Center for Clinical Genomics and Advanced Technology
About Us
Jeremiah Karrs, DO
Jeremiah Karrs, DO
Jeremiah Karrs, DO
CGAT Associate Director; Director Molecular Hematology
Wahab Khan, PhD
Jeremiah Karrs, DO
Jeremiah Karrs, DO
CGAT Associate Director, Director Molecular and Cytogenetics
Joel Lefferts, PhD
Jeremiah Karrs, DO
Joel Lefferts, PhD
CGAT Associate Director, Director Molecular Infectious Diseases
Nidhi Shah, MD
Jeremiah Karrs, DO
Joel Lefferts, PhD
CGAT Assistant Director, Assistant Director Molecular Genetics
Parth Shah, MD
Shrey Sukhadia, PhD
Shrey Sukhadia, PhD
CGAT Associate Director, Director Genomic Informatics
Shrey Sukhadia, PhD
Shrey Sukhadia, PhD
Shrey Sukhadia, PhD
CGAT Assistant Director, Assistant Director Genomic Informatics
Laura Tafe, MD
Shrey Sukhadia, PhD
Samantha Allen, BS
CGAT Associate Director, Director Molecular Oncology
Samantha Allen, BS
Shrey Sukhadia, PhD
Samantha Allen, BS
Laboratory Supervisor
Torrey Gallagher, MS
Gregory J. Tsongalis, PhD
Heather Steinmetz, MBA
Laboratory Supervisor
Heather Steinmetz, MBA
Gregory J. Tsongalis, PhD
Heather Steinmetz, MBA
CGAT Manager
Gregory J. Tsongalis, PhD
Gregory J. Tsongalis, PhD
Gregory J. Tsongalis, PhD
CGAT Director
CGAT Fellows
Joel A. Lefferts
Ahmad N. Abou Tayoun
Joel A. Lefferts
Fellow 2006-2009
Current: Assistant Director-CGAT
Dartmouth Hitchcock Medical Center Lebanon, NH
Soya Sam
Ahmad N. Abou Tayoun
Joel A. Lefferts
Fellow: 2011-2013
Current: Lifespan
Providene, RI
Ahmad N. Abou Tayoun
Ahmad N. Abou Tayoun
Ahmad N. Abou Tayoun
Fellow: 2011-2013
Current: Associate Professor of Genetics, MBRU and Al Jalila Children's Specialty Hospital, Dubai
Scott A. Turner
Aaron E. Atkinson
Ahmad N. Abou Tayoun
Fellow: 2014-2016
Current: Assistant Director, Molecular Pathology Virginia Commonwealth University Richmomnd, VA
Hou-Sung Jung
Aaron E. Atkinson
Aaron E. Atkinson
Fellow: 2015-2017
Current: Director, Molecular Diagnostics
Tufts University Medical Center
Aaron E. Atkinson
Aaron E. Atkinson
Aaron E. Atkinson
Fellow: 2016-2018
Current: Huntsman Cancer Institute, Salt Lake City, UT
M. Rabie Al-Turkmani
M. Rabie Al-Turkmani
M. Rabie Al-Turkmani
Fellow: 2017-2019
Current: Chief Scientific Officer and Medical Director, Labtech Diagnostics. San Antonio, TX
Lauren M. Petersen
M. Rabie Al-Turkmani
M. Rabie Al-Turkmani
Fellow: 2018-2020
Current: Invitae
Diana M. Toledo
M. Rabie Al-Turkmani
Shivaprasad H. Sathyanarayana
Fellow: 2019-2021
Current: The Broad Institute, Cambridge, MA
Shivaprasad H. Sathyanarayana
Shivaprasad H. Sathyanarayana
Shivaprasad H. Sathyanarayana
Fellow: 2021-current
Lauren Wainman
Shivaprasad H. Sathyanarayana
Lauren Wainman
Fellow: 2022-current
Publications
2023
2023
Periductal stromal tumor of the beast with a TERT promoter mutation: First case report with comprehensive molecular analysis. Anderson B, Marotti JD, Lefferts JA, Muller KE.Int J Surg Pathol. 2023 Feb 23:10668969231157306. doi: 10.1177/10668969231157306. Online ahead of print.PMID: 3682378
Validation of a rapid HLA-DQA1*05 pharmacogenomics assay to identify at risk resistance to anti-tumor necrosis factor therapy among patients with inflammatory bowel disease. DelBaugh RM, Cook LJ, Siegel CA, Tsongalis GJ, Khan WA. Am J Clin Pathol. 2023 Aug 1;160(2):194-199. doi: 10.1093/ajcp/aqad036.PMID: 37086490
Multiple adult onset xanthogranulomas associated with skin dysbiosis: A presenting sign of common variable immune deficiency supported by next generation sequencing. Salem I, Hodson EL, Davis MJ, Khan WA, Hughes EG, Cook LJ, Aaron DM, Sriharan A. JAAD Case Rep. 2023 Apr 5;36:4-7. doi: 10.1016/j.jdcr.2023.03.009. eCollection 2023 Jun.PMID: 37179956
Validation of a droplet digital PCR (ddPCR) assay to detect Cyanobacterial 16S rRNA in human lung tissue. Barney RE, Huang G, Gallagher TL, Tischbein M, DeWitt J, Martindale R, LaRochelle EMP, Tsongalis GJ, Stommel EW. Toxics. 2023 Jun 14;11(6):531. doi: 10.3390/toxics11060531.PMID: 37368631
Providing diagnostic pathology services in low and middle income countries. Ruhangaza D, Kennedy LS, Tsongalis GJ.Hematol Oncol Clin North Am. 2023 Jun 14:S0889-8588(23)00070-9. doi: 10.1016/j.hoc.2023.05.015. Online ahead of print.PMID: 37328312 Review.
A novel method to detect copy number variation in melanoma: Droplet digital PCR for quantitation of the CDKN2A gene, a proof of concept study. McFadden JR, Syku M, Barney RE, Stevanovic M, Chaudhari AS, O'Hern KJ, Chambers M, Baker CM, LeBlanc RE, Doan L, Tsongalis GJ, Hughes EG, Sriharan A. Am J Dermatopathol. 2023 Jul 1;45(7):454-462. doi: 10.1097/DAD.0000000000002436. Epub 2023 May 2.PMID: 37130203
Inferring spatial transcriptomics markers from whole sldie images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study. Fatemi M, Feng E, Sharma C, Azher Z, Goel T, Ramwala O, Palisoul SM, Barney RE, Perreard L, Kolling FW, Salas LA, Christensen BC, Tsongalis GJ, Vaickus LJ, Levy JJ.J Pathol Inform. 2023 Mar 29;14:100308. doi: 10.1016/j.jpi.2023.100308. eCollection 2023.PMID: 371140.
Identification of spatial proteomic signatures of colon tumor metastasis: A digital spatial profiling appraoch. Levy JJ, Zavras JP, Veziroglu EM, Nasir-Moin M, Kolling FW, Christensen BC, Salas LA, Barney RE, Palisoul SM, Ren B, Liu X, Kerr DA, Pointer KB, Tsongalis GJ, Vaickus LJ.Am J Pathol. 2023 Jun;193(6):778-795. doi: 10.1016/j.ajpath.2023.02.020. Epub 2023 Apr 8.PMID: 37037284
Gain of CCND1 may occur too infrequently in cutaneous melanoma and too late in melanogenesis to be diagnsotically useful: Genome analysis of 88 cases. McFadden JR, Chaudhari AS, Stevanovic M, Tsongalis GJ, Hughes EG, Sriharan A. Am J Dermatopathol. 2023 May 1;45(5):311-319. doi: 10.1097/DAD.0000000000002420. Epub 2023 Mar 20.PMID: 36939129
Utility of retrospective molecular analysis in diagnostically challenging mesenchymal neoplasms. Mindiola Romero AE, Tafe LJ, Green DC, Deharvengt SJ, Winnick KN, Tsongalis GJ, Baker ML, Linos K, Levy JJ, Kerr DA.Int J Surg Pathol. 2023 Mar 13:10668969231157783. doi: 10.1177/10668969231157783. Online ahead of print.PMID: 36911994
Molecular diagnostics and the laboratory developed test: A tale of success and the potential impacts of increased regulation. Tsongalis GJ.J Mass Spectrom Adv Clin Lab. 2023 Feb 1;28:27-29. doi: 10.1016/j.jmsacl.2023.01.007. eCollection 2023 Apr.PMID: 36825239
Potential impact of pharmacogenomic single nucleotide variants in a rural caucasian population. Williams GR, Tsongalis GJ, Lewis LD, Barney RE, Cook LJ, Aaron Geno K, Nerenz RD. J Appl Lab Med. 2023 Mar 6;8(2):251-263. doi: 10.1093/jalm/jfac091.PMID: 36611001
2022
Using molecular testing to improve the management of thyroid nodules with indeterminate cytology: an institutional expeerience with review of molecular alterations. Glass RE, Marotti JD, Kerr DA, Levy JJ, Vaickus LJ, Gutmann EJ, Tafe LJ, Motanagh SA, Sorensen MJ, Davies L, Liu X. J Am Soc Cytopathol. 2022 Mar-Apr;11(2):79-86. PMID: 34627720
Living the best of both worlds: A personal scientific journey. Tsongalis GJ. FASEB Bioadv. 2021 Nov 5;4(2):95-101. PMID: 35141473
Mammary-type Myofibroblastoma with Leiomyomatous Differentiation: A Rare Variant with Potential Pitfalls. Strait AM, Bridge JA, Iafrate AJ, Li MM, Xu F, Tsongalis GJ, Linos K. Int J Surg Pathol. 2022 Apr;30(2):200-206. PMID: 34338561
Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers. Levy JJ, Bobak CA, Nasir-Moin M, Veziroglu EM, Palisoul SM, Barney RE, Salas LA, Christensen BC, Tsongalis GJ, Vaickus LJ. Pac Symp Biocomput. 2022;27:175-186. PMID: 34890147
Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing. Tadimety A, Zhang Y, Molinski JH, Palinski TJ, Tsongalis GJ, Zhang JXJ. Methods Mol Biol. 2022;2393:73-87. PMID: 34837175
2021
CRISPR-cas13 enzymology rapidly detects SARS-CoV-2 fragments in a clinical setting. Khan WA, Barney RE, Tsongalis GJ. J Clin Virol. 2021 Dec;145:105019. PMID: 34753073
High-Throughput CRISPR-Cas13 SARS-CoV-2 Test. Manning BJ, Khan WA, Peña JM, Fiore ES, Boisvert H, Tudino MC, Barney RE, Wilson MK, Singh S, Mowatt JA, Thompson HJ, Tsongalis GJ, Blake WJ. Clin Chem. 2021 Dec 30;68(1):172-180. PMID: 34718481
Expanding Our Understanding of Nevogenesis: Copy Number Gain of Chromosome 15q in Melanocytic Nevi Is Associated With Distinct Histomorphologic Findings. Olson LC, Lefferts JA, LeBlanc RE, Yan S, Momtahen S, Sriharan A, Linos K. Am J Surg Pathol. 2021 Feb 9. doi: 10.1097/PAS.0000000000001683. Online ahead of print.Am J Surg Pathol. 2021. PMID: 33577183
Implementation of Reverse Transcriptase PCR Testing for Severe Acute Respiratory Syndrome Coronavirus 2 under the US Food and Drug Administration Emergency Use Authorization. Lefferts JA, Allen SF, Steinmetz HB, Tsongalis GJ. Clin Chem. 2021 Jan 30;67(2):434-435. PMID: 33315063
Cross reactivity of NRASQ61R antibody in a subset of Spitz nevi with 11p gain: A potential confounding factor in the era of pathway-based diagnostic approach. Parra O, Lefferts JA, Tafe LJ, Gru AA, Linos K. Hum Pathol. 2021 Feb 23:S0046-8177(21)00026-5. doi: 10.1016/j.humpath.2021.02.001. Online ahead of print.Hum Pathol. 2021. PMID: 33636207
Rare Activating BRAF Alteration Involving the β3-αC Kinase Domain in Ganglioglioma. Lin CC, Lefferts JA, Chan AM, Zanazzi G. J Neuropathol Exp Neurol. 2021 Feb 21:nlab013. doi: 10.1093/jnen/nlab013. Online ahead of print.J Neuropathol Exp Neurol. 2021. PMID: 33611593
Cytologic features of a case of mixed medullary and follicular cell-derived thyroid carcinoma with review of the literature. Chambers M, Tafe LJ, Gutmann EJ, Kerr DA. Diagn Cytopathol. 2021 Mar;49(3):E125-E129. PMID: 32936534
2020
Proliferative potential and response to nivolumab in clear cell renal cell carcinoma patients. Zhang T, Pabla S, Lenzo FL, Conroy JM, Nesline MK, Glenn ST, Papanicolau-Sengos A, Burgher B, Giamo V, Andreas J, Wang Y, Bshara W, Madden KG, Shirai K, Dragnev K, Tafe LJ, Gupta R, Zhu J, Labriola M, McCall S, George DJ, Ghatalia P, Dayyani F, Edwards R, Park MS, Singh R, Jacob R, George S, Xu B, Zibelman M, Kurzrock R, Morrison C. Oncoimmunology. 2020 Jun 10;9(1):1773200. doi: 10.1080/2162402X.2020.1773200.Oncoimmunology. 2020. PMID: 32923131
Novel LRRFIP2-RAF1 fusion identified in an acral melanoma: A review of the literature on melanocytic proliferations with RAF1 fusions and the potential therapeutic implications. LeBlanc RE, Lefferts JA, Baker ML, Linos KD. J Cutan Pathol. 2020 Dec;47(12):1181-1186. PMID: 32700768
A Novel Case of Mammary-Type Myofibroblastoma With Sarcomatous Features. Strait AM, Linos K, Tafe LJ, Muller KE. Int J Surg Pathol. 2020 Aug 5:1066896920947465. doi: 10.1177/1066896920947465. Online ahead of print.Int J Surg Pathol. 2020. PMID: 32752900
Concordance Analysis of the 23-Gene Expression Signature (myPath Melanoma) With Fluorescence In Situ Hybridization Assay and Single Nucleotide Polymorphism Array in the Analysis of Challenging Melanocytic Lesions: Results From an Academic Medical Center. Castillo SA, Pham AK, Dagrosa AT, Yan S, Barton DT, Lefferts JA, Linos K. Am J Dermatopathol. 2020 Dec;42(12):939-947. PMID: 32675469
Molecular matching and treatment strategies for advanced stage lung cancer at Dartmouth-Hitchcock Medical Center: A three-year review of a Molecular Tumor Board. Bernhardt EB, Chamberlin MD, Gorlov IP, de Abreu FB, Bloch KJ, Peterson JD, Tsongalis GJ, Shirai K, Dragnev KH, Miller TW, Tafe LJ. Pract Lab Med. 2020 Jun 12;21:e00174. PMID: 32613070
Lessons learned from Direct-to-Consumer genetic testing. Petersen LM, Lefferts JA.Clin Lab Med. 2020 Mar;40(1):83-92. PMID: 32008642
Primary cutaneous Ewing sarcoma with diffuse S100/SOX10 positivity and pseudoalveolar pattern: An extraordinarily rare case highlighting a potential pitfall with significant repercussions. Evangelou Z, Zhang L, Tafe LJ, Azzouz L, Grada Z, Linos K. J Cutan Pathol. 2021 Feb;48(2):302-308. PMID: 32592167
A case of molecularly confirmed BAP1 Inactivated Melanocytic Tumor with retention of immunohistochemical expression: A confounding factor. Linos K, Atkinson A, Yan S, Tsongalis GJ, Lefferts JA. J Cutan Pathol. 2020 (May); 47:485-489. PMID: 31891422
Salivary-Like Tumors of the Thyroid: A Comprehensive Review of Three Rare Carcinomas.Chambers M, Nosé V, Sadow PM, Tafe LJ, Kerr DA. Head Neck Pathol. 2020 Jun 19. doi: 10.1007/s12105-020-01193-5. Online ahead of print.Head Neck Pathol. 2020. PMID: 32562215
Feasibility of brigade-style, multiphasic cancer screening in rural Honduras. Lyons KD, Kennedy LS, LaRochelle EPM, Tsongalis GJ, Reyes HS, Zuniga-Moya JC, Chamberlin MD, Bruce ML, BejaranoS. Global Oncol 2020 March;6:453-461. PMID:32160013
A case report of papillary thyroid carcinoma dedifferentiated to squamous cell carcinoma presenting as a lung metastasis: A potential diagnostic pitfall Gadde R, Tafe LJ, Tsapakos MJ, Liu X. Diagn Cytopathol. 2020 Apr 9. doi: 10.1002/dc.24422. [Epub ahead of print] PMID: 32271487
CD10 and p63 expression in a sarcomatid undifferentiated melanoma: A cautionary (and molecularlay annotated) tale. Lefferts JA, Loehrer AP, Yan S, Green DC, Deharvengt SJ, LeBlanc RE.J Cutan Pathol. 2020 Jan 14. PMID: 31943331
Rapid EGFR mutation testing in lung cancer tissue samples using a fully automated system and single-use cartridge. Al Turkmani MR, Suriawinata MA, Deharvengt SJ, Green DC, Black CC, Shirai K, Dragnev KH, Tsongalis GJ. J Pract Lab Med 2020 (Mar),PMID: 32181314.
Multi-Institutional Evaluation of Interrater Agreement of Variant Classification Based on the 2017 Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer. Sirohi D, Schmidt RL, Aisner DL, Behdad A, Betz BL, Brown N, Coleman JF, Corless CL, Deftereos G, Ewalt MD, Fernandes H, Hsiao SJ, Mansukhani MM, Murray SS, Niu N, Ritterhouse LL, Suarez CJ, Tafe LJ, Thorson JA, Segal JP, Furtado LV. J Mol Diagn. 2020 Feb;22(2):284-293. PMID: 31837433
Non-Small Cell Lung Cancer as a Precision Oncology Paradigm: Emerging Targets and Tumor Mutational Burden (TMB). Tafe LJ. Adv Anat Pathol. 2020 Jan;27(1):3-10. PMID: 31567128
Comparison of tissue molecular biomarker testing turnaround times and concordance between standard of care and the Biocartis Idylla™ platform in colorectal cancer patients. Tsongalis GJ, Al Turkmani MR, Suriawinata MA, Babcock MJ, Mitchell K, Ding Y, Scicchitano L, Tira A, Buckingham L, Atkinson S, Lax A, Aisner DL, Davies KD, Wood HN, O’Neill SS, Levine EA, Sequeira J, Harada S, DeFrank G, Paluri R, Tan BA, Colabella H, Snead C, Cruz-Correa M, Ramirez V, Rojas A, Huang H, Mackinnon AC, Garcia FU, Cavone SM, Elfaha M, Abel G, Vasef MA, Judd A, Linder MW, Alkhateeb K, Skinner WL, Boccia R, Patel K.Am J Clin Pathol. 2020, in press.
Molecular genetic profiling reveals novel association between FLT3 mutation and survival in glioma. Shee K, Chambers M, Hughes EG, Almiron DA, Deharvengt SJ, Green D, Lefferts JA, Andrew AS, Hickey WF, Tsongalis GJ. J Neurooncol. 2020 Jul;148(3):473-480. PMID: 32583303
2019
MicroRNAs in graft-versus-host disease: a review of the latest data. Newmarch M, Kostantin E, Tsongalis GJ, Guimond M, Roy J, De Guire V, Ahmad I.Bone Marrow Transplant. 2019 Dec 3. PMID: 31796872
BRAF V600E mutations are not an oncogenic driver of solitary xanthogranuloma and reticulohistiocytoma: Testing may be useful in screening for Erdheim-Chester disease. Hoyt BS, Yan S, Linos KD, Momtahen S, Sriharan A, Tran TA, Tsongalis GJ, O’Meara RR, Green DC, LeBlanc RE. Exp Molec Pathol 2019 Dec. PMID:31639332
Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing. Petersen LM, Martin IW, Moschetti WE, Kershaw CM,Tsongalis GJ. J Clin Microbiol 2019 Oct. PMID:31619531.
Clinical validation of a 108-SNV MALDI-ToF MS pharmacogenomic panel. Williams GR, Cook L, Lewis LD, Tsongalis GJ, Nerenz RD. J Appl Lab Med 2019; in press.
Pure erythroid leukemia, presenting with pancytopenia. Images in Hematology. Linnik Y, Batukbhai B, Loo E.Clin Case Rep. 2019 Aug 13;7(9):1829-1830.
Significant expansion of real time PCR multiplexing with traditional chemistries using amplitude modulation. Rajagopal A, Yurk D, Shin C, Menge K, Jacky L, Frasser S, Tombrello TA, Tsongalis GJ. Nat Sci Rep 2019;9:1053. PMID:30705333
Design of peptide nucleic acid probes on plasmonic gold nanorods for detection of circulating tumor DNA point mutations. Tadimety A, Zhang Y, Kready KM, Palinski TJ, Tsongalis GJ, Zhang JXJ. Bioelectron. 2019 (Jan);130:236-244. PMID: 30769288
Pancreatic cyst fluid harboring a KRAS mutation. Al-Turkmani MR, Gordon SR, Smith KD, Tsongalis GJ, Liu X. Cold Spring Harb Mol Case Stud 2019 (Apr);5:1-6. PMID: 30936197
Screening for Human Papillomavirus in a Low- and Middle-Income Country. Atkinson AE, Mandujano CAM, Bejarano S, Kennedy LS, Tsongalis GJ. J Glob Oncol. 2019 (May);5:JGO1800233. doi: 10.1200/JGO.18.00233. PMID: 31050922
How close are miRNAs from clinical practice? A perspective on the diagnostic and therapeutic market. Bonneau E, Neveu B, Kostantin E, Tsongalis GJ, De Guire V. EJIFCC. 2019 (Jun) 24;30(2):114-127. PMID:31263388
2018
Identifying Associations between Somatic Mutations and Clinicopathologic Findings in Lung Cancer Pathology Reports.Kumar N, Tafe LJ, Higgins JH, Peterson JD, de Abreu FB, Deharvengt SJ, Tsongalis GJ, Amos CI, Hassanpour S.Methods Inf Med. 2018 Feb;57(1):63-73. doi: 10.3414/ME17-01-0039. Epub 2018 Apr 5. PMID: 29621832
Rural distribution of human papilloma virus in low- and middle-income countries.Atkinson A, Studwell C, Bejarano S, Castellón AMZ, Espinal JAP, Deharvengt S, LaRochelle EPM, Kennedy LS, Tsongalis GJ.Exp Mol Pathol. 2018 Apr;104(2):146-150. doi: 10.1016/j.yexmp.2018.03.001. Epub 2018 Mar 16. PMID: 29551573
Potential of STAT Somatic Mutation Testing at Resection.Al-Turkmani MR, Schutz SN, Tsongalis GJ.Clin Chem. 2018 May;64(5):865-866. doi: 10.1373/clinchem.2017.285759. Epub 2018 Feb 26. No abstract available.
PMID: 29483108
Frequency of Somatic TP53 Mutations in Combination with Known Pathogenic Mutations in Colon Adenocarcinoma, Non-Small Cell Lung Carcinoma, and Gliomas as Identified by Next-Generation Sequencing.Shajani-Yi Z, de Abreu FB, Peterson JD, Tsongalis GJ.Neoplasia. 2018 Mar;20(3):256-262. doi: 10.1016/j.neo.2017.12.005. Epub 2018 Feb 16. PMID: 29454261
Pharmacogenetics of opiod use and implications for pain management. Nerenz RD, Tsongalis GJ. J Apll Lab Med 2018 (Jan);1:622-632.
Rapid somatic mutation testing in colorectal cancer by use of a fully automated system and single-use cartridge: A comparison with next generation sequencing. Al-Turkmani MR, Godwin KN, Peterson JD, Tsongalis GJ. J Appl Lab Med 2018 (Sept);3:178-184.
Maternally inherited 133 kb deletion of 14q32 causing Kagami-Ogata Syndrome. Jung HS, Vallee SE, Dinulos MB, Tsongalis GJ, Lefferts JA. J Hum Genet 2018 (Sept), PMID:30232357.
Identifying aerosolized cyanobacteria in the human respiratory tract: A proposed mechanism for cyanotoxin-associated diseases. Facciponte DN, Bough MW, Seidler D, Carroll JL, Ashare A, Andrew AS, Tsongalis GJ, Vaickus LJ, Henegan PL, Butt TH, Stommel EW. Sci Total Environ. 2018 (Dec), 15;645:1003-1013. PMID: 30248825
Ductal Carcinoma in Situ Biomarkers in a Precision Medicine Era: Current and Future Molecular-Based Testing. Shee K, Muller KE, Marotti J, Miller TW, Wells WA, Tsongalis GJ. Am J Pathol. 2018 (Oct). PMID: 30385093
2017
Somatic Mutation Analysis of Human Cancers: Challenges in Clinical Practice.Tsongalis GJ, Coleman WB.J Clin Pharmacol. 2017 Oct;57 Suppl 10:S60-S66. doi: 10.1002/jcph.934.
PMID: 28921651
Somatic mutation analysis in melanoma using targeted next generation sequencing.Miraflor AP, de Abreu FB, Peterson JD, Turner SA, Amos CI, Tsongalis GJ, Yan S.Exp Mol Pathol. 2017 Oct;103(2):172-177. PMID: 28822769
The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care.Kaul KL, Sabatini LM, Tsongalis GJ, Caliendo AM, Olsen RJ, Ashwood ER, Bale S, Benirschke R, Carlow D, Funke BH, Grody WW, Hayden RT, Hegde M, Lyon E, Murata K, Pessin M, Press RD, Thomson RB. Acad Pathol. 2017 Jul 16;4:2374289517708309. doi: 10.1177/2374289517708309. eCollection 2017 Jan-Dec.
PMID: 28815200
Triple-Negative Breast Cancer: Next-Generation Sequencing for Target Identification.Marotti JD, de Abreu FB, Wells WA, Tsongalis GJ.Am J Pathol. 2017 Oct;187(10):2133-2138. PMID: 28734944
Development of HLA-B*57:01 Genotyping Real-Time PCR with Optimized Hydrolysis Probe Design.Jung HS, Tsongalis GJ, Lefferts JA.J Mol Diagn. 2017 Sep;19(5):742-754. PMID: 28732216
Not all good things come in big packages.Guire V, Fabbri M, Tsongalis GJ.Clin Chem Lab Med. 2017 May 1;55(5):605-607. PMID: 28343175
miRNA analysis in pancreatic cancer: the Dartmouth experience.Abreu FB, Liu X, Tsongalis GJ.Clin Chem Lab Med. 2017 May 1;55(5):755-762.
PMID: 28343174
Hyper-Methylated Loci Persisting from Sessile Serrated Polyps to Serrated Cancers.Andrew AS, Baron JA, Butterly LF, Suriawinata AA, Tsongalis GJ, Robinson CM, Amos CI.Int J Mol Sci. 2017 Mar 2;18(3). pii: E535. doi: 10.3390/ijms18030535.
PMID: 28257124
Variant call concordance between two laboratory-developed, solid tumor targeted genomic profiling assays using distinct workflows and sequencing instruments.Hampel KJ, de Abreu FB, Sidiropoulos N, Peterson JD, Tsongalis GJ.Exp Mol Pathol. 2017 Apr;102(2):215-218. PMID: 28192086
HS3ST1 genotype regulates antithrombin's inflammomodulatory tone and associates with atherosclerosis.Smits NC, Kobayashi T, Srivastava PK, Skopelja S, Ivy JA, Elwood DJ, Stan RV, Tsongalis GJ, Sellke FW, Gross PL, Cole MD, DeVries JT, Kaplan AV, Robb JF, Williams SM, Shworak NW.Matrix Biol. 2017 Nov;63:69-90. PMID: 28126521
Immune modulation associated with vascular endothelial growth factor (VEGF) blockade in patients with glioblastoma.Thomas AA, Fisher JL, Hampton TH, Christensen BC, Tsongalis GJ, Rahme GJ, Whipple CA, Steel SE, Davis MC, Gaur AB, Lewis LD, Ernstoff MS, Fadul CE.Cancer Immunol Immunother. 2017 Mar;66(3):379-389. PMID: 27942839
A Phase II Trial of Dovitinib in BCG-Unresponsive Urothelial Carcinoma with FGFR3 Mutations or Overexpression: Hoosier Cancer Research Network Trial HCRN 12-157.Hahn NM, Bivalacqua TJ, Ross AE, Netto GJ, Baras A, Park JC, Chapman C, Masterson TA, Koch MO, Bihrle R, Foster RS, Gardner TA, Cheng L, Jones DR, McElyea K, Sandusky GE, Breen T, Liu Z, Albany C, Moore ML, Loman RL, Reed A, Turner SA, De Abreu FB, Gallagher T, Tsongalis GJ, Plimack ER, Greenberg RE, Geynisman DM.Clin Cancer Res. 2017 Jun 15;23(12):3003-3011. PMID: 27932416
2016
Role of microRNAs in regulation of the TNF/TNFR gene superfamily in chronic lymphocytic leukemia.Srivastava S, Tsongalis GJ, Kaur P.Clin Biochem. 2016 Nov;49(16-17):1307-1310.
PMID: 27544753
Improving Adequacy of Small Biopsy and Fine-Needle Aspiration Specimens for Molecular Testing by Next-Generation Sequencing in Patients With Lung Cancer: A Quality Improvement Study at Dartmouth-Hitchcock Medical Center.Padmanabhan V, Steinmetz HB, Rizzo EJ, Erskine AJ, Fairbank TL, de Abreu FB, Tsongalis GJ, Tafe LJ.Arch Pathol Lab Med. 2017 Mar;141(3):402-409.
PMID: 27763790
Detection of CALR Mutation in Clonal and Nonclonal Hematologic Diseases Using Fragment Analysis and Next-Generation Sequencing.Gardner JA, Peterson JD, Turner SA, Soares BL, Lancor CR, Dos Santos LL, Kaur P, Ornstein DL, Tsongalis GJ, de Abreu FB.Am J Clin Pathol. 2016 Oct;146(4):448-55. PMID: 27686171
The Use of Targeted Therapies for Precision Medicine in Oncology.White Al-Habeeb N, Kulasingam V, Diamandis EP, Yousef GM, Tsongalis GJ, Vermeulen L, Zhu Z, Kamel-Reid S.Clin Chem. 2016 Dec;62(12):1556-1564.
PMID: 27679436
Clinical Genotyping of Non-Small Cell Lung Cancers Using Targeted Next-Generation Sequencing: Utility of Identifying Rare and Co-mutations in Oncogenic Driver Genes.Tafe LJ, Pierce KJ, Peterson JD, de Abreu F, Memoli VA, Black CC, Pettus JR, Marotti JD, Gutmann EJ, Liu X, Shirai K, Dragnev KH, Amos CI, Tsongalis GJ.Neoplasia. 2016 Sep;18(9):577-83.
PMID: 27659017
The genomic profile of pancreatic adenocarcinoma and its relationship to metastatic disease.Pierce KJ, de Abreu FB, Peterson JD, Suriawinata AA, Tsongalis GJ, Liu X.Exp Mol Pathol. 2016 Oct;101(2):172-175.
PMID: 27498048
Alpha-synuclein (SNCA) polymorphisms exert protective effects on memory after mild traumatic brain injury.Shee K, Lucas A, Flashman LA, Nho K, Tsongalis GJ, McDonald BC, Saykin AJ, McAllister TW, Rhodes CH.Neurosci Lett. 2016 Sep 6;630:241-246. PMID: 27478013
Somatic gene mutation analysis of triple negative breast cancers.Dillon JL, Mockus SM, Ananda G, Spotlow V, Wells WA, Tsongalis GJ, Marotti JD.Breast. 2016 Oct;29:202-7.
PMID: 27397723
Targeted next-generation sequencing detects a high frequency of potentially actionable mutations in metastatic breast cancers.Muller KE, Marotti JD, de Abreu FB, Peterson JD, Miller TW, Chamberlin MD, Tsongalis GJ, Tafe LJ.Exp Mol Pathol. 2016 Jun;100(3):421-5. PMID: 27095739
The potential utility of re-mining results of somatic mutation testing: KRAS status in lung adenocarcinoma.Biernacka A, Tsongalis PD, Peterson JD, de Abreu FB, Black CC, Gutmann EJ, Liu X, Tafe LJ, Amos CI, Tsongalis GJ.Cancer Genet. 2016 May;209(5):195-8.
PMID: 27068338
2015
Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial. Kapp JR, Diss T, Spicer J, Gandy M, Schrijver I, Jennings LJ, Li MM, Tsongalis GJ, Gonzalez de Castro D, Bridge JA, Wallace A, Deignan JL, Hing S, Butler R, Verghese E, Latham GJ, Hamoudi RA. J Clin Pathol 2015 Feb;68(2):111-8. PMID:25430497.
A Multiplex PCR Assay for the Simultaneous Detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis. Abou Tayoun AN, Burchard PR, Caliendo AM, Scherer A, Tsongalis GJ. Exp Mol Pathol. 2015 Apr; 98(2):214-218. PMID:25595915
Regulatory T cells are not a strong predictor of survival for patients with glioblastoma. 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. Neuro Oncol. 2015 Jun; 17(6):801-809. PMID: 25618892
Rapid fluorescence in situ hybridisation (FISH) for HER2 (ERBB2) assessment in breast and gastro-oesophageal cancer. Tafe LJ, Steinmetz HB, Allen SF, Dokus BJ, Tsongalis GJ. J Clin Pathol. 2015 Apr; 68(4):306-308. PMID: 25576545
A 78-year old women with brain metastases. Tafe LJ, Tsongalis GJ. Clin Chem 2015 Apr 61(4):584-586.
Implementation of a Molecular Tumor Board: The Impact on Treatment Decisions for 35 Patients Evaluated at Dartmouth-Hitchcock Medical Center. Tafe LJ, Gorlov IP, de Abreu FB, Lefferts JA, Liu X, Pettus JR, Marotti JD, Bloch KJ, Memoli VA, Suriawinata AA, Dragnev KH, Fadul CE, Schwartz GN, Morgan CR, Holderness BM, Peterson JD, Tsongalis GJ, Miller TW, Chamberlin MD. Oncologist. 2015 Sep;20(9):1011-8. PMID:26205736
Molecular profiling of intrahepatic and extrahepatic cholangiocarcinoma using next generation sequencing. Putra J, de Abreu FB, Peterson JD, Pipas JM, Mody K, Amos CI, Tsongalis GJ, Suriawinmata AA. Exp Molec Pathol 2015; 99:240-244. PMID:26189129
Rat-bite fever: An uncommon cause of fever and rash in a 9-year-old patient. Miraflor AP, Ghajar LD, Subramaniam S, de Abreu FB, Castanedo-Tardan MP, Samie FH, Mann JA, Holmes AV, Tsongalis GJ, Yan S. J Am Acad Dermatol Case Reports 2015 (Oct), 1:371-374.
Discovery of a novel cystathionine-beta-synthae mutation and diagnosis of homocystinuria by whole exome sequencing in a family from rural Honduras. Case report. Turner SA, Dinulos MBP, Vallee SE, Kennedy L, Mason P, Seibert D, Martinez MT, Steinmetz HB, Tsongalis GJ, Lefferts JA. Clin Pathol 2015 Sept;2(3):59-65.
2019 CGAT Test Menu
Genetic Disease Testing
Alpha-1-antitrypsin
Cystic fibrosis transmembrane conductance regulator (CFTR) - 139
Chromosomal microarray (Cytoscan)
Factor (Prothrombin) - 20210G>A
Factor V (Factor V leiden) - 1691 G>A
Fragile X Syndrome
Hemochromatosis
IL28B
Methylene tetrahydrofolate reductase (MTHFR) - 677C>T
Identity
SRY
Twinship
Hematopathology
Bcl-2
BCR-ABL1
Calreticulin (CALR)
Chimerism
FLT3
IgH rearrangements
JAK2
TruSight Myeloid (54 genes)
NPM1
TCR rearrangements
Infectious disease testing
BKV
Bordetella holmseii
Bordetella parapertussis
Bodetella pertussis
CMV VL
Chlamydida trachomatis
HBV VL
HCV VL
HCV genotyping
HIV-1 VL
Human papillomavirus (HPV)
HPV genotyping
MRSA
Neisseria gonnorhoeae
Parvo B19
Oncology
ALK FISH
AmpliSeq 50 gene Cancer Hotspot Panel
BRAF V600E
EGFR del
ERBB2 FISH
EWSR FISH
FGFR3
HRAS
IDH1
IDH2
KIT
KRAS
MDM2 FISH
MGMT methylation
MLH1 methylation
NRAS
Oncoscan microarray
PDGFRa
ROS1 FISH
1p19q del
Pharmacogenomics
CYP2C9
CYP2C19
CYP2D6
GSTP1
PGX 74
UGT1A1
VKORC1
