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Coker SM, McInnes K, Vallee E, Biggs P, Pomroy WE, Howe L, Morgan KJ. Molecular characterisation and additional morphological descriptions of Eimeria spp. (Apicomplexa: Eimeriidae) from brown kiwi (Apteryx mantelli Bartlett). Syst Parasitol 2023; 100:269-281. [PMID: 36826706 PMCID: PMC10129925 DOI: 10.1007/s11230-023-10086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023]
Abstract
Brown kiwi (Apteryx mantelli Bartlett), a ratite endemic to New Zealand, is currently listed as "Vulnerable" under the IUCN classification system due to predation by introduced mammals. Operation Nest Egg (ONE) raises chicks and juveniles in predator-proof enclosures until they are large enough to defend themselves. These facilities experience an environmental accumulation of coccidial oocysts, which leads to severe morbidity and mortality of these kiwi. Four species of coccidia have been morphologically described from sporulated oocysts with additional opportunistic descriptions of endogenous stages. This research continues the morphological descriptions of these species of Eimeria with an additional novel morphotype also morphologically described. It also provides the first genetic characterisation targeting the mitochondrial cytochrome c oxidase I (COI) gene. Based on these findings, it was determined there are at least five morphotypes of Eimeria that infect brown kiwi and co-infections are common at the ONE facilities surveyed. The COI amplicon targeted for this study was sufficient to provide differentiation from other members of this genus. Sanger sequencing yielded ambiguous bases, indicating the need for more in-depth sequencing.
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Affiliation(s)
- Sarah M Coker
- School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Kate McInnes
- Department of Conservation, PO Box 10-420, Wellington, 6143, New Zealand
| | - Emilie Vallee
- School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Patrick Biggs
- School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, New Zealand.,School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - William E Pomroy
- School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, New Zealand
| | - Laryssa Howe
- School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, New Zealand.
| | - Kerri J Morgan
- School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, New Zealand.,Wildbase, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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2
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Ritu K, Kumar P, Singh A, Nupur K, Spalgias S, Mrigpuri P, Rajkumar. Untangling the KRAS mutated lung cancer subsets and its therapeutic implications. MOLECULAR BIOMEDICINE 2021; 2:40. [PMID: 34918209 PMCID: PMC8677854 DOI: 10.1186/s43556-021-00061-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
The Kirsten rat sarcoma virus transforming protein (KRAS) mutations (predominate in codons 12, 13, and 61) and genomically drive nearly one-third of lung carcinomas. These mutations have complex functions in tumorigenesis, and influence the tumor response to chemotherapy and tyrosine kinase inhibitors resulting in a poorer patient prognosis. Recent attempts using targeted therapies against KRAS alone have met with little success. The existence of specific subsets of lung cancer based on KRAS mutations and coexisting mutations are suggested. Their interactions need further elaboration before newer promising targeted therapies for KRAS mutant lung cancers can be used as earlier lines of therapy. We summarize the existing knowledge of KRAS mutations and their coexisting mutations that is relevant to lung cancer treatment, in this review. We elaborate on the prognostic impact of clinical and pathologic characteristics of lung cancer patients associated with KRAS mutations. We briefly review the currently available techniques for KRAS mutation detection on biopsy and cytology samples. Finally, we discuss the new therapeutic strategies for targeting KRAS-mutant non-small cell lung cancer (NSCLC). These may herald a new era in the treatment of KRASG12Cmutated NSCLC as well as be helpful to develop demographic subsets to predict targeted therapies and prognosis of lung cancer patients.
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3
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de Biase D, Acquaviva G, Visani M, Sanza V, Argento CM, De Leo A, Maloberti T, Pession A, Tallini G. Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel. Diagnostics (Basel) 2020; 10:diagnostics10040250. [PMID: 32340363 PMCID: PMC7236002 DOI: 10.3390/diagnostics10040250] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/05/2023] Open
Abstract
Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
- Correspondence: ; Tel.: +39-051-2144717; Fax: +39-051-6363689
| | - Viviana Sanza
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Chiara M. Argento
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Antonio De Leo
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
| | - Thais Maloberti
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology, Molecular Diagnostic Unit, University of Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (D.d.B.); (C.M.A.); (T.M.); (A.P.)
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale), Molecular Diagnostic Unit, University of Bologna, Azienda USL di Bologna, viale Ercolani 4/2, 40138 Bologna, Italy; (G.A.); (V.S.); (A.D.L.); (G.T.)
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Igarashi T, Shimizu K, Usui K, Yokobori T, Ohtaki Y, Nakazawa S, Obayashi K, Yajima T, Nobusawa S, Ohkawa T, Katoh R, Motegi Y, Ogawa H, Harimoto N, Ichihara T, Mitani Y, Yokoo H, Mogi A, Shirabe K. Significance of RAS mutations in pulmonary metastases of patients with colorectal cancer. Int J Clin Oncol 2019; 25:641-650. [PMID: 31773354 DOI: 10.1007/s10147-019-01582-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND RAS/BRAF mutations of colorectal cancer (CRC) play a crucial role in carcinogenesis and cancer progression and need to be considered for the therapeutic strategy choice. We used next-generation-sequencing (NGS) technology to assess RAS/BRAF mutation differences between primary CRC and corresponding pulmonary metastases (PMs). METHODS We examined the mutation statuses of the KRAS 12/13/61/146, NRAS 12/13/61/146, and BRAF 600 codons in genomic DNA from fresh-frozen or formalin-fixed paraffin-embedded tissues derived from 34 primary lesions and 52 corresponding PMs from 36 patients with CRC. RESULTS We found RAS mutations in 76% (26/34) of primary CRC lesions and in 86% (31/36) of PMs. While 27% (7/26) of the primary CRC RAS mutations were heterogeneous, all the RAS mutations in PMs were homogeneous. Of the mutations in PMs, 71% (22/31) were KRAS G>A transitions, of which 82% (18/22) were KRAS G12D or G13D. The RAS mutation discordance between primary tumors and PMs was 12.1% (4/33). RAS mutations with the same genotyping were detected in all synchronous and metachronous PMs from 9 patients. We found no BRAF mutations in either primary or pulmonary tissues. CONCLUSION Our NGS analysis suggests that RAS mutations of PM of patients with CRC are more common than initially thought. The presence of KRAS mutations in CRC specimens, especially G12D or G13D mutations, seems to promote PM formation.
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Affiliation(s)
- Takamichi Igarashi
- Department of Hepatobiliary and Pancreatic Surgery, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kimihiro Shimizu
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan. .,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
| | - Kengo Usui
- Genetic Diagnosis Technology Unit, RIKEN Center of Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takehiko Yokobori
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Department of Innovative Cancer Immunotherapy, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Gunma University Initiative for Advanced Research (GIAR), Maebashi, Gunma, 371-8511, Japan
| | - Yoichi Ohtaki
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Seshiru Nakazawa
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kai Obayashi
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Toshiki Yajima
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Department of Innovative Cancer Immunotherapy, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Sumihito Nobusawa
- Department of Human Pathology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Takahiro Ohkawa
- Genetic Diagnosis Technology Unit, RIKEN Center of Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryuji Katoh
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Yoko Motegi
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Hiroomi Ogawa
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Norifumi Harimoto
- Department of Hepatobiliary and Pancreatic Surgery, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Tatsuo Ichihara
- K.K. DNAFORM, 75-1 Ono-machi, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan
| | - Yasumasa Mitani
- K.K. DNAFORM, 75-1 Ono-machi, Tsurumi-ku, Yokohama, Kanagawa, 230-0046, Japan
| | - Hideaki Yokoo
- Department of Human Pathology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Akira Mogi
- Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Division of General Thoracic Surgery, Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Ken Shirabe
- Department of Hepatobiliary and Pancreatic Surgery, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.,Integrative Center of General Surgery, Gunma University Hospital, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
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5
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Hong KH, Song S, Shin W, Kang K, Cho CS, Hong YT, Han K, Moon JH. A case of interdigitating dendritic cell sarcoma studied by whole-exome sequencing. Genes Genomics 2018; 40:1279-1285. [PMID: 30099721 DOI: 10.1007/s13258-018-0724-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/24/2018] [Indexed: 12/18/2022]
Abstract
Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.
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Affiliation(s)
- Ki Hwan Hong
- Department of Otolaryngology-Head and Neck Surgery, Chonbuk National University Medical School, Jeonju, 54896, Republic of Korea
| | - Soyoung Song
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Wonseok Shin
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Chun-Sung Cho
- Department of Neurosurgery, College of Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yong Tae Hong
- Department of Otolaryngology-Head and Neck Surgery, Chonbuk National University Medical School, Jeonju, 54896, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Jeong Hwan Moon
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
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6
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Al-Ogaidi AJM, Stefan-van Staden RI, Gugoasa LA, Rosu MC, Socaci C. Electrochemical Determination of the KRAS Genetic Marker for Colon Cancer with Modified Graphete and Graphene Paste Electrodes. ANAL LETT 2018. [DOI: 10.1080/00032719.2018.1453516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ahmed Jassim Muklive Al-Ogaidi
- University Politehnica, Bucharest, Romania
- Applied Sciences Department, Branch of Applied Chemistry, University of Technology, Baghdad, Iraq
| | - Raluca-Ioana Stefan-van Staden
- University Politehnica, Bucharest, Romania
- Laboratory of Electrochemistry and PATLAB Bucharest, National Institute of Research for Electrochemistry and Condensed Matter, Bucharest, Romania
| | - Livia Alexandra Gugoasa
- Laboratory of Electrochemistry and PATLAB Bucharest, National Institute of Research for Electrochemistry and Condensed Matter, Bucharest, Romania
| | - Marcela-Corina Rosu
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Crina Socaci
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
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7
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Xiao N, Tang YT, Li ZS, Cao R, Wang R, Zou JM, Pei J. Performance of probe polymerization-conjunction-agarose gel electrophoresis in the rapid detection of KRAS gene mutation. Genet Mol Biol 2018; 41:555-561. [PMID: 30080912 PMCID: PMC6136376 DOI: 10.1590/1678-4685-gmb-2017-0197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/30/2017] [Indexed: 11/22/2022] Open
Abstract
This study aimed to develop a simple and rapid method to detect KRAS gene mutations for conventional clinical applications under laboratory conditions. The genotype of mutation sites was determined based on the occurrence of target bands in the corresponding lanes of the reaction tubes through polymerization-conjunction of the probes, probe purification and amplification, and agarose gel electrophoresis. Circulating DNA samples were obtained from the plasma of 72 patients with lung cancer, which were identified based on six mutation sites (G12S, G12R, G12C, G12D, G12A, and G12V) of codon 12 of the KRAS gene. The detection results were compared with direct sequencing data. The proposed detection method is characterized by simple operation, high specificity, and high sensitivity (2%). This method can detect the mutations of three samples at G12S, G12R, and G12A. In the direct sequencing spectra of these samples, the genotype could not be determined due to the lack of evident sequencing peaks that correspond to the basic group of mutations. In conclusion, a simple and rapid method was established based on probe polymerization-conjunction-agarose gel electrophoresis for detecting KRAS gene mutations. This method can be applied to the conventional mutation detection of inhomogeneous samples.
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Affiliation(s)
- Na Xiao
- Medical College of Hubei University of Arts and Science, Xiangyang, China
| | - Yi-Tong Tang
- Medical College of Hubei University of Arts and Science, Xiangyang, China
| | - Zhi-Shan Li
- Department of Clinical Laboratory, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Rui Cao
- Department of Internal Medicine, Maternal and Child Health Care Hospital of Dongguan, Dongguan, China
| | - Rong Wang
- Department of Clinical Laboratory, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Jiu-Ming Zou
- Department of Clinical Laboratory, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Jiao Pei
- Department of Clinical Laboratory, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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Cazacu IM, Luzuriaga Chavez AA, Saftoiu A, Vilmann P, Bhutani MS. A quarter century of EUS-FNA: Progress, milestones, and future directions. Endosc Ultrasound 2018; 7:141-160. [PMID: 29941723 PMCID: PMC6032705 DOI: 10.4103/eus.eus_19_18] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/21/2018] [Indexed: 12/11/2022] Open
Abstract
Tissue acquisition using EUS has considerably evolved since the first EUS-FNA was reported 25 years ago. Its introduction was an important breakthrough in the endoscopic field. EUS-FNA has now become a part of the diagnostic and staging algorithm for the evaluation of benign and malignant diseases of the gastrointestinal tract and of the organs in its proximity, including lung diseases. This review aims to present the history of EUS-FNA development and to provide a perspective on the recent developments in procedural techniques and needle technologies that have significantly extended the role of EUS and its clinical applications. There is a bright future ahead for EUS-FNA in the years to come as extensive research is conducted in this field and various technologies are continuously implemented into clinical practice.
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Affiliation(s)
- Irina Mihaela Cazacu
- Department of Gastroenterology, Research Center of Gastroenterology and Hepatology, University of Medicine and Pharmacy, Craiova, Romania
- Department of Gastroenterology, Hepatology, and Nutrition, University of Texas – MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Adrian Saftoiu
- Department of Gastroenterology, Research Center of Gastroenterology and Hepatology, University of Medicine and Pharmacy, Craiova, Romania
| | - Peter Vilmann
- Gastrounit, Division of Surgery, Copenhagen University Hospital Herlev, Copenhagen, Denmark
| | - Manoop S. Bhutani
- Department of Gastroenterology, Hepatology, and Nutrition, University of Texas – MD Anderson Cancer Center, Houston, Texas, USA
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9
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Yang Z, Sun G. High-frequency, low-coverage "false positives" mutations may be true in GS Junior sequencing studies. Sci Rep 2017; 7:13751. [PMID: 29062110 PMCID: PMC5653793 DOI: 10.1038/s41598-017-13116-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
The GS Junior sequencer provides simplified procedures for library preparation and data processing. Errors in pyrosequencing generate some biases during library construction and emulsion PCR amplification. False-positive mutations are identified by related characteristics described in the manufacturer’s manual, and some detected mutations may have ‘borderline’ characteristics when they are detected in few reads or at low frequency. Among these mutations, however, some may be true positives. This study aimed to improve the accuracy of identifying true positives among mutations with borderline false-positive characteristics detected with GS Junior sequencing. Mutations with the borderline features were tested for validity with Sanger sequencing. We examined 10 mutations detected in coverages <20-fold at frequencies >30% (group A) and 16 mutations detected in coverages >20-fold at frequencies < 30% (group B). In group A, two mutations were not confirmed, and two mutations with 100% frequency were confirmed as heterozygous alleles. No mutation in group B was confirmed. The two groups had significantly different false-positive prevalences (p = 0.001). These results suggest that mutations detected at frequencies less than 30% can be confidently identified as false-positives but that mutations detected at frequencies over 30%, despite coverages less than 20-fold, should be verified with Sanger sequencing.
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Affiliation(s)
- Zhiliang Yang
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China.
| | - Guilian Sun
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China
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10
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Thierry AR, Pastor B, Jiang ZQ, Katsiampoura AD, Parseghian C, Loree JM, Overman MJ, Sanchez C, Messaoudi SE, Ychou M, Kopetz S. Circulating DNA Demonstrates Convergent Evolution and Common Resistance Mechanisms during Treatment of Colorectal Cancer. Clin Cancer Res 2017; 23:4578-4591. [PMID: 28400427 PMCID: PMC5562356 DOI: 10.1158/1078-0432.ccr-17-0232] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 02/09/2017] [Accepted: 04/06/2017] [Indexed: 02/06/2023]
Abstract
Purpose: Liquid biopsies allow the tracking of clonal dynamics and detection of mutations during treatment.Experimental Design: We evaluated under blinded conditions the ability of cell-free DNA (cfDNA) to detect RAS/BRAF mutations in the plasma of 42 metastatic colorectal cancer patients treated on a phase Ib/II trial of FOLFOX and dasatinib, with or without cetuximab.Results: Prior to treatment, sequencing of archival tissue detected mutations in 25 of 42 patients (60%), while the cfDNA assay detected mutations in 37 of 42 patients (88%). Our cfDNA assay detected mutations with allele frequencies as low as 0.01%. After exposure to treatment, 41 of 42 patients (98%) had a cfDNA-detected RAS/BRAF mutation. Of 21 patients followed with serial measurements who were RAS/BRAF mutant at baseline, 11 (52%) showed additional point mutation following treatment and 3 (14%) no longer had detectable levels of another mutant allele. Of RAS/BRAF wild-type tumors at baseline, 4 of 5 (80%) showed additional point mutations. cfDNA quantitative measurements from this study closely mirrored changes in CEA and CT scan results, highlighting the importance of obtaining quantitative data beyond the mere presence of a mutation.Conclusions: Our findings demonstrate the development of new RAS/BRAF mutations in patients regardless of whether they had preexisting mutations in the pathway, demonstrating a convergent evolutionary pattern. Clin Cancer Res; 23(16); 4578-91. ©2017 AACR.
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Affiliation(s)
- Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Zhi-Qin Jiang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anastasia D Katsiampoura
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christine Parseghian
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Safia El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- DiaDx SAS, Montpellier, France
| | - Marc Ychou
- IRCM, Institut de Recherche en Cancérologie de Montpellier, Montpellier, France
- INSERM, U1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Service de Chirurgie Digestive, Institut Régional du Cancer de Montpellier, Montpellier, France
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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11
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Riva A, BØrgesen M, Guldmann-Christensen M, Hauge Kyneb M, Voogd K, Andersen C, Epistolio S, Merlo E, Yding Wolff T, Hamilton-Dutoit S, Lorenzen J, Christensen UB, Frattini M. SensiScreen®KRAS exon 2-sensitive simplex and multiplex real-time PCR-based assays for detection of KRAS exon 2 mutations. PLoS One 2017. [PMID: 28636636 PMCID: PMC5479524 DOI: 10.1371/journal.pone.0178027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Activating mutations in codon 12 and codon 13 of the KRAS (Kirsten rat sarcoma viral oncogene homolog) gene are implicated in the development of several human cancer types and influence their clinical evaluation, treatment and prognosis. Numerous different methods for KRAS genotyping are currently available displaying a wide range of sensitivities, time to answer and requirements for laboratory equipment and user skills. Here we present SensiScreen® KRAS exon 2 simplex and multiplex CE IVD assays, that use a novel real-time PCR-based method for KRAS mutation detection based on PentaBase's proprietary DNA analogue technology and designed to work on standard real-time PCR instruments. By means of the included BaseBlocker™ technology, we show that SensiScreen® specifically amplifies the mutated alleles of interest with no or highly subdued amplification of the wild type allele. Furthermore, serial dilutions of mutant DNA in a wild type background demonstrate that all SensiScreen® assays display a limit of detection that falls within the range of 0.25-1%. Finally, in three different colorectal cancer patient populations, SensiScreen® assays confirmed the KRAS genotype previously determined by commonly used methods for KRAS mutation testing, and notably, in two of the populations, SensiScreen® identified additional mutant positive cases not detected by common methods.
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Affiliation(s)
- Alice Riva
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | | | | | | | - Kirsten Voogd
- Laboratory of Research and Development, Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Samantha Epistolio
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Elisabetta Merlo
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
| | - Tine Yding Wolff
- Life Science Division, Danish Technological Institute, Aarhus, Denmark
| | - Stephen Hamilton-Dutoit
- Laboratory of Research and Development, Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Jan Lorenzen
- Life Science Division, Danish Technological Institute, Aarhus, Denmark
| | | | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Locarno, Switzerland
- * E-mail: (UBC); (MF)
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12
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Lee HS, Kim WH, Kwak Y, Koh J, Bae JM, Kim KM, Chang MS, Han HS, Kim JM, Kim HW, Chang HK, Choi YH, Park JY, Gu MJ, Lhee MJ, Kim JY, Kim HS, Cho MY. Molecular Testing for Gastrointestinal Cancer. J Pathol Transl Med 2017; 51:103-121. [PMID: 28219002 PMCID: PMC5357760 DOI: 10.4132/jptm.2017.01.24] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 12/20/2022] Open
Abstract
With recent advances in molecular diagnostic methods and targeted cancer therapies, several molecular tests have been recommended for gastric cancer (GC) and colorectal cancer (CRC). Microsatellite instability analysis of gastrointestinal cancers is performed to screen for Lynch syndrome, predict favorable prognosis, and screen patients for immunotherapy. The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor has been approved in metastatic CRCs with wildtype RAS (KRAS and NRAS exon 2-4). A BRAF mutation is required for predicting poor prognosis. Additionally, amplification of human epidermal growth factor receptor 2 (HER2) and MET is also associated with resistance to EGFR inhibitor in metastatic CRC patients. The BRAF V600E mutation is found in sporadic microsatellite unstable CRCs, and thus is helpful for ruling out Lynch syndrome. In addition, the KRAS mutation is a prognostic biomarker and the PIK3CA mutation is a molecular biomarker predicting response to phosphoinositide 3-kinase/AKT/mammalian target of rapamycin inhibitors and response to aspirin therapy in CRC patients. Additionally, HER2 testing should be performed in all recurrent or metastatic GCs. If the results of HER2 immunohistochemistry are equivocal, HER2 silver or fluorescence in situ hybridization testing are essential for confirmative determination of HER2 status. Epstein-Barr virus-positive GCs have distinct characteristics, including heavy lymphoid stroma, hypermethylation phenotype, and high expression of immune modulators. Recent advances in next-generation sequencing technologies enable us to examine various genetic alterations using a single test. Pathologists play a crucial role in ensuring reliable molecular testing and they should also take an integral role between molecular laboratories and clinicians.
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Affiliation(s)
- Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mee Soo Chang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Hye Seung Han
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Joon Mee Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Hwal Woong Kim
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
| | - Hee Kyung Chang
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Young Hee Choi
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
| | - Ji Y. Park
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Mi Jin Gu
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
| | - Min Jin Lhee
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
| | - Jung Yeon Kim
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
| | - Hee Sung Kim
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Mee-Yon Cho
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Gastrointestinal Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
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13
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Dolatkhah R, Somi MH, Kermani IA, Farassati F, Dastgiri S. A novel KRAS gene mutation report in sporadic colorectal cancer, from Northwest of Iran. Clin Case Rep 2017; 5:338-341. [PMID: 28265402 PMCID: PMC5331244 DOI: 10.1002/ccr3.779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/19/2016] [Accepted: 11/23/2016] [Indexed: 12/14/2022] Open
Abstract
While the role of KRAS gene mutations has been widely accepted for predicting responses to anti‐EGFR therapy in patients with colorectal cancer, although this study was based on observation of a single case it gives hope that some KRAS gene mutation may have favorable prognosis. More studies are required on patients with similar mutation to validate this finding.
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Affiliation(s)
- Roya Dolatkhah
- Hematology and Oncology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Iraj Asvadi Kermani
- Hematology and Oncology Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Faris Farassati
- The University of Kansas Medical School-Molecular Medicine Laboratory Kansas City Kansas USA
| | - Saeed Dastgiri
- Hematology and Oncology Research Center Tabriz University of Medical Sciences Tabriz Iran; Tabriz Health Services Research Center Tabriz University of Medical Sciences Tabriz Iran
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14
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Loree JM, Kopetz S, Raghav KPS. Current companion diagnostics in advanced colorectal cancer; getting a bigger and better piece of the pie. J Gastrointest Oncol 2017; 8:199-212. [PMID: 28280626 PMCID: PMC5334060 DOI: 10.21037/jgo.2017.01.01] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
While the treatment of colorectal cancer continues to rely heavily on conventional cytotoxic therapy, an increasing number of targeted agents are under development. Many of these treatments require companion diagnostic tests in order to define an appropriate population that will derive benefit. In addition, a growing number of biomarkers provide prognostic information about a patient's malignancy. As we learn more about these biomarkers and their assays, selecting the appropriate companion diagnostic becomes increasingly important. In the case of many biomarkers, there are numerous assays which could provide the same information to a treating physician, however each assay has strengths and weaknesses. Institutions must balance cost, assay sensitivity, turn-around time, and labor resources when selecting which assay to offer. In this review we will discuss the current state of companion diagnostics available in metastatic colorectal cancer and explore emerging biomarkers and their assays. We will focus on KRAS, BRAF, HER2, and PIK3CA testing, as well as microsatellite stability assessment and multigene panels.
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Affiliation(s)
- Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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15
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de Biase D, Genestreti G, Visani M, Acquaviva G, Di Battista M, Cavallo G, Paccapelo A, Cancellieri A, Trisolini R, Degli Esposti R, Bartolini S, Pession A, Tallini G, Brandes AA. The percentage of Epidermal Growth Factor Receptor (EGFR)-mutated neoplastic cells correlates to response to tyrosine kinase inhibitors in lung adenocarcinoma. PLoS One 2017; 12:e0177822. [PMID: 28520821 PMCID: PMC5433779 DOI: 10.1371/journal.pone.0177822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Epidermal Growth Factor Receptor (EGFR) molecular analysis is performed to assess the responsiveness to Tyrosine Kinase Inhibitors (TKIs) in patients with Non-Small Cell Lung Cancer (NSCLC). The existence of molecular intra-tumoral heterogeneity has been observed in lung cancers. The aim of the present study is to investigate if the percentage of mutated neoplastic cells within the tumor sample might influence the responsiveness to TKIs treatment. MATERIAL AND METHODS A total of 931 cases of NSCLC were analyzed for EGFR mutational status (exon 18, 19, 20, 21) using Next Generation Sequencer. The percentage of mutated neoplastic cells was calculated after normalizing the percentage of mutated alleles obtained after next generation sequencer analysis with the percentage of neoplastic cells in each tumor. RESULTS Next generation sequencing revealed an EGFR mutation in 167 samples (17.9%), mainly deletions in exon 19. In 18 patients treated with TKIs and with available follow-up, there was a significant correlation between the percentage of mutated neoplastic cells and the clinical response (P = 0.017). Patients with a percentage of mutated neoplastic cells greater than 56%, have a statistical trend (P = 0.081) for higher Overall Survival (26.3 months) when compared to those with a rate of mutated neoplastic cells lower than 56% (8.2 months). CONCLUSIONS The percentage of EGFR-mutated neoplastic cells in the tumor is associated with response to TKIs. A "quantitative result" of EGFR mutational status might provide useful information in order to recognize those patients which might have the greatest benefit from TKIs.
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Affiliation(s)
- Dario de Biase
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
- * E-mail: (DdB); (GG)
| | - Giovenzio Genestreti
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
- * E-mail: (DdB); (GG)
| | - Michela Visani
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Giorgia Acquaviva
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Monica Di Battista
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Giovanna Cavallo
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Alexandro Paccapelo
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | - Rocco Trisolini
- Interventional Pulmology, Sant'Orsola, Malpighi Hospital, Bologna, Italy
| | - Roberta Degli Esposti
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Stefania Bartolini
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacy and Biotechnology (Dipartimento di Farmacia e Biotecnologie) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale) - Molecular Diagnostic Unit, Azienda USL di Bologna, University of Bologna School of Medicine, Bologna, Italy
| | - Alba A. Brandes
- Department of Oncology, AUSL Bologna – IRCCS Institute of Neurological Sciences, Bologna, Italy
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16
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Dolatkhah R, Somi MH, Asvadi Kermani I, Bonyadi M, Sepehri B, Boostani K, Azadbakht S, Fotouhi N, Farassati F, Dastgiri S. Association between proto-oncogene mutations and clinicopathologic characteristics and overall survival in colorectal cancer in East Azerbaijan, Iran. Onco Targets Ther 2016; 9:7385-7395. [PMID: 27994469 PMCID: PMC5153263 DOI: 10.2147/ott.s116373] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Colorectal cancer (CRC) is the third-most common cancer in Iran. The increasing incidence of CRC in the past three decades has made it a major public health burden in the country. This study aimed to determine any relationship of specific mutations in CRCs with clinicopathologic aspects and outcome of patients. Materials and methods This study was conducted on 100 CRC patients by the case-only method. Polymerase chain-reaction products were analyzed by Sanger sequencing, and sequence results were compared with the significant KRAS and BRAF gene mutations in the My Cancer Genome database. Logistic regression models were used to detect associations of clinicopathologic characteristics with each of the mutations. Kaplan–Meier and Cox regression models were constructed to estimate overall survival in patients. Results A total of 26 subjects (26%) had heterozygote-mutant KRAS, and mutations were not detected in the amplified exon of BRAF in both tumor and normal tissues of the 100 CRCs. Rectal tumors had 1.53-fold higher likelihood of KRAS mutations than colon tumors, and men had 1.37-fold higher odds than women. The presence of metastasis increased the likelihood of KRAS mutations 2.36-fold over those with nonmetastatic CRCs. Compared to patients with KRAS wild-type cancers, those with KRAS mutations had significantly higher mortality (hazard ratio 3.74, 95% confidence interval 1.44–9.68; log-rank P=0.003). Conclusion Better understanding of the causality of CRC can be established by combining epidemiology and research on molecular mechanisms of the disease.
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Affiliation(s)
- Roya Dolatkhah
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Iraj Asvadi Kermani
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Bonyadi
- Center of Excellence for Biodiversity, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Bita Sepehri
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kamal Boostani
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saleh Azadbakht
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nikou Fotouhi
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faris Farassati
- Molecular Medicine Laboratory, University of Kansas Medical School, Kansas City, KS, USA
| | - Saeed Dastgiri
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Tabriz Health Services Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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17
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Lee HK, Lee CK, Tang JWT, Loh TP, Koay ESC. Contamination-controlled high-throughput whole genome sequencing for influenza A viruses using the MiSeq sequencer. Sci Rep 2016; 6:33318. [PMID: 27624998 PMCID: PMC5022032 DOI: 10.1038/srep33318] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/24/2016] [Indexed: 12/04/2022] Open
Abstract
Accurate full-length genomic sequences are important for viral phylogenetic studies. We developed a targeted high-throughput whole genome sequencing (HT-WGS) method for influenza A viruses, which utilized an enzymatic cleavage-based approach, the Nextera XT DNA library preparation kit, for library preparation. The entire library preparation workflow was adapted for the Sentosa SX101, a liquid handling platform, to automate this labor-intensive step. As the enzymatic cleavage-based approach generates low coverage reads at both ends of the cleaved products, we corrected this loss of sequencing coverage at the termini by introducing modified primers during the targeted amplification step to generate full-length influenza A sequences with even coverage across the whole genome. Another challenge of targeted HTS is the risk of specimen-to-specimen cross-contamination during the library preparation step that results in the calling of false-positive minority variants. We included an in-run, negative system control to capture contamination reads that may be generated during the liquid handling procedures. The upper limits of 99.99% prediction intervals of the contamination rate were adopted as cut-off values of contamination reads. Here, 148 influenza A/H3N2 samples were sequenced using the HTS protocol and were compared against a Sanger-based sequencing method. Our data showed that the rate of specimen-to-specimen cross-contamination was highly significant in HTS.
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Affiliation(s)
- Hong Kai Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Julian Wei-Tze Tang
- Department of Infection, Immunity, Inflammation, University of Leicester, Leicester, UK.,Clinical Microbiology, Leicester Royal Infirmary, Leicester, UK
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
| | - Evelyn Siew-Chuan Koay
- Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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18
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Gao J, Wu H, Wang L, Zhang H, Duan H, Lu J, Liang Z. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR. BMJ Open 2016; 6:e009532. [PMID: 26747035 PMCID: PMC4716245 DOI: 10.1136/bmjopen-2015-009532] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE To validate the targeted next-generation sequencing (NGS) platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion real-time PCR. SETTING Beijing, China. PARTICIPANTS 51 archived FFPE CRC samples (36 men, 15 women) were retrospectively randomly selected and then checked by an experienced pathologist for sequencing based on histological confirmation of CRC and availability of sufficient tissue. METHODS RAS mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger sequencing and the Therascreen KRAS assay, respectively. Agreement among the 3 methods was assessed. Assay sensitivity was further determined by sequencing serially diluted DNA from FFPE cell lines with known mutation statuses. RESULTS 13 of 51 (25.5%) cases had a mutation in KRAS exon 2, as determined by PGM analysis. PGM analysis showed 100% (51/51) concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04% (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1) for detecting KRAS exon 2 mutations, respectively. The only discrepant case harboured a KRAS exon 2 mutation (c.37G>T) that was not covered by the Therascreen kit. The dilution series experiment results showed that PGM was able to detect KRAS mutations at a frequency of as low as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were also detected in 10 samples by PGM. Furthermore, mutations in other CRC-related genes could be simultaneously detected in a single test by PGM. CONCLUSIONS The targeted NGS platform is specific and sensitive for KRAS exon 2 mutation detection and is appropriate for use in routine clinical testing. Moreover, it is sample saving and cost-efficient and time-efficient, and has great potential for clinical application to expand testing to include mutations in RAS and other CRC-related genes.
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Affiliation(s)
- Jie Gao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Li Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Huanli Duan
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Junliang Lu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
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Kriegsmann M, Arens N, Endris V, Weichert W, Kriegsmann J. Detection of KRAS, NRAS and BRAF by mass spectrometry - a sensitive, reliable, fast and cost-effective technique. Diagn Pathol 2015; 10:132. [PMID: 26220423 PMCID: PMC4518505 DOI: 10.1186/s13000-015-0364-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/09/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND According to current clinical guidelines mutational analysis for KRAS and NRAS is recommended prior to EGFR-directed therapy of colorectal cancer (CRC) in the metastatic setting. Therefore, reliable, fast, sensitive and cost-effective methods for routine tissue based molecular diagnostics are required that allow the assessment of the CRC mutational status in a high throughput fashion. METHODS We have developed a custom designed assay for routine mass-spectrometric (MS) (MassARRAY, Agena Bioscience) analysis to test the presence/absence of 18 KRAS, 14 NRAS and 4 BRAF mutations. We have applied this assay to 93 samples from patients with CRC and have compared the results with Sanger sequencing and a chip hybridization assay (KRAS LCD-array Kit, Chipron). In cases with discordant results, next-generation sequencing (NGS) was performed. RESULTS MS detected a KRAS mutation in 46/93 (49%), a NRAS mutation in 2/93 (2%) and a BRAF mutation in 1/93 (1%) of the cases. MS results were in agreement with results obtained by combination of the two other methods in 92 (99%) of 93 cases. In 1/93 (1%) of the cases a G12V mutation has been detected by Sanger sequencing and MS, but not by the chip assay. In this case, NGS has confirmed the G12V mutation in KRAS. CONCLUSIONS Mutational analysis by MS is a reliable method for routine diagnostic use, which can be easily extended for testing of additional mutations.
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Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | | | - Volker Endris
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | - Wilko Weichert
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
- National Center of Tumor Diseases, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Jörg Kriegsmann
- Institute of Molecular Pathology, Trier, Germany.
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany.
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Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC. PLoS One 2015; 10:e0129280. [PMID: 26076459 PMCID: PMC4468211 DOI: 10.1371/journal.pone.0129280] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/06/2015] [Indexed: 01/21/2023] Open
Abstract
The recent FDA approval of the MiSeqDx platform provides a unique opportunity to develop targeted next generation sequencing (NGS) panels for human disease, including cancer. We have developed a scalable, targeted panel-based assay termed UNCseq, which involves a NGS panel of over 200 cancer-associated genes and a standardized downstream bioinformatics pipeline for detection of single nucleotide variations (SNV) as well as small insertions and deletions (indel). In addition, we developed a novel algorithm, NGScopy, designed for samples with sparse sequencing coverage to detect large-scale copy number variations (CNV), similar to human SNP Array 6.0 as well as small-scale intragenic CNV. Overall, we applied this assay to 100 snap-frozen lung cancer specimens lacking same-patient germline DNA (07–0120 tissue cohort) and validated our results against Sanger sequencing, SNP Array, and our recently published integrated DNA-seq/RNA-seq assay, UNCqeR, where RNA-seq of same-patient tumor specimens confirmed SNV detected by DNA-seq, if RNA-seq coverage depth was adequate. In addition, we applied the UNCseq assay on an independent lung cancer tumor tissue collection with available same-patient germline DNA (11–1115 tissue cohort) and confirmed mutations using assays performed in a CLIA-certified laboratory. We conclude that UNCseq can identify SNV, indel, and CNV in tumor specimens lacking germline DNA in a cost-efficient fashion.
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Bolton L, Reiman A, Lucas K, Timms J, Cree IA. KRAS mutation analysis by PCR: a comparison of two methods. PLoS One 2015; 10:e0115672. [PMID: 25568935 PMCID: PMC4287618 DOI: 10.1371/journal.pone.0115672] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/26/2014] [Indexed: 01/04/2023] Open
Abstract
Background KRAS mutation assays are important companion diagnostic tests to guide anti-EGFR antibody treatment of metastatic colorectal cancer. Direct comparison of newer diagnostic methods with existing methods is an important part of validation of any new technique. In this this study, we have compared the Therascreen (Qiagen) ARMS assay with Competitive Allele-Specific TaqMan PCR (castPCR, Life Technologies) to determine equivalence for KRAS mutation analysis. Methods DNA was extracted by Maxwell (Promega) from 99 colorectal cancers. The ARMS-based Therascreen and a customized castPCR assay were performed according to the manufacturer’s instructions. All assays were performed on either an Applied Biosystems 7500 Fast Dx or a ViiA7 real-time PCR machine (both from Life Technologies). The data were collected and discrepant results re-tested with newly extracted DNA from the same blocks in both assay types. Results Of the 99 tumors included, Therascreen showed 62 tumors to be wild-type (WT) for KRAS, while 37 had KRAS mutations on initial testing. CastPCR showed 61 tumors to be wild-type (WT) for KRAS, while 38 had KRAS mutations. Thirteen tumors showed BRAF mutation in castPCR and in one of these there was also a KRAS mutation. The custom castPCR plate included several other KRAS mutations and BRAF V600E, not included in Therascreen, explaining the higher number of mutations detected by castPCR. Re-testing of discrepant results was required in three tumors, all of which then achieved concordance for KRAS. CastPCR assay Ct values were on average 2 cycles lower than Therascreen. Conclusion There was excellent correlation between the two methods. Although castPCR assay shows lower Ct values than Therascreen, this is unlikely to be clinically significant.
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Affiliation(s)
- Louise Bolton
- Department of Pathology, Queen Alexandra Hospital, Portsmouth, United Kingdom
| | - Anne Reiman
- Department of Pathology and Warwick Medical School, University Hospitals Coventry and Warwickshire, Coventry, United Kingdom
| | - Katie Lucas
- Department of Pathology and Warwick Medical School, University Hospitals Coventry and Warwickshire, Coventry, United Kingdom
| | - Judith Timms
- Department of Pathology and Warwick Medical School, University Hospitals Coventry and Warwickshire, Coventry, United Kingdom
| | - Ian A. Cree
- Department of Pathology and Warwick Medical School, University Hospitals Coventry and Warwickshire, Coventry, United Kingdom
- * E-mail:
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Sakai K, Yoneshige A, Ito A, Ueda Y, Kondo S, Nobumasa H, Fujita Y, Togashi Y, Terashima M, De Velasco MA, Tomida S, Nishio K. Performance of a novel KRAS mutation assay for formalin-fixed paraffin embedded tissues of colorectal cancer. SPRINGERPLUS 2015; 4:7. [PMID: 25674493 PMCID: PMC4320212 DOI: 10.1186/2193-1801-4-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/16/2014] [Indexed: 01/06/2023]
Abstract
We compared the performance of the 3D-Gene® mutation assay (3D-Gene® KRAS mutation assay kit) with the Scorpion-ARMS (therascreen® KRAS RGQ PCR Kit) and Luminex (MEBGEN™ KRAS kit) assays for the detection of KRAS mutations in formalin-fixed, paraffin-embedded tissue samples from 150 patients diagnosed with colorectal cancer. DNA was extracted from the paraffin-embedded tissue samples with or without macrodissection under hematoxylin and eosin staining and the KRAS mutation status was independently determined using these assays. Discordant results were re-analyzed by Sanger sequencing. Mutation detection analysis was successfully performed in all 150 specimens using the 3D-Gene® mutation assay without an invalid case. The concordance rate between the 3D-Gene® mutation assay and Scorpion-ARMS or Luminex was 98.7% (148/150). KRAS mutations were detected at a frequency of 35.3% (53/150) in colorectal cancer specimens. Three discrepant cases were found between the three assays. Overall, our results demonstrate a high concordance rate of between the 3D-Gene® mutation assay and the two existing in-vitro diagnostics kits. All three assays proved to be validated methods for detecting clinically significant KRAS mutations in paraffin-embedded tissue samples.
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Affiliation(s)
- Kazuko Sakai
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Azusa Yoneshige
- Department of Pathology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Akihiko Ito
- Department of Pathology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Yoji Ueda
- New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa, Japan
| | - Satoshi Kondo
- New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa, Japan
| | - Hitoshi Nobumasa
- New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa, Japan
| | - Yoshihiko Fujita
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Yosuke Togashi
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Masato Terashima
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Marco A De Velasco
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Shuta Tomida
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
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Ming Z, Jiang D, Hu Q, Li X, Huang J, Xu Y, Liu Y, Xu C, Hua X, Hou Y. Diagnostic application of PIK3CA mutation analysis in Chinese esophageal cancer patients. Diagn Pathol 2014; 9:153. [PMID: 25106743 PMCID: PMC4149237 DOI: 10.1186/s13000-014-0153-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/29/2014] [Indexed: 02/06/2023] Open
Abstract
Background The PIK3CA gene mutation was found to associate with prognosis and might affect molecular targeted therapy in esophageal carcinoma (EC). The aim of this study is to compare different methods for analyzing the PIK3CA gene mutation in EC. Methods Genomic DNA was extracted from 106 surgically resected EC patient tissues. The PIK3CA mutation status (exons 9 and 20) were screened by mutant-enrich liquid chip (ME-Liquidchip), Sanger sequencing, and pyrosequencing. And all samples with mutations were independently reassessed using amplification refractory mutation system (ARMS) methods again. Results PIK3CA mutation rates were identified as 11.3% (12/106) by ME-Liquidchip. 10 mutations occurred in exon 9 and 2 in exon 20, including G1624A:E542K (n = 4), G1633A:E545K (n = 6) and A3140G:H1047R (n = 2). The results were further verified by ARMS methods. Among these 12 cases characterized for PIK3CA mutation, however, only 7 and 6 cases were identified by Sanger sequencing (6.6%,7/106) and pyrosequencing (5.7%,6/106), respectively. Conclusion Sanger sequencing and pyrosequencing are less sensitive and are not efficiently applicable to the detection of PIK3CA mutation in EC samples. Choosing between ME-Liquidchip and ARMS will depend on laboratory facilities and expertise. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_153
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiuguo Hua
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Siraj AK, Bu R, Prabhakaran S, Bavi P, Beg S, Al Hazmi M, Al-Rasheed M, Alobaisi K, Al-Dayel F, AlManea H, Al-Sanea N, Uddin S, Al-Kuraya KS. A very low incidence of BRAF mutations in Middle Eastern colorectal carcinoma. Mol Cancer 2014; 13:168. [PMID: 25005754 PMCID: PMC4109832 DOI: 10.1186/1476-4598-13-168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 06/24/2014] [Indexed: 02/08/2023] Open
Abstract
Background Recent studies emphasize the role of BRAF as a genetic marker for prediction, prognosis and risk stratification in colorectal cancer. Earlier studies have reported the incidence of BRAF mutations in the range of 5-20% in colorectal carcinomas (CRC) and are predominantly seen in the serrated adenoma-carcinoma pathway characterized by microsatellite instability (MSI-H) and hypermethylation of the MLH1 gene in the setting of the CpG island methylator phenotype (CIMP). Due to the lack of data on the true incidence of BRAF mutations in Saudi Arabia, we sought to analyze the incidence of BRAF mutations in this ethnic group. Methods 770 CRC cases were analyzed for BRAF and KRAS mutations by direct DNA sequencing. Results BRAF gene mutations were seen in 2.5% (19/757) CRC analyzed and BRAF V600E somatic mutation constituted 90% (17/19) of all BRAF mutations. BRAF mutations were significantly associated with right sided tumors (p = 0.0019), MSI-H status (p = 0.0144), CIMP (p = 0.0017) and a high proliferative index of Ki67 expression (p = 0.0162). Incidence of KRAS mutations was 28.6% (216/755) and a mutual exclusivity was noted with BRAF mutations (p = 0.0518; a trend was seen). Conclusion Our results highlight the low incidence of BRAF mutations and CIMP in CRC from Saudi Arabia. This could be attributed to ethnic differences and warrant further investigation to elucidate the effect of other environmental and genetic factors. These findings indirectly suggest the possibility of a higher incidence of familial hereditary colorectal cancers especially Hereditary non polyposis colorectal cancer (HNPCC) syndrome /Lynch Syndrome (LS) in Saudi Arabia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, MBC#98-16, P,O, Box 3354 Riyadh 11211, Saudi Arabia.
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Berenstein R, Blau IW, Kar A, Cay R, Sindram A, Seide C, Blau O. Comparative examination of various PCR-based methods for DNMT3A and IDH1/2 mutations identification in acute myeloid leukemia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:44. [PMID: 24887327 PMCID: PMC4045877 DOI: 10.1186/1756-9966-33-44] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/10/2014] [Indexed: 12/29/2022]
Abstract
Background Mutations in epigenetic modifiers were reported in patients with acute myeloid leukaemia (AML) including mutations in DNA methyltransferase 3A gene (DNMT3A) in 20%-30% patients and mutations in isocitrate dehydrogenase 1/2 gene (IDH1/2) in 5%-15% patients. Novel studies have shown that mutations in DNMT3A and IDH1/2 influence prognosis, indicating an increasing need to detect these mutations during routine laboratory analysis. DNA sequencing for the identification of these mutations is time-consuming and cost-intensive. This study aimed to establish rapid screening tests to identify mutations in DNMT3A and IDH1/2 that could be applied in routine laboratory procedures and that could influence initial patient management. Methods In this study we developed an endonuclease restriction method to identify the most common DNMT3A mutation (R882H) and an amplification-refractory mutation system (ARMS) to analyse IDH2 R140Q mutations. Furthermore, we compared these methods with HRM analysis and evaluated the latter for the detection of IDH1 mutations. Results Of 230 samples from patients with AML 30 (13%) samples had DNMT3A mutations, 16 (7%) samples had IDH2 R140Q mutations and 36 (16%) samples had IDH1 mutations. Sensitivity assays performed using serial dilutions of mutated DNA showed that ARMS analysis had a sensitivity of 4.5%, endonuclease restriction had a sensitivity of 0.05% and HRM analysis had a sensitivity of 5.9%–7.8% for detecting different mutations. HRM analysis was the best screening method to determine the heterogeneity of IDH1 mutations. Furthermore, for the identification of mutations in IDH2 and DNMT3A, endonuclease restriction and ARMS methods showed a perfect concordance (100%) with Sanger sequencing while HRM analysis showed a near-perfect concordance (approximately 98%). Conclusion Our study suggested that all the developed methods were rapid, specific and easy to use and interpret. HRM analysis is the most timesaving and cost-efficient method to rapidly screen all the 3 genes at diagnosis in samples obtained from patients with AML. Endonuclease restriction and ARMS assays can be used separately or in combination with HRM analysis to obtain more reliable results. We propose that early screening of mutations in patients with AML having normal karyotype could facilitate risk stratification and improve treatment options.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Hindenburgdamm 30, 12200 Berlin, Germany.
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Real-time bidirectional pyrophosphorolysis-activated polymerization for quantitative detection of somatic mutations. PLoS One 2014; 9:e96420. [PMID: 24769870 PMCID: PMC4000192 DOI: 10.1371/journal.pone.0096420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/07/2014] [Indexed: 12/24/2022] Open
Abstract
Detection of somatic mutations for targeted therapy is increasingly used in clinical settings. However, due to the difficulties of detecting rare mutations in excess of wild-type DNA, current methods often lack high sensitivity, require multiple procedural steps, or fail to be quantitative. We developed real-time bidirectional pyrophosphorolysis-activated polymerization (real-time Bi-PAP) that allows quantitative detection of somatic mutations. We applied the method to quantify seven mutations at codons 12 and 13 in KRAS, and 2 mutations (L858R, and T790M) in EGFR in clinical samples. The real-time Bi-PAP could detect 0.01% mutation in the presence of 100 ng template DNA. Of the 34 samples from the colon cancer patients, real-time Bi-PAP detected 14 KRAS mutant samples whereas the traditional real-time allele-specific PCR missed two samples with mutation abundance <1% and DNA sequencing missed nine samples with mutation abundance <10%. The detection results of the two EGFR mutations in 45 non-small cell lung cancer samples further supported the applicability of the real-time Bi-PAP. The real-time Bi-PAP also proved to be more efficient than the real-time allele-specific PCR in the detection of templates prepared from formalin-fixed paraffin-embedded samples. Thus, real-time Bi-PAP can be used for rapid and accurate quantification of somatic mutations. This flexible approach could be widely used for somatic mutation detection in clinical settings.
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de Biase D, Visani M, Baccarini P, Polifemo AM, Maimone A, Fornelli A, Giuliani A, Zanini N, Fabbri C, Pession A, Tallini G. Next generation sequencing improves the accuracy of KRAS mutation analysis in endoscopic ultrasound fine needle aspiration pancreatic lesions. PLoS One 2014; 9:e87651. [PMID: 24504548 PMCID: PMC3913642 DOI: 10.1371/journal.pone.0087651] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/27/2013] [Indexed: 02/05/2023] Open
Abstract
The use of endoscopic ultrasonography has allowed for improved detection and pathologic analysis of fine needle aspirate material for pancreatic lesion diagnosis. The molecular analysis of KRAS has further improved the clinical sensitivity of preoperative analysis. For this reason, the use of highly analytical sensitive and specific molecular tests in the analysis of material from fine needle aspirate specimens has become of great importance. In the present study, 60 specimens from endoscopic ultrasonography fine needle aspirate were analyzed for KRAS exon 2 and exon 3 mutations, using three different techniques: Sanger sequencing, allele specific locked nucleic acid PCR and Next Generation sequencing (454 GS-Junior, Roche). Moreover, KRAS was also tested in wild-type samples, starting from DNA obtained from cytological smears after pathological evaluation. Sanger sequencing showed a clinical sensitivity for the detection of the KRAS mutation of 42.1%, allele specific locked nucleic acid of 52.8% and Next Generation of 73.7%. In two wild-type cases the re-sequencing starting from selected material allowed to detect a KRAS mutation, increasing the clinical sensitivity of next generation sequencing to 78.95%. The present study demonstrated that the performance of molecular analysis could be improved by using highly analytical sensitive techniques. The Next Generation Sequencing allowed to increase the clinical sensitivity of the test without decreasing the specificity of the analysis. Moreover we observed that it could be useful to repeat the analysis starting from selectable material, such as cytological smears to avoid false negative results.
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Affiliation(s)
- Dario de Biase
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
- * E-mail:
| | - Michela Visani
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Paola Baccarini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Anna Maria Polifemo
- Unit of Gastroenterology, Azienda Unità Sanitaria Locale di Bologna - Bellaria Hospital, Bologna, Italy
| | | | - Adele Fornelli
- Anatomic Pathology Unit, Azienda Unità Sanitaria Locale di Bologna - Maggiore Hospital, Bologna, Italy
| | - Adriana Giuliani
- Indiana University, Bloomington, Indiana, United States of America
| | - Nicola Zanini
- Unit of General Surgery, Azienda Unità Sanitaria Locale di Bologna - Maggiore Hospital, Bologna, Italy
| | - Carlo Fabbri
- Unit of Gastroenterology, Azienda Unità Sanitaria Locale di Bologna - Bellaria Hospital, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
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de Biase D, Visani M, Malapelle U, Simonato F, Cesari V, Bellevicine C, Pession A, Troncone G, Fassina A, Tallini G. Next-generation sequencing of lung cancer EGFR exons 18-21 allows effective molecular diagnosis of small routine samples (cytology and biopsy). PLoS One 2013; 8:e83607. [PMID: 24376723 PMCID: PMC3871524 DOI: 10.1371/journal.pone.0083607] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/05/2013] [Indexed: 02/05/2023] Open
Abstract
Selection of lung cancer patients for therapy with tyrosine kinase inhibitors directed at EGFR requires the identification of specific EGFR mutations. In most patients with advanced, inoperable lung carcinoma limited tumor samples often represent the only material available for both histologic typing and molecular analysis. We defined a next generation sequencing protocol targeted to EGFR exons 18-21 suitable for the routine diagnosis of such clinical samples. The protocol was validated in an unselected series of 80 small biopsies (n=14) and cytology (n=66) specimens representative of the material ordinarily submitted for diagnostic evaluation to three referral medical centers in Italy. Specimens were systematically evaluated for tumor cell number and proportion relative to non-neoplastic cells. They were analyzed in batches of 100-150 amplicons per run, reaching an analytical sensitivity of 1% and obtaining an adequate number of reads, to cover all exons on all samples analyzed. Next generation sequencing was compared with Sanger sequencing. The latter identified 15 EGFR mutations in 14/80 cases (17.5%) but did not detected mutations when the proportion of neoplastic cells was below 40%. Next generation sequencing identified 31 EGFR mutations in 24/80 cases (30.0%). Mutations were detected with a proportion of neoplastic cells as low as 5%. All mutations identified by the Sanger method were confirmed. In 6 cases next generation sequencing identified exon 19 deletions or the L858R mutation not seen after Sanger sequencing, allowing the patient to be treated with tyrosine kinase inhibitors. In one additional case the R831H mutation associated with treatment resistance was identified in an EGFR wild type tumor after Sanger sequencing. Next generation sequencing is robust, cost-effective and greatly improves the detection of EGFR mutations. Its use should be promoted for the clinical diagnosis of mutations in specimens with unfavorable tumor cell content.
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Affiliation(s)
- Dario de Biase
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Michela Visani
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesca Simonato
- Department of Medicine (DIMED) – Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Valentina Cesari
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Annalisa Pession
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ambrogio Fassina
- Department of Medicine (DIMED) – Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
- * E-mail:
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