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Putra J, de Abreu FB, Peterson JD, Pipas JM, Mody K, Amos CI, Tsongalis GJ, Suriawinata AA. Molecular profiling of intrahepatic and extrahepatic cholangiocarcinoma using next generation sequencing. Exp Mol Pathol 2015; 99:240-4. [PMID: 26189129 DOI: 10.1016/j.yexmp.2015.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 12/24/2022]
Abstract
Cholangiocarcinoma is a heterogeneous malignant process, which is further classified into intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC). The poor prognosis of the disease is partly due to the lack of understanding of the disease mechanism. Multiple gene alterations identified by various molecular techniques have been described recently. As a result, multiple targeted therapies for ICC and ECC are being developed. In this study, we identified and compared somatic mutations in ICC and ECC patients using next generation sequencing (NGS) (Ampliseq Cancer Hotspot Panel v2 and Ion Torrent 318v2 chips). Eleven of 16 samples passed internal quality control established for NGS testing. ICC cases (n=3) showed IDH1 (33.3%) and NRAS (33.3%) mutations. Meanwhile, TP53 (75%), KRAS (50%), and BRAF (12.5%) mutations were identified in ECC cases (n=8). Our study confirmed the molecular heterogeneity of ICC and ECC using NGS. This information will be important for individual patients as targeted therapies for ICC and ECC become available in the future.
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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103
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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104
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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105
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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106
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107
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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108
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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109
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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110
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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111
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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112
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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113
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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] [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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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] [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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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] [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] [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] [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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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] [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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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] [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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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] [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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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] [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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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] [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] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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