care institution can vary in utility by patient indication.
Objective.—
To evaluate exome sequencing (ES) ordering practices and the effects of applying criteria to support ES stewardship. Exome sequencing can provide molecular diagnostic information for patients with known or suspected genetic diseases, but it is relatively expensive, and the cost is often borne by patients, institutions, and payers.
Design.—
We examined ordering patterns of ES approved by board-certified geneticists at our tertiary pediatric care center, as well as preauthorization outcomes for ES requests. We compared positivity rates among patients by patient phenotype, composite insurance coverage criteria, and insurance preauthorization outcome.
Results.—
Patients who met composite coverage criteria were more likely to receive a positive result from ES compared to patients who did not meet composite coverage criteria, though this trend was not statistically significant. There was no significant difference in ES results between patients who were denied or not denied preauthorization by insurance payers.
Conclusions.—
Insurance payers should consider implementing and/or expanding coverage criteria for ES, and institutions should implement stewardship programs to support appropriate ES practices.
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Affiliation(s)
- Claire L. Wittowski
- From the Department of Laboratories (Wittowski, Clowes Candadai, Perrone, Gallego, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
| | - Sarah Clowes Candadai
- From the Department of Laboratories (Wittowski, Clowes Candadai, Perrone, Gallego, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
- Patient-Centered Laboratory Utilization Guidance Services (PLUGS) (Clowes Candadai, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
| | - Marie E. Perrone
- From the Department of Laboratories (Wittowski, Clowes Candadai, Perrone, Gallego, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
- The Department of Laboratory Medicine, University of Washington, Seattle (Perrone, Gallego, Dickerson)
| | - Daniel F. Gallego
- From the Department of Laboratories (Wittowski, Clowes Candadai, Perrone, Gallego, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
- The Department of Laboratory Medicine, University of Washington, Seattle (Perrone, Gallego, Dickerson)
| | - Jessie H. Conta
- From the Department of Laboratories (Wittowski, Clowes Candadai, Perrone, Gallego, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
- Patient-Centered Laboratory Utilization Guidance Services (PLUGS) (Clowes Candadai, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
| | - Jane A. Dickerson
- From the Department of Laboratories (Wittowski, Clowes Candadai, Perrone, Gallego, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
- Patient-Centered Laboratory Utilization Guidance Services (PLUGS) (Clowes Candadai, Conta, Dickerson), Seattle Children's Hospital, Seattle, Washington
- The Department of Laboratory Medicine, University of Washington, Seattle (Perrone, Gallego, Dickerson)
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Perrone ME, Alvarez R, Vo TT, Chung MW, Chhieng DC, Paulson VA, Colbert BG, Q Konnick E, Huang EC. Validating cell-free DNA from supernatant for molecular diagnostics on cytology specimens. Cancer Cytopathol 2021; 129:956-965. [PMID: 34265180 DOI: 10.1002/cncy.22491] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Cytology specimens are often used for biomarker testing in the setting of neoplasia. On occasion, formalin-fixed paraffin-embedded (FFPE) cell blocks unfortunately may not yield sufficient material for testing. Recent studies have suggested that residual supernatant fluid from cell block preparation is a valuable source of DNA: both cellular and cell-free DNA (cfDNA). In the present study, the use of cfDNA from supernatant is compared against DNA from FFPE materials. METHODS cfDNA was extracted prospectively from residual supernatants of 30 cytology samples (29 neoplastic cases and 1 benign ascitic fluid from a patient with a history of melanoma). Samples were tested using clinically validated next-generation-sequencing platforms and the results were compared with data from paired FFPE cell blocks in a real-time prospective clinical setting. Thirteen samples were tested on an amplicon-based assay (Solid Tumor Hotspot), and 17 samples were tested using a comprehensive capture-based assay (UW-Oncoplex). RESULTS Neoplastic content was estimated by mutational variant allele fraction, with a mean content of 24.0% and 25.8% in supernatant and FFPE, respectively. The variant concordance between paired samples was 90%, and identical results were detected in both supernatant and FFPE samples in 74% of cases. CONCLUSIONS This study confirmed that cfDNA from supernatant is a viable alternative to FFPE cell blocks for molecular biomarker testing using both amplicon-based and capture-based assays with potential for decreasing additional tissue sampling and faster turnaround time.
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Affiliation(s)
- Marie E Perrone
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Rebeca Alvarez
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Tawnie T Vo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Moon-Wook Chung
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - David C Chhieng
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Vera A Paulson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Brice G Colbert
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Eric Q Konnick
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Eric C Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
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Perrone ME, Chang A, Henriksen KJ. Medical renal diseases are frequent but often unrecognized in adult autopsies. Mod Pathol 2018; 31:365-373. [PMID: 28984299 DOI: 10.1038/modpathol.2017.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 02/02/2023]
Abstract
Kidney diseases affect many hospitalized patients and contribute to morbidity and mortality. Therefore, kidney disease should be prevalent, but the frequency and spectrum of medical renal pathology in autopsy specimens has not been well documented. We sought to determine the spectrum of medical renal pathology in adult autopsy specimens and the frequency of overlooked diagnoses. We reviewed the hematoxylin- and eosin-stained kidney sections from 140 adult autopsies performed at a large teaching hospital over a 2-year period. Fifty-eight cases (41%) had findings warranting further analysis, including alterations in glomerular matrix and/or cellularity, atypical or pigmented casts, thrombi, tubulointerstitial or vascular inflammation, or deposition of amorphous material. After additional studies and clinical correlation, the pathologic changes in 43 cases (31%) were categorized as follows: diabetic nephropathy, bile cast nephropathy, thrombotic microangiopathy, infection-related glomerulonephritis, focal necrotizing/crescentic glomerulonephritis, oxalate nephropathy, light-chain cast nephropathy, amyloidosis, urate nephropathy, hemosiderosis, antineutrophil cytoplasmic antibody-associated vasculitis, polyoma virus nephropathy, atheroembolic disease, and nephrocalcinosis. These diagnoses were not reported in 26 (60%) cases during the initial autopsy evaluation. This study demonstrates that medical renal diseases are common in autopsy cases, but significant diagnoses can be easily overlooked. Autopsy kidney specimens are a rich source of renal pathology and their evaluation should be emphasized in anatomic pathology residency training. Ultimately, our understanding of how kidney disease contributes to morbidity and mortality will benefit from accurate recognition of renal pathology in autopsy specimens.
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Affiliation(s)
- Marie E Perrone
- Department of Pathology, The University of Washington, Seattle, WA, USA
| | - Anthony Chang
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Kammi J Henriksen
- Department of Pathology, The University of Chicago, Chicago, IL, USA
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Perrone ME, Carmody D, Philipson LH, Greeley SAW. An online monogenic diabetes discussion group: supporting families and fueling new research. Transl Res 2015; 166:425-31. [PMID: 26184072 PMCID: PMC4744474 DOI: 10.1016/j.trsl.2015.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 04/21/2015] [Revised: 06/03/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
Many online support groups are available for patients with rare disorders, but scant evidence is available on how effectively such groups provide useful information or valuable psychosocial support to their participants. It is also unclear to what extent physicians and researchers may learn more about these disorders by participating in such groups. To formally assess the utility of the Kovler Monogenic Diabetes Registry online discussion group for patients and families affected by KATP channel-related monogenic neonatal diabetes in providing psychosocial and informational support and in identifying concerns unique to patients with this rare form of diabetes. We qualitatively analyzed all 1,410 messages from the online group that consisted of 64 participants affected by KATP channel monogenic diabetes and 11 researchers. We utilized the Social Behavior Support Code to assign each message to a support category and deductive thematic analysis to identify discussion topics addressed by each message. 44% of messages provided/requested informational support, whereas 31.4% of the messages contained psychosocial/emotional support. The most popular topics of postings to the forums were diabetes treatment (503 messages) and neurodevelopmental concerns (472 messages). Participation in the discussion led researchers to modify survey instruments and design new studies focusing on specific topics of concern, such as sleep. We demonstrate that an online support group for a monogenic form of diabetes is an effective informational tool that also provides psychosocial support. Participation by researchers and care providers can inform future research directions and highlight issues of patient concern.
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Affiliation(s)
- Marie E Perrone
- Department of Medicine, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill; Department of Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill
| | - David Carmody
- Department of Medicine, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill; Department of Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill
| | - Louis H Philipson
- Department of Medicine, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill; Department of Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill
| | - Siri Atma W Greeley
- Department of Medicine, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill; Department of Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Ill.
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Carmody D, Park SY, Ye H, Perrone ME, Alkorta-Aranburu G, Highland HM, Hanis CL, Philipson LH, Bell GI, Greeley SAW. Continued lessons from the INS gene: an intronic mutation causing diabetes through a novel mechanism. J Med Genet 2015; 52:612-6. [PMID: 26101329 DOI: 10.1136/jmedgenet-2015-103220] [Citation(s) in RCA: 21] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/03/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Diabetes in neonates usually has a monogenic aetiology; however, the cause remains unknown in 20-30%. Heterozygous INS mutations represent one of the most common gene causes of neonatal diabetes mellitus. METHODS Clinical and functional characterisation of a novel homozygous intronic mutation (c.187+241G>A) in the insulin gene in a child identified through the Monogenic Diabetes Registry (http://monogenicdiabetes.uchicago.edu). RESULTS The proband had insulin-requiring diabetes from birth. Ultrasonography revealed a structurally normal pancreas and C-peptide was undetectable despite readily detectable amylin, suggesting the presence of dysfunctional β cells. Whole-exome sequencing revealed the novel mutation. In silico analysis predicted a mutant mRNA product resulting from preferential recognition of a newly created splice site. Wild-type and mutant human insulin gene constructs were derived and transiently expressed in INS-1 cells. We confirmed the predicted transcript and found an additional transcript created via an ectopic splice acceptor site. CONCLUSIONS Dominant INS mutations cause diabetes via a mutated translational product causing endoplasmic reticulum stress. We describe a novel mechanism of diabetes, without β cell death, due to creation of two unstable mutant transcripts predicted to undergo nonsense and non-stop-mediated decay, respectively. Our discovery may have broader implications for those with insulin deficiency later in life.
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Affiliation(s)
- David Carmody
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
| | - Soo-Young Park
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
| | - Honggang Ye
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
| | - Marie E Perrone
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
| | - G Alkorta-Aranburu
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Heather M Highland
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Louis H Philipson
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
| | - Graeme I Bell
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
| | - Siri Atma W Greeley
- Departments of Medicine and Pediatrics, Section of Adult and Pediatric Endocrinology, Diabetes, & Metabolism, The University of Chicago, Chicago, Illinois, USA
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