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Peterson JD, de Abreu F, Kaur P, Ornstein DL, Tsongalis GJ. Implementation and Routine Clinical Use of the TruSight Myeloid Sequencing Panel in Patients with Myeloid Malignancies. Cancer Genet 2015. [DOI: 10.1016/j.cancergen.2015.05.015] [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] [Indexed: 10/23/2022]
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102
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Turner SA, de Abreau FB, Peterson JD, Tsongalis GJ, Tafe LJ. Clinical Validation and Implementation of a Targeted Sequencing Panel for Predisposition to Inherited Cancer. Cancer Genet 2015. [DOI: 10.1016/j.cancergen.2015.05.017] [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] [Indexed: 10/23/2022]
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103
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Lefferts JA, Turner SA, Liu EZ, Reader EI, Linos K, Tafe LJ, Tsongalis GJ. Analytical Validation of Chromosomal Microarray Analysis with Solid Tumor FFPE Specimens. Cancer Genet 2015. [DOI: 10.1016/j.cancergen.2015.05.013] [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] [Indexed: 11/16/2022]
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104
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Vallee SE, Tafe LJ, Reader E, Dinulos MBP, Bao L, Tsongalis GJ, Lefferts JA. Bilateral Radial Ray Defects: An Atypical Presentation of 16p11.2 Microdeletion Syndrome. Cancer Genet 2015. [DOI: 10.1016/j.cancergen.2015.05.027] [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] [Indexed: 11/28/2022]
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Affiliation(s)
- Laura J Tafe
- Department of Pathology and Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, and the Geisel School of Medicine at Dartmouth, Hanover, NH.
| | - Gregory J Tsongalis
- Department of Pathology and Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, and the Geisel School of Medicine at Dartmouth, Hanover, NH
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106
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Tafe LJ, Gorlov IP, Blumental de Abreu FB, Lefferts JA, Liu X, Pettus JR, Bloch KJ, Marotti JD, Memoli VA, Suriawinata AA, Peterson JD, Tsongalis GJ, Holderness BM, Morgan CR, Miller TW, Chamberlin MD. The impact of a molecular tumor board on treatment decisions for 35 patients: The Dartmouth experience. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1550] [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: 11/20/2022] Open
Affiliation(s)
- Laura J. Tafe
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
| | | | | | | | - Xiaoying Liu
- Geisel School of Medicine at Dartmouth, Hanover, NH
| | | | | | | | | | | | | | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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107
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Potter CS, Patterson SE, Woo XY, Stafford GA, Tsongalis GJ, Mockus SM. Ranking therapies for clinical trial selection based on somatic mutation profiles. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e22089] [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: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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Mockus SM, Liu R, Ananda G, Potter CS, Bult CJ, Pipas JM, Tsongalis GJ. A proposal for community standards in clinical trials descriptions and reporting. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e12537] [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: 11/20/2022] Open
Affiliation(s)
| | - Roger Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | | | | | - J. Marc Pipas
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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109
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Patterson SE, Potter CS, Stafford GA, Woo XY, Spotlow V, Mitchell T, Liu R, Ananda G, Tsongalis GJ, Mockus SM. Solid tumor profiling via next-generation sequencing to identify tumor-specific actionable variants. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1539] [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: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | - Talia Mitchell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Roger Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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110
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Potter CS, Mockus SM, Patterson SE, Spotlow V, Mitchell T, Liu R, Ananda G, York EB, Tsongalis GJ, Tafe LJ. Somatic mutation profiling in ovarian Brenner and associated mucinous tumors. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e16585] [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: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Talia Mitchell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Roger Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Eric B. York
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
| | - Laura J. Tafe
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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111
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Patterson SE, Potter CS, Spotlow V, Mitchell T, Liu R, Ananda G, Tsongalis GJ, Tafe LJ, Mockus SM. Potential driver mutations in ovarian Brenner tumors. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e22087] [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: 11/20/2022] Open
Affiliation(s)
| | | | | | - Talia Mitchell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Roger Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | | | - Laura J. Tafe
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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112
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Thomas AA, Fisher JL, Rahme GJ, Hampton TH, Baron U, Olek S, Schwachula T, Rhodes CH, Gui J, Tafe LJ, Tsongalis GJ, Lefferts JA, Wishart H, Kleen J, Miller M, Whipple CA, de Abreu FB, Ernstoff MS, Fadul CE. Regulatory T cells are not a strong predictor of survival for patients with glioblastoma. Neuro Oncol 2015; 17:801-9. [PMID: 25618892 DOI: 10.1093/neuonc/nou363] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 07/25/2014] [Accepted: 12/26/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Regulatory T cells (Tregs) are potentially prognostic indicators in patients with glioblastoma. If differences in frequency of Tregs in tumor or blood account for substantial variation in patient survival, then reliably measuring Tregs may enhance treatment selection and improve outcomes. METHODS We measured Tregs and CD3+ T cells in tumors and blood from 25 patients with newly diagnosed glioblastoma. Tumor-infiltrating Tregs and CD3+ T cells, measured by quantitative DNA demethylation analysis (epigenetic qPCR) and by immunohistochemistry, and peripheral blood Treg proportions measured by flow cytometry were correlated with patient survival. Additionally, we analyzed data from The Cancer Genome Atlas (TCGA) to correlate the expression of Treg markers with patient survival and glioblastoma subtypes. RESULTS Tregs, as measured in tumor tissue and peripheral blood, did not correlate with patient survival. Although there was a correlation between tumor-infiltrating Tregs expression by epigenetic qPCR and immunohistochemistry, epigenetic qPCR was more sensitive and specific. Using data from TCGA, mRNA expression of Forkhead box protein 3 (FoxP3) and Helios and FoxP3 methylation level did not predict survival. While the classical glioblastoma subtype corresponded to lower expression of Treg markers, these markers did not predict survival in any of the glioblastoma subtypes. CONCLUSIONS Although immunosuppression is a hallmark of glioblastoma, Tregs as measured in tissue by gene expression, immunohistochemistry, or demethylation and Tregs in peripheral blood measured by flow cytometry do not predict survival of patients. Quantitative DNA demethylation analysis provides an objective, sensitive, and specific way of identifying Tregs and CD3+ T cells in glioblastoma.
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Affiliation(s)
- Alissa A Thomas
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Jan L Fisher
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Gilbert J Rahme
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Thomas H Hampton
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Udo Baron
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Sven Olek
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Tim Schwachula
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - C Harker Rhodes
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Jiang Gui
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Laura J Tafe
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Gregory J Tsongalis
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Joel A Lefferts
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Heather Wishart
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Jonathan Kleen
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Michael Miller
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Chery A Whipple
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Francine B de Abreu
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Marc S Ernstoff
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
| | - Camilo E Fadul
- Department of Neurology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (A.A.T.); Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.L.F.); Department of Genetics, Geisel School of Medicine at Dartmouth, Norris Cotton Cancer Center, Dartmouth College, Lebanon, New Hampshire (G.J.R.); Epiontis GmbH, Berlin, Germany (U.B., S.O., T.S.); Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.H.R., L.J.T., G.J.T., J.A.L., F.B.d.A.); Section of Biostatistics and Epidemiology, Department of Family and Community Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.G.); Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire (T.H.H.); Department of Psychiatry, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (H.W.); Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire (J.K., M.M.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.A.W.); Melanoma Program, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, Ohio (M.S.E.); Department of Medicine, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire (C.E.F.)
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Abou Tayoun AN, Burchard PR, Caliendo AM, Scherer A, Tsongalis GJ. A multiplex PCR assay for the simultaneous detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis. Exp Mol Pathol 2015; 98:214-8. [PMID: 25595915 DOI: 10.1016/j.yexmp.2015.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 11/17/2022]
Abstract
INTRODUCTION For developing countries, sexually transmitted infections (STIs) and their complications are ranked in the top 5 disease categories for which adults seek medical treatment. Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Trichomonas vaginalis (TV) are the three most common STIs worldwide, with TV accounting for over half of the cases. In developing countries, traditional methods for diagnosing STIs are laborious, often not very sensitive, and have a long turnaround time with most recent commercially available diagnostic tests targeting one or, at most, two of these STIs at a time. Here, we describe the development of a highly sensitive, rapid and affordable sample-to-answer multiplex PCR-based assay for the simultaneous detection of Trichomonas vaginalis, Neisseria gonorrhoeae, and Chlamydia trachomatis. MATERIALS AND METHODS We designed a multiplex PCR assay for the detection of 4 targets (CT, TV, NG, and process/PCR control) using melt curve analysis. To establish the limit of detection (LOD) for each pathogen, we used previously extracted and quantified TV, NG, and CT genomic DNA (Vircell, Spain). For each target, the LOD was determined by lowering its copy number while increasing the other two STI loads in a stepwise fashion. The process/PCR control remained constant in the optimized assay and was spiked into each sample before extraction. For a concordance study, we tested urine, vaginal and rectal swab specimens from 26 patients positive for one or more of the tested STIs. In addition, 56 liquid cytology specimens (Thinprep) were used to assess specificity. RESULTS This assay has a turnaround time of less than 2h and has a limit of detection as low as 7-31 copies for each STI in the presence of the other 2 targets. Our assay also demonstrated 100% concordance with 26 known clinical samples from urine, vaginal and rectal swab specimens. TV, NG, CT, and our process/PCR control were consistently identified at 78°C, 82.3°C, 85.7°C, and ~92°C, respectively. When applied to DNA extracted from residual Thinprep specimens, the assay was negative in 54/56 samples. Two samples were found to be co-infected with CT. CONCLUSIONS Our multiplex assay combines a rapid and cost-effective approach to molecular diagnostics with the versatility required for use within a variety of laboratory settings. These performance characteristics make this multiplex STI assay highly suitable for use in a clinical laboratory.
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Affiliation(s)
- Ahmad N Abou Tayoun
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Paul R Burchard
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Angela M Caliendo
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Axel Scherer
- Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Gregory J Tsongalis
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States.
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Tafe LJ, Steinmetz HB, Allen SF, Dokus BJ, Tsongalis GJ. Rapid fluorescence in situ hybridisation (FISH) for HER2 (ERBB2) assessment in breast and gastro-oesophageal cancer. J Clin Pathol 2015; 68:306-8. [DOI: 10.1136/jclinpath-2014-202787] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Evaluation of HER2 (ERBB2) gene amplification or protein expression is standard of care in breast (BR) and advanced stage gastro-oesophageal cancers to identify patients eligible for anti-HER2 therapies. Here, we evaluate a rapid fluorescence in situ hybridisation (FISH) technology (HER2 instant quality (IQ) FISH pharmDx Kit) for detection of HER2 in patients with BR and gastro-oesophageal cancer using 30 FFPE samples that had been previously evaluated with the PathVysion HER2 DNA Probe Kit. Cases were scored as positive (HER2:CEN-17 ≥2.0), negative (HER2:CEN-17 <2.0) or equivocal according to the ASCO/CAP 2013 BR cancer guidelines. Ten samples were positive for HER2 amplification while 20 were negative; none were equivocal. The IQ FISH was able to detect low level amplification (HER2:CEN-17 ratio 2.4). The HER2 IQ FISH pharmDx Kit is a FDA approved kit that offers a rapid turnaround time (approximately 3.5 h) and in our laboratory was 100% concordant with prior PathVysion results.
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Tsongalis GJ, Peterson JD, de Abreu FB, Tunkey CD, Gallagher TL, Strausbaugh LD, Wells WA, Amos CI. Routine use of the Ion Torrent AmpliSeq™ Cancer Hotspot Panel for identification of clinically actionable somatic mutations. Clin Chem Lab Med 2014; 52:707-14. [PMID: 24334431 DOI: 10.1515/cclm-2013-0883] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/23/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND Somatic mutation analysis is standard of practice for solid tumors in order to identify therapeutic sensitizing and resistance mutations. Our laboratory routinely performed standalone PCR-based methods for mutations in several genes. Rapid discovery and introduction of new therapeutics has demanded additional genomic information for adequate management of the cancer patient. We evaluated a next generation sequencing assay, the Ion Torrent AmpliSeq Cancer Hotspot Panelv2 (CHPv2), capable of identifying multiple somatic mutations in 50 genes in a single assay. METHODS Accuracy, precision, limit of detection, and specificity were evaluated using DNA from well-characterized cell lines, genetically engineered cell lines fixed and embedded in paraffin, and previously tested mutation positive or negative, formalin-fixed, paraffin-embedded (FFPE) tissues. Normal kidney, tonsil and colon FFPE tissues were used as controls. RESULTS Accuracy studies showed 100% concordance in each patient sample between previous PCR results and the corresponding variants identified using the Ion Torrent panel. Precision studies gave consistent results when libraries were prepared from the same original DNA and were run on multiple 316 chips. The limit of detection was determined to be 5% for single nucleotide variants (SNVs) and 20% for insertions and deletions (indels). Specificity studies using normal FFPE tissue previously tested by PCR methods were also 100%. CONCLUSIONS We have evaluated the performance of the AmpliSeq Cancer Panel Hotspotv2 and show that it is suitable for clinical testing. This next generation sequencing panel has allowed the laboratory to consolidate a broader range of molecular oncology testing to a single platform and single assay.
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Kapp JR, Diss T, Spicer J, Gandy M, Schrijver I, Jennings LJ, Li MM, Tsongalis GJ, de Castro DG, Bridge JA, Wallace A, Deignan JL, Hing S, Butler R, Verghese E, Latham GJ, Hamoudi RA. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial. J Clin Pathol 2014; 68:111-8. [PMID: 25430497 PMCID: PMC4316935 DOI: 10.1136/jclinpath-2014-202644] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aims Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. Methods 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. Results Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p<0.0001), and yield variation from engineered samples was not significant (p=0.3782). Two laboratories failed DNA extraction from samples that may be attributed to operator error. DNA extraction protocols themselves were not found to contribute significant variation. 10/13 labs reported yields averaging 235.8 ng (95% CI 90.7 to 380.9) from cell-negative samples, which was attributed to issues with spectrophotometry. DNA measurements using Qubit Fluorometry demonstrated a median fivefold overestimation of DNA quantity by Nanodrop Spectrophotometry. DNA integrity and PCR inhibition were factors not found to contribute significant variation. Conclusions In this study, we provide evidence demonstrating that variation in pre-PCR steps is prevalent and may detrimentally affect the patient's ability to receive critical therapy. We provide recommendations for preanalytical workflow optimisation that may reduce errors in down-stream sequencing and for next-generation sequencing library generation.
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Affiliation(s)
- Joshua R Kapp
- Division of Surgery and Interventional Sciences, University College London, London, UK
| | - Tim Diss
- University College London Advanced Diagnostics, University College London, London, UK
| | - James Spicer
- Division of Research Oncology, Guy's and St. Thomas' Hospital NHS Trust, London, UK
| | - Michael Gandy
- University College London Advanced Diagnostics, University College London, London, UK
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, USA
| | - Lawrence J Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Marilyn M Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | | | | | - Julia A Bridge
- Department of Pathology, University of Nebraska Medical Center, Omaha, USA
| | - Andrew Wallace
- Regional Genetics Laboratory, Central Manchester University Hospital NHS Trust, Manchester, UK
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, USA
| | - Sandra Hing
- Paediatric Malignancy Department, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Rachel Butler
- All Wales Genetics Laboratory, Cardiff and Vale NHS Trust, Cardiff, UK
| | - Eldo Verghese
- Pathology and Tumour biology, University of Leeds, Leeds, UK
| | | | - Rifat A Hamoudi
- Division of Surgery and Interventional Sciences, University College London, London, UK
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Schink JC, Trosman JR, Weldon CB, Siziopikou KP, Tsongalis GJ, Rademaker AW, Patel JD, Benson AB, Perez EA, Gradishar WJ. Biomarker testing for breast, lung, and gastroesophageal cancers at NCI designated cancer centers. J Natl Cancer Inst 2014; 106:dju256. [PMID: 25217578 PMCID: PMC4176043 DOI: 10.1093/jnci/dju256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 12/05/2013] [Revised: 04/03/2014] [Accepted: 07/17/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Molecular biomarkers, a cornerstone of precision oncology, are critical in breast, gastroesophageal, and non-small cell lung cancer management (BC, GEC, NSCLC). Testing practices are intensely debated, impacting diagnostic quality and affecting pathologists, oncologists and patients. However, little is known about testing approaches used in practice. Our study described biomarker practices in BC, GEC, and NSCLC at the leading US cancer centers. METHODS We conducted a survey of the National Cancer Institute (NCI) designated centers on BC, GEC, and NSCLC biomarker testing. We used simple frequencies to describe practices, two-sided Fisher's exact test and two-sided McNemar's test for cross-cancer comparison. All statistical tests were two-sided. RESULTS For BC human epidermal growth factor receptor 2 (HER2), 39% of centers combine guidelines by using in situ hybridization (ISH) and immunohistochemistry (IHC) concurrently, and 21% reflex-test beyond guideline-recommended IHC2+. For GEC HER2, 44% use ISH and IHC concurrently, and 28% reflex-test beyond IHC2+. In NSCLC, the use of IHC is limited to 4% for epidermal growth factor receptor (EGFR) and 7% for anaplastic lymphoma kinase (ALK). 43.5% test NSCLC biomarkers on oncologist order; 34.5% run all biomarkers upfront, and 22% use a sequential protocol. NSCLC external testing is statistically significantly higher than BC (P < .0001) and GEC (P < .0001). NSCLC internally developed tests are statistically significantly more common than BC (P < .0001) and GEC (P < .0001). CONCLUSIONS At the NCI cancer centers, biomarker testing practices vary, but exceeding guidelines is a common practice for established biomarkers and emerging practice for newer biomarkers. Use of internally developed tests declines as biomarkers mature. Implementation of multibiomarker protocols is lagging. Our study represents a step toward developing a biomarker testing practice landscape.
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Affiliation(s)
- Julian C Schink
- * Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Julia R Trosman
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Christine B Weldon
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Kalliopi P Siziopikou
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Gregory J Tsongalis
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Alfred W Rademaker
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Jyoti D Patel
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Al B Benson
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - Edith A Perez
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI
| | - William J Gradishar
- Northwestern University Feinberg School of Medicine, Chicago, IL (JCS, JRT, CBW, KPS, AWR, JDP, ABB, WJG); Center for Business Models in Healthcare, Chicago, IL (JRT, CBW); UCSF Center for Translational and Policy Research on Personalized Medicine, Department of Clinical Pharmacy, University of California, San Francisco, CA (JRT); Department of Pathology, Dartmouth Hitchcock Medical Center and the Audrey and Theodor Geisel School of Medicine, Dartmouth College, Lebanon, NH (GJT); Mayo Clinic Cancer Center, Mayo Clinic, Jacksonville, FL (EAP).* Current affiliation: Spectrum Health Medical Group, Grand Rapids, MI.
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Burchard PR, Abou Tayoun AN, Lefferts JA, Lewis LD, Tsongalis GJ, Cervinski MA. Development of a rapid clinical TPMT genotyping assay. Clin Biochem 2014; 47:126-9. [PMID: 25093923 DOI: 10.1016/j.clinbiochem.2014.07.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Thiopurine compounds are commonly used in the treatment of childhood acute lymphoblastic leukemia, and as immunosuppressants following organ transplantation or for treatment of various autoimmune disorders. Thiopurine S-methyltransferase (TPMT) is required for detoxification, through S-methylation, of 6-thioguanine nucleotides (TGNs), a byproduct of thiopurine metabolism. Single nucleotide polymorphisms (SNPs) in the TPMT gene have been shown to affect its function, with some variants associated with serious clinical manifestations including severe to fatal myelosuppression and organ transplant rejection following treatment with standard thiopurine doses. In this study, we describe a TaqMan real time PCR allelic discrimination assay requiring minimal DNA input for TPMT genotyping. DESIGN AND METHODS We designed controls for the homozygous wild type and allelic variants of TPMT*2, *3B, and *3C. Genomic DNA was extracted from an additional 412 human blood samples. The samples were tested for the TPMT*2, *3B, *3C, and *3A polymorphisms by TaqMan genotyping assays using the AB 7500 FAST Real-Time PCR instrument. Allelic discrimination plots were used to identify each mutation. RESULTS The TaqMan assay correctly genotyped all custom control DNA samples. Of the 412 tested samples, our assay identified 375 samples as wild-type *1/*1 (91.02%), 3 as *1/*2 (0.73%), 1 as *1/*3B (0.24%), 3 as *1/*3C (0.73%), 27 presumed to be *1/*3A (6.55%), and 3 as *3B/*3A (0.73%). CONCLUSIONS The clinical implications of TPMT genotyping, along with the simplicity and specificity of the TaqMan genotyping assays make this test highly suitable for use in a clinical laboratory.
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Affiliation(s)
- Paul R Burchard
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Ahmad N Abou Tayoun
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Joel A Lefferts
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Lionel D Lewis
- Department of Medicine, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Mark A Cervinski
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.
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Liu X, Mody K, de Abreu FB, Pipas JM, Peterson JD, Gallagher TL, Suriawinata AA, Ripple GH, Hourdequin KC, Smith KD, Barth RJ, Colacchio TA, Tsapakos MJ, Zaki BI, Gardner TB, Gordon SR, Amos CI, Wells WA, Tsongalis GJ. Molecular Profiling of Appendiceal Epithelial Tumors Using Massively Parallel Sequencing to Identify Somatic Mutations. Clin Chem 2014; 60:1004-11. [DOI: 10.1373/clinchem.2014.225565] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Some epithelial neoplasms of the appendix, including low-grade appendiceal mucinous neoplasm and adenocarcinoma, can result in pseudomyxoma peritonei (PMP). Little is known about the mutational spectra of these tumor types and whether mutations may be of clinical significance with respect to therapeutic selection. In this study, we identified somatic mutations using the Ion Torrent AmpliSeq Cancer Hotspot Panel v2.
METHODS
Specimens consisted of 3 nonneoplastic retention cysts/mucocele, 15 low-grade mucinous neoplasms (LAMNs), 8 low-grade/well-differentiated mucinous adenocarcinomas with pseudomyxoma peritonei, and 12 adenocarcinomas with/without goblet cell/signet ring cell features. Barcoded libraries were prepared from up to 10 ng of extracted DNA and multiplexed on single 318 chips for sequencing. Data analysis was performed using Golden Helix SVS. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer.
RESULTS
A single Janus kinase 3 (JAK3) mutation was detected in the mucocele group. Eight mutations were identified in the V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and GNAS complex locus (GNAS) genes among LAMN samples. Additional gene mutations were identified in the AKT1 (v-akt murine thymoma viral oncogene homolog 1), APC (adenomatous polyposis coli), JAK3, MET (met proto-oncogene), phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA), RB1 (retinoblastoma 1), STK11 (serine/threonine kinase 11), and tumor protein p53 (TP53) genes. Among the PMPs, 6 mutations were detected in the KRAS gene and also in the GNAS, TP53, and RB1 genes. Appendiceal cancers showed mutations in the APC, ATM (ataxia telangiectasia mutated), KRAS, IDH1 [isocitrate dehydrogenase 1 (NADP+)], NRAS [neuroblastoma RAS viral (v-ras) oncogene homolog], PIK3CA, SMAD4 (SMAD family member 4), and TP53 genes.
CONCLUSIONS
Our results suggest molecular heterogeneity among epithelial tumors of the appendix. Next generation sequencing efforts have identified mutational spectra in several subtypes of these tumors that may suggest a phenotypic heterogeneity showing mutations that are relevant for targeted therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Christopher I Amos
- Center for Genomic Medicine and Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH and Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH
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Burchard PR, Abou Tayoun AN, Scherer A, Tsongalis GJ. A rapid RT-PCR assay for the detection of HIV-1 in human plasma specimens. Exp Mol Pathol 2014; 97:111-5. [PMID: 24945443 DOI: 10.1016/j.yexmp.2014.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/16/2014] [Indexed: 10/25/2022]
Abstract
INTRODUCTION The CDC estimates that there are currently over 1million people living with human immunodeficiency virus (HIV-1) in the United States, with new cases increasing by approximately 50,000 each year. HIV-1 consists of four distinct groups: the major M group, and the rare N, O, and P groups, each comprising of various subtypes. Without proper care, HIV-1 can lead to cardiovascular, kidney, and liver diseases, cancer, and rapid progression into acquired immune deficiency syndrome (AIDS). Here, we describe a novel, rapid, and highly sensitive assay for the detection of HIV-1 using intercalating dye based RT-PCR and melt curve analysis. MATERIALS AND METHODS We designed an RT-PCR assay for the detection of the major M subtypes in addition to the rare (O, N, and P) HIV-1 groups, as well as an extraction/RT-PCR control, using melt curve analysis. Viral RNA was extracted using the automated Qiagen EZ1 robotic system (Qiagen, Valencia, CA). To establish the limit of detection (LOD) for this assay, we diluted the AcroMetrix HIV-1 panel (LifeTechnologies, Grand Island, NY) to concentrations ranging from 25 to 500 copies/ml. Armored RNA BCR/ABL b3/a2 (Asuragen, Austin, Texas) was used as our extraction and RT-PCR control. Specificity and accuracy were assessed by testing plasma specimens from 48 anonymized patients negative for HIV-1. RESULTS This assay has a turnaround time of less than 2.5h and has a limit of detection of 50 copies/ml of plasma. Our assay also demonstrated 100% concordance with 53 previously quantified plasma patient specimens, including 48 negative samples and 5 positive samples. HIV-1 and our extraction/RT-PCR control were consistently identified at 79 °C and 82.5 °C, respectively. CONCLUSIONS We developed a comprehensive, easy to use assay for the detection of HIV-1 in human plasma. Our assay combines a rapid and cost-effective method for molecular diagnostics with the versatility necessary for widespread laboratory use. These performance characteristics make this HIV-1 detection assay highly suitable for use in a clinical laboratory.
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Affiliation(s)
- Paul R Burchard
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Ahmad N Abou Tayoun
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States
| | - Axel Scherer
- Department of Electrical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Gregory J Tsongalis
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, United States.
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Valle SE, Tafe LJ, Reader EI, Bao L, Dinulos MBP, Tsongalis GJ, Lefferts JA. A Mosaic Copy Number Gain of 5p15.3p13.3. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.010] [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] [Indexed: 10/24/2022]
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Tsongalis GJ. The thrills and agonies of using next-generation sequencing for somatic mutation detection in cancer. Per Med 2014; 11:369-371. [PMID: 29783481 DOI: 10.2217/pme.14.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mody K, Shatzel JJ, James SL, Wang R, Colacchio TA, Barth RJ, Zaki BI, Tsapakos MJ, Suriawinata AA, Sutton JE, Gordon SR, Gardner TB, Smith KD, Ripple GH, Hourdequin KC, Tsongalis GJ, McGrath EB, Pipas JM. Prognostic value of serum carbohydrate 19-9 in patients receiving gemcitabine-based neoadjuvant therapy for pancreatic cancer. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e15189] [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: 11/20/2022] Open
Affiliation(s)
- Kabir Mody
- Dartmouth Hitchcock Medical Center, Lebanon, NH
| | | | | | | | | | | | | | | | | | - John E. Sutton
- White River Junction VA Medical Center, White River Junction, VT
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Shatzel JJ, Wang R, Mody K, James SL, Dulai PS, Colacchio TA, Barth RJ, Zaki BI, Tsapakos MJ, Suriawinata AA, Sutton JE, Gordon SR, Smith KD, Ripple GH, Gardner TB, Hourdequin KC, Tsongalis GJ, McGrath EB, Pipas JM. Effects of dose reduction on gemcitabine-based neoadjuvant chemoradiotherapy for localized pancreatic cancer. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e15262] [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: 11/20/2022] Open
Affiliation(s)
| | | | - Kabir Mody
- Dartmouth Hitchcock Medical Center, Lebanon, NH
| | | | | | | | | | | | | | | | - John E. Sutton
- White River Junction VA Medical Center, White River Junction, VT
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125
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Ahles TA, Li Y, McDonald BC, Schwartz GN, Kaufman PA, Tsongalis GJ, Moore JH, Saykin AJ. Longitudinal assessment of cognitive changes associated with adjuvant treatment for breast cancer: the impact of APOE and smoking. Psychooncology 2014; 23:1382-90. [PMID: 24789331 DOI: 10.1002/pon.3545] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [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: 08/29/2013] [Revised: 03/10/2014] [Accepted: 03/17/2014] [Indexed: 01/11/2023]
Abstract
PURPOSE This study examined the association of post-treatment changes in cognitive performance, apolipoprotein E (APOE), and smoking in breast cancer patients treated with adjuvant therapy. PARTICIPANTS AND METHODS Breast cancer patients treated with chemotherapy (N = 55, age = 51.9 ± 7.1, education = 15.7 ± 2.6) were evaluated with a battery of neuropsychological tests prior to chemotherapy and at 1, 6, and 18 months post-chemotherapy. Matched groups of breast cancer patients not exposed to chemotherapy (N = 68, age = 56.8 ± 8.3, education = 14.8 ± 2.2) and healthy controls (N = 43, age = 53.0 ± 10.1, education = 15.2 ± 2.6) were evaluated at similar intervals. APOE epsilon 4 carrier status (APOE4+) and smoking history were also evaluated. RESULTS The detrimental effect of APOE4+ genotype on post-treatment cognitive functioning was moderated by smoking history, that is, patients without a smoking history had significantly lower performance on measures of processing speed and working memory compared with those with a smoking history and healthy controls. Exploratory analyses revealed that APOE4+ patients without a smoking history who were exposed to chemotherapy showed a decline in performance in processing speed, compared with patients with a smoking history. A similar but less pronounced pattern was seen in the no chemotherapy group (primarily endocrine treatment). For working memory, the APOE4+ by smoking interaction was observed in the no chemotherapy group only. CONCLUSIONS The association between APOE status, breast cancer treatment, and cognitive functioning was moderated by smoking history suggesting that both chemotherapy and endocrine therapy interact with APOE status and smoking to influence cognition. A putative mechanism is that smoking corrects a deficit in nicotinic receptor functioning and dopamine levels in APOE4+ individuals.
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Affiliation(s)
- Tim A Ahles
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Department of Psychiatry and Center for Psycho-Oncology Research, the Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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Cervinski MA, Sam SS, Steinmetz HB, Wood B, Tsongalis GJ. Validation of interleukin 28B genotyping assay for clinical use. Clin Biochem 2014; 47:478-80. [PMID: 24462832 DOI: 10.1016/j.clinbiochem.2014.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 11/19/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The favorable CC genotype at rs12979860 upstream of the interleukin (IL)-28B gene is correlated with a greater post-treatment sustained virologic response rate in chronic hepatitis C infected patients. We report on our validation of a clinical genotyping assay for rs12979860 polymorphisms in the IL28B locus. DESIGN AND METHODS The rs12979860 genotype was determined using a TaqMan® Real-Time PCR allelic discrimination assay with primers and probes specific for the C and T alleles on the Applied Biosystems 7500 Fast Real-Time PCR System. RESULTS The rs12979860 genotype determined by our assay was concordant with the genotypes obtained from a reference laboratory. The allelic frequency was similar to that reported in the HapMap project (rs12979860 C=0.65, T=0.35) and did not deviate from Hardy-Weinberg equilibrium. CONCLUSION Clinical availability of this assay in conjunction with other factors will allow the prediction of the individual patient's response to therapy.
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Affiliation(s)
- Mark A Cervinski
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States.
| | - Soya S Sam
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
| | - Heather B Steinmetz
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
| | - Brendan Wood
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
| | - Gregory J Tsongalis
- Department of Pathology, The Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH, United States
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Koestler DC, Li J, Baron JA, Tsongalis GJ, Butterly LF, Goodrich M, Lesseur C, Karagas MR, Marsit CJ, Moore JH, Andrew AS, Srivastava A. Distinct patterns of DNA methylation in conventional adenomas involving the right and left colon. Mod Pathol 2014; 27:145-55. [PMID: 23868178 PMCID: PMC3880603 DOI: 10.1038/modpathol.2013.104] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/05/2013] [Accepted: 05/11/2013] [Indexed: 12/17/2022]
Abstract
Recent studies have shown two distinct non-CIMP methylation clusters in colorectal cancer, raising the possibility that DNA methylation, involving non-CIMP genes, may play a role in the conventional adenoma-carcinoma pathway. A total of 135 adenomas (65 left colon and 70 right colon) were profiled for epigenome-wide DNA methylation using the Illumina HumanMethylation450 BeadChip. A principal components analysis was performed to examine the association between variability in DNA methylation and adenoma location. Linear regression and linear mixed effects models were used to identify locus-specific differential DNA methylation in adenomas of right and left colon. A significant association was present between the first principal component and adenoma location (P=0.007), even after adjustment for subject age and gender (P=0.009). A total of 168 CpG sites were differentially methylated between right- and left-colon adenomas and these loci demonstrated enrichment of homeobox genes (P=3.0 × 10(-12)). None of the 168 probes were associated with CIMP genes. Among CpG loci with the largest difference in methylation between right- and left-colon adenomas, probes associated with PRAC (prostate cancer susceptibility candidate) gene showed hypermethylation in right-colon adenomas whereas those associated with CDX2 (caudal type homeobox transcription factor 2) showed hypermethylation in left-colon adenomas. A subgroup of left-colon adenomas enriched for current smokers (OR=6.1, P=0.004) exhibited a methylation profile similar to right-colon adenomas. In summary, our results indicate distinct patterns of DNA methylation, independent of CIMP genes, in adenomas of the right and left colon.
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Affiliation(s)
- Devin C Koestler
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Jing Li
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - John A Baron
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Lynn F Butterly
- Department of Gastroenterology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Martha Goodrich
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Corina Lesseur
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Margaret R Karagas
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jason H Moore
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA,Department of Genetics, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Angeline S Andrew
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
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de Abreu FB, Gallagher TL, Liu EZ, Tsongalis GJ. Determining methylation status of methylguanine DNA methyl transferase (MGMT) from formalin-fixed, paraffin embedded tumor tissue. MethodsX 2014; 1:42-8. [PMID: 26150933 PMCID: PMC4472848 DOI: 10.1016/j.mex.2014.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/04/2014] [Accepted: 05/07/2014] [Indexed: 10/27/2022] Open
Abstract
O-6-methylguanine-DNA methyltransferase (MGMT) has been associated with resistance to alkylating agent cancer therapy in Glioblastoma (GBM), the most common and aggressive primary brain tumor in adults. Lower expression or silencing of the MGMT protein by promoter methylation has been reported to improve survival in patients with GBM [1]. This protocol describes bisulfite conversion, methylation sensitive PCR amplification and data analysis/interpretation. This protocol differs from published protocols in that it:•Describes a detailed method to measure MGMT using DNA extracted from solid tumor tissue. We have optimized the DNA extraction by using FFPE tissue blocks that contain greater than 50% tumor tissue, when non-tumor tissue was also present. Performance of this assay is compromised when lower quantities of tumor cells are used as the methylation status of tumor cells is diluted out by methylation status of normal cells.•The measurement of MGMT could be further (enhanced) optimized using a percentage of methylation ration cutoff of 2 as methylated.•The machine specifications detailed here are specific to measuring MGMT from PPFE tumor tissue.
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Affiliation(s)
- Francine B de Abreu
- Dartmouth Medical School and Dartmouth-Hitchcock Medical Center and The Audrey and Theodor Geisel School of Medicine at Dartmouth, Department of Pathology, 1 Medical Center Drive, Lebanon, NH 03756, United States
| | - Torrey L Gallagher
- Dartmouth Medical School and Dartmouth-Hitchcock Medical Center and The Audrey and Theodor Geisel School of Medicine at Dartmouth, Department of Pathology, 1 Medical Center Drive, Lebanon, NH 03756, United States
| | - Emmeline Z Liu
- Dartmouth Medical School and Dartmouth-Hitchcock Medical Center and The Audrey and Theodor Geisel School of Medicine at Dartmouth, Department of Pathology, 1 Medical Center Drive, Lebanon, NH 03756, United States
| | - Gregory J Tsongalis
- Dartmouth Medical School and Dartmouth-Hitchcock Medical Center and The Audrey and Theodor Geisel School of Medicine at Dartmouth, Department of Pathology, 1 Medical Center Drive, Lebanon, NH 03756, United States
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Abstract
OBJECTIVES Infectious diseases that are largely treatable continue to pose a tremendous burden on the developing world despite the availability of highly potent drugs. The high mortality and morbidity rates of these diseases are largely due to a lack of affordable diagnostics that are accessible to resource-limited areas and that can deliver high-quality results. In fact, modified molecular diagnostics for infectious diseases were rated as the top biotechnology to improve health in developing countries. METHODS In this review, we describe the characteristics of accessible molecular diagnostic tools and discuss the challenges associated with implementing such tools at low infrastructure sites. RESULTS We highlight our experience as part of the "Grand Challenge" project supported by the Gates Foundation for addressing global health inequities and describe issues and solutions associated with developing adequate technologies or molecular assays needed for broad access in the developing world. CONCLUSIONS We believe that sharing this knowledge will facilitate the development of new molecular technologies that are extremely valuable for improving global health.
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Affiliation(s)
| | - Paul R. Burchard
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Imran Malik
- Department of Electrical Engineering, California Institute of Technology, Pasadena, CA
| | - Axel Scherer
- Department of Electrical Engineering, California Institute of Technology, Pasadena, CA
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Mandavilli SR, Cartun RW, Ricci A, Tsongalis GJ. Immunohistochemical Evaluation of Genetic and Epigenetic Factors in Primary Breast Cancers. J Histotechnol 2013. [DOI: 10.1179/his.1997.20.1.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Abstract
BACKGROUND Lynch syndrome (LS) is the most common form of the hereditary colon cancer syndromes. Because of its high prevalence, a nationwide campaign has begun to screen all colorectal cancers for the genetic abnormalities associated with LS. CONTENT Next to colorectal cancer, endometrial cancer is the most common form of malignancy found in women with LS. Identifying individuals who harbor the well-characterized mismatch-repair gene mutations via immunohistochemistry, microsatellite instability analysis, or direct gene sequencing is critical to managing the LS patient and to surveillance for the development of other associated tumor types. SUMMARY Although many institutions have begun screening all colorectal tumors for LS, the evidence is sufficient to warrant the testing of all endometrial cancers for LS as well. Various testing algorithms, along with genetic-counseling efforts, can lead to a cost-efficient and beneficial screening program.
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Peterson JD, de Abreu F, Gallagher TL, Burchard PR, Amos CI, Wells WA, Pipas JM, Ernstoff MS, Fadul CE, Rigas JR, Tsongalis GJ. Abstract B179: Targeted next generation sequencing for somatic mutations in human cancer. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-b179] [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: 11/16/2022]
Abstract
Abstract
Objective: We have replaced single gene PCR-based methods for the detection of BRAF, KRAS and EGFR variants in routine clinical practice with next generation sequencing assays for the Ion Torrent AmpliSeq Cancer Hotspot Panel v2 (50 genes) and the Illumina TruSeq Amplicon Cancer panel (48 genes). Implementation of these panels requires constant optimization of technical and analytical procedures as reagents and software continue to be developed. In this study we describe somatic mutation findings from our clinical laboratory service.
Methods: DNA was extracted from 90 formalin fixed, paraffin embedded tissue specimens that included 50 lung cancer, 24 colon cancer and 16 other cancers. Barcoded libraries were prepared from up to 10ng of extracted DNA and multiplexed on single 318 chips. Data analysis was performed using Golden Helix SVS for the Ion Torrent panel and Variant Studio for the Illumina panel. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer (IGV).
Results: Of the 90 cancer cases sequenced, each panel returned on average 20 variants. Of these, there was 100% concordance between the two panels with respect to the clinically actionable mutations identified.
Conclusions: We have implemented next generation sequencing technologies for the detection of somatic mutations in human cancers. Two platforms, the Ion Torrent PGM and the Illumina MiSeq, have been used for the routine analysis of FFPE cancer tissues in a clinical setting with actionable and non-actionable variants reported and archived.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B179.
Citation Format: Jason D. Peterson, Francine de Abreu, Torrey L. Gallagher, Paul R. Burchard, Christopher I. Amos, Wendy A. Wells, J. Marc Pipas, Marc S. Ernstoff, Camilo E. Fadul, James R. Rigas, Gregory J. Tsongalis. Targeted next generation sequencing for somatic mutations in human cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B179.
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Affiliation(s)
- Jason D. Peterson
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Francine de Abreu
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Torrey L. Gallagher
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Paul R. Burchard
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Christopher I. Amos
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Wendy A. Wells
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - J. Marc Pipas
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Marc S. Ernstoff
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Camilo E. Fadul
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - James R. Rigas
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
| | - Gregory J. Tsongalis
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical and Norris Cotton Cancer Center, Lebanon, NH
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Gardner TB, Glass LM, Smith KD, Ripple GH, Barth RJ, Klibansky DA, Colacchio TA, Tsapakos MJ, Suriawinata AA, Tsongalis GJ, Pipas JM, Gordon SR. Pancreatic cyst prevalence and the risk of mucin-producing adenocarcinoma in US adults. Am J Gastroenterol 2013; 108:1546-50. [PMID: 24091499 PMCID: PMC4115202 DOI: 10.1038/ajg.2013.103] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [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: 12/11/2022]
Abstract
OBJECTIVES The presence of a pancreatic cyst often prompts concern, although the rate of malignant transformation to mucin-producing adenocarcinoma is not known. We aimed to determine the prevalence rate of mucin-producing adenocarcinoma in US adults with pancreatic cysts. METHODS This retrospective, population-based cross-sectional study calculated the annual number of mucin-producing adenocarcinomas using the Surveillance Epidemiology and End Results (SEER 18) database and the 2010 US census. The overall prevalence rate of cysts in the population was found using data from large cross-sectional imaging studies of incidental cyst prevalence. Prevalence rates were then calculated by dividing the annual number of mucin-producing adenocarcinomas by the cyst prevalence rate. RESULTS Between 2005 and 2009, 1,137 mucin-producing adenocarcinomas were estimated to be found annually in a US adult population of 137,154,960. The total number of pancreas cysts, given a cyst prevalence rate of 2.5%, was 3,428,874. Therefore, the prevalence rate of mucin-producing adenocarcinoma arising in patients with pancreatic cysts was 33.2 per 100,000 (95% confidence interval (CI): 21.9-44.5). The prevalence rate was 32.8 per 100,000 (95% CI: 21.6-44.0) in women and 33.5 per 100,000 (95% CI: 22.2-44.8) in men. As expected, the rate of malignant transformation increased linearly with advancing age (highest 38.6 per 100,000 in 80- to 84-year-old men). CONCLUSIONS Malignant transformation of pancreatic cysts into mucin-producing adenocarcinoma in US adults is a very rare event. Current clinical guidelines and resource allocation for pancreatic cyst disease should be reconsidered given these findings.
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Affiliation(s)
- Timothy B. Gardner
- Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Lisa M. Glass
- Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | | | - Gregory H. Ripple
- Section of Hematology and Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Richard J. Barth
- Department of Surgery, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - David A. Klibansky
- Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Thomas A. Colacchio
- Section of Hematology and Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | | | | | | | - J. Marc Pipas
- Section of Hematology and Oncology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Stuart R. Gordon
- Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH
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135
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Affiliation(s)
- Gregory J Tsongalis
- Director of Molecular Pathology and Co-Director of the Translational Research Program, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Elizabeth Chao
- Director of Translational Medicine, Ambry Genetics, Aliso Viejo, CA
| | - Jill M Hagenkord
- Chief Medical Officer and Senior Vice President, Complete Genomics, Inc., Mountain View, CA
| | - Tina Hambuch
- Illumina Clinical Services Laboratory, Illumina, Mountain View, CA
| | - Jason H Moore
- Professor of Genetics and Community and Family Medicine, Director of the Institute for Quantitative Biomedical Sciences, Associate Director for Bioinformatics, Norris-Cotton Cancer Center, and Editor-in-Chief of BioData Mining, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Lebanon, NH
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136
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Xue Y, Abou Tayoun AN, Abo KM, Pipas JM, Gordon SR, Gardner TB, Barth RJ, Suriawinata AA, Tsongalis GJ. MicroRNAs as diagnostic markers for pancreatic ductal adenocarcinoma and its precursor, pancreatic intraepithelial neoplasm. Cancer Genet 2013; 206:217-21. [PMID: 23933230 DOI: 10.1016/j.cancergen.2013.05.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [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: 02/11/2013] [Revised: 05/24/2013] [Accepted: 05/28/2013] [Indexed: 12/18/2022]
Abstract
Since the discovery of small non-coding RNAs, the analysis of microRNA (miRNA) expression patterns in human cancer have provided new insights into cancer biology. Evidence suggests that deregulated miRNA expression is associated with pancreatic cancer development. In this study, we analyzed the expression of several miRNAs in different types of pancreatic disease to determine if miRNA expression could aid in the diagnosis of pancreatic ductal adenocarcinoma (PDAC) and its precursor, pancreatic intraepithelial neoplasm (PanIN). Pancreatic resection specimens were selected, which included PDAC (n = 16), benign pancreatic parenchyma from corresponding carcinoma cases (n = 16), chronic pancreatitis (n = 4), normal pancreatic parenchyma (n = 5), and PanIN (n = 5). The expression levels of five miRNA (miR-148a, miR-217, miR-21, miR-196a, and miR-10b) were assessed by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) assays. Our data demonstrate that compared to the normal pancreatic parenchyma, miR-148a and miR-217 expression levels were down-regulated in PanIN, particularly in PanIN II-III and PDAC, whereas the level of miR-196 was significantly up-regulated in PDAC and its precursor, PanIN II-III. In addition, we observed that miR-21 was significantly overexpressed in PDAC, and miR-10b was highly expressed in PanIN II-III. Our study demonstrates that certain miRNAs, especially miR-148a, miR-217, and miR-196a, are significantly deregulated in PDAC, including in the early stage of PDAC. These markers can potentially be used as diagnostic markers to distinguish PDAC and its precursor from benign lesions.
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Affiliation(s)
- Yue Xue
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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137
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Hourdequin KC, Lefferts JA, Brennick JB, Ernstoff MS, Tsongalis GJ, Pipas JM. Merkel cell polyomavirus and extrapulmonary small cell carcinoma. Oncol Lett 2013; 6:1049-1052. [PMID: 24137462 PMCID: PMC3796380 DOI: 10.3892/ol.2013.1483] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 02/13/2013] [Accepted: 07/05/2013] [Indexed: 12/02/2022] Open
Abstract
The Merkel cell polyomavirus (MCV) is involved in the development of up to 100% of Merkel cell cancer (MCC) cases. Early studies have reported that the virus was infrequently detected in other small cell or neuroendocrine lung carcinomas, which share histological features with MCC. The present study investigated the presence of MCV in cases of extrapulmonary small cell carcinoma (ESCC), which also shares histological features with MCC. A total of 25 cases of ESCC that were diagnosed between 2004 and 2009 were identified at The Dartmouth Hitchcock Medical Center. Archived tissue was available for testing in 16 of these cases. A total of 11 tissue specimens of MCC were used as positive controls. DNA that was extracted from the archived tissue was subjected to five separate quantitative (q)PCR assays for the detection of four MCV genomic targets. MCV DNA was detected in 3/16 (19%) of the ESCCs and in all 11 MCCs. In the three MCV-positive ESCCs, the viral target was only detected by either one or two of the PCR assays. In 8/11 MCV-positive MCCs, the DNA tested positive by either three or all four assays and the remaining three MCCs tested positive by either one or two assays. The β-globin endogenous control was detected in all the samples that were tested. Although MCC and ESCC share numerous histological features, MCV is detected at a lower frequency in ESCC. The possible role for MCV in the etiology of ESCC remains uncertain and may account for the rare cases of ESCC with no other identifiable etiology. The failure of other assays to detect MCV may be due to sequence variability in the MCV genome.
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Affiliation(s)
- Kathryn C Hourdequin
- Department of Medicine, Section of Hematology/Oncology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA ; Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
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138
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Gowarty MA, Zaki BI, Tsapakos MJ, Gordon SR, Suriawinata AA, Tsongalis GJ, Sutton JE, Pipas JM. Successful retreatment with chemoradiotherapy for local recurrence of pancreatic adenocarcinoma after neoadjuvant therapy and pancreaticoduodenectomy. Gastrointest Cancer Res 2013; 6:118-119. [PMID: 24147160 PMCID: PMC3782873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Minda A Gowarty
- Gastrointestinal Oncology Program Norris Cotton Cancer Center Dartmouth-Hitchcock Medical Center Lebanon, NH
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139
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Abou Tayoun AN, Tunkey CD, Pugh TJ, Ross T, Shah M, Lee CC, Harkins TT, Wells WA, Tafe LJ, Amos CI, Tsongalis GJ. A comprehensive assay for CFTR mutational analysis using next-generation sequencing. Clin Chem 2013; 59:1481-8. [PMID: 23775370 DOI: 10.1373/clinchem.2013.206466] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cystic fibrosis is a life-threatening genetic disorder that has been associated with mutations in the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene. Hundreds of CFTR mutations have been detected to date. Current CFTR genotyping assays target a subset of these mutations, particularly a mutation panel recommended by the American College of Medical Genetics for carrier screening of the general population. Fast sequencing of the entire coding sequence in a scalable manner could expand the detection of CFTR mutations and facilitate management of costs and turnaround times in the clinical laboratory. METHODS We describe a proof-of-concept CFTR assay that uses PCR target enrichment and next-generation sequencing on the Ion Torrent Personal Genome Machine™ (PGM™) platform. RESULTS The scalability of the assay was demonstrated, with an average mean depth of coverage ranging from 500× to 3500×, depending on the number of multiplexed patient samples and the Ion Torrent chip used. In a blinded study of 79 previously genotyped patient DNA samples and cell lines, our assay detected most of the mutations, including single-nucleotide variants, small insertions and deletions, and large copy-number variants. The reproducibility was 100% for detecting mutations in independent runs. Our assay demonstrated high specificity, with only 2 false-positive calls (at 2184delA) found in 2 samples caused by a sequencing error in a homopolymer stretch of sequence. The detection rate for variants of unknown significance was very low in the targeted region. CONCLUSIONS With continued optimization and system refinements, PGM sequencing promises to be a powerful, rapid, and scalable means of clinical diagnostic sequencing.
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Affiliation(s)
- Ahmad N Abou Tayoun
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, and Dartmouth-Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH
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140
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Roengvoraphoj M, Tsongalis GJ, Dragnev KH, Rigas JR. Epidermal growth factor receptor tyrosine kinase inhibitors as initial therapy for non-small cell lung cancer: focus on epidermal growth factor receptor mutation testing and mutation-positive patients. Cancer Treat Rev 2013; 39:839-50. [PMID: 23768755 DOI: 10.1016/j.ctrv.2013.05.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [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: 11/27/2012] [Revised: 05/02/2013] [Accepted: 05/04/2013] [Indexed: 01/24/2023]
Abstract
Activation of the epidermal growth factor receptor (EGFR) pathway has been implicated in tumorigenesis in non-small cell lung cancer (NSCLC), the most common type of lung cancer. As a result, EGFR has become a key focus for the development of personalized therapy, with several molecular biomarkers having been investigated as potential predictors of response with EGFR tyrosine kinase inhibitors (TKIs) in NSCLC (e.g., EGFR expression, EGFR gene copy gain, and EGFR mutations). Of these, activating mutations in EGFR have thus far given the most consistent results based on the available evidence from preclinical studies and clinical trials. In an attempt to identify patients who are most likely to benefit from treatment with EGFR TKIs, EGFR mutation testing is being increasingly utilized in clinical practice. Currently in the United States, no EGFR TKI or accompanying mutational test is approved for the identification and first-line treatment of patients with advanced NSCLC. However, the first-generation EGFR TKIs, erlotinib and gefitinib, as well as investigational ErbB family TKIs and EGFR mutation testing methods are being evaluated in this setting. This review will discuss EGFR mutation testing as a biomarker of response to EGFR TKIs and the evolution of EGFR mutational analysis in NSCLC. Completed and ongoing clinical trials evaluating currently available or investigational EGFR TKIs as first-line therapy in molecularly and clinically selected patients with NSCLC, with a focus on trials in patients whose tumors have EGFR mutations, will also be reviewed.
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Affiliation(s)
- Monic Roengvoraphoj
- Comprehensive Thoracic Oncology Program, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH 03756-0001, USA; The Geisel School of Medicine at Dartmouth, One Rope Ferry Road, Hanover, NH 03755-1404, USA.
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141
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Affiliation(s)
- Gregory J Tsongalis
- Department of Pathology, Audrey and Theodor Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical Center, Norris Cotton Cancer Center, United States.
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142
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Abou Tayoun AN, de Abreu FB, Lefferts JA, Tsongalis GJ. A clinical PCR fragment analysis assay for TA repeat sizing in the UGT1A1 promoter region. Clin Chim Acta 2013; 422:1-4. [DOI: 10.1016/j.cca.2013.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 03/19/2013] [Accepted: 03/21/2013] [Indexed: 10/27/2022]
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Abstract
e15010 Background: HER2 testing in gastric and esophageal cancers (GEC) is a new area with evolving research on which testing methods are best. Based on the ToGA trial, guidelines recommend IHC/reflex to FISH, but studies show effectiveness of other protocols as well (e.g. Yan et al, J Clin Pathol 2011). Our study provides a benchmark on practices for GEC HER2 testing at NCI Cancer Centers. Methods: We conducted an IRB approved web survey of 58 NCI cancer centers (pathologists and oncologists) providing adult GEC care. The survey included 14 questions on HER2 testing methods, reflex and retest practices and awareness of institutional lab accreditation. Results: The study achieved a response rate of 93% (54/58 sites). In this cohort, 41% (22/54) of sites conduct HER2 GEC tests using concurrent FISH and IHC methods. An IHC testing method with reflex to FISH is used at 39% (21/54) of sites, of which all 21 sites reflex IHC 2+ results, and 9 of 21 automatically reflex IHC beyond 2+ (see table, results are not mutually exclusive). FISH only testing is done at 15% (8/54); concurrent FISH and CISH testing at 2% (1/54); concurrent SISH and IHC testing at 2% (1/54), and SISH only testing at 2% (1/54) of sites. The survey separately asked about HER2 testing methods for breast cancer (BC), which were compared by site to GEC HER2 practices: 65% (35/54) of sites conduct HER2 testing in a similar manner - analogous methods in similar order (p= 0.0471); 19% (10/54) of sites use primary IHC in GEC but primary FISH in BC, and 17% (9/54) of sites conduct primary or concurrent FISH testing in GEC but primary IHC in BC. Lab CAP certification for their sites was known by 89% (56/63) of GEC pathologists vs 34% (19/56) of GEC oncologists (p < .0001). 67% (42/63) of GEC pathologists were aware of whether their lab underwent a HER2 IHC and/or FISH proficiency test, vs 4% (2/56) of GEC oncologists (p<.0001). Conclusions: For gastric and esophageal HER2 testing, concurrent FISH and IHC and expanded reflex testing, beyond IHC 2+ results, are the common practice at the NCI cancer centers. [Table: see text]
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Affiliation(s)
| | | | | | - Julian C. Schink
- Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Al Bowen Benson
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
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144
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Schink JC, Trosman JR, Weldon CB, Siziopikou KP, Gradishar WJ, Tsongalis GJ, Patel JD, Benson AB, Perez EA. Biomarker testing methods in breast, gastric, and lung cancers: A benchmarking survey of NCI cancer centers. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.e22093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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
e22093 Background: Biomarkers are an integral part of cancer care. A variety of testing methods exist, allowing institutional selection of which technologies to use and in what order to run them. This descriptive study provides a benchmark on methods used in practice for biomarker testing in breast (BC), gastric/esophageal (GC), and non-small cell lung cancers (NSCLC). Methods: We conducted an IRB-approved web survey of the 58 NCI designated cancer centers (pathologists and oncologists) providing adult care in BC, GC, and NSCLC. We developed a survey instrument with 14 BC, 5 GC, and 10 NSCLC items asking about methods used, order of testing, turn around time (TAT) and if tests are internally developed (ID). Results: For BC, 32% (18/57) of sites run concurrent rather than reflex HER2 FISH and IHC testing, citing quality assurance reasons. Average TAT for concurrent vs reflex testing is 6.5 and 9.5 days. Rates of ID tests are 14% (8/57) for PgR, 12% (7/57) for ER and 7% (4/57) for HER2. For GC, 39% (21/54) of sites run concurrent HER2 FISH and IHC tests, citing reasons of quality assurance and evolving guidelines. TAT for concurrent vs reflex testing is 6.3 and 9.5 days. 19% (10/54) of sites use ID HER2 tests. All reporting sites use EGFR and ALK testing in NSCLC and 96% use KRAS. 24% (13/55) of sites run them concurrently with an average TAT of 7.6 days, while the average TAT for sites with sequential testing is 22.8 days. CAP recommends a 10 day TAT for NSCLC tests, and 92% (12/13) of sites with concurrent testing meet this guideline vs only 11% (4/38) of sites with sequential testing (p<.0001). Rates of ID tests are 57% (30/53) for KRAS, 47% (26/55) for EGFR and 35% (19/55) for ALK, for which a kit is listed on the FDA drug label. There is a difference in the use of ID tests between BC and NSCLC, p<.0148. Conclusions: Concurrent testing for BC and GC HER2, and for NSCLC markers is a common practice at NCI cancer centers; and it improves TAT. Concurrent NSCLC testing allows meeting CAP TAT guideline, but sequential testing does not. New markers (GC HER2, EGFR, KRAS and ALK) are commonly adopted, with a higher rate of internally developed tests than for BC HER2. [Table: see text]
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Affiliation(s)
- Julian C. Schink
- Northwestern University, Feinberg School of Medicine, Chicago, IL
| | | | | | | | | | | | - Jyoti D. Patel
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Al Bowen Benson
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
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145
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Weldon CB, Trosman JR, Benson AB, Tsongalis GJ, Siziopikou KP, Gradishar WJ, Schink JC. Are oncologists involved in cancer biomarker decisions at their institutions? J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.6617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
6617 Background: Biomarkers play a critical role in oncology, but differences in accuracy and quality exist between different testing methods for specific markers. ASCO/CAP guidelines call for oncologists, on behalf of patients, to seek information on testing quality and to obtain assurance that testing laboratories are appropriately accredited (Wolff et al, JCO, 2007). We surveyed oncologists and pathologists from the NCI designated cancer centers to collect individual perception of their institution’s decision making on biomarkers, and awareness of lab quality accreditation. Methods: We conducted an IRB approved web survey of pathologists and oncologists at the 58 NCI designated cancer centers providing adult breast, gastric, esophageal and non small cell lung cancer care. The survey included 12 questions on institutional decision processes and lab quality accreditation. We analyzed results using simple frequencies and the Fisher's exact test. Results: The study achieved a response rate of 98% (57/58 sites), with survey responses from 115 pathologists and 156 oncologists. The perception that their institution uses a formal organizational review and decision process on new biomarker tests was reported by 47% (54/115) of pathologists and 31% (48/156) of oncologists (p= .0078). 22% (33/153) of oncologists report they are always involved in institutional decision making on biomarker method selection for their specialty. Awareness of CAP certification status for their institutional laboratory was reported by 88% (99/112) of pathologists and 46% (65/142) of oncologists (p <0.0001). Awareness of whether their institutional laboratory underwent CAP HER2 IHC and/or FISH proficiency testing was reported by 70% (53/76) of pathologists and by 21% (13/63) of oncologists who treat breast cancer (p<.0001). Conclusions: Oncologists are typically not actively involved in their institution’s decision making process to select biomarker testing methods, nor are many of them aware of their institutional lab’s quality accreditation. With the ever increasing role of biomarkers in cancer care, oncologists’ awareness of biomarker testing performance and their participation in decision making related to biomarkers will become critical.
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Affiliation(s)
| | | | - Al Bowen Benson
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | | | | | | | - Julian C. Schink
- Northwestern University, Feinberg School of Medicine, Chicago, IL
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146
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Ma T, Galimberti F, Erkmen CP, Memoli V, Chinyengetere F, Sempere L, Beumer JH, Anyang BN, Nugent W, Johnstone D, Tsongalis GJ, Kurie JM, Li H, Direnzo J, Guo Y, Freemantle SJ, Dragnev KH, Dmitrovsky E. Comparing histone deacetylase inhibitor responses in genetically engineered mouse lung cancer models and a window of opportunity trial in patients with lung cancer. Mol Cancer Ther 2013; 12:1545-55. [PMID: 23686769 DOI: 10.1158/1535-7163.mct-12-0933] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Histone deacetylase inhibitor (HDACi; vorinostat) responses were studied in murine and human lung cancer cell lines and genetically engineered mouse lung cancer models. Findings were compared with a window of opportunity trial in aerodigestive tract cancers. In human (HOP62, H522, and H23) and murine transgenic (ED-1, ED-2, LKR-13, and 393P, driven, respectively, by cyclin E, degradation-resistant cyclin E, KRAS, or KRAS/p53) lung cancer cell lines, vorinostat reduced growth, cyclin D1, and cyclin E levels, but induced p27, histone acetylation, and apoptosis. Other biomarkers also changed. Findings from transgenic murine lung cancer models were integrated with those from a window of opportunity trial that measured vorinostat pharmacodynamic responses in pre- versus posttreatment tumor biopsies. Vorinostat repressed cyclin D1 and cyclin E expression in murine transgenic lung cancers and significantly reduced lung cancers in syngeneic mice. Vorinostat also reduced cyclin D1 and cyclin E expression, but increased p27 levels in post- versus pretreatment human lung cancer biopsies. Notably, necrotic and inflammatory responses appeared in posttreatment biopsies. These depended on intratumoral HDACi levels. Therefore, HDACi treatments of murine genetically engineered lung cancer models exert similar responses (growth inhibition and changes in gene expression) as observed in lung cancer cell lines. Moreover, enhanced pharmacodynamic responses occurred in the window of opportunity trial, providing additional markers of response that can be evaluated in subsequent HDACi trials. Thus, combining murine and human HDACi trials is a strategy to translate preclinical HDACi treatment outcomes into the clinic. This study uncovered clinically tractable mechanisms to engage in future HDACi trials.
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Affiliation(s)
- Tian Ma
- Departments of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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147
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Burchard PR, Malhotra S, Kaur P, Tsongalis GJ. Detection of the FCGR3a polymorphism using a real-time polymerase chain reaction assay. Cancer Genet 2013; 206:130-4. [PMID: 23680410 DOI: 10.1016/j.cancergen.2013.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/18/2013] [Accepted: 03/18/2013] [Indexed: 10/26/2022]
Abstract
The fragment crystallizable (Fc) region of the immunoglobulin G, low affinity III A receptor (FCGR3a, also known as CD16) belongs to the Fc gamma receptor family (FCGR), which plays an important role in immunoinflammatory processes. It is a low affinity, transmembrane receptor that is mainly expressed in monocytes, natural killer cells, and macrophages. It has been implicated in various inflammatory conditions, and recently a polymorphism (rs396991) in this gene has been shown to influence response to rituximab (anti-CD20) therapy in various disorders. We evaluated two molecular methods to genotype this polymorphism. Archived, formalin-fixed, paraffin-embedded samples from 26 biopsies of diffuse large B-cell lymphoma were retrieved and DNA was extracted. The samples were tested for the FCGR3a polymorphism using real-time polymerase chain reaction (PCR) followed by melt curve analysis or by a standard TaqMan allelic discrimination assay using the ABI 7500 FAST real-time PCR instrument. With the TaqMan allelic discrimination assay, we found that 16 cases were the wild type genotype, homozygous phenylalanine (F/F), for the FCGR3a receptor, whereas two cases had the homozygous valine (V/V) polymorphism and eight cases were heterozygous with a V/F genotype. Results with the real-time PCR followed by melt curve analysis were similar for 25 cases; however, four samples did not have sufficient DNA for the melt curve analysis method, and the result from one sample was discordant. The new TaqMan assay offers several advantages over previously published assays, such as faster turnaround time and ease of interpretation. These performance characteristics make it highly suitable for use in a clinical laboratory.
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Affiliation(s)
- Paul R Burchard
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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148
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Sam SS, Steinmetz HB, Tsongalis GJ, Tafe LJ, Lefferts JA. Validation of a solid-phase electrochemical array for genotyping hepatitis C virus. Exp Mol Pathol 2013; 95:18-22. [PMID: 23583628 DOI: 10.1016/j.yexmp.2013.04.001] [Citation(s) in RCA: 17] [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: 03/15/2013] [Accepted: 04/03/2013] [Indexed: 12/14/2022]
Abstract
Hepatitis C viral infection is a major cause of progressive liver disease. HCV genotype is one of the most significant baseline predictors of response to HCV antiviral therapy. The objective was to evaluate an HCV genotyping method that targets the 5'-untranslated region (UTR) to detect genotypes/subtypes using the GenMark eSensor® XT-8 system. The HCV amplicon of major genotypes/subtypes from the Roche TaqMan® HCV assay served as a template for the nested PCR followed by a direct analysis on the XT-8 detection system. The assay was validated for limit of detection (LOD), specificity, accuracy and precision. The LOD determined was below 175 IU/ml for all the subtypes except 6ab. The genotypes detected using this assay were in concordance with the LiPA assay. The high performance characteristics (LOD, specificity, intra- and inter-assay precision, and accuracy), make this assay particularly well suited for clinical HCV genotyping in order to guide antiviral therapy.
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Affiliation(s)
- Soya S Sam
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA.
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Sam S, Schned AR, Tsongalis GJ, Tafe LJ. Profiling miRNAs in Renal Neoplasms for Diagnosis and Biomarker Discovery. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.53.3] [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: 11/11/2022]
Affiliation(s)
- Soya Sam
- Dartmouth‐Hitchcock Medical CenterLebanonNH
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Ash GI, Eicher JD, Tsongalis GJ, Thompson PD, Pescatello LS. Clinical and Genetic Determinants of Blood Pressure Under Ambulatory Conditions on Days With and Without Acute Exercise. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.910.15] [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: 11/11/2022]
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