ARUP Journal Article Publications Archive—2017

The Institute for Clinical and Experimental Research® is focused on the development of new diagnostic assays in a wide range of disciplines. Researchers at the institute regularly publish in respected, peer-reviewed journals, give presentations at national and international organizations, author books and book chapters, and develop new tests.

There are currently 76 total entries for the year 2017.

Lloyd IE, Kohlmann WK, Gligorich K, Hall A, Lyon E, Downs-Kelly E, Samowitz WS, Bronner MP. A Clinicopathologic Evaluation of Incidental Fundic Gland Polyps With Dysplasia: Implications for Clinical Management. American Journal of Gastroenterology 2017;8(17):27839-27853.
Chiaro TR, Soto R, Zac Stephens W, Kubinak JL, Petersen C, Gogokhia L, Bell R, Delgado JC, Cox J, Voth W, Brown J, Stillman DJ, O'Connell RM, Tebo AE, Round JL. A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Science Translational Medicine 2017;9(380).
Reading NS, Ruiz-Bonilla J, Christensen RD, Caceres-Perkins W, Prchal JT. A Patient with Both Methemoglobinemia and G6PD Deficiency: A Therapeutic Conundrum. American Journal of Hematology 2017;92(5):474-477.
Greene DN, Elliott-Jelf MC, Grenache DG. AAT Phenotype Identification by Isoelectric Focusing. Methods in Molecular Biology 2017;1639:33-44.
Yang H, Kircher DA, Kim KH, Grossmann AH, VanBrocklin MW, Holmen SL, Robinson JP. Activated MEK cooperates with Cdkn2a and Pten loss to promote the development and maintenance of melanoma. Oncogene 2017;36(27):3842-3851.
Maese L, Li KD, Xu X, Afify Z, Paxton CN, Putnam A. Acute Leukemia and Concurrent Mediastinal Germ Cell Tumor: Case Report and Literature Review. Fetal and Pediatric Pathology. 2017;36(2):168-176.
Kendall BA, Tkach VV, Gutierrez Y, Longino JT, Couturier MR. Answer to August 2017 Photo Quiz. Journal of Clinical Microbiology 2017;55(8):2562-2563
Gardiner JD, Abegglen LM, Huang X, Carter BE, Schackmann EA, Stucki M, Paxton CN, Randall RL, Amatruda JF, Putnam AR, Kovar H, Lessnick SL, Schiffman JD. C/EBPβ-1 promotes transformation and chemoresistance in Ewing sarcoma cells. Oncotarget 2017;8(16):26013-26026.
Hong B, Zunich J, Openshaw A, Toydemir RM. Clinical features of trisomy 12 mosaicism-Report and review. American Journal of Medical Genetics. Part A. 2017;173(6):1681-1686.
Shea S, Kubota KA, Maguire H, Gladbach S, Woron A, Atkinson-Dunn R, Couturier MR, Miller MB. Clinical Microbiology Laboratories' Adoption of Culture Independent Diagnostic Tests Are a Threat to Food-Borne Disease Surveillance in the United States. Journal of Clinical Microbiology 2017;55(1):10-19.
Patel J, Schumacher JA, Frizzell K, Sorrells S, Shen W, Clayton A, Jattani R, Kelley TW. Coexisting and Cooperating Mutations in NPM1-mutated Acute Myeloid Leukemia. Leukemia Research 2017;56:7-12.
Samadder NJ, Valentine JF, Guthery S, Singh, H, Bernstein C, Wan Y, Wong J, Boucher K, Pappas L, Rowe K, Bronner M, Ulrich N, Burt RW, Curtin K and Smith KR. Colorectal Cancer in Inflammatory Bowel Diseases: A Population-Based Study in Utah. Digestive Diseases and Sciences 2017;62(8):2126-2132.
La'ulu SL, Suh-Lailam BB, Davis KW, Straseski JA, Tebo AE. Comparative analysis of neutrophil gelatinase-associated lipocalin and other laboratory markers for lupus nephritis: a cross-sectional investigation. Annals of Clinical Biochemistry 2017;54(2):240-245.
Lin D, Genzen J. Comparison of Breast Cancer Tumor Marker Test Results: A Retrospective Analysis of Paired CA 15-3 and CA 27.29 Testing at a National Reference Laboratory. American Journal of Clinical Pathology 2017;147(suppl_2):S159-S160.
Sweeney M, Galli J, McNally S, Tebo A, Haven T, Thulin P, Clardy SL. Delayed LGI1 seropositivity in voltage-gated potassium channel (VGKC)-complex antibody limbic encephalitis. BMJ Case Reports 2017;2017.
Wittwer CT. Democratizing the Real-Time PCR. Clinical Chemistry 2017;63(4):924-925.
Schumacher J, Szankasi P, Kelley TW. Detection and Quantification of Acute Myeloid Leukemia-Associated Fusion Transcripts. Methods in Molecular Biology 2017;1633:151-161.
Naylor BC, Porter MT, Wilson E, Herring A, Lofthouse S, Hannemann A, Piccolo SR, Rockwood AL, Price JC. DeuteRater: a Tool for Quantifying Peptide Isotope Precision and Kinetic Proteomics. Bioinformatics 2017;33(10):1514-1520.
Tardif, KD, Schlaberg R. Development of a Real-Time PCR Assay for the Direct Detection of Candida species Causing Vulvovaginal Candidiasis. Diagnostic Microbiology and Infectious Disease 2017;88(1):39-40.
De Biase I, Viau KS, Liu A, Yuzyuk T, Botto LD, Pasquali M, Longo N. Diagnosis, treatment and clinical outcome of patients with long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency. JIMD Reports 2017;31:63-71.
Walker BS, Barakauskas VE, Grenache DG, Schmidt RL. Effect of Preanalytical Factors on the Stability of Maternal Serum Biomarkers and Calculated Risk for Trisomy 21, Trisomy 18, and Open Neural Tube Defect. The Journal of Applied Laboratory Medicine 2017;1(6): 1.
Best DH, Sumner KL, Smith BP, Damjanovich-Colmenares K, Nakayama I, Brown LM, Ha Y, Paul E, Morris A, Jama MA, Dodson MW, Bayrak-Toydemir P, Elliott CG. EIF2AK4 Mutations in Patients Diagnosed with Pulmonary Arterial Hypertension. Chest 2017;151(4):821-828.
Cannon RB, Dundar Y, Thomas A, Monroe MM, Buchmann LO, Witt BL, Sowder AM, Hunt JP. Elective Neck Dissection for Head and Neck Cutaneous Squamous Cell Carcinoma with Skull Base Invasion. Otolaryngology Head and Neck Surgery 2017;156(4):671-676.
Kumánovics A, Lee YN, Close DW, Coonrod EM, Ujhazi B, Chen K, MacArthur D, Krivan G, Notarangelo LD, Walter JE . Estimated disease incidence of RAG1/2 mutations: a case report and querying the Exome Aggregation Consortium. The Journal of Allergy and Clinical Immunology 2017;139(2):690-692.
Amengual O, Forastiero R, Sugiura-Ogasawara M, Otomo K, Oku K, Favas C, Delgado Alves J. Evaluation of phosphatidylserine-dependent antiprothrombin antibody testing for the diagnosis of antiphospholipid syndrome: results of an international multicentre study.Lupas 2017;26(3):266-276.
Mallory MA, Lucic D, Ebbert MTW, Cloherty GA, Toolsie D, Hillyard DR. Evaluation of the Abbott RealTime HCV Genotype II Plus RUO (PLUS) Assay with Reference to Core and NS5B Sequencing. Journal of Clinical Virology 2017;90:26-31.
Wong SH, Johnson-Davis KL, Garrison K, Rankin JD, Muhammad CS. Everolimus TDM using Thermo Fisher QMS immunoassay on Indiko, Beckman DxC, AU680, and AU5800 analyzers. Clinical Biochemistry 2017;50(7-8):425-430.
Affolter K, Gligorich K, Samadder NJ, Samowitz WS, Curtin K. Feasibility of Large-Scale Identification of Sessile Serrated Polyp Patients Using Electronic Records: A Utah Study. Digestive Diseases and Sciences 2017;62(6):1455-1463.
Tsewang T, Reading NS, Wuren T, Moore L, Hu H, Tang F, Shestakova A, Lorenzo F, Burjanivova T, Guchchait P, Koul P, Wittwer C, Julian C, Shah B, Huff C, Gordeuk V, Prchal J, Ge R-L. Gain-of-function ELGN1 prolyl hydroxylase (PHD2 D4E:C127S) in combination with EPAS1 (HIF2). Methods in Molecular Medicine 2017;95(6), 665-670.
Shaco-Levy R, Jasperson KW, Martin K, Samadder NJ, Burt RW, Ying J, Bronner MP. Gastrointestinal Polyposis in Cowden Syndrome. Journal of Clinical Gastroenterology 2017;51(7):e60-e67.
Patel S, Mason CC, Glenn MJ, Paxton CN, South ST, Cessna MH, Asch J, Cobain EF, Bixby DL, Smith LB, Reshmi S, Gastier-Foster JM, Schiffman JD, Miles RR. Genomic analysis of adult B-ALL identifies potential markers of shorter survival. Leukemia Research 2017;56:44-51.
Meyer JA, Zhou D, Mason CC, Downie JM, Rodic V, Abromowitch M, Wistinghausen B, Termuhlen AM, Angiolillo AL, Perkins SL, Barnette P, Schiffman JD, Miles RR. Genomic characterization of pediatric B-lymphoblastic lymphoma and B-lymphoblastic leukemia using formalin-fixed tissues. Pediatric Blood & Cancer 2017;64(7).
Powers J, Best H, Grenache D. Genotype-Phenotype Associations for Low Glucose-6-Phosphate Dehydrogenase Activity in Red Blood Cells. American Journal of Clinical Pathology 2017;147(suppl_2):S177-S178.
Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. The Journal of Molecular Diagnostics 2017;19(3):341-365.
Profaizer T, Lazar-Molnar E, Delgado J, Kumanovics A. HLA genotyping using the Illumina HLA TruSight next-generation sequencing kits: A comparison. International Journal of Immunogenetics 2017;44:164-168.
Schlaberg R, Ampofo K, Tardif KD, Stockmann C, Simmon KE, Hymas W, Flygare S, Kennedy B, Blaschke A, Eilbeck K, Yandell M, McCullers JA, Williams DJ, Edwards K, Arnold SR, Bramley A, Jain S, Pavia AT. Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia. The Journal of Infectious Diseases 2017;216(6):688-696.
Imaging and Outcomes for A New Entity: Low-Grade Sinonasal Sarcoma with Neural and Myogenic Features. AAT Phenotype Identification by Isoelectric Focusing. Journal of Neurological Surgery Reports 2017;78(1):15-19.
Evans AJ, Salama ME, Henricks WH, Pantanowitz L. Implementation of Whole Slide Imaging for Clinical Purposes: Issues to Consider From the Perspective of Early Adopters. Archives of Pathology & Laboratory Medicine 2017;141(7):944-959.
Clark Z, Ballock S, Calton L, Mason D. Interference Testing and Mitigation in LC-MS/MS Assays: tackling the good, the bad, and the ugly. Clinical Laboratory News 2017;22-25.
Taylor LL, Flint NA, Ma V, Hill BM, Clark CJ, Strathmann FG. Internal Hydrolysis Indicator for Sample Specific Monitoring of. Journal of Analytical Toxicology 2017;41(5):407-411.
De Biase I, Diaz-Ochu M, Rindler M, Hobson-Rohrer WL. Introduction to biochemical genetics from the clinical laboratory prospective: a case-based discussion. MedEdPORTAL Publications 2017;13:10586.
Goodwin AJ, Higgins RA, Moser KA, Smock KJ, Chandler WL, Kottke-Marchant K, Hartman SK, Volod O, Brown AF, Johari VP, Burr S, Polyakov N, Chen D. Issues Surrounding Age-Adjusted d-Dimer Cutoffs That Practicing Physicians Need to Know When Evaluating Patients With Suspected Pulmonary Embolism. Annals of Internal Medicine 2017;166(5):361-363.
Merrigan SD, Kish-Trier E, Seegmiller J, Johnson-Davis K. LC-MS/MS Method for Quantitation of Mycophenolic Acid, Mycophenolic Acid Acyl-Glucuronide, and 7-O-Mycophenolic Acid Glucuronide in Serum. Clinical Mass Spectrometry 2017;3:41-48.
Wu F, Slawson MH, Johnson-Davis KL. Metabolic Patterns of Fentanyl, Meperidine, Methylphenidate, Tapentadol and Tramadol Observed in Urine, Serum or Plasma. Journal of Analytical Toxicology 2017;41(4):289-299.
Wortmann SB, Chen MA, Colombo R, Pontoglio A, Alhaddad B, Botto LD, Yuzyuk T, Coughlin CR, Descartes M, Gr. AMild orotic aciduria in UMPS heterozygotes: a metabolic finding without clinical consequences. Journal of Inherited Metabolic Disease 2017;40(3):423-431.
Denys GA, Collazo-Velez V, Young S, Daly JA, Couturier MR, Faron ML, Buchan BW, Ledeboer N. Multicenter evaluation of the Portrait Staph ID/R blood culture panel for the rapid identification of Staphylococci and detection of mecA gene. Journal of Clinical Microbiology 2017;55(4):1140-1146.
Mollaoglu G, Guthrie MR, B. MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition. Cancer Cell 2017;31(2):270-285.
Kuzman JA, Stenehjem DD, Merriman J, Agarwal AM, Patel SB, Hahn AW, Alex A, Albertson D, Gill DM, Agarwal N. Neutrophil-lymphocyte ratio as a predictive biomarker for response to high dose interleukin-2 in patients with renal cell carcinoma. BMC Urology 2017;17(1):1.
Taylor JR, Thompson PJ, Genzen JR, Hickner J, Marques MB. Opportunities to Enhance Laboratory Professionals' Role On the Diagnostic Team. Laboratory Medicine 2017;48(1):97-103.
Rudosph J, Jackson BR, Smock KJ, Wilson AR, Schmidt RL. Organizational Benchmarks for Test Utilization Performance: An Example Based on Positivity Rates for Genetic Tests. American Journal of Clinical Pathology 2017;147(4):382-389.
Carlston CM, O'Donnell-Luria AH, Underhill HR, Cummings BB, Weisburd B, Minikel EV, Birnbaum DP; Exome Aggregation Consortium., Tvrdik T, MacArthur DG, Mao R. Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome. Human Mutation 2017;38(5):517-523.
Brown AF, Salama ME, Patel JL, Paxton CN, Xu X, Perkins SL, Li KD. PD-L1 protein expression in most EBV-driven lymphoproliferative disorders is not associated with 9p24.1 amplification. San Diego Society of Hematopathology 2017;2(1):58-68.
Zhou Z, Reyes-Vargas E, Escobar H, Chang KY, Barker AP, Rockwood AL, Delgado JC, He X, Jensen PE. Peptidomic analysis of type 1 diabetes associated HLA-DQ molecules and the impact of HLA-DM on peptide repertoire editing. European Journal of Immunology 2017;47(2):314-326.
Kendall BA, Tkach VV, Gutierrez Y, Longino JT, Couturier MR. Photo Quiz: Motile Structures in the Stool of a Field Biologist. Journal of Clinical Microbiology 2017;55(8):2293.
Sirdah MM, Shubair ME, Al-Kahlout MS, Al-Tayeb, JM, Prchal JT, Reading NS. Possible Association of 3' UTR +357 A>G, IVS11-nt 93 T>C, c.1311 C>T Polymorphism with G6PD Deficiency Hematology. Hematology 2017;22(6):370-374.
Cohen AL, Factor RE, Mooney K, Salama ME, Wade M, Serpico V, Ostrander E, Nelson E, Porretta J, Matsen C, Bernard P, Boucher K, Neumayer L. POWERPIINC (PreOperative Window of Endocrine Therapy Provides Information to Increase Compliance) trial: Changes in tumor proliferation index and quality of life with 7 days of preoperative tamoxifen. Breast 2017;31:219-223.
Clark ZD, Cutler JM, Frank EL. APractical LC-MS/MS Method for 5-Hydroxyindoleacetic Acid in Urine. Journal of Applied Laboratory Medicine 2017;1(4)387-399.
Kuo CY, Garcia-Lloret MI, Slev P, Bohnsack JF, Chen K. Profound T-cell lymphopenia associated with prenatal exposure to purine antagonists detected by TREC newborn screening. The Journal of Allergy and Clinical Immunology. In Practice. 2017;5(1):198-200.
Zhou W, Geiersbach K, Chadwick B. Rapid removal of cytology slide coverslips for DNA and RNA isolation. Journal of the American Society of Cytopathology 2017;6(1):24-27.
Greene DN, Elliott-Jelf MC, Grenache DG. SCF-KIT signaling induces endothelin-3 synthesis and secretion: Thereby activates and regulates endothelin-B-receptor for generating temporally- and spatially-precise nitric oxide to modulate SCF- and or KIT-expressing. PLOS One 2017;12(9):e0184154.
Pyne MT, Mallory MA, Xie HB, Mei Y, Schlaberg R, Hillyard DR. Sequencing of the Hepatitis D Virus RNA WHO International Standard. Journal of Clinical Virology 2017;90:52-56.
Zhang Y, Sakthivel SK,, Bramley A, Jain S, Haynes A, Chappell JD, Hymas W, Lenny N, Patel A, Qi C, Ampofo K, Arnold SR, Self WH, Williams DJ, Hillyard D, Anderson EJ, Grijalva CG, Zhu Y, Wunderink RG, Edwards KM, Pavia. Serology Enhances Molecular Diagnosis of Respiratory Virus Infections Other than Influenza in Children and Adults Hospitalized with Community-Acquired Pneumonia. Journal of Clinical Microbiology 2017;55(1):79-89.
Clark ZD, Cutler JM, Pavlov IY, Strathmann FG, Frank EL. Simple dilute-and-shoot method for urinary vanillylmandelic acid and homovanillic acid by liquid chromatography tandem mass spectrometry. Clinica Chimica Acta 2017;468(2017) 201.
Tang H, Lee M, Kim EH, Bishop D, Rodgers GM. siRNA-knockdown of ADAMTS-13 modulates endothelial cell angiogenesis. Microvascular Research 2017;113:65-70.
Wu F, Marin SJ, McMillin GA. Stability of 21 cocaine, opioid and benzodiazepine druganalytes in meconium at three temperatures. Journal of Analytical Toxicology 2017;41(3):196-204.
Wu F, Marin SJ, Clark CJ, McMillin GA. Stability of 21 Cocaine, Opioid, and Benzodiazepine Drug Analytes in Meconium at 3 Temperatures. American Journal of Clinical Pathology 2017;1639:33-44.
Schmidt RL, Chute DJ, Colbert-Getz JM, Firpo-Betancourt A, James DS, Karp KJ, Miller DC, Milner DA, Smock KJ, Sutton AT, White KL, Walker BS, Wilson AR, Wojcik EM, Yared MA, Factor RE. Statistical literacy among academic pathologists: A Survey to Gauge Knowledge of Frequently Used Statistical Tests Among Faculty and Trainees. Archives of Pathology and Laboratory Medicine 2017;141(2):279-287.
Rasmussen NN, Cichelli J, Adler C, Barker A, Strathmann FG. The Best of Both Worlds: LC/Q-TOF as a method to detect a targeted list of 35 drugs and metabolites in urine with retrospective data mining capabilities. Agilent Technologies, Inc 2017;5991-7955EN.
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. The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care. Academic Pathology 2017;4:2374289517708309.
Lee S, Luo W, Shah T, Yin C, O'Connell T, Chung TH, Perkins SL, Miles RR, Ayello J, Morris E, Harrison L, van de Ven C, Cairo MS. The effects of DLEU1 gene expression in Burkitt lymphoma (BL): potential mechanism of chemoimmunotherapy resistance in BL. Oncotarget 2017;8(17):27839-27853.
Staats PN, Witt BL. The significance of NIFTP for thyroid cytology. CAP Today 2017;31(1):33-35.
Straseski JA, Whale C, Wilson A, Strathmann FG. The significance of reporting to the thousandths place: Figuring out the laboratory limitations. Practical Laboratory Medicine 2017;7:1-5.
Margraf RL, VanSant-Webb C, Sant D, Carey J, Hanson H, D'Astous J, Viskochil D, Stevenson DA, Mao R. Utilization of Whole-Exome Next-Generation Sequencing Variant Read Frequency for Detection of Lesion-Specific, Somatic Loss of Heterozygosity in a Neurofibromatosis Type 1 Cohort with Tibial Pseudarthrosis. The Journal of Molecular Diagnostics 2017;19(3):468-474.
Schlaberg R, Queen K, Simmon K, Tardif K, Stockmann C, Flygare S, Kennedy B, Voelkerding K, Bramley A, Zhang J, Eilbeck K, Yandell M, Jain S, Pavia AT, Tong S, Ampofo K. Viral Pathogen Detection by Metagenomics and Pan Viral Group PCR in Children with Pneumonia Lacking Identifiable Etiology. The Journal of Infectious Diseases 2017;215(9):1407-1415.