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Marya NB, Hartley C, Powers PD, Bois MC, Kerr SE, Graham RP, Levy MJ. Development of a Computer-aided Prediction Tool for Evaluating Brushing Samples of Biliary Strictures. Clin Gastroenterol Hepatol 2024; 22:185-187.e3. [PMID: 36967098 DOI: 10.1016/j.cgh.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/03/2023] [Accepted: 03/11/2023] [Indexed: 04/22/2023]
Affiliation(s)
- Neil B Marya
- Division of Gastroenterology, UMass Chan Medical School, Worcester, Massachusetts; Program in Digital Medicine, UMass Chan Medical School, Worcester, Massachusetts.
| | - Christopher Hartley
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patrick D Powers
- Program in Digital Medicine, UMass Chan Medical School, Worcester, Massachusetts
| | - Melanie C Bois
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- Allina Health Laboratory, Minneapolis, Minnesota
| | - Rondell P Graham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michael J Levy
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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Bakkum-Gamez JN, Sherman ME, Slettedahl SW, Mahoney DW, Lemens MA, Laughlin-Tommaso SK, Hopkins MR, VanOosten A, Shridhar V, Staub JK, Cao X, Foote PH, Clarke MA, Burger KN, Berger CK, O'Connell MC, Doering KA, Podratz KC, DeStephano CC, Schoolmeester JK, Kerr SE, Wentzensen N, Taylor WR, Kisiel JB. Detection of endometrial cancer using tampon-based collection and methylated DNA markers. Gynecol Oncol 2023; 174:11-20. [PMID: 37141817 DOI: 10.1016/j.ygyno.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/26/2022] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 05/06/2023]
Abstract
OBJECTIVE Alterations in DNA methylation are early events in endometrial cancer (EC) development and may have utility in EC detection via tampon-collected vaginal fluid. METHODS For discovery, DNA from frozen EC, benign endometrium (BE), and benign cervicovaginal (BCV) tissues underwent reduced representation bisulfite sequencing (RRBS) to identify differentially methylated regions (DMRs). Candidate DMRs were selected based on receiver operating characteristic (ROC) discrimination, methylation level fold-change between cancers and controls, and absence of background CpG methylation. Methylated DNA marker (MDM) validation was performed using qMSP on DNA from independent EC and BE FFPE tissue sets. Women ≥45 years of age with abnormal uterine bleeding (AUB) or postmenopausal bleeding (PMB) or any age with biopsy-proven EC self-collected vaginal fluid using a tampon prior to clinically indicated endometrial sampling or hysterectomy. Vaginal fluid DNA was assayed by qMSP for EC-associated MDMs. Random forest modeling analysis was performed to generate predictive probability of underlying disease; results were 500-fold in-silico cross-validated. RESULTS Thirty-three candidate MDMs met performance criteria in tissue. For the tampon pilot, 100 EC cases were frequency matched by menopausal status and tampon collection date to 92 BE controls. A 28-MDM panel highly discriminated between EC and BE (96% (95%CI 89-99%) specificity; 76% (66-84%) sensitivity (AUC 0.88). In PBS/EDTA tampon buffer, the panel yielded 96% (95% CI 87-99%) specificity and 82% (70-91%) sensitivity (AUC 0.91). CONCLUSION Next generation methylome sequencing, stringent filtering criteria, and independent validation yielded excellent candidate MDMs for EC. EC-associated MDMs performed with promisingly high sensitivity and specificity in tampon-collected vaginal fluid; PBS-based tampon buffer with added EDTA improved sensitivity. Larger tampon-based EC MDM testing studies are warranted.
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Affiliation(s)
- Jamie N Bakkum-Gamez
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Surgery, Mayo Clinic, Rochester, MN, United States of America.
| | - Mark E Sherman
- Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, United States of America
| | - Seth W Slettedahl
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States of America
| | - Douglas W Mahoney
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States of America
| | - Maureen A Lemens
- Surgery Research, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Shannon K Laughlin-Tommaso
- Department of Obstetrics and Gynecology, Division of Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Matthew R Hopkins
- Department of Obstetrics and Gynecology, Division of Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Ann VanOosten
- Surgery Research, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Viji Shridhar
- Department of Laboratory Medicine and Pathology, Experimental Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Julie K Staub
- Department of Laboratory Medicine and Pathology, Experimental Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Xiaoming Cao
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Patrick H Foote
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Megan A Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Kelli N Burger
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Calise K Berger
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Maria C O'Connell
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Karen A Doering
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Karl C Podratz
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Surgery, Mayo Clinic, Rochester, MN, United States of America
| | - Christopher C DeStephano
- Department of Obstetrics and Gynecology, Division of Minimally Invasive Gynecology, Mayo Clinic, Jacksonville, FL, United States of America
| | - J Kenneth Schoolmeester
- Department of Laboratory Medicine and Pathology, Anatomic Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Sarah E Kerr
- Hospital Pathology Associates, Minneapolis, MN, United States of America
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - William R Taylor
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - John B Kisiel
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
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Ghosh T, Greipp PT, Knutson D, Kloft-Nelson S, Jenkins S, Mounajjed T, Said S, La Rosa S, Vanoli A, Sessa F, Naini BV, Bellizzi A, Zhang L, Kerr SE, Graham RP. BRAF Rearrangements and BRAF V600E Mutations Are Seen in a Subset of Pancreatic Carcinomas With Acinar Differentiation. Arch Pathol Lab Med 2022; 146:840-845. [PMID: 34614142 DOI: 10.5858/arpa.2020-0739-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Comprehensive genomic profiling has demonstrated that approximately 20% of pancreatic carcinomas with acinar differentiation harbor potentially targetable BRAF fusions that activate the MAPK pathway. OBJECTIVES.— To validate the above finding by BRAF break-apart fluorescence in situ hybridization (FISH) in a large series of pure acinar cell carcinomas (ACCs), evaluate tumors for the presence of BRAF V600E mutations, and compare clinicopathologic features of tumors with BRAF rearrangements with those without. DESIGN.— Thirty cases of pure ACC and 6 cases of mixed acinar-neuroendocrine carcinoma (ACC-NEC) were retrieved. A break-apart FISH probe was used to detect BRAF rearrangements. Immunohistochemistry for BRAF V600E was performed. RESULTS.— BRAF rearrangements by FISH were found in 6 of 36 cases (17%), 5 of which were pure ACC and 1 was a mixed ACC-NEC. Follow-up was available in 29 of 36 cases (81%). The median survival was 22 months for BRAF-rearranged cases and 16 months for BRAF-intact cases; the 2-year overall survival was 50% for BRAF-rearranged cases and 35% for BRAF-intact cases. No significant clinicopathologic differences were identified in cases with BRAF rearrangement compared with those without BRAF rearrangement. BRAF V600E mutation was identified in 2 of 34 cases (6%), both of which were pure ACC and were BRAF-intact by FISH. CONCLUSIONS.— This study supports the finding that BRAF rearrangements are present in approximately 20% of cases and identified BRAF V600E mutations in approximately 5% of cases. These cases may benefit from targeted therapy.
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Affiliation(s)
- Toshi Ghosh
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Darlene Knutson
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Sara Kloft-Nelson
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Sarah Jenkins
- From the Department of Health Sciences Research (Jenkins), Mayo Clinic, Rochester, Minnesota
| | - Taofic Mounajjed
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Samar Said
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Stefano La Rosa
- From the Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland (La Rosa)
| | - Alessandro Vanoli
- From the Anatomic Pathology Unit, Department of Molecular Medicine, University of Pavia, and IRCCS San Matteo Hospital, Pavia, Italy (Vanoli)
| | - Fausto Sessa
- From the Anatomic Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy (Sessa)
| | - Bita V Naini
- From the Department of Pathology, University of California, Los Angeles (Naini)
| | - Andrew Bellizzi
- From the Department of Pathology, University of Iowa, Iowa City (Bellizzi)
| | - Lizhi Zhang
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
| | - Rondell P Graham
- From the Department of Laboratory Medicine and Pathology (Ghosh, Greipp, Knutson, Kloft-Nelson, Mounajjed, Said, Zhang, Kerr, Graham), Mayo Clinic, Rochester, Minnesota
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Marinelli LM, Kisiel JB, Slettedahl SW, Mahoney DW, Lemens MA, Shridhar V, Taylor WR, Staub JK, Cao X, Foote PH, Burger KN, Berger CK, O'Connell MC, Doering KA, Giakoumopoulos M, Berg H, Volkmann C, Solsrud A, Allawi HT, Kaiser M, Vaccaro AM, Albright Crawford C, Moehlenkamp C, Shea G, Deist MS, Schoolmeester JK, Kerr SE, Sherman ME, Bakkum-Gamez JN. Methylated DNA markers for plasma detection of ovarian cancer: Discovery, validation, and clinical feasibility. Gynecol Oncol 2022; 165:568-576. [DOI: 10.1016/j.ygyno.2022.03.018] [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] [Received: 12/12/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
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DeJong SR, Bakkum-Gamez JN, Clayton AC, Henry MR, Keeney GL, Zhang J, Kroneman TN, Laughlin-Tommaso SK, Ahlberg LJ, VanOosten AL, Weaver AL, Wentzensen N, Kerr SE. Tao brush endometrial cytology is a sensitive diagnostic tool for cancer and hyperplasia among women presenting to clinic with abnormal uterine bleeding. Cancer Med 2021; 10:7040-7047. [PMID: 34532991 PMCID: PMC8525073 DOI: 10.1002/cam4.4235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/29/2021] [Revised: 08/09/2021] [Accepted: 08/14/2021] [Indexed: 12/21/2022] Open
Abstract
Background Abnormal uterine bleeding requires the investigation of the endometrium. Histology is typically used but there remains room for the improvement and use of cytology. Methods Women presenting for clinically indicated office endometrial biopsy were prospectively enrolled. Tao endometrial brushing and office endometrial biopsy were performed, and surgical procedure if clinically indicated. Tao brush cytology specimens were blindly reviewed by up to three pathologists, consensus obtained, and scored as: benign, atypical (favor benign), suspicious, positive for malignancy, or non‐diagnostic. Cytology and histology were compared to surgical pathology to determine sensitivity, specificity, positive, and negative predictive values to detect AH (atypical hyperplasia) or EC (endometrial cancer). Results Clinical indications of 197 enrolled patients included postmenopausal bleeding (90, 45.7%), abnormal uterine bleeding (94, 47.7%), and abnormal endometrium on ultrasound without bleeding (13, 6.6%). Of the 197 patients, 185 (93.9%) had cytology score consensus and a total of 196 (99.5%) had consensus regarding cytology positivity. Surgical pathology diagnoses (N = 85) were 13 (15.3%) FIGO grade 1 or 2 EC, 3 (3.5%) AH, and 69 (81.2%) benign endometrium. Sensitivity and specificity to detect EC or AH were 93.7% and 100%, respectively, via endometrial biopsy; 87.5% and 63.8%, respectively, via endometrial cytology when scores of malignancy, suspicious, or atypical were considered positive. Conclusions In a high‐risk population, Tao brush endometrial cytology showed high sensitivity to detect AH and EC comparable to biopsy histology when considering scores of malignancy, suspicious, atypical, and non‐diagnostic. Revisiting the potential value of endometrial cytology in the contemporary era of endometrial diagnostic workup is warranted.
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Affiliation(s)
- Stephanie R DeJong
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Jamie N Bakkum-Gamez
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Amy C Clayton
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael R Henry
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Gary L Keeney
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jun Zhang
- Department of Anatomic Pathology, Mayo Clinic, Phoenix, AZ, USA
| | | | | | - Lisa J Ahlberg
- Department of Obstetrics and Gynecology, Division of Gynecology, Mayo Clinic, Rochester, MN, USA
| | - Ann L VanOosten
- Department of Obstetrics and Gynecology, Division of Obstetrics and Gynecology Research, Mayo Clinic, Rochester, MN, USA
| | - Amy L Weaver
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sarah E Kerr
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA.,Currently: Hospital Pathology Associates, Minneapolis, MN, USA
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Murphy SJ, Levy MJ, Smadbeck JB, Karagouga G, McCune AF, Harris FR, Udell JB, Johnson SH, Kerr SE, Cheville JC, Kipp BR, Vasmatzis G, Gleeson FC. Theragnostic chromosomal rearrangements in treatment-naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound. J Cell Mol Med 2021; 25:4110-4123. [PMID: 33704908 PMCID: PMC8051743 DOI: 10.1111/jcmm.16381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 06/12/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 12/15/2022] Open
Abstract
A crucial mutational mechanism in malignancy is structural variation, in which chromosomal rearrangements alter gene functions that drive cancer progression. Herein, the presence and pattern of structural variations were investigated in twelve prospectively acquired treatment‐naïve pancreatic cancers specimens obtained via endoscopic ultrasound (EUS). In many patients, this diagnostic biopsy procedure and specimen is the only opportunity to identify somatic clinically relevant actionable alterations that may impact their care and outcome. Specialized mate pair sequencing (MPseq) provided genome‐wide structural variance analysis (SVA) with a view to identifying prognostic markers and possible therapeutic targets. MPseq was successfully performed on all specimens, identifying highly rearranged genomes with complete SVA on all specimens with > 20% tumour content. SVA identified chimeric fusion proteins and potentially immunogenic readthrough transcripts, change of function truncations, gains and losses of key genes linked to tumour progression. Complex localized rearrangements, termed chromoanagenesis, with broad pattern heterogeneity were observed in 10 (83%) specimens, impacting multiple genes with diverse cellular functions that could influence theragnostic evaluation and responsiveness to immunotherapy regimens. This study indicates that genome‐wide MPseq can be successfully performed on very limited clinically EUS obtained specimens for chromosomal rearrangement detection and potential theragnostic targets.
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Affiliation(s)
- Stephen J Murphy
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael J Levy
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
| | - James B Smadbeck
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Giannoula Karagouga
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexa F McCune
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Faye R Harris
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Julia B Udell
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sarah H Johnson
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sarah E Kerr
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - John C Cheville
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - George Vasmatzis
- Biomarker Discovery Laboratory, Centre for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ferga C Gleeson
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN, USA
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DiGuardo MA, Davila JI, Jackson RA, Nair AA, Fadra N, Minn KT, Atiq MA, Zarei S, Blommel JH, Knight SM, Jen J, Eckloff BW, Voss JS, Rumilla KM, Kerr SE, Lam-Himlin DM, Bellizzi AM, Graham RP, Kipp BR, Jenkins RB, Halling KC. RNA-Seq Reveals Differences in Expressed Tumor Mutation Burden in Colorectal and Endometrial Cancers with and without Defective DNA-Mismatch Repair. J Mol Diagn 2021; 23:555-564. [PMID: 33549857 DOI: 10.1016/j.jmoldx.2021.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
Tumor mutation burden (TMB) is an emerging biomarker of immunotherapy response. RNA sequencing in FFPE tissue samples was used for determining TMB in microsatellite-stable (MSS) and microsatellite instability-high (MSI-H) tumors in patients with colorectal or endometrial cancer. Tissue from tumors and paired normal tissue from 46 MSI-H and 12 MSS cases were included. Of the MSI-H tumors, 29 had defective DNA mismatch-repair mutations, and 17 had MLH1 promoter hypermethylation. TMB was measured using the expressed somatic nucleotide variants (eTMB). A method of accurate measurement of eTMB was developed that removes FFPE-derived artifacts by leveraging mutation signatures. There was a significant difference in the median eTMB values observed between MSI-H and MSS cases: 27.3 versus 6.7 mutations/megabase (mut/Mb) (P = 3.5 × 10-9). Among tumors with defective DNA-mismatch repair, those with mismatch-repair mutations had a significantly higher median eTMB than those with hypermethylation: 28.1 versus 17.5 mut/Mb (P = 0.037). Multivariate analysis showed that MSI status, tumor type (endometrial or colorectal), and age were significantly associated with eTMB. Additionally, using whole-exome sequencing in a subset of these patients, it was determined that DNA TMB correlated well with eTMB (Spearman correlation coefficient, 0.83). These results demonstrate that RNA sequencing can be used for measuring eTMB in FFPE tumor specimens.
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Affiliation(s)
- Margaret A DiGuardo
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jaime I Davila
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota; Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, Minnesota
| | - Rory A Jackson
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Asha A Nair
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Numrah Fadra
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kay T Minn
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mazen A Atiq
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shabnam Zarei
- Robert J Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Joseph H Blommel
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Shannon M Knight
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jin Jen
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Bruce W Eckloff
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jesse S Voss
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kandelaria M Rumilla
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- Hospital Pathology Associates, Minneapolis, Minnesota
| | - Dora M Lam-Himlin
- Department of Laboratory Medicine and Pathology, Divisions of Laboratory Genetics and Experimental Pathology, and Health Sciences Research, Mayo Clinic, Phoenix, Arizona
| | - Andrew M Bellizzi
- Holden Comprehensive Cancer Center, Department of Pathology, University of Iowa, Iowa City, Iowa
| | - Rondell P Graham
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Benjamin R Kipp
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robert B Jenkins
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kevin C Halling
- Division of Laboratory Genetics and Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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Delarue EMP, Kerr SE, Rymer TL. Habitat and sex effects on behaviour in fawn-footed mosaic-tailed rats (Melomys cervinipes). Aust Mammalogy 2021. [DOI: 10.1071/am19065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Habitat complexity reflects resource availability and predation pressure – both factors that influence behaviour. We investigated whether exploratory behaviour and activity varied in fawn-footed mosaic-tailed rats (Melomys cervinipes) from two habitats that were categorised differently based on vegetation. We conducted vegetation surveys to determine structural complexity and vegetation cover, confirming that an abandoned hoop-pine (Araucaria cunninghami) plantation forest was structurally less complex, with lower vegetation cover than a variable secondary rainforest. We then tested mosaic-tailed rats from both sites in four behavioural tests designed to assess exploratory and activity behaviours (open field, novel object, light-dark box, acoustic startle), predicting that rats from the less structurally complex habitat would be less exploratory, and show lower activity. Our results provide some evidence for a context-specific trade-off between exploratory behaviour and predation risk in rats from the abandoned hoop pine plantation, as rats were less active, and showed a freezing strategy in the light-dark box. We also found context-specific sex differences in behaviour in response to a novel object and sound. Our results suggest that small-scale variation in habitat structure and complexity, as well as sex differences, is associated with variation in behaviour, most likely through effects on resource availability and/or predation risk.
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Van Treeck BJ, Lotfalla M, Czeczok TW, Mounajjed T, Moreira RK, Allende DS, Reid MD, Naini BV, Westerhoff M, Adsay NV, Kerr SE, Rizvi SH, Smoot RL, Liu Y, Davila J, Graham RP. Molecular and Immunohistochemical Analysis of Mucinous Cystic Neoplasm of the Liver. Am J Clin Pathol 2020; 154:837-847. [PMID: 32880620 DOI: 10.1093/ajcp/aqaa115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Mucinous cystic neoplasm of the liver is characterized by neoplastic mucinous and/or biliary epithelium surrounded by ovarian-type stroma. Immunohistochemical studies have shown that the ovarian-type stroma expresses estrogen receptor, suggesting potential hormonal responsiveness. The molecular biology of mucinous cystic neoplasm of the liver remains poorly studied. METHODS Transcriptome sequencing and immunohistochemistry were performed on a series of mucinous cystic neoplasms. RESULTS Mucinous cystic neoplasm of the liver exhibited significantly increased RNA expression of ovarian stromal markers WT1, PR, and ER2 and sex cord stromal markers SF-1, inhibin-α, and calretinin compared with nonneoplastic liver. Immunohistochemistry confirmed the RNA-level data. Evidence for sex hormone biosynthesis was identified by significant overexpression of multiple estrogen biosynthetic enzymes. Expression of 17β-hydroxysteroid dehydrogenase 1 was confirmed immunohistochemically. Pathway analysis also identified significant upregulation of the hedgehog and Wnt pathways and significant downregulation of T-helper 1 and T-helper 2 pathways. CONCLUSIONS Mucinous cystic neoplasm of the liver recapitulates ovarian stroma at the morphologic, DNA, RNA, and protein levels. These data support the concept that this tumor likely arises from ectopic primitive gonadal tissue and/or stromal cells with capacity to transdifferentiate to ovarian cortical cells.
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Affiliation(s)
| | - Mira Lotfalla
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | | | | | | | | | | | - Bita V Naini
- Department of Pathology, University of California, Los Angeles
| | | | - N Volkan Adsay
- Department of Pathology, Koc University, Istanbul, Turkey
| | | | - Sumera H Rizvi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Rory L Smoot
- Department of Surgery, Mayo Clinic, Rochester, MN
| | - Yuanhang Liu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Jaime Davila
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
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10
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Venable ER, Kerr SE, Lopes MBS, Jones KA, Bellizzi AM, Mounajjed T, Raghunathan A, Hamidi O, Halfdanarson TR, Ryder M, Graham RP. Liver metastases from pituitary carcinomas mimicking visceral well-differentiated neuroendocrine tumors: a series of four cases. Diagn Pathol 2020; 15:81. [PMID: 32622369 PMCID: PMC7335443 DOI: 10.1186/s13000-020-00997-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/26/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Background Pathologists frequently encounter neuroendocrine tumors (NETs) presenting as multiple liver masses in routine practice. Most often, these are well-differentiated tumors with characteristic histologic features. In contrast, pituitary carcinoma is very rare, and there is limited data on its natural history and pathologic characterization. Methods The aim of this study was to describe clinical characteristics, histomorphology, immunophenotype and follow-up of pituitary carcinoma involving the liver and mimicking well-differentiated NETs of visceral origin. We selected a group of well-differentiated NETs of the pancreas to use as immunophenotypic controls. We identified 4 patients (age range, 51 to 73) with pituitary corticotroph carcinoma with liver metastases. Three patients presented with Cushing syndrome. Results All cases histologically resembled well-differentiated NETs of visceral origin with Ki-67 proliferation indices of 5–42% and expression of T-PIT; metastatic tumors were not immunoreactive with CDX2, Islet 1 or TTF-1. Conclusions Frequently, these cases display adrenocorticotropic hormone (ACTH) secretion and pituitary-specific transcription factor immunohistochemistry may be used as a reliable marker to distinguish metastatic pituitary carcinoma from NETs of visceral origin in addition to delineating a corticotroph carcinoma from somatotroph, lactotroph, thyrotroph, and gonadotroph lineage. Although rare, the differential diagnosis of pituitary carcinoma should be considered in metastatic well-differentiated NETs in which the site of origin is uncertain. In summary, pituitary corticotroph carcinoma can metastasize to the liver and mimic well-differentiated NET.
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Affiliation(s)
- Elise R Venable
- Division of Anatomic Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Sarah E Kerr
- Division of Anatomic Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - M Beatriz S Lopes
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Karra A Jones
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | | | - Taofic Mounajjed
- Division of Anatomic Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Aditya Raghunathan
- Division of Anatomic Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Oksana Hamidi
- Division of Endocrinology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Endocrinology and Metabolism, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Mabel Ryder
- Division of Endocrinology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rondell P Graham
- Division of Anatomic Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
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11
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Enninga EAL, Raber P, Quinton RA, Ruano R, Ikumi N, Gray CM, Johnson EL, Chakraborty R, Kerr SE. Maternal T Cells in the Human Placental Villi Support an Allograft Response during Noninfectious Villitis. J Immunol 2020; 204:2931-2939. [PMID: 32321754 DOI: 10.4049/jimmunol.1901297] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/26/2020] [Indexed: 12/15/2022]
Abstract
During human pregnancy, proinflammatory responses in the placenta can cause severe fetal complications, including growth restriction, preterm birth, and stillbirth. Villitis of unknown etiology (VUE), an inflammatory condition characterized by the infiltration of maternal CD8+ T cells into the placenta, is hypothesized to be secondary to either a tissue rejection response to the haploidentical fetus or from an undiagnosed infection. In this study, we characterized the global TCR β-chain profile in human T cells isolated from placentae diagnosed with VUE compared with control and infectious villitis-placentae by immunoSEQ. Immunosequencing demonstrated that VUE is driven predominantly by maternal T cell infiltration, which is significantly different from controls and infectious cases; however, these T cell clones show very little overlap between subjects. Mapping TCR clones to common viral epitopes (CMV, EBV, and influenza A) demonstrated that Ag specificity in VUE was equal to controls and significantly lower than CMV-specific clones in infectious villitis. Our data indicate VUE represents an allograft response, not an undetected infection. These observations support the development of screening methods to predict those at risk for VUE and the use of specific immunomodulatory therapies during gestation to improve outcomes in affected fetuses.
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Affiliation(s)
| | | | - Reade A Quinton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Rodrigo Ruano
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN 55905
| | - Nadia Ikumi
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa 7791
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa 7791
| | - Erica L Johnson
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
| | - Rana Chakraborty
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN 55905.,Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905.,Department of Immunology, Mayo Clinic, Rochester, MN 55905; and
| | - Sarah E Kerr
- Hospital Pathology Associates, Minneapolis, MN 55407
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12
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Kerr SE. Mismatch repair from Lynch syndrome to immunotherapy: A brief primer for cytopathologists. Cancer Cytopathol 2020; 128:515-517. [PMID: 32196978 DOI: 10.1002/cncy.22263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 02/18/2020] [Indexed: 11/05/2022]
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13
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Enninga EAL, Leontovich AA, Fedyshyn B, Wakefield L, Gandhi M, Markovic SN, Ruano R, Kerr SE. Upregulation of HLA-Class I and II in Placentas Diagnosed with Villitis of Unknown Etiology. Reprod Sci 2020; 27:1129-1138. [PMID: 32046454 DOI: 10.1007/s43032-019-00101-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 05/23/2019] [Accepted: 09/17/2019] [Indexed: 11/26/2022]
Abstract
The placenta utilizes many mechanisms to protect the haploidentical fetus from recognition by the maternal immune system. However, in cases of villitis of unknown etiology (VUE), maternal lymphocytes gain access into the placenta, causing significant health risks for the fetus. Evidence suggests that VUE is a rejection response between the mother and the haploidentical fetus. Therefore, we profiled human leukocyte antigen (HLA), an important predictor of transplant rejection, in VUE using placental tissue from ten patients with VUE and ten gestational age matched controls. Placentas were stained using novel multiplexed immunofluorescence (MxIF) to investigate morphology and HLA classes I and II. Gene expression was evaluated by microarray, and where available, tissue typing of mother/baby pairs was completed to determine HLA type. MxIF demonstrated strong CD8+ T cell infiltration and HLA class I staining both the distal and stem villi of VUE placentas. Compared to controls, VUE cases had significantly higher expression of HLA class II mRNA and pathway analysis demonstrated that 40% of the differentially expressed genes in VUE are related to tissue rejection. The data suggest that VUE resembles a rejection response between the mother and the fetus. It remains unknown what initiates immune recognition and why some mothers appear to be at higher risk for developing this condition than others. Understanding this etiology will be critical for developing effective interventions or prevention strategies during pregnancy.
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Affiliation(s)
- Elizabeth Ann L Enninga
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
| | | | - Bohdana Fedyshyn
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Laurie Wakefield
- Department of Transfusion Medicine, Mayo Clinic, Rochester, MN, USA
| | - Manish Gandhi
- Department of Transfusion Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Rodrigo Ruano
- Department of Obstetrics and Gynecology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sarah E Kerr
- Department of Laboratory Pathology, Mayo Clinic, Rochester, MN, USA
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14
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Phillips AL, Cetta F, Kerr SE, Cheek EH, Rose CH, Bonnichsen CR, Phillips SD. The placenta: A site of end-organ damage after Fontan operation. A case series. Int J Cardiol 2019; 289:52-55. [PMID: 30765280 DOI: 10.1016/j.ijcard.2019.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Received: 09/28/2018] [Revised: 01/07/2019] [Accepted: 02/04/2019] [Indexed: 01/27/2023]
Abstract
BACKGROUND Placental insufficiency may be the cause of the high preterm birth rate in women after Fontan operation. In this study we reviewed the clinical course and pregnancy outcome of women with Fontan physiology with a focus on placental pathology. METHODS We reviewed clinical charts and placental pathology from 7 women with Fontan physiology who had pregnancies at Mayo Clinic, Rochester, Minnesota. The review was limited to cases where placental pathologic specimens were rigorously examined. RESULTS Seven women had 13 deliveries between 2002 and 2018. Only 2 of 13 deliveries were at term (>37 weeks). Mean maternal age at time of last delivery was 27.5 ± 3.2 years. Preeclampsia was noted during 2 pregnancies and 2 women had preterm premature rupture of membranes at 24 and 35 weeks gestation, respectively. Placental abruption with bleeding occurred in 2 pregnancies. An additional 4 pregnancies were complicated by intrauterine growth restriction (IUGR). Median placental weight was 441.5 g (IQR 305.5-622.5 g). Median placental weight percentile for gestational age was 10th to 25th, but varied greatly; two placentas were <10th percentile and 5 were >90th percentile for gestational age. Two umbilical cords contained a single umbilical artery. Prominent subchorionic fibrin deposition was a consistent feature in all placentas. Villous hypermaturity was noted in 4 placentas. CONCLUSIONS Fontan physiology may be associated with poor placental health. High systemic venous pressure and low cardiac output may contribute to stagnation of placental blood flow and result in subchorionic fibrin deposition and variable villous hypoplasia. This may explain the high preterm birth rate in women with Fontan physiology. Preterm deliveries and small-for-gestational-age (SGA) newborns should be anticipated in this patient population. Analysis of placental pathology may help determine both candidacy for future pregnancy and long-term effects of pregnancy for women with Fontan physiology.
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Affiliation(s)
- Amanda L Phillips
- Wanek Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States of America
| | - Frank Cetta
- Wanek Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, MN, United States of America; Division of Pediatric Cardiology, Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States of America; Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, United States of America.
| | - Sarah E Kerr
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - E Heidi Cheek
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Carl H Rose
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, United States of America
| | - Crystal R Bonnichsen
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, United States of America
| | - Sabrina D Phillips
- Department of Cardiovascular Diseases, Mayo Clinic, Jacksonville, FL, United States of America
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15
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Lin S, Wang C, Zarei S, Bell DA, Kerr SE, Runger GC, Kocher JPA. A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas. BMC Genomics 2018; 19:841. [PMID: 30482155 PMCID: PMC6258141 DOI: 10.1186/s12864-018-5177-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 12/14/2017] [Accepted: 10/16/2018] [Indexed: 12/19/2022] Open
Abstract
Background Copy Number Alternations (CNAs) is defined as somatic gain or loss of DNA regions. The profiles of CNAs may provide a fingerprint specific to a tumor type or tumor grade. Low-coverage sequencing for reporting CNAs has recently gained interest since successfully translated into clinical applications. Ovarian serous carcinomas can be classified into two largely mutually exclusive grades, low grade and high grade, based on their histologic features. The grade classification based on the genomics may provide valuable clue on how to best manage these patients in clinic. Based on the study of ovarian serous carcinomas, we explore the methodology of combining CNAs reporting from low-coverage sequencing with machine learning techniques to stratify tumor biospecimens of different grades. Results We have developed a data-driven methodology for tumor classification using the profiles of CNAs reported by low-coverage sequencing. The proposed method called Bag-of-Segments is used to summarize fixed-length CNA features predictive of tumor grades. These features are further processed by machine learning techniques to obtain classification models. High accuracy is obtained for classifying ovarian serous carcinoma into high and low grades based on leave-one-out cross-validation experiments. The models that are weakly influenced by the sequence coverage and the purity of the sample can also be built, which would be of higher relevance for clinical applications. The patterns captured by Bag-of-Segments features correlate with current clinical knowledge: low grade ovarian tumors being related to aneuploidy events associated to mitotic errors while high grade ovarian tumors are induced by DNA repair gene malfunction. Conclusions The proposed data-driven method obtains high accuracy with various parametrizations for the ovarian serous carcinoma study, indicating that it has good generalization potential towards other CNA classification problems. This method could be applied to the more difficult task of classifying ovarian serous carcinomas with ambiguous histology or in those with low grade tumor co-existing with high grade tumor. The closer genomic relationship of these tumor samples to low or high grade may provide important clinical value.
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Affiliation(s)
- Sangdi Lin
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, 85281, AZ, USA
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, 55905, MN, USA
| | - Shabnam Zarei
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Debra A Bell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, 55905, MN, USA
| | - George C Runger
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, 85281, AZ, USA.,Department of Biomedical Informatics, Arizona State University, Scottsdale, 85259, AZ, USA
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16
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Affiliation(s)
- Wendy A Callaway
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Ayla A Turner
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Oscar B Croshaw
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Jade A Ferguson
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Zachary J -N Julson
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Trevor M Volp
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Sarah E Kerr
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
- Centre for Tropical Environmental and Sustainability Sciences, James Cook University, Cairns, Queensland, Australia
| | - Tasmin L Rymer
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
- Centre for Tropical Environmental and Sustainability Sciences, James Cook University, Cairns, Queensland, Australia
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17
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Levy MJ, Kipp BR, Milosevic D, Schneider AR, Voss JS, Avula R, Kerr SE, Henry MR, Highsmith E, Liu MC, Gleeson FC. Analysis of Cell-Free DNA to Assess Risk of Tumoremia Following Endoscopic Ultrasound Fine-Needle Aspiration of Pancreatic Adenocarcinomas. Clin Gastroenterol Hepatol 2018. [PMID: 29526691 DOI: 10.1016/j.cgh.2018.02.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 02/07/2023]
Abstract
BACKGROUND & AIMS Cellular and nuclear material from tumors disseminates into the bloodstream (tumoremia), but it is not clear whether medical procedures cause release of this material or contribute to formation of metastases. We performed a prospective study of blood samples from patients with pancreatic adenocarcinoma (PDAC) to determine whether endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) associates with markers of tumoremia. METHODS We obtained peripheral blood from 104 patients (35 with PDAC) before and after EUS-FNA of primary tumors; blood samples from 69 healthy individuals were used as controls. Plasma concentrations of cell-free DNA (cfDNA) were measured, and cfDNA and primary tumor samples were analyzed to detect activating mutations in KRAS. Potential development of tumoremia was defined by an increase in cfDNA of 2-fold or more, and/or detection of mutant KRAS in samples collected after FNA from patients whose blood samples did not contain detectable mutant KRAS before FNA. RESULTS Peripheral blood concentrations of cfDNA were 1200 ng/ml (500-3300 ng/ml) before FNA vs 1400 ng/ml (900-4000 ng/ml) after FNA (P = .391). Tumoremia was detected in 10/35 patients (28.6%): 7 patients had a ≥2-fold increase in cfDNA concentration (20.6%) and 3 patients had circulating tumor DNA with KRAS mutations after FNA that were not detected before FNA (8.8%). New distant metastases were detected in 1.3 ± 0.82 patients with tumoremia vs 0.64 ± 0.81 without (P = .0375). Overall mortality did not differ significantly between patients with tumoremia (10/10 deaths, 100%) vs those without (19/25 deaths, 76%) nor did survival times of deceased patients (13.3 months for patients with tumoremia; range, 5.8-14.9 months vs 11.1 months for patients without tumoremia; range, 5.5-14.5 months). However, 6 patients without tumoremia were alive at a mean 23.9 months after EUS-FNA (range, 19.9-25 months after EUS-FNA) vs none of the patients with tumoremia. CONCLUSION In patients with PDAC, EUS-FNA associates with increased plasma concentration of cfDNA and increased detection of mutant KRAS after the procedure (markers of tumoremia and possible new distant metastasis). Although levels of cfDNA and activating mutations in KRAS are logical markers of tumoremia, they may not serve as the ideal biomarkers of this process. These findings are preliminary and do not indicate a need to modify current practice, yet further studies are needed.
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Affiliation(s)
- Michael J Levy
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Amber R Schneider
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Rajeswari Avula
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michael R Henry
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Edward Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Minetta C Liu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Ferga C Gleeson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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18
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Mouchli MA, Kerr SE, Roberts L. An Enlarging Metastatic Calcified Liver Lesion of an Occult Melanoma. Case Rep Oncol 2018; 11:388-391. [PMID: 30022941 PMCID: PMC6047565 DOI: 10.1159/000489555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 12/03/2022] Open
Abstract
Calcified liver lesions are caused by a wide variety of factors. The most common lesions are inflammatory liver lesions followed by benign and malignant neoplasms. Hemangioma, one of the most common benign hepatic neoplasm in adults, often contains calcifications, in up to 20% of cases secondary to fibrosis and thrombosis of blood vessels. These calcifications are typically large, coarse, and located in the center of the lesions. Liver metastases, the most common malignant lesions found in the noncirrhotic liver, may contain areas of calcification. Radiologists should be aware of morphologic imaging features of calcified liver lesions to help differentiate benign from malignant lesions. Liver biopsy should be offered when the diagnosis is doubtful.
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Affiliation(s)
- Mohamad A Mouchli
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA.,Division of Gastroenterology and Hepatology, Carilion Clinic, Roanoke, Virginia, USA
| | - Sarah E Kerr
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lewis Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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19
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Bryce AH, Egan JB, Borad MJ, Stewart AK, Nowakowski GS, Chanan-Khan A, Patnaik MM, Ansell SM, Banck MS, Robinson SI, Mansfield AS, Klee EW, Oliver GR, McCormick JB, Huneke NE, Tagtow CM, Jenkins RB, Rumilla KM, Kerr SE, Kocher JPA, Beck SA, Fernandez-Zapico ME, Farrugia G, Lazaridis KN, McWilliams RR. Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery. Oncotarget 2018; 8:27145-27154. [PMID: 28423702 PMCID: PMC5432324 DOI: 10.18632/oncotarget.16057] [Citation(s) in RCA: 45] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/15/2017] [Indexed: 01/16/2023] Open
Abstract
Background The ability to analyze the genomics of malignancies has opened up new possibilities for off-label targeted therapy in cancers that are refractory to standard therapy. At Mayo Clinic these efforts are organized through the Center for Individualized Medicine (CIM). Results Prior to GTB, datasets were analyzed and integrated by a team of bioinformaticians and cancer biologists. Therapeutically actionable mutations were identified in 65% (92/141) of the patients tested with 32% (29/92) receiving genomically targeted therapy with FDA approved drugs or in an independent clinical trial with 45% (13/29) responding. Standard of care (SOC) options were continued by 15% (14/92) of patients tested before exhausting SOC options, with 71% (10/14) responding to treatment. Over 35% (34/92) of patients with actionable targets were not treated with 65% (22/34) choosing comfort measures or passing away. Materials and Methods Patients (N = 165) were referred to the CIM Clinic between October 2012 and December 2015. All patients received clinical genomic panel testing with selected subsets receiving array comparative genomic hybridization and clinical whole exome sequencing to complement and validate panel findings. A genomic tumor board (GTB) reviewed results and, when possible, developed treatment recommendations. Conclusions Treatment decisions driven by tumor genomic analysis can lead to significant clinical benefit in a minority of patients. The success of genomically driven therapy depends both on access to drugs and robustness of bioinformatics analysis. While novel clinical trial designs are increasing the utility of genomic testing, robust data sharing of outcomes is needed to optimize clinical benefit for all patients.
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Affiliation(s)
- Alan H Bryce
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Jan B Egan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Mitesh J Borad
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - A Keith Stewart
- Hematology/Oncology, Mayo Clinic, Phoenix, AZ, U.S.A.,Mayo Clinic Cancer Center, Phoenix, AZ, U.S.A.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Grzegorz S Nowakowski
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Asher Chanan-Khan
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology/Oncology, Mayo Clinic, Jacksonville, FL, U.S.A
| | - Mrinal M Patnaik
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Stephen M Ansell
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Hematology, Mayo Clinic, Rochester, MN, U.S.A
| | - Michaela S Banck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Steven I Robinson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Aaron S Mansfield
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Norine E Huneke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Colleen M Tagtow
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Robert B Jenkins
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Sarah E Kerr
- Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | - Jean-Pierre A Kocher
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Health Sciences Research, Mayo Clinic, Rochester, MN, U.S.A
| | - Scott A Beck
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A
| | - Martin E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A
| | - Gianrico Farrugia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Gastroenterology, Mayo Clinic, Rochester, MN, U.S.A
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Gastroenterology, Mayo Clinic, Rochester, MN, U.S.A
| | - Robert R McWilliams
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, U.S.A.,Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A.,Mayo Clinic Cancer Center, Rochester, MN, U.S.A
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Brachtel EF, Operaña TN, Sullivan PS, Kerr SE, Cherkis KA, Schroeder BE, Dry SM, Schnabel CA. Molecular classification of cancer with the 92-gene assay in cytology and limited tissue samples. Oncotarget 2017; 7:27220-31. [PMID: 27034010 PMCID: PMC5053644 DOI: 10.18632/oncotarget.8449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 03/20/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Detailed molecular evaluation of cytology and limited tissue samples is increasingly becoming the standard for cancer care. Reproducible and accurate diagnostic approaches with reduced demands on cellularity are an ongoing unmet need. This study evaluated the performance of a 92-gene assay for molecular diagnosis of tumor type/subtype in cytology and limited tissue samples. METHODS Clinical validation of accuracy for the 92-gene assay in limited tissue samples such as cytology cell blocks, core biopsies and small excisions was conducted in a blinded multi-institutional study (N = 109, 48% metastatic, 53% grade II and III). Analytical success rate and diagnostic utility were evaluated in a consecutive series of 644 cytology cases submitted for clinical testing. RESULTS The 92-gene assay demonstrated 91% sensitivity (95% CI [0.84, 0.95]) for tumor classification, with high accuracy maintained irrespective of specimen type (100%, 92%, and 86% in FNA/cytology cell blocks, core biopsies, and small excisions, respectively; p = 0.26). The assay performed equally well for metastatic versus primary tumors (90% vs 93%, p = 0.73), and across histologic grades (100%, 90%, 89%, in grades I, II, and III, respectively; p = 0.75). In the clinical case series, a molecular diagnosis was reported in 87% of the 644 samples, identifying 23 different tumor types and allowing for additional mutational analysis in selected cases. CONCLUSIONS These findings demonstrate high accuracy and analytical success rate of the 92-gene assay, supporting its utility in the molecular diagnosis of cancer for specimens with limited tissue.
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Affiliation(s)
- Elena F Brachtel
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Peggy S Sullivan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Sarah M Dry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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Egan JB, Marks DL, Hogenson TL, Vrabel AM, Sigafoos AN, Tolosa EJ, Carr RM, Safgren SL, Enriquez Hesles E, Almada LL, Romecin-Duran PA, Iguchi E, Ala’Aldeen A, Kocher JPA, Oliver GR, Prodduturi N, Mead DW, Hossain A, Huneke NE, Tagtow CM, Ailawadhi S, Ansell SM, Banck MS, Bryce AH, Carballido EM, Chanan-Khan AA, Curtis KK, Resnik E, Gawryletz CD, Go RS, Halfdanarson TR, Ho TH, Joseph RW, Kapoor P, Mansfield AS, Meurice N, Nageswara Rao AA, Nowakowski GS, Pardanani A, Parikh SA, Cheville JC, Feldman AL, Ramanathan RK, Robinson SI, Tibes R, Finnes HD, McCormick JB, McWilliams RR, Jatoi A, Patnaik MM, Silva AC, Wieben ED, McAllister TM, Rumilla KM, Kerr SE, Lazaridis KN, Farrugia G, Stewart AK, Clark KJ, Kennedy EJ, Klee EW, Borad MJ, Fernandez-Zapico ME. Molecular Modeling and Functional Analysis of Exome Sequencing–Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma. JCO Precis Oncol 2017; 2017. [PMID: 30761385 PMCID: PMC6369924 DOI: 10.1200/po.17.00018] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Genomic testing has increased the quantity of information available to oncologists. Unfortunately, many identified sequence alterations are variants of unknown significance (VUSs), which thus limit the clinician’s ability to use these findings to inform treatment. We applied a combination of in silico prediction and molecular modeling tools and laboratory techniques to rapidly define actionable VUSs. Materials and Methods Exome sequencing was conducted on 308 tumors from various origins. Most single nucleotide alterations within gene coding regions were VUSs. These VUSs were filtered to identify a subset of therapeutically targetable genes that were predicted with in silico tools to be altered in function by their variant sequence. A subset of receptor tyrosine kinase VUSs was characterized by laboratory comparison of each VUS versus its wild-type counterpart in terms of expression and signaling activity. Results The study identified 4,327 point mutations of which 3,833 were VUSs. Filtering for mutations in genes that were therapeutically targetable and predicted to affect protein function reduced these to 522 VUSs of interest, including a large number of kinases. Ten receptor tyrosine kinase VUSs were selected to explore in the laboratory. Of these, seven were found to be functionally altered. Three VUSs (FGFR2 F276C, FGFR4 R78H, and KDR G539R) showed increased basal or ligand-stimulated ERK phosphorylation compared with their wild-type counterparts, which suggests that they support transformation. Treatment of a patient who carried FGFR2 F276C with an FGFR inhibitor resulted in significant and sustained tumor response with clinical benefit. Conclusion The findings demonstrate the feasibility of rapid identification of the biologic relevance of somatic mutations, which thus advances clinicians’ ability to make informed treatment decisions.
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Affiliation(s)
- Jan B. Egan
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - David L. Marks
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Tara L. Hogenson
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Anne M. Vrabel
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Ashley N. Sigafoos
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Ezequiel J. Tolosa
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Ryan M. Carr
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Stephanie L. Safgren
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Elisa Enriquez Hesles
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Luciana L. Almada
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Paola A. Romecin-Duran
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Eriko Iguchi
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Aryan Ala’Aldeen
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Jean-Pierre A. Kocher
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Gavin R. Oliver
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Naresh Prodduturi
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - David W. Mead
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Asif Hossain
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Norine E. Huneke
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Colleen M. Tagtow
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Sikander Ailawadhi
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Stephen M. Ansell
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Michaela S. Banck
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Alan H. Bryce
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Estrella M. Carballido
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Asher A. Chanan-Khan
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Kelly K. Curtis
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Ernesto Resnik
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Chelsea D. Gawryletz
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Ronald S. Go
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Thorvardur R. Halfdanarson
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Thai H. Ho
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Richard W. Joseph
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Prashant Kapoor
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Aaron S. Mansfield
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Nathalie Meurice
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Amulya A. Nageswara Rao
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Grzegorz S. Nowakowski
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Animesh Pardanani
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Sameer A. Parikh
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - John C. Cheville
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Andrew L. Feldman
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Ramesh K. Ramanathan
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Steven I. Robinson
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Raoul Tibes
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Heidi D. Finnes
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Jennifer B. McCormick
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Robert R. McWilliams
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Aminah Jatoi
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Mrinal M. Patnaik
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Alvin C. Silva
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Eric D. Wieben
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | | | | | | | | | - Gianrico Farrugia
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - A. Keith Stewart
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Karl J. Clark
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Eileen J. Kennedy
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Eric W. Klee
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Mitesh J. Borad
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
| | - Martin E. Fernandez-Zapico
- David L. Marks, Tara L. Hogenson, Anne M. Vrabel, Ashley N. Sigafoos, Ezequiel J. Tolosa, Ryan M. Carr, Stephanie L. Safgren, Elisa Enriquez Hesles, Luciana L. Almada, Paola A. Romecin-Duran, Eriko Iguchi, Aryan Ala’Aldeen, Jean-Pierre A. Kocher, Gavin R. Oliver, Naresh Prodduturi, David W. Mead, Asif Hossain, Norine E. Huneke, Colleen M. Tagtow, Sikander Ailawadhi, Stephen M. Ansell, Michaela S. Banck, Asher A. Chanan-Khan, Ronald S. Go, Thorvardur R. Halfdanarson, Richard W. Joseph, Prashant Kapoor,
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McAuliffe MJ, Fletcher AR, Kerr SE, O'Beirne GA, Anderson T. Effect of Dysarthria Type, Speaking Condition, and Listener Age on Speech Intelligibility. Am J Speech Lang Pathol 2017; 26:113-123. [PMID: 28124068 DOI: 10.1044/2016_ajslp-15-0182] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
PURPOSE The aim of this study was to examine the effect of loud and slow speech cues on younger and older listeners' comprehension of dysarthric speech, specifically, (a) whether one strategy, as opposed to the other, promoted greater intelligibility gains for different speaker groups; (b) whether older and younger listeners' understandings were differentially affected by these strategies; and (c) which acoustic changes best predicted intelligibility gain in individual speakers. METHOD Twenty younger and 40 older listeners completed a perceptual task. Six individuals with dysarthria produced phrases across habitual, loud, and slow conditions. The primary dependent variable was proportion of words correct; follow-up acoustic analyses linked perceptual outcomes to changes in acoustic speech features. RESULTS Regardless of dysarthria type, the loud condition produced significant intelligibility gains. Overall, older listeners' comprehension was reduced relative to younger listeners. Follow-up analysis revealed considerable interspeaker differences in intelligibility outcomes across conditions. Although the most successful speaking mode varied, intelligibility gains were strongly associated with the degree of change participants made to their vowel formants. CONCLUSIONS Perceptual outcomes vary across speaking modes, even when speakers with dysarthria are grouped according to similar perceptual profiles. Further investigation of interspeaker differences is needed to inform individually tailored intervention approaches.
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Affiliation(s)
- Megan J McAuliffe
- Department of Communication Disorders, University of Canterbury, Christchurch, New ZealandNew Zealand Institute of Language, Brain & Behaviour, University of Canterbury, Christchurch, New Zealand
| | - Annalise R Fletcher
- Department of Communication Disorders, University of Canterbury, Christchurch, New ZealandNew Zealand Institute of Language, Brain & Behaviour, University of Canterbury, Christchurch, New Zealand
| | - Sarah E Kerr
- Department of Communication Disorders, University of Canterbury, Christchurch, New ZealandNew Zealand Institute of Language, Brain & Behaviour, University of Canterbury, Christchurch, New Zealand
| | - Greg A O'Beirne
- Department of Communication Disorders, University of Canterbury, Christchurch, New ZealandNew Zealand Institute of Language, Brain & Behaviour, University of Canterbury, Christchurch, New Zealand
| | - Tim Anderson
- New Zealand Brain Research Institute, Christchurch, New Zealand
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23
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Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ. Molecular cytology genotyping of primary and metastatic GI stromal tumors by using a custom two-gene targeted next-generation sequencing panel with therapeutic intent. Gastrointest Endosc 2016; 84:950-958.e3. [PMID: 27118626 DOI: 10.1016/j.gie.2016.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 04/15/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS In an era of precision medicine, customized genotyping of GI stromal tumors by screening for driver mutations will become the standard of care. The fidelity of genotype concordance between paired cytology smears and surgical pathology specimens is unknown. In patients with either primary or metastatic sporadic disease, we sought to determine the frequency of KIT and PDGFRA pathogenic alterations within such specimens, imatinib sensitivity, and the concordance of pathogenic alterations between paired specimens. METHODS DNA obtained from cytology smears from 36 patients, 24 of whom had paired surgical pathology specimens, underwent targeted next-generation sequencing by using a custom panel to evaluate somatic mutations within KIT (exon 2, 9, 10, 11, 13, 14, 15, 17, 18) and PDGFRA (exon 12, 14, 15, 18) genes. Patients with KIT and PDGRFA wild-type genes completed the Qiagen Human Comprehensive Cancer GeneRead DNAseq Targeted Array V2. RESULTS Genotyping revealed KIT and PDGFRA mutations in 68% and 15% of patients. The wild-type population did not harbor mutations in BRAF, RAS family, SDHB, SETD2, or NF1. Imatinib sensitivity based on the oncogenic kinase mutation prevalence was estimated to be 68%. Mutational concordance between paired cytology and surgical pathology specimens was 96%. CONCLUSIONS Our data have demonstrated the ability to stratify either primary or metastatic gastrointestinal stromal tumors by mutational subtype using a targeted next-generation sequencing 2 gene mutation panel. We highlight the ability to use cytology specimens obtained via minimally invasive techniques as a surrogate to surgical specimens given the high mutational landscape concordance between paired specimens.
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Affiliation(s)
- Ferga C Gleeson
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas M Minot
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Zheng Jin Tu
- Division of Biomedical Statics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael R Henry
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C Cheville
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Konstantinos N Lazaridis
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael J Levy
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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24
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Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Graham RP, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ. Targeted next generation sequencing of endoscopic ultrasound acquired cytology from ampullary and pancreatic adenocarcinoma has the potential to aid patient stratification for optimal therapy selection. Oncotarget 2016; 7:54526-54536. [PMID: 27203738 PMCID: PMC5342360 DOI: 10.18632/oncotarget.9440] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 04/24/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND & AIMS Less than 10% of registered drug intervention trials for pancreatic ductal adenocarcinoma (PDAC) include a biomarker stratification strategy. The ability to identify distinct mutation subsets via endoscopic ultrasound fine needle aspiration (EUS FNA) molecular cytology could greatly aid clinical trial patient stratification and offer predictive markers. We identified chemotherapy treatment naïve ampullary adenocarcinoma and PDAC patients who underwent EUS FNA to assess multigene mutational frequency and diversity with a surgical resection concordance assessment, where available. METHODS Following strict cytology smear screening criteria, targeted next generation sequencing (NGS) using a 160 cancer gene panel was performed. RESULTS Complete sequencing was achieved in 29 patients, whereby 83 pathogenic alterations were identified in 21 genes. Cytology genotyping revealed that the majority of mutations were identified in KRAS (93%), TP53 (72%), SMAD4 (31%), and GNAS (10%). There was 100% concordance for the following pathogenic alterations: KRAS, TP53, SMAD4, KMT2D, NOTCH2, MSH2, RB1, SMARCA4, PPP2R1A, PIK3R1, SCL7A8, ATM, and FANCD2. Absolute multigene mutational concordance was 83%. Incremental cytology smear mutations in GRIN2A, GATA3 and KDM6A were identified despite re-examination of raw sequence reads in the corresponding resection specimens. CONCLUSIONS EUS FNA cytology genotyping using a 160 cancer gene NGS panel revealed a broad spectrum of pathogenic alterations. The fidelity of cytology genotyping to that of paired surgical resection specimens suggests that EUS FNA represents a suitable surrogate and may complement the conventional stratification criteria in decision making for therapies and may guide future biomarker driven therapeutic development.
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Affiliation(s)
- Ferga C. Gleeson
- Division of Gastroenterology & Hepatology, Mayo Clinic Rochester, MN, USA
| | - Sarah E. Kerr
- Department of Laboratory Medicine & Pathology, Mayo Clinic Rochester, MN, USA
| | - Benjamin R. Kipp
- Department of Laboratory Medicine & Pathology, Mayo Clinic Rochester, MN, USA
| | - Jesse S. Voss
- Department of Laboratory Medicine & Pathology, Mayo Clinic Rochester, MN, USA
| | - Douglas M. Minot
- Department of Laboratory Medicine & Pathology, Mayo Clinic Rochester, MN, USA
| | - Zheng Jin Tu
- Division of Biomedical Statics & Informatics, Department of Health Sciences Research, Mayo Clinic Rochester, MN, USA
| | - Michael R. Henry
- Department of Laboratory Medicine & Pathology, Mayo Clinic Rochester, MN, USA
| | - Rondell P. Graham
- Department of Laboratory Medicine & Pathology, Mayo Clinic Rochester, MN, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - John C. Cheville
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N. Lazaridis
- Division of Gastroenterology & Hepatology, Mayo Clinic Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael J. Levy
- Division of Gastroenterology & Hepatology, Mayo Clinic Rochester, MN, USA
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Affiliation(s)
- Rodica Gincul
- Gastroenterology Department, Mayo Clinic, Rochester, Minnesota, USA
| | - Victoria Gomez
- Gastroenterology Department, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael J Levy
- Gastroenterology Department, Mayo Clinic, Rochester, Minnesota, USA
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Leventakos K, Mansfield AS, Murphy SJ, Johnson SH, Kerr SE, Aubry MC, Vasmatzis G, Molina JR. Abstract 4513: A prognostic model for pulmonary carcinoid tumors based on large chromosomal alterations. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4513] [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: 11/16/2022]
Abstract
Abstract
PURPOSE: Previous mutational analyses have failed to identify a predictive or prognostic marker for pulmonary carcinoid tumors (PCT). The heterogeneity of PCTs coupled with a lack of detailed information about the tumor biology, impedes patient stratification into groups based on tumor phenotypes or treatment response. We sought to use high-throughput next-generation sequencing to improve prognostication.
METHODS: We stratified 37 patients with resected PCTs as low risk (n = 17) and high risk (n = 20) based on a 5 year long follow up for recurrence. Patients with no recurrence within 5 years from initial treatment were deemed low risk. Macrodissection was followed by genomic DNA isolation and next-generation sequencing was performed using an Illumina Mate Pair library protocol. Sequence reads were mapped to the human genome, and primers spanning the fusion junctions were used for validation polymerase chain reaction.
RESULTS:
Carcinoids commonly harbor rearrangements (median 3.5, range 1-167). Large chromosomal gains or losses were found in 24 of the cases (64.8%). We developed a prognostic score that included the total amount of genetic alterations (deletions and translocations). ROC analysis revealed an AUC of 0.76. High risk patients had a mean score of 20 and low risk patients had a mean score of 5.45 (p value = 0.03, Welch Two Sample t-test). Further analysis of the specific genetic alterations harbored by high and low risk PCTs and correlation with the pathologic and immunohistochemical information is currently underway.
CONCLUSION:
Large chromosomal rearrangements and aneuploidy portend a poor prognosis for patients with PCTs. Mate Pair sequencing of PCTs provides valuable prognostic information for this highly heterogeneous group of cancers.
Citation Format: Konstantinos Leventakos, Aaron S. Mansfield, Stephen J. Murphy, Sarah H. Johnson, Sarah E. Kerr, Marie Christine Aubry, George Vasmatzis, Julian R. Molina. A prognostic model for pulmonary carcinoid tumors based on large chromosomal alterations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4513.
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Nassar A, Reynolds JP, Kerr SE, Jenkins SM, Lackore KA, Bernet V. Survey of cytopathologists and cytotechnologists for the clinical impact of the use of atypia or follicular lesion of undetermined significance. Cytojournal 2015. [PMID: 26195986 PMCID: PMC4485319 DOI: 10.4103/1742-6413.159246] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background: The cytologic diagnosis of atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS) is controversial because of variation in how it is applied in practice, as well as uncertainty about patient management. We aimed to assess the percentage of thyroid fine-needle aspiration biopsies (FNABs) with AUS/FLUS diagnoses in different North American and European practice settings (e.g. community, academic, etc.), assess whether patients were managed according to current guidelines, and determine patient outcomes. Materials and Methods: A detailed questionnaire survey was posted in secure websites used separately by cytopathologists and cytotechnologists. The questionnaire was posted from August 1 through December 31, 2013. Results: Endocrinologists and cytopathologists performed 51.7% and 37.1% of thyroid FNABs, respectively. The Bethesda reporting system for thyroid FNAB was used in 90% of practices. The rate of AUS/FLUS varied widely among institutions, with 46.1% of represented institutions reporting AUS/FLUS rates of 3–10%. The median follow-up rate of patients with an initial AUS/FLUS diagnosis was 70% (range, 10–100%). For the majority of represented institutions (86.4%), patients with initial AUS/FLUS diagnosis had follow-up with endocrinologists. Of repeat AUS/FLUS thyroid FNABs, a median of 52% was considered benign, and 18% were suspicious of or positive for malignancy (median, 10% and 7.5%, respectively). Conclusions: Reporting of the AUS/FLUS category varied widely among different institutions. The median follow-up rate was lower than published guidelines. The most common follow-up diagnosis was benign thyroid nodule. Improved standardization of cytologic criteria should be adopted to reduce such variation.
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Affiliation(s)
- Aziza Nassar
- Address: Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | - Jordan P Reynolds
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah E Kerr
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah M Jenkins
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Kandace A Lackore
- Division of Health Care Policy and Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Victor Bernet
- Division of Endocrinology, Mayo Clinic, Jacksonville, Florida, USA
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Bakkum-Gamez JN, Wentzensen N, Maurer MJ, Hawthorne KM, Voss JS, Kroneman TN, Famuyide AO, Clayton AC, Halling KC, Kerr SE, Cliby WA, Dowdy SC, Kipp BR, Mariani A, Oberg AL, Podratz KC, Shridhar V, Sherman ME. Detection of endometrial cancer via molecular analysis of DNA collected with vaginal tampons. Gynecol Oncol 2015; 137:14-22. [PMID: 25677060 DOI: 10.1016/j.ygyno.2015.01.552] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/31/2015] [Indexed: 01/05/2023]
Abstract
OBJECTIVE We demonstrate the feasibility of detecting EC by combining minimally-invasive specimen collection techniques with sensitive molecular testing. METHODS Prior to hysterectomy for EC or benign indications, women collected vaginal pool samples with intravaginal tampons and underwent endometrial brushing. Specimens underwent pyrosequencing for DNA methylation of genes reported to be hypermethylated in gynecologic cancers and recently identified markers discovered by profiling over 200 ECs. Methylation was evaluated individually across CpGs and averaged across genes. Differences between EC and benign endometrium (BE) were assessed using two-sample t-tests and area under the curve (AUC). RESULTS Thirty-eight ECs and 28 BEs were included. We evaluated 97 CpGs within 12 genes, including previously reported markers (RASSF1, HSP2A, HOXA9, CDH13, HAAO, and GTF2A1) and those identified in discovery work (ASCL2, HTR1B, NPY, HS3ST2, MME, ADCYAP1, and additional CDH13 CpG sites). Mean methylation was higher in tampon specimens from EC v. BE for 9 of 12 genes (ADCYAP1, ASCL2, CDH13, HS3ST2, HTR1B, MME, HAAO, HOXA9, and RASSF1) (all p<0.05). Among these genes, relative hypermethylation was observed in EC v. BE across CpGs. Endometrial brush and tampon results were similar. Within tampon specimens, AUC was highest for HTR1B (0.82), RASSF1 (0.75), and HOXA9 (0.74). This is the first report of HOXA9 hypermethylation in EC. CONCLUSION DNA hypermethylation in EC tissues can also be identified in vaginal pool DNA collected via intravaginal tampon. Identification of additional EC biomarkers and refined collection methods are needed to develop an early detection tool for EC.
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Affiliation(s)
- Jamie N Bakkum-Gamez
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA.
| | - Nicolas Wentzensen
- Hormonal and Reproductive Branch (HREB), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), USA
| | - Matthew J Maurer
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Kieran M Hawthorne
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Trynda N Kroneman
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Abimbola O Famuyide
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Amy C Clayton
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kevin C Halling
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics, Mayo Clinic, Rochester, MN, USA
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - William A Cliby
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sean C Dowdy
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrea Mariani
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Ann L Oberg
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Karl C Podratz
- Department of Obstetrics and Gynecology, Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Viji Shridhar
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mark E Sherman
- Hormonal and Reproductive Branch (HREB), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), USA
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Bogani G, Liu MC, Dowdy SC, Cliby WA, Kerr SE, Kalli KR, Kipp BR, Halling KC, Campion MB, Mariani A. Detection of circulating tumor cells in high-risk endometrial cancer. Anticancer Res 2015; 35:683-687. [PMID: 25667446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
AIM To evaluate the presence of circulating tumor cells (CTCs) in patients with high-risk endometrial cancer (EC). PATIENTS AND METHODS We prospectively included 28 patients with a preoperative diagnosis of grade 3 EC undergoing surgery from June 2010 to December 2011. Their preoperative blood samples were tested for the presence of CTCs using an immunomagnetic and immunofluorescence assay technique. RESULTS Overall, 2 out of 28 patients (7%) were positive for CTCs. The presence of positive CTCs was significantly associated with myometrial invasion (MI) (33% vs. 0% for MI>50% vs. ≤50%; p=0.04) and lymph node positivity (40% vs. 0% for positive vs. negative nodes; p=0.03). Only patients with endometrioid histology had positive CTCs (29% in endometrioid vs. 0% in nonendometrioid; p=0.06). CONCLUSION The presence of positive CTCs was associated with deep MI and lymph node positivity. The absence of CTCs in patients with type II histology suggests the need to find other markers in this sub-group of patients.
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Affiliation(s)
- Giorgio Bogani
- Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, U.S.A
| | - Minetta C Liu
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, U.S.A. Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | - Sean C Dowdy
- Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, U.S.A
| | - William A Cliby
- Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, U.S.A
| | - Sarah E Kerr
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Benjamin R Kipp
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | - Kevin C Halling
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, U.S.A
| | | | - Andrea Mariani
- Division of Gynecologic Surgery, Mayo Clinic, Rochester, MN, U.S.A.
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Gleeson FC, Kipp BR, Kerr SE, Voss JS, Lazaridis KN, Katzka DA, Levy MJ. Characterization of endoscopic ultrasound fine-needle aspiration cytology by targeted next-generation sequencing and theranostic potential. Clin Gastroenterol Hepatol 2015; 13:37-41. [PMID: 25424571 DOI: 10.1016/j.cgh.2014.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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] [Received: 10/22/2014] [Accepted: 10/22/2014] [Indexed: 02/07/2023]
Abstract
Determination of tumor genetic architecture based on tissue analysis yields important information on signaling pathways involved in cancer pathogenesis and plays a growing role in choosing the optimal medical management of malignancies. Specifically, the advent of next-generation sequencing has led to a rapidly evolving era of relatively inexpensive, high-throughput DNA sequencing of tumors. One such example is multiplexed tumor genotyping (ie, panel testing) of more than 2800 mutations across 50 commonly mutated cancer-associated genes. This resulting mutational landscape shows medically actionable pathogenic alterations to optimize antitumor therapy. We recently assessed the performance and outcome of targeted next-generation sequencing with archived endoscopic ultrasound fine-needle aspirates across a broad range of primary and metastatic sites with encouraging accuracy. As a result, endoscopic ultrasound has the potential to move from a test for diagnosis or confirmation of malignancy, to one in which it could facilitate the personalization of cancer-directed therapy.
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Affiliation(s)
- Ferga C Gleeson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jesse S Voss
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Konstantinos N Lazaridis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - David A Katzka
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Michael J Levy
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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McAuliffe MJ, Kerr SE, Gibson EMR, Anderson T, LaShell PJ. Cognitive-perceptual examination of remediation approaches to hypokinetic dysarthria. J Speech Lang Hear Res 2014; 57:1268-1283. [PMID: 24687031 DOI: 10.1044/2014_jslhr-s-12-0349] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PURPOSE To determine how increased vocal loudness and reduced speech rate affect listeners' cognitive-perceptual processing of hypokinetic dysarthric speech associated with Parkinson's disease. METHOD Fifty-one healthy listener participants completed a speech perception experiment. Listeners repeated phrases produced by 5 individuals with dysarthria across habitual, loud, and slow speaking modes. Listeners were allocated to habitual ( n = 17), loud ( n = 17), or slow ( n = 17) experimental conditions. Transcripts derived from the phrase repetition task were coded for overall accuracy (i.e., intelligibility), and perceptual error analyses examined how these conditions affected listeners' phonemic mapping (i.e., syllable resemblance) and lexical segmentation (i.e., lexical boundary error analysis). RESULTS Both speech conditions provided obvious perceptual benefits to listeners. Overall, transcript accuracy was highest in the slow condition. In the loud condition, however, improvement was evidenced across the experiment. An error analysis suggested that listeners in the loud condition prioritized acoustic-phonetic cues in their attempts to resolve the degraded signal, whereas those in the slow condition appeared to preferentially weight lexical stress cues. CONCLUSIONS Increased loudness and reduced rate exhibited differential effects on listeners' perceptual processing of dysarthric speech. The current study highlights the insights that may be gained from a cognitive-perceptual approach.
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Gleeson FC, Kipp BR, Levy MJ, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Lazaridis KN, Kerr SE. Lung cancer adrenal gland metastasis: Optimal fine-needle aspirate and touch preparation smear cellularity characteristics for successful theranostic next-generation sequencing. Cancer Cytopathol 2014; 122:822-32. [DOI: 10.1002/cncy.21464] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/16/2014] [Accepted: 06/18/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Ferga C. Gleeson
- Divison of Gastroenterology and Hepatology; Mayo Clinic Rochester; Rochester Minnesota
| | - Benjamin R. Kipp
- Department of Laboratory Medicine and Pathology; Mayo Clinic Rochester; Rochester Minnesota
| | - Michael J. Levy
- Divison of Gastroenterology and Hepatology; Mayo Clinic Rochester; Rochester Minnesota
| | - Jesse S. Voss
- Department of Laboratory Medicine and Pathology; Mayo Clinic Rochester; Rochester Minnesota
| | - Michael B. Campion
- Department of Laboratory Medicine and Pathology; Mayo Clinic Rochester; Rochester Minnesota
| | - Douglas M. Minot
- Department of Laboratory Medicine and Pathology; Mayo Clinic Rochester; Rochester Minnesota
| | - Zheng J. Tu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research; Mayo Clinic Rochester; Rochester Minnesota
| | - Eric W. Klee
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research; Mayo Clinic Rochester; Rochester Minnesota
| | - Konstantinos N. Lazaridis
- Divison of Gastroenterology and Hepatology; Mayo Clinic Rochester; Rochester Minnesota
- Center for Individualized Medicine; Mayo Clinic Rochester; Rochester Minnesota
| | - Sarah E. Kerr
- Department of Laboratory Medicine and Pathology; Mayo Clinic Rochester; Rochester Minnesota
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Kerr SE, Barr Fritcher EG, Campion MB, Voss JS, Kipp BR, Halling KC, Lewis JT. Biliary dysplasia in primary sclerosing cholangitis harbors cytogenetic abnormalities similar to cholangiocarcinoma. Hum Pathol 2014; 45:1797-804. [PMID: 25027853 DOI: 10.1016/j.humpath.2014.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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] [Received: 01/18/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 12/28/2022]
Abstract
Grading criteria for biliary dysplasia associated with primary sclerosing cholangitis (PSC) have been recently described. Although a dysplasia to cholangiocarcinoma (CCA) sequence is implied, supportive data are lacking. Seventeen liver explants with biliary dysplasia from patients with PSC were selected. Formalin-fixed, paraffin-embedded blocks from each patient were evaluated to identify areas of normal/reactive biliary epithelium, intestinal metaplasia, low-grade dysplasia, high-grade dysplasia, and CCA. Areas of interest were assessed for chromosomal alteration with fluorescence in situ hybridization using probes directed to locus 9p21 and centromeres 3, 7, and 17. The cutoffs for calling probe copy number abnormalities for polysomy, single locus gain, and homozygous 9p21 loss were established by receiver operating characteristic curve analysis. Of 4 areas of intestinal metaplasia, 19 low-grade dysplasias, 19 high-grade dysplasias, and 5 CCAs, 0%, 11%, 58%, and 40% displayed polysomy and 0%, 0%, 16%, and 40% exhibited homozygous 9p21 loss as the most severe abnormality, respectively. Patients with prior or current CCA were more likely to display polysomy in dysplasia than patients without CCA (70% versus 14%; P = .05); however, high-grade dysplasia was proportionally more common in the CCA-associated dysplasia group. Polysomy and homozygous 9p21 loss are detected in biliary dysplasia and CCA. These findings support a dysplasia-carcinoma sequence in PSC patients and suggest that fluorescence in situ hybridization analysis could help refine the grading of biliary dysplasia in these patients.
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Affiliation(s)
- Sarah E Kerr
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905.
| | | | | | - Jesse S Voss
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Benjamin R Kipp
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Kevin C Halling
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Jason T Lewis
- Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL 32224
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McAuliffe MJ, Gibson EMR, Kerr SE, Anderson T, LaShell PJ. Vocabulary influences older and younger listeners' processing of dysarthric speech. J Acoust Soc Am 2013; 134:1358-1368. [PMID: 23927132 DOI: 10.1121/1.4812764] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This study examined younger (n = 16) and older (n = 16) listeners' processing of dysarthric speech-a naturally occurring form of signal degradation. It aimed to determine how age, hearing acuity, memory, and vocabulary knowledge interacted in speech recognition and lexical segmentation. Listener transcripts were coded for accuracy and pattern of lexical boundary errors. For younger listeners, transcription accuracy was predicted by receptive vocabulary. For older listeners, this same effect existed but was moderated by pure-tone hearing thresholds. While both groups employed syllabic stress cues to inform lexical segmentation, older listeners were less reliant on this perceptual strategy. The results were interpreted to suggest that individuals with larger receptive vocabularies, with their presumed greater language familiarity, were better able to leverage cue redundancies within the speech signal to form lexical hypothesis-leading to an improved ability to comprehend dysarthric speech. This advantage was minimized as hearing thresholds increased. While the differing levels of reliance on stress cues across the listener groups could not be attributed to specific individual differences, it was hypothesized that some combination of larger vocabularies and reduced hearing thresholds in the older participant group led to them prioritize lexical cues as a segmentation frame.
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Affiliation(s)
- Megan J McAuliffe
- Department of Communication Disorders and New Zealand Institute of Language, Brain and Behaviour, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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Voss JS, Holtegaard LM, Kerr SE, Fritcher EGB, Roberts LR, Gores GJ, Zhang J, Highsmith WE, Halling KC, Kipp BR. Molecular profiling of cholangiocarcinoma shows potential for targeted therapy treatment decisions. Hum Pathol 2013; 44:1216-22. [DOI: 10.1016/j.humpath.2012.11.006] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 11/16/2012] [Accepted: 11/21/2012] [Indexed: 01/26/2023]
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Reungwetwattana T, Mandrekar SJ, Kroneman T, Foster NR, Aubry MC, Yi ES, Kerr SE, Yang P, Grothey A, Shridhar V, Voss JS, Kipp B, Molina JR. A Ki-67 proliferation index cutoff value of 1% to predict 5-year RFS and OS in patients with pulmonary carcinoid tumors. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.11119] [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: 11/20/2022] Open
Abstract
11119 Background: Evaluation of prognostic factors in carcinoid tumors of the lung is limited due to the rarity of disease. This study assessed Ki-67 expression and other clinical variables as prognostic factors in 262 patients. Methods: A systematic search of Mayo Clinic lung cancer epidemiology and tumor registry databases from 1997 to 2009 identified 449 consecutive patients, with 262 having available tissue blocks [40 atypical carcinoids (AC) and 222 typical carcinoids (TC)]. Clinical data were collected by chart review. Tissue blocks were reviewed by 1/3 pathologists using WHO criteria. Tumors were tested for the Ki-67 index using digital image analysis (tumor tracing) by two operators. The association and predictive value of the factors with recurrence-free and overall survival (RFS and OS) were explored using univariable Cox proportional Hazards model and concordance (c) index. Results: Age, stage, smoking history, lymph node (LN) involvement and Ki-67 index were significant prognostic factors for RFS and OS. Median follow-up on alive-patients is 5 years (range: 0.006-5). Median percentage of Ki-67 index of AC and TC were 1.61% and 0.56% (P<0.0001), respectively. Patients with Ki-67 ≥ 1% had significantly worse RFS (HR=3.69, P<0.0001) and OS (HR=3.69, P=0.0007) compared with Ki-67 < 1% group. The c-index of Ki-67 (0.65) was comparable to the pathologic distinction between AC and TC (0.62 for original diagnosis and 0.63 for central-reviewed diagnosis). Conclusions: Ki-67 index cutoff value of 1% is a valuable prognostic biomarker for pulmonary carcinoids based on this large cohort. Our data also provide strong evidence for clinical variables such as age, stage, smoking history, and LN involvement as clinical prognostic factors in pulmonary carcinoids. A prognostic calculator incorporating Ki-67 and clinical variables is under development. [Table: see text]
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Affiliation(s)
| | | | | | | | | | - Eunhee S. Yi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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McGregor DC, Kerr SE, Krockenberger AK. The distribution and abundance of an island population of Koalas (Phascolarctos cinereus) in the far north of their geographic range. PLoS One 2013; 8:e59713. [PMID: 23527258 PMCID: PMC3601071 DOI: 10.1371/journal.pone.0059713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/17/2013] [Indexed: 11/18/2022] Open
Abstract
Koalas are an iconic species of charismatic megafauna, of substantial social and conservation significance. They are widely distributed, often at low densities, and individuals can be difficult to detect, making population surveys challenging and costly. Consequently, koala population estimates have been limited and the results inconsistent. The aims of this study were to estimate the distribution, relative abundance and population size of the koalas on Magnetic Island, far north Queensland. Population densities were estimated in 18 different vegetation types present on the island using a Fecal Standing Crop Method. Koala density ranged from 0.404 ha(-1), recorded in forest red gum and bloodwood woodland, to absence from eight of the vegetation types surveyed. The second highest density of 0.297 koalas ha(-1) was recorded in mixed eucalypt woodland, which covers 45% of the island. The total abundance of koalas on Magnetic Island, not including those present in urban areas, was estimated at 825±175 (SEM). The large variation in koala density across vegetation types reinforces the need for sampling stratification when calculating abundance over large areas, as uniformity of habitat quality cannot be assumed. In this context, koala populations also occur in low densities in areas generally regarded as poor quality koala habitat. These results highlight the importance of protecting vegetation communities not traditionally considered to have high conservation value to koalas, as these habitats may be essential for maintaining viable, widespread, low-density populations. The results from this study provide a baseline to assess future trends in koala distribution, density and abundance on Magnetic Island.
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Affiliation(s)
- Denise C. McGregor
- Centre for Tropical Environmental and Sustainability Science, and School of Marine and Tropical Biology, James Cook University, Cairns, Queensland, Australia
| | - Sarah E. Kerr
- Centre for Tropical Environmental and Sustainability Science, and School of Marine and Tropical Biology, James Cook University, Cairns, Queensland, Australia
| | - Andrew K. Krockenberger
- Centre for Tropical Environmental and Sustainability Science, and School of Marine and Tropical Biology, James Cook University, Cairns, Queensland, Australia
- * E-mail:
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Kerr SE, Schnabel CA, Sullivan PS, Zhang Y, Singh V, Carey B, Erlander MG, Highsmith WE, Dry SM, Brachtel EF. Multisite validation study to determine performance characteristics of a 92-gene molecular cancer classifier. Clin Cancer Res 2012; 18:3952-60. [PMID: 22648269 DOI: 10.1158/1078-0432.ccr-12-0920] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [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
PURPOSE Accurate tumor classification is essential for cancer management as patient outcomes improve with use of site- and subtype-specific therapies. Current clinicopathologic evaluation is varied in approach, yet standardized diagnoses are critical for determining therapy. While gene expression-based cancer classifiers may potentially meet this need, imperative to determining their application to patient care is validation in rigorously designed studies. Here, we examined the performance of a 92-gene molecular classifier in a large multi-institution cohort. EXPERIMENTAL DESIGN Case selection incorporated specimens from more than 50 subtypes, including a range of tumor grades, metastatic and primary tumors, and limited tissue samples. Formalin-fixed, paraffin-embedded tumors passed pathologist-adjudicated review between three institutions. Tumor classification using a 92-gene quantitative reverse transcriptase polymerase chain reaction (RT-PCR) assay was conducted on blinded tumor sections from 790 cases and compared with adjudicated diagnoses. RESULTS The 92-gene assay showed overall sensitivities of 87% for tumor type [95% confidence interval (CI), 84-89] and 82% for subtype (95% CI, 79-85). Analyses of metastatic tumors, high-grade tumors, or cases with limited tissue showed no decrease in comparative performance (P = 0.16, 0.58, and 0.16). High specificity (96%-100%) was showed for ruling in a primary tumor in organs commonly harboring metastases. The assay incorrectly excluded the adjudicated diagnosis in 5% of cases. CONCLUSIONS The 92-gene assay showed strong performance for accurate molecular classification of a diverse set of tumor histologies. Results support potential use of the assay as a standardized molecular adjunct to routine clinicopathologic evaluation for tumor classification and primary site diagnosis.
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Affiliation(s)
- Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Schnabel CA, Kerr SE, Sullivan PS, Zhang Y, Singh V, Carey B, Erlander MG, Highsmith WE, Dry SM, Brachtel EF. Multisite validation of a 92-gene molecular classifier: Diagnostic accuracy and clinical utility in metastatic cancer. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.10588] [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: 11/20/2022] Open
Abstract
10588 Background: Accurate tumor classification is increasingly critical to individualized care as patient outcomes improve with use of targeted cancer therapies and predictive biomarkers. In metastatic cancers of uncertain or unknown origin, identification of a primary site remains equivocal in a significant number of cases. Gene expression signatures may improve accuracy and specificity of tumor classification, however, large-scale, blinded validation studies that demonstrate stable performance in metastatic and poorly differentiated cases are currently lacking. Methods: Seven hundred and ninety cases (51% female, 44% metastatic, 63% grade 2 and 3, 14% limited tissue specimens) representing 28 tumor types and 50 subtypes were processed and adjudicated between Mayo Clinic, UCLA and Massachusetts General Hospital. Blinded FFPE tumor sections were submitted and tested using a 92-gene RT-PCR assay (CancerTYPE ID, bioTheranostics Inc.). Molecular predictions were evaluated for concordance with the reference diagnosis; diagnostic accuracy between clinical subsets was compared. Results: The 92-gene assay demonstrated overall sensitivities of 87% for tumor classification and 82% for subtyping. Forty-seven (5.9%) cases were considered unclassifiable. Comparative analysis of performance between metastatic (n=329) and primary (n=414) tumors showed no statistically significant difference in accuracy (85% vs 88%, p=0.16). Similarly, no significant decreases in performance were observed across histological grades (p=0.58) and when comparing limited tissue to excisional biopsy specimens (p=0.16). Strong precision was demonstrated for accurate identification of a primary tumor in tissues biopsied from common metastatic sites, reported as positive predictive values of 100% for lung, brain and peritoneum, 92% for ovary and 80% for liver. Conclusions: Results from this multisite, blinded study validate the diagnostic accuracy of the 92-gene assay for classifying a diverse set of tumors, and support its clinical utility in the diagnosis of metastatic tumors to determine tissue of origin, and in the differential diagnosis of metastatic vs new primary disease.
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Affiliation(s)
| | - Sarah E Kerr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Peggy S Sullivan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Yi Zhang
- bioTheranostics, Inc., San Diego, CA
| | | | - Brittany Carey
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | - W Edward Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Sarah M Dry
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Elena F Brachtel
- Department of Pathology, Massachusetts General Hospital, Boston, MA
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Kipp BR, Voss JS, Kerr SE, Barr Fritcher EG, Graham RP, Zhang L, Highsmith WE, Zhang J, Roberts LR, Gores GJ, Halling KC. Isocitrate dehydrogenase 1 and 2 mutations in cholangiocarcinoma. Hum Pathol 2012; 43:1552-8. [PMID: 22503487 DOI: 10.1016/j.humpath.2011.12.007] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 02/07/2023]
Abstract
Somatic mutations in isocitrate dehydrogenase 1 and 2 genes are common in gliomas and help stratify patients with brain cancer into histologic and molecular subtypes. However, these mutations are considered rare in other solid tumors. The aims of this study were to determine the frequency of isocitrate dehydrogenase 1 and 2 mutations in cholangiocarcinoma and to assess histopathologic differences between specimens with and without an isocitrate dehydrogenase mutation. We sequenced 94 formalin-fixed, paraffin-embedded cholangiocarcinoma (67 intrahepatic and 27 extrahepatic) assessing for isocitrate dehydrogenase 1 (codon 132) and isocitrate dehydrogenase 2 (codons 140 and 172) mutations. Multiple histopathologic characteristics were also evaluated and compared with isocitrate dehydrogenase 1/2 mutation status. Of the 94 evaluated specimens, 21 (22%) had a mutation including 14 isocitrate dehydrogenase 1 and 7 isocitrate dehydrogenase 2 mutations. Isocitrate dehydrogenase mutations were more frequently observed in intrahepatic cholangiocarcinoma than in extrahepatic cholangiocarcinoma (28% versus 7%, respectively; P = .030). The 14 isocitrate dehydrogenase 1 mutations were R132C (n = 9), R132S (n = 2), R132G (n = 2), and R132L (n = 1). The 7 isocitrate dehydrogenase 2 mutations were R172K (n = 5), R172M (n = 1), and R172G (n = 1). Isocitrate dehydrogenase mutations were more frequently observed in tumors with clear cell change (P < .001) and poorly differentiated histology (P = .012). The results of this study show for the first time that isocitrate dehydrogenase 1 and 2 genes are mutated in cholangiocarcinoma. The results of this study are encouraging because it identifies a new potential target for genotype-directed therapeutic trials and may represent a potential biomarker for earlier detection of cholangiocarcinoma in a subset of cases.
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Affiliation(s)
- Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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Kochar O, Wick MR, Kerr SE, Oglesbee D, Cathro HP. Unexpected Fabry disease in a renal allograft kidney: an underrecognized cause of poor allograft function. Ultrastruct Pathol 2011; 35:92-6. [PMID: 21299350 DOI: 10.3109/01913123.2010.538136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fabry disease is an X-linked recessive lysosomal storage disease caused by a deficiency of α-galactosidase A, with characteristic ultrastructural cytoplasmic myelin-like inclusions. Renal lesions are seen in male and variably in heterozygous female patients. One previous report has described Fabry disease involving a renal allograft from a deceased female donor with no history of Fabry disease. The authors describe another case, in which suspicion for Fabry disease was raised ultrastructurally. This serves as a reminder that proteinuria after renal transplantation may be due to donor-derived disease. Fabry disease is probably an underrecognized cause of graft dysfunction. This case provides further justification for ultrastructural examination of renal allograft biopsies.
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Affiliation(s)
- Olga Kochar
- Department of Pathology and Laboratory Medicine, University of Virginia, Charlottesville, Virginia 22908, USA
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Dunn BE, Choi H, Recla DL, Kerr SE, Wagenman BL. Robotic surgical telepathology between the Iron Mountain and Milwaukee Department of Veterans Affairs Medical Centers: a twelve year experience. Semin Diagn Pathol 2009; 26:187-93. [DOI: 10.1053/j.semdp.2009.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Dunn BE, Choi H, Recla DL, Kerr SE, Wagenman BL. Robotic surgical telepathology between the Iron Mountain and Milwaukee Department of Veterans Affairs Medical Centers: a 12-year experience. Hum Pathol 2009; 40:1092-9. [DOI: 10.1016/j.humpath.2009.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
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Kerr SE, Bellizzi AM, Stelow EB, Frierson HF, Policarpio-Nicolas MLC. Initial assessment of fine-needle aspiration specimens by telepathology: validation for use in pathology resident-faculty consultations. Am J Clin Pathol 2008; 130:409-13. [PMID: 18701414 DOI: 10.1309/na7y7thptbf112a0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Telepathology is useful when distance is an obstacle to timely diagnosis. Performance of fine-needle aspiration (FNA) at locations distant from cytopathologists can limit timely assessment of adequacy and preliminary diagnosis. We evaluated a telepathology system for consultation between residents and faculty for assessment of FNA specimen adequacy and preliminary diagnosis using 100 consecutive cases. We compared findings with the original assessment of adequacy, preliminary interpretation, and final diagnosis. Two residents initially screened 50 cases, and images were then transmitted to cytopathologists, who communicated by telephone. We found 97% diagnostic concordance and 99% accuracy. The screening time ranged from 41 seconds to 30:19 minutes (mean, 6:35 minutes). The viewing time ranged from 10 seconds to 12:50 minutes (mean, 3:52 minutes). Our telepathology system is efficient and accurate for the initial assessment and preliminary diagnosis of FNA specimens, but we recommend its use by more senior and experienced trainees.
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Abstract
Endometrial stromal sarcomas are uncommon tumors of the uterus, and the cytologic features have only been reported in a number of case reports that mostly discuss the features of higher grade undifferentiated sarcomas. This article discusses the cytologic features of a large series of low-grade endometrial stromal sarcomas (ESSs) sampled by a variety of methods. We reviewed our histologic files for all confirmed cases of low-grade ESS, and followed this by a computerized search for any corresponding cytologic specimens. We identified 12 Papanicolaou tests and 9 nongynecologic specimens. Most cases showed moderate to marked cellularity with a combination of single cells and stromal fragments. Blood vessels, interspersed between the clusters of stromal cells, were seen in 15 cases; 4 of these had supporting hyaline matrix. The cells were predominantly spindle shaped with scant to moderate cytoplasm, round to ovoid nuclei, and fine chromatin. Mitotic figures and nucleoli were rare. Most cases had a clean background.
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Abstract
OBJECTIVE To describe how people with HIV understand and experience the problem of adhering to antiretroviral medication regimens. DESIGN We performed a qualitative study based on interviews with HIV-infected patients, including 46 clients of AIDS service organizations, who were sampled according to age, ethnicity, and injection drug use history, and a convenience sample of 15 patients. Interviews were conducted in English or Spanish and were audiotaped and transcribed. PARTICIPANTS Of 52 respondents who had prescriptions for antiretroviral therapy, 25 were randomly selected for in-depth analysis. Of these, 5 reported having an AIDS diagnosis, 15 reported symptoms they attributed to HIV, and 5 reported having no symptoms of HIV disease. MEASUREMENTS AND MAIN RESULTS Investigators prepared structured abstracts of interviews to extract adherence-related data. One investigator compared the abstracts with the original transcripts to confirm the interpretations, and used the abstracts to organize and classify the findings. Most subjects (84%) reported recent nonadherent behavior, including ceasing treatment, medication "holidays," sleeping through doses, forgetting doses, skipping doses due to side effects, and following highly asymmetric schedules. Initially, most reported that they were not significantly nonadherent, and many did not consider their behavior nonadherent. Only a minority clearly understood the possible consequences of missing doses. Most said they had not discussed their nonadherence with their physicians. CONCLUSIONS Many people rationalize their difficulty in adhering to HIV treatment by deciding that the standard of adherence they can readily achieve is appropriate. Physicians should inquire about adherence-related behavior in specific detail, and ensure that patients understand the consequences of not meeting an appropriate standard.
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Affiliation(s)
- M B Laws
- Latino Health Institute Center for Research on Culture and Health and the Department of Family Medicine and Community Health, Tufts University School of Medicine, Boston, Mass, USA.
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Hlynka JN, Danforth DH, Kerr SE. Drug usage review. Part two: Implementing the ambulatory program. Can Pharm J 1981; 114:467-70. [PMID: 10253716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Ridenhour CE, Henzel JH, DeWeese MS, Kerr SE. Thymoma arising from undescended cervical thymus. Surgery 1970; 67:614-9. [PMID: 5435909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Kerr SE, Kfoury GA, Djibelian LG. Preparation of brain polyphosphoinositides. J Lipid Res 1964; 5:481-3. [PMID: 4289247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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