1
|
Suda K, Sakai K, Ohira T, Chikugo T, Satou T, Matsubayashi J, Nagao T, Ikeda N, Tsutani Y, Mitsudomi T, Nishio K. Performance of Ultra-Rapid Idylla™ EGFR Mutation Test in Non-Small-Cell Lung Cancer and Its Potential at Clinical Molecular Screening. Cancers (Basel) 2023; 15:cancers15092648. [PMID: 37174112 PMCID: PMC10177517 DOI: 10.3390/cancers15092648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The Idylla™ EGFR Mutation Test is an ultra-rapid single-gene test that detects epidermal growth factor receptor (EGFR) mutations using formalin-fixed paraffin-embedded specimens. Here, we compared the performance of the Idylla EGFR Mutation Test with the Cobas® EGFR Mutation Test v2. METHODS Surgically resected NSCLC specimens obtained at two Japanese institutions (N = 170) were examined. The Idylla EGFR Mutation Test and the Cobas EGFR Mutation Test v2 were performed independently and the results were compared. For discordant cases, the Ion AmpliSeq Colon and Lung Cancer Research Panel V2 was performed. RESULTS After the exclusion of five inadequate/invalid samples, 165 cases were evaluated. EGFR mutation analysis revealed 52 were positive and 107 were negative for EGFR mutation in both assays (overall concordance rate: 96.4%). Analyses of the six discordant cases revealed that the Idylla EGFR Mutation Test was correct in four and the Cobas EGFR Mutation Test v2 was correct in two. In a trial calculation, the combination of the Idylla EGFR Mutation Test followed by a multi-gene panel test will reduce molecular screening expenses if applied to a cohort with EGFR mutation frequency >17.9%. CONCLUSIONS We demonstrated the accuracy and potential clinical utility of the Idylla EGFR Mutation Test as a molecular screening platform in terms of turnaround time and molecular testing cost if applied to a cohort with a high EGFR mutation incidence (>17.9%).
Collapse
Affiliation(s)
- Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Tatsuo Ohira
- Department of Surgery, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Takaaki Chikugo
- Department of Diagnostic Pathology, Kindai University Hospital, Osakasayama 589-8511, Japan
| | - Takao Satou
- Department of Diagnostic Pathology, Kindai University Hospital, Osakasayama 589-8511, Japan
| | - Jun Matsubayashi
- Department of Anatomic Pathology, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Toshitaka Nagao
- Department of Anatomic Pathology, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Norihiko Ikeda
- Department of Surgery, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Yasuhiro Tsutani
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| |
Collapse
|
2
|
Angrisani A, Di Fiore A, Di Trani CA, Fonte S, Petroni M, Lospinoso Severini L, Bordin F, Belloni L, Ferretti E, Canettieri G, Moretti M, De Smaele E. Specific Protein 1 and p53 Interplay Modulates the Expression of the KCTD-Containing Cullin3 Adaptor Suppressor of Hedgehog 2. Front Cell Dev Biol 2021; 9:638508. [PMID: 33898425 PMCID: PMC8060498 DOI: 10.3389/fcell.2021.638508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
The Hedgehog (Hh) signaling pathway plays a crucial role in normal embryonic development and adult tissue homeostasis. On the other end, dysregulated Hh signaling triggers a prolonged mitogenic response that may prompt abnormal cell proliferation, favoring tumorigenesis. Indeed, about 30% of medulloblastomas (MBs), the most common malignant childhood cerebellar tumors, exhibit improper activation of the Hh signaling. The oncosuppressor KCASH2 has been described as a suppressor of the Hh signaling pathway, and low KCASH2 expression was observed in Hh-dependent MB tumor. Therefore, the study of the modulation of KCASH2 expression may provide fundamental information for the development of new therapeutic approaches, aimed to restore physiological KCASH2 levels and Hh inhibition. To this end, we have analyzed the TATA-less KCASH2 proximal promoter and identified key transcriptional regulators of this gene: Sp1, a TF frequently overexpressed in tumors, and the tumor suppressor p53. Here, we show that in WT cells, Sp1 binds KCASH2 promoter on several putative binding sites, leading to increase in KCASH2 expression. On the other hand, p53 is involved in negative regulation of KCASH2. In this context, the balance between p53 and Sp1 expression, and the interplay between these two proteins determine whether Sp1 acts as an activator or a repressor of KCASH2 transcription. Indeed, in p53–/– MEF and p53 mutated tumor cells, we hypothesize that Sp1 drives promoter methylation through increased expression of the DNA methyltransferase 1 (DNMT1) and reduces KCASH2 transcription, which can be reversed by Sp1 inhibition or use of demethylating agents. We suggest therefore that downregulation of KCASH2 expression in tumors could be mediated by gain of Sp1 activity and epigenetic silencing events in cells where p53 functionality is lost. This work may open new venues for novel therapeutic multidrug approaches in the treatment of Hh-dependent tumors carrying p53 deficiency.
Collapse
Affiliation(s)
| | | | | | - Simone Fonte
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | | | | | - Fabio Bordin
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Laura Belloni
- Department of Internal, Anesthesiological and Cardiovascular Clinical Sciences, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Rome, Italy.,Istituto Pasteur, Fondazione Cenci-Bolognetti, Sapienza University, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University, Rome, Italy.,Istituto Pasteur, Fondazione Cenci-Bolognetti, Sapienza University, Rome, Italy
| | - Marta Moretti
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| |
Collapse
|
3
|
Belardinilli F, Pernazza A, Mahdavian Y, Cerbelli B, Bassi M, Gradilone A, Coppa A, Pignataro MG, Anile M, Venuta F, Della Rocca C, Giannini G, d'Amati G. A multidisciplinary approach for the differential diagnosis between multiple primary lung adenocarcinomas and intrapulmonary metastases. Pathol Res Pract 2021; 220:153387. [PMID: 33647865 DOI: 10.1016/j.prp.2021.153387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/13/2021] [Indexed: 11/26/2022]
Abstract
PURPOSE The distinction between multiple primary lung cancers (MPLCs) and intrapulmonary metastases has a significant impact on tumor staging and therapeutic choices. Several criteria have been proposed to solve this diagnostic issue, but a definitive consensus is still missing. We tested the efficacy of a combined clinical, histopathological and molecular ("real world") approach for the correct classification of multiple lung tumors in a selected cohort of patients. METHODS 24 multiple lung tumors with a diagnosis of adenocarcinoma from 10 patients were retrospectively reviewed. Radiological, pathological and clinical information, including follow-up, were integrated with molecular profiling via a routine multigene panel sequencing. RESULTS Comprehensive histologic assessment revealed readily distinguishable histologic patterns between multiple tumors suggesting unrelated lesions in 7 cases, in agreement with clinical, radiological and molecular data, thus leading to final diagnosis of MPLCs. In the remaining 3 cases, the differential diagnosis between MPLCs and intrapulmonary metastases was challenging, since the histologic features of the lesions were similar or identical. The final interpretation (2 MPLCs and 1 most likely intrapulmonary metastases) was reached thanks to the integration of all available data, and was confirmed by follow-up. CONCLUSIONS A multidisciplinary approach including a routinely affordable multigene panel sequencing is a useful tool to discriminate MPLCs from intrapulmonary metastases in multiple lung nodules sharing the adenocarcinoma histotype.
Collapse
Affiliation(s)
- Francesca Belardinilli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Angelina Pernazza
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Bruna Cerbelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Massimiliano Bassi
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | | | - Maria Gemma Pignataro
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University, Rome, 00161, Italy
| | - Marco Anile
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Federico Venuta
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Carlo Della Rocca
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy.
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University, Rome, 00161, Italy.
| |
Collapse
|
4
|
Nicolussi A, Belardinilli F, Ottini L, Petroni M, Capalbo C, Giannini G, Coppa A. A novel BRCA2 splice variant identified in a young woman. Mol Genet Genomic Med 2020; 8:e1513. [PMID: 33159495 PMCID: PMC7767566 DOI: 10.1002/mgg3.1513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/07/2020] [Accepted: 09/02/2020] [Indexed: 11/08/2022] Open
Abstract
Background BRCA1/2 VUSs represent an important clinical issue in risk assessment for the breast/ovarian cancer families (HBOC) families. Among them, some occurring within the intron‐exon boundary may lead to aberrant splicing process by altering or creating de novo splicing regulatory elements or unmasking cryptic splice site. Defining the impact of these potential splice variants at functional level is important to establish their pathogenic role. Methods Genomic DNA was extracted from peripheral blood sample of a young woman affected with breast cancer belonging to a HBOC family and the entire coding regions of the BRCA1 and BRCA2 genes were amplified using the Ion AmpliSeq BRCA1 and BRCA2 Panel. The BRCA2 c.682‐2delA variant has been characterized by RT‐PCR analysis performed on mRNA extracted from blood and lymphoblastoid cell line. Results We demonstrated that a novel BRCA2 c.682‐2delA variant at the highly conserved splice consensus site in intron 8 disrupts the canonical splice acceptor site generating a truncated protein as predicted by several bioinformatics tools. Segregations analysis in the family and LOH performed on proband breast cancer tissue further confirmed its classification as pathogenic variant. Conclusion Combining different methodologies, we characterized this new BRCA2 variant and provided findings of clinical utility for its classification as pathogenic variant.
Collapse
Affiliation(s)
- Arianna Nicolussi
- Department of Experimental MedicineUniversity of Roma “La Sapienza”RomaItaly
| | | | - Laura Ottini
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
| | - Marialaura Petroni
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
| | - Carlo Capalbo
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
| | - Giuseppe Giannini
- Department of Molecular MedicineUniversity of Roma “La Sapienza”RomaItaly
- Istituto Pasteur‐Fondazione Cenci BolognettiRomaItaly
| | - Anna Coppa
- Department of Experimental MedicineUniversity of Roma “La Sapienza”RomaItaly
| |
Collapse
|
5
|
CTNNB1 p.L31P mutation in an ovarian endometrioid carcinoma with synchronous uterine endometrioid carcinoma. Pathol Res Pract 2020; 216:153260. [PMID: 33120166 DOI: 10.1016/j.prp.2020.153260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 11/20/2022]
Abstract
We performed next generation sequencing of DNA extracted from the neoplastic tissues obtained from a patient who underwent surgery for a large right ovarian carcinoma (OC) of endometrioid type associated with endometrial cancer (EC). This was done in order to ascertain whether the tumors were synchronous endometrial/ovarian cancers or an advanced metastatic stage from either the ovary or the uterus. Pathologic criteria favoured synchronous EC/OC. We identified a PTEN c.959 T > G (p.L320X) truncating mutation occurring with similar allele frequency in both neoplastic tissues (ovary: 88 %, endometrium 89 %) and a CTNNB1 c.100C > G (p.S37C) activating mutation, with a comparable allelic frequency in both tumor tissues (ovary 51 %, endometrium 52 %). The shared genetic mutations, and the presence of PTEN c.959 T > G (p.L320X) truncating mutation, albeit at low allelic frequency (6 %), in the healthy peritumoral endometrial tissue, appear to confirm the recent literature on a primary endometrial origin for synchronous EC/OC. A third mutation was CTNNB1 c.92 T > C (p.L31 P), a missense mutation occurring with a low allele frequency (3.7 %) only in the ovarian cancer tissue. This mutation is only occasionally described in hepatocellular carcinomas.
Collapse
|
6
|
Belardinilli F, Capalbo C, Malapelle U, Pisapia P, Raimondo D, Milanetti E, Yasaman M, Liccardi C, Paci P, Sibilio P, Pepe F, Bonfiglio C, Mezi S, Magri V, Coppa A, Nicolussi A, Gradilone A, Petroni M, Di Giulio S, Fabretti F, Infante P, Coni S, Canettieri G, Troncone G, Giannini G. Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer. Front Oncol 2020; 10:560. [PMID: 32457828 PMCID: PMC7221020 DOI: 10.3389/fonc.2020.00560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Extensive molecular characterization of human colorectal cancer (CRC) via Next Generation Sequencing (NGS) indicated that genetic or epigenetic dysregulation of a relevant, but limited, number of molecular pathways typically occurs in this tumor. The molecular picture of the disease is significantly complicated by the frequent occurrence of individually rare genetic aberrations, which expand tumor heterogeneity. Inter- and intratumor molecular heterogeneity is very likely responsible for the remarkable individual variability in the response to conventional and target-driven first-line therapies, in metastatic CRC (mCRC) patients, whose median overall survival remains unsatisfactory. Implementation of an extensive molecular characterization of mCRC in the clinical routine does not yet appear feasible on a large scale, while multigene panel sequencing of most commonly mutated oncogene/oncosuppressor hotspots is more easily achievable. Here, we report that clinical multigene panel sequencing performed for anti-EGFR therapy predictive purposes in 639 formalin-fixed paraffin-embedded (FFPE) mCRC specimens revealed previously unknown pairwise mutation associations and a high proportion of cases carrying actionable gene mutations. Most importantly, a simple principal component analysis directed the delineation of a new molecular stratification of mCRC patients in eight groups characterized by non-random, specific mutational association patterns (MAPs), aggregating samples with similar biology. These data were validated on a The Cancer Genome Atlas (TCGA) CRC dataset. The proposed stratification may provide great opportunities to direct more informed therapeutic decisions in the majority of mCRC cases.
Collapse
Affiliation(s)
| | - Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Pasquale Pisapia
- Department of Public Health, University Federico II, Naples, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Mahdavian Yasaman
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Carlotta Liccardi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Paola Paci
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Pasquale Sibilio
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II, Naples, Italy
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Bari, Italy
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, Rome, Italy
| | - Valentina Magri
- Department of Surgery Pietro Valdoni, Faculty of Medicine and Dentistry, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sonia Coni
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | | | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| |
Collapse
|
7
|
Nicolussi A, Belardinilli F, Silvestri V, Mahdavian Y, Valentini V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Di Giulio S, Fabretti F, Fratini B, Gradilone A, Ottini L, Giannini G, Coppa A, Capalbo C. Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data. PeerJ 2019; 7:e7972. [PMID: 31741787 PMCID: PMC6859874 DOI: 10.7717/peerj.7972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/30/2022] Open
Abstract
Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.
Collapse
Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Valentina Silvestri
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science @ Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Francesca Fabretti
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Beatrice Fratini
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| |
Collapse
|
8
|
Nicolussi A, Belardinilli F, Mahdavian Y, Colicchia V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Valentini V, Ottini L, Giannini G, Capalbo C, Coppa A. Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer. PeerJ 2019; 7:e6661. [PMID: 31065452 PMCID: PMC6482939 DOI: 10.7717/peerj.6661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.
Collapse
Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Valeria Colicchia
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy.,U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science@Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| |
Collapse
|
9
|
Capalbo C, Belardinilli F, Raimondo D, Milanetti E, Malapelle U, Pisapia P, Magri V, Prete A, Pecorari S, Colella M, Coppa A, Bonfiglio C, Nicolussi A, Valentini V, Tessitore A, Cardinali B, Petroni M, Infante P, Santoni M, Filetti M, Colicchia V, Paci P, Mezi S, Longo F, Cortesi E, Marchetti P, Troncone G, Bellavia D, Canettieri G, Giannini G. A Simplified Genomic Profiling Approach Predicts Outcome in Metastatic Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11020147. [PMID: 30691222 PMCID: PMC6406354 DOI: 10.3390/cancers11020147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
The response of metastatic colorectal cancer (mCRC) to the first-line conventional combination therapy is highly variable, reflecting the elevated heterogeneity of the disease. The genetic alterations underlying this heterogeneity have been thoroughly characterized through omic approaches requiring elevated efforts and costs. In order to translate the knowledge of CRC molecular heterogeneity into a practical clinical approach, we utilized a simplified Next Generation Sequencing (NGS) based platform to screen a cohort of 77 patients treated with first-line conventional therapy. Samples were sequenced using a panel of hotspots and targeted regions of 22 genes commonly involved in CRC. This revealed 51 patients carrying actionable gene mutations, 22 of which carried druggable alterations. These mutations were frequently associated with additional genetic alterations. To take into account this molecular complexity and assisted by an unbiased bioinformatic analysis, we defined three subgroups of patients carrying distinct molecular patterns. We demonstrated these three molecular subgroups are associated with a different response to first-line conventional combination therapies. The best outcome was achieved in patients exclusively carrying mutations on TP53 and/or RAS genes. By contrast, in patients carrying mutations in any of the other genes, alone or associated with mutations of TP53/RAS, the expected response is much worse compared to patients with exclusive TP53/RAS mutations. Additionally, our data indicate that the standard approach has limited efficacy in patients without any mutations in the genes included in the panel. In conclusion, we identified a reliable and easy-to-use approach for a simplified molecular-based stratification of mCRC patients that predicts the efficacy of the first-line conventional combination therapy.
Collapse
Affiliation(s)
- Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | | | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | | | - Umberto Malapelle
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Valentina Magri
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Alessandra Prete
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Silvia Pecorari
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | | | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Castellana Grotte, 70013 Bari, Italy.
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Virginia Valentini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Campus A. Buzzati-Traverso, 00015 Monterotondo Scalo, Italy.
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy.
| | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy.
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62012 Macerata, Italy.
| | - Marco Filetti
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | - Valeria Colicchia
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, 00185 Rome, Italy.
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Flavia Longo
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Enrico Cortesi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Paolo Marchetti
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | - Giancarlo Troncone
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Diana Bellavia
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, 00161 Rome, Italy.
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, 00161 Rome, Italy.
| |
Collapse
|
10
|
Gall TMH, Gerrard G, Frampton AE, Castellano L, Ahmad R, Habib N, Spalding D, Pai M, Foroni L, Jiao LR. Can we predict long-term survival in resectable pancreatic ductal adenocarcinoma? Oncotarget 2019; 10:696-706. [PMID: 30774772 PMCID: PMC6366827 DOI: 10.18632/oncotarget.26511] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/12/2018] [Indexed: 01/06/2023] Open
Abstract
Objective Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumour associated with poor 5-year survival. We aimed to determine factors which differentiate short and long-term survivors and identify a prognostic biomarker. Methods Over a ten-year period, patients with resected PDAC who developed disease recurrence within 12 months (Group I) and those who had no disease recurrence for 24 months (Group II) were identified. Clinicopathological data was analysed. Ion Torrent high-throughput sequencing on DNA extracted from FFPE tumour samples was used to identify mutations. Additionally, peripheral blood samples were analysed for variants in cell-free DNA, circulating tumour cells (CTCs), and microRNAs. Results Multivariable analysis of clinicopathological factors showed that a positive medial resection margin was significantly associated with short disease-free survival (p = 0.007). Group I patients (n = 21) had a higher frequency of the KRAS mutant mean variant allele (16.93% ± 11.04) compared to those in Group II (n = 13; 7.55% ± 5.76, p = 0.0078). Group I patients also trended towards having a KRAS c.35G>A p.Gly12Asp mutation in addition to variants in other genes, such as TP53, CDKN2A, and SMAD4. Mutational status of cell-free DNA, and number of CTCs, was not found to be useful in this study. A circulating miRNA (hsa-miR-548ah-5p) was found to be significantly differentially expressed. Conclusions Medial resection margin status and the frequency of KRAS mutation in the tumour tissue are independent prognostic indicators for resectable PDAC. Circulating miRNA hsa-miR-548ah-5p has the potential to be used as a prognostic biomarker.
Collapse
Affiliation(s)
- Tamara M H Gall
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Gareth Gerrard
- Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom.,Current address: Sarah Cannon Molecular Diagnostics, HCA Healthcare UK, London WC1E 6JA, United Kingdom
| | - Adam E Frampton
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Leandro Castellano
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Raida Ahmad
- Department of Histopathology, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Nagy Habib
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Duncan Spalding
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Madhava Pai
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Letizia Foroni
- Department of Histopathology, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| | - Long R Jiao
- Department of Surgery and Cancer, Imperial College, Hammersmith Hospital Campus, London W12 0HS, United Kingdom
| |
Collapse
|
11
|
Belardinilli F, Gradilone A, Gelibter A, Zani M, Occhipinti M, Ferraro S, Nicolazzo C, Coppa A, Giannini G. Coexistence of three EGFR mutations in an NSCLC patient: A brief report. Int J Biol Markers 2018; 33:1724600818782200. [PMID: 29945477 DOI: 10.1177/1724600818782200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
BACKGROUND The epidermal growth factor receptor (EGFR) represents a molecular target for tyrosine kinase inhibitors for non-small cell lung cancer (NSCLC) patients with a mutation in the EGFR gene. Mutations of the EGFR gene that occur at a single position in NSCLC tissue are found as single, whereas two or more mutations on the same allele are poorly detected and investigated. PATIENT AND METHODS We investigated the presence of the EGFR gene mutations in tumor tissue by Sanger sequencing and ion torrent sequencing in an NSCLC patient at Stage IV of disease. RESULTS We found the presence of three coexisting mutations on the EGFR gene-two of which on exon 21 are present on the same allele, and the third, on exon 20, was analyzed by Sanger sequencing of the peripheral blood lymphocytes. The patient staged as cT4N0M1c (Stage IV) and started afatinib 40 mg daily 8 months ago, showing a clinical benefit. CONCLUSION In this report we describe the case of an NSCLC patient harboring three coexisting mutations on the EGFR gene, two of which are present on the same allele. This mutation pattern may represent, for patient progeny, a genetic risk of cancer development. Therefore it should be possible to obtain screening guidelines to improve the risk calculation for lung cancer susceptibility in the future.
Collapse
Affiliation(s)
| | - Angela Gradilone
- 1 Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Roma, Italia
| | - Alain Gelibter
- 2 Dipartimento di Scienze Radiologiche, Oncologiche ed Anatomopatologiche, Sapienza Università di Roma, Roma, Italia
| | - Massimo Zani
- 1 Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Roma, Italia
| | - Mario Occhipinti
- 2 Dipartimento di Scienze Radiologiche, Oncologiche ed Anatomopatologiche, Sapienza Università di Roma, Roma, Italia
| | - Sergio Ferraro
- 1 Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Roma, Italia
| | - Chiara Nicolazzo
- 1 Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Roma, Italia
| | - Anna Coppa
- 3 Dipartimento di Medicina Sperimentale, Sapienza Università di Roma, Roma, Italia
| | - Giuseppe Giannini
- 1 Dipartimento di Medicina Molecolare, Sapienza Università di Roma, Roma, Italia
- 4 Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italia
| |
Collapse
|
12
|
Capalbo C, Belardinilli F, Filetti M, Parisi C, Petroni M, Colicchia V, Tessitore A, Santoni M, Coppa A, Giannini G, Marchetti P. Effective treatment of a platinum-resistant cutaneous squamous cell carcinoma case by EGFR pathway inhibition. Mol Clin Oncol 2018; 9:30-34. [PMID: 29977536 DOI: 10.3892/mco.2018.1634] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/30/2018] [Indexed: 12/25/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most common type of non-melanoma skin cancer. Platinum-based regimens have been an integral part of palliative care for patients with locally advanced or metastatic disease. There is no evidence of efficacy for later lines of chemotherapy and no targeted therapy has been introduced as 'standard of care'. Here we report on the case of an elderly cSCC patient, resistant to conventional therapy, however successfully treated with anti-epidermal growth factor receptor (EGFR) agent (Cetuximab) in addition to a daily dose of Curcumin phospholipid. The patient responded to treatment and experienced no recurrence for 11 months with only minor skin-related toxicity. To our knowledge, this is the first report of clinical evidence that an anti EGFR targeted therapy with a daily oral dose of Curcumin phospholipid is well tolerated and results in a highly effective disease control in a heavily pretreated cSCC patient.
Collapse
Affiliation(s)
- Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy.,Medical Oncology Sant'Andrea Hospital, I-00189 Rome, Italy
| | | | - Marco Filetti
- Medical Oncology Sant'Andrea Hospital, I-00189 Rome, Italy
| | - Claudia Parisi
- Medical Oncology Sant'Andrea Hospital, I-00189 Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, I-00161 Rome, Italy
| | - Valeria Colicchia
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | | | - Matteo Santoni
- Oncology Unit, Macerata Hospital, I-62100 Macerata, Italy
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, I-00161 Rome, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, I-00161 Rome, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, I-00161 Rome, Italy
| | | |
Collapse
|
13
|
Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
Collapse
Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| |
Collapse
|
14
|
Coppa A, Nicolussi A, D'Inzeo S, Capalbo C, Belardinilli F, Colicchia V, Petroni M, Zani M, Ferraro S, Rinaldi C, Buffone A, Bartolazzi A, Screpanti I, Ottini L, Giannini G. Optimizing the identification of risk-relevant mutations by multigene panel testing in selected hereditary breast/ovarian cancer families. Cancer Med 2018; 7:46-55. [PMID: 29271107 PMCID: PMC5773970 DOI: 10.1002/cam4.1251] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/05/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022] Open
Abstract
The introduction of multigene panel testing for hereditary breast/ovarian cancer screening has greatly improved efficiency, speed, and costs. However, its clinical utility is still debated, mostly due to the lack of conclusive evidences on the impact of newly discovered genetic variants on cancer risk and lack of evidence-based guidelines for the clinical management of their carriers. In this pilot study, we aimed to test whether a systematic and multiparametric characterization of newly discovered mutations could enhance the clinical utility of multigene panel sequencing. Out of a pool of 367 breast/ovarian cancer families Sanger-sequenced for BRCA1 and BRCA2 gene mutations, we selected a cohort of 20 BRCA1/2-negative families to be subjected to the BROCA-Cancer Risk Panel massive parallel sequencing. As a strategy for the systematic characterization of newly discovered genetic variants, we collected blood and cancer tissue samples and established lymphoblastoid cell lines from all available individuals in these families, to perform segregation analysis, loss-of-heterozygosity and further molecular studies. We identified loss-of-function mutations in 6 out 20 high-risk families, 5 of which occurred on BRCA1, CHEK2 and ATM and are esteemed to be risk-relevant. In contrast, a novel RAD50 truncating mutation is most likely unrelated to breast cancer. Our data suggest that integrating multigene panel testing with a pre-organized, multiparametric characterization of newly discovered genetic variants improves the identification of risk-relevant alleles impacting on the clinical management of their carriers.
Collapse
Affiliation(s)
- Anna Coppa
- Department of Experimental MedicineUniversity La SapienzaV.le R. Elena 324Rome00161Italy
| | - Arianna Nicolussi
- Department of Experimental MedicineUniversity La SapienzaV.le R. Elena 324Rome00161Italy
| | - Sonia D'Inzeo
- Department of Experimental MedicineUniversity La SapienzaV.le R. Elena 324Rome00161Italy
| | - Carlo Capalbo
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | | | - Valeria Colicchia
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Marialaura Petroni
- Center for Life Nano Science@SapienzaIstituto Italiano di TecnologiaRome00161Italy
| | - Massimo Zani
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Sergio Ferraro
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Christian Rinaldi
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Amelia Buffone
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Armando Bartolazzi
- Department of PathologySant'Andrea HospitalUniversity La SapienzaVia di Grottarossa 1035Rome00189Italy
| | - Isabella Screpanti
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Laura Ottini
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
| | - Giuseppe Giannini
- Department of Molecular MedicineUniversity La SapienzaV.le R. Elena 291Rome00161Italy
- Istituto Pasteur‐Fondazione Cenci BolognettiRome00161Italy
| |
Collapse
|
15
|
Hou H, Liu D, Zhang C, Jiang Y, Lu G, Zhou N, Yang X, Zhang X, Li Z, Zhu H, Qian Z, Zhang X. Targeted next generation sequencing in Chinese colorectal cancer patients guided anti-EGFR treatment and facilitated precision cancer medicine. Oncotarget 2017; 8:105072-105080. [PMID: 29285234 PMCID: PMC5739621 DOI: 10.18632/oncotarget.21349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Colorectal cancer (CRC) patients with both RAS and BRAF wild-type tumors determined by non-next generation sequencing (NGS) testing may still not respond due to the presence of additional mutated genes such as PIK3CA or PTEN. In this study, a broad, hybrid capture-based NGS assay was used to identify RAS, BRAF and additional targetable genetic alterations from Chinese CRC tissues. METHODS Fifty-seven cases of CRC were enrolled, and all the patients signed the informed consent. In total, 7708 exons of 508 tumor-related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, INDELs, copy number alterations, and gene fusions. RESULTS The study found that 50.9% (29/57) of the tumors harbored KRAS mutations, 3.5% (2/57) harbored NRAS mutations and 3.5% (2/57) harbored BRAF mutations. More specifically, 89.7% (26/29) of RAS mutations were located in codon 12. Except for RAS and RAF, anti-EGFR therapy response genetic mutations in PTEN (n=2) and PIK3CA (n=1) were found in 4.7% (3/64) of the samples. Actionable alterations were found in HER2 (n = 7), CCND2 (n = 2), NF1 (n = 1), and BRCA1 (n = 1). CONCLUSIONS Our results illustrated that 82.5% (47/57) of the samples harbored at least one actionable genetic alteration identified by NGS. HER2 amplifications or mutations, which were identified in 12.3% of the tissues, defined a unique molecular subtype of CRC. The study suggests that high-throughput NGS testing in CRC tissues is a comprehensive and efficient genomic profiling assay to guide personalized therapy.
Collapse
Affiliation(s)
- Helei Hou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Dong Liu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Chuantao Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Guifang Lu
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Na Zhou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Xiaonan Yang
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Xiaoping Zhang
- Department of Clinical Laboratory, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhuokun Li
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Hongmei Zhu
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Zhaoyang Qian
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xiaochun Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| |
Collapse
|
16
|
Selective targeting of HDAC1/2 elicits anticancer effects through Gli1 acetylation in preclinical models of SHH Medulloblastoma. Sci Rep 2017; 7:44079. [PMID: 28276480 PMCID: PMC5343431 DOI: 10.1038/srep44079] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/02/2017] [Indexed: 02/06/2023] Open
Abstract
SHH Medulloblastoma (SHH-MB) is a pediatric brain tumor characterized by an inappropriate activation of the developmental Hedgehog (Hh) signaling. SHH-MB patients treated with the FDA-approved vismodegib, an Hh inhibitor that targets the transmembrane activator Smoothened (Smo), have shown the rapid development of drug resistance and tumor relapse due to novel Smo mutations. Moreover, a subset of patients did not respond to vismodegib because mutations were localized downstream of Smo. Thus, targeting downstream Hh components is now considered a preferable approach. We show here that selective inhibition of the downstream Hh effectors HDAC1 and HDAC2 robustly counteracts SHH-MB growth in mouse models. These two deacetylases are upregulated in tumor and their knockdown inhibits Hh signaling and decreases tumor growth. We demonstrate that mocetinostat (MGCD0103), a selective HDAC1/HDAC2 inhibitor, is a potent Hh inhibitor and that its effect is linked to Gli1 acetylation at K518. Of note, we demonstrate that administration of mocetinostat to mouse models of SHH-MB drastically reduces tumor growth, by reducing proliferation and increasing apoptosis of tumor cells and prolongs mouse survival rate. Collectively, these data demonstrate the preclinical efficacy of targeting the downstream HDAC1/2-Gli1 acetylation in the treatment of SHH-MB.
Collapse
|
17
|
Fontanges Q, De Mendonca R, Salmon I, Le Mercier M, D'Haene N. Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers. Int J Mol Sci 2016; 17:ijms17122117. [PMID: 27999270 PMCID: PMC5187917 DOI: 10.3390/ijms17122117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 01/01/2023] Open
Abstract
Promising targeted therapy and personalized medicine are making molecular profiling of tumours a priority. For colorectal cancer (CRC) patients, international guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-epidermal growth factor receptor agents (anti-EGFR). Daily, new data emerge on the theranostic and prognostic role of molecular biomarkers, which is a strong incentive for a validated, sensitive and broadly available molecular screening test in order to implement and improve multi-modal therapy strategy and clinical trials. Next generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. Targeted NGS is a method that allows parallel sequencing of thousands of short DNA sequences in a single test offering a cost-effective approach for detecting multiple genetic alterations with a minimum amount of DNA. In the present review, we collected data concerning the clinical application of NGS technology in the setting of colorectal cancer.
Collapse
Affiliation(s)
- Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Ricardo De Mendonca
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| |
Collapse
|
18
|
Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R, Tommasi S, Pinto R. Next-generation sequencing: advances and applications in cancer diagnosis. Onco Targets Ther 2016; 9:7355-7365. [PMID: 27980425 PMCID: PMC5144906 DOI: 10.2147/ott.s99807] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Technological advances have led to the introduction of next-generation sequencing (NGS) platforms in cancer investigation. NGS allows massive parallel sequencing that affords maximal tumor genomic assessment. NGS approaches are different, and concern DNA and RNA analysis. DNA sequencing includes whole-genome, whole-exome, and targeted sequencing, which focuses on a selection of genes of interest for a specific disease. RNA sequencing facilitates the detection of alternative gene-spliced transcripts, posttranscriptional modifications, gene fusion, mutations/single-nucleotide polymorphisms, small and long noncoding RNAs, and changes in gene expression. Most applications are in the cancer research field, but lately NGS technology has been revolutionizing cancer molecular diagnostics, due to the many advantages it offers compared to traditional methods. There is greater knowledge on solid cancer diagnostics, and recent interest has been shown also in the field of hematologic cancer. In this review, we report the latest data on NGS diagnostic/predictive clinical applications in solid and hematologic cancers. Moreover, since the amount of NGS data produced is very large and their interpretation is very complex, we briefly discuss two bioinformatic aspects, variant-calling accuracy and copy-number variation detection, which are gaining a lot of importance in cancer-diagnostic assessment.
Collapse
Affiliation(s)
- Simona Serratì
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| |
Collapse
|
19
|
Khodakov D, Wang C, Zhang DY. Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches. Adv Drug Deliv Rev 2016; 105:3-19. [PMID: 27089811 DOI: 10.1016/j.addr.2016.04.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/21/2016] [Accepted: 04/06/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics.
Collapse
|
20
|
Jesinghaus M, Pfarr N, Endris V, Kloor M, Volckmar AL, Brandt R, Herpel E, Muckenhuber A, Lasitschka F, Schirmacher P, Penzel R, Weichert W, Stenzinger A. Genotyping of colorectal cancer for cancer precision medicine: Results from the IPH Center for Molecular Pathology. Genes Chromosomes Cancer 2016; 55:505-21. [PMID: 26917275 DOI: 10.1002/gcc.22352] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/02/2016] [Accepted: 02/05/2016] [Indexed: 12/19/2022] Open
Abstract
Cancer precision medicine has opened up new avenues for the treatment of colorectal cancer (CRC). To fully realize its potential, high-throughput sequencing platforms that allow genotyping beyond KRAS need to be implemented and require performance assessment. We comprehensively analyzed first-year data of 202 consecutive formalin-fixed paraffin embedded (FFPE) CRC samples for which prospective genotyping at our institution was requested. Deep targeted genotyping was done using a semiconductor-based sequencing platform and a self-designed panel of 30 CRC-related genes. Additionally, microsatellite status (MS) was determined. Ninety-seven percent of tumor samples were suitable for sequencing and in 88% MS could be assessed. The minimal drop-out rates of 6 and 25 cases, respectively were due to too low amounts or heavy degradation of DNA. Of 557 nonsynonymous mutations, 90 (16%) have not been described in COSMIC at the time of data query. Forty-three cases (22%) had double- or triple mutations affecting a single gene. Sixty-four percent had genetic alterations influencing oncological therapy. Eight percent of patients (MSI phenotype: 6%; mutated POLE: 2%) were potentially eligible for treatment with immune checkpoint inhibitors. Of 56% of KRASwt CRC that potentially qualified for anti-EGFR treatment, 30% presented with mutations in BRAF/NRAS. Mutated PIK3CA was detected in 21%. In conclusion, we here present real-life routine diagnostics data that not only demonstrate the robustness and feasibility of deep targeted sequencing and MS-analysis of FFPE CRC samples but also contribute to the understanding of CRC genetics. Most importantly, in more than half of the patients our approach enabled the selection of the best treatment currently available. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Moritz Jesinghaus
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, 81675, Germany
| | - Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, 81675, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Matthias Kloor
- Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Regine Brandt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Esther Herpel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | | | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, 81675, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Member of the German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, 69120, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,National Center for Tumor Diseases-Heidelberg School of Oncology (NCT-HSO), Heidelberg, Germany
| |
Collapse
|
21
|
de Leng WWJ, Gadellaa-van Hooijdonk CG, Barendregt-Smouter FAS, Koudijs MJ, Nijman I, Hinrichs JWJ, Cuppen E, van Lieshout S, Loberg RD, de Jonge M, Voest EE, de Weger RA, Steeghs N, Langenberg MHG, Sleijfer S, Willems SM, Lolkema MP. Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material. PLoS One 2016; 11:e0149405. [PMID: 26919633 PMCID: PMC4769293 DOI: 10.1371/journal.pone.0149405] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022] Open
Abstract
Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5% concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detection of low-frequency variants. The reliability of mutation analysis could be further improved with manual inspection of sequence data. Conclusion Targeted NGS can be reliably implemented in cancer diagnostics using both FFPE and FF tissue when using appropriate analysis settings, even with low input DNA.
Collapse
Affiliation(s)
- Wendy W. J. de Leng
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Christa G. Gadellaa-van Hooijdonk
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Françoise A. S. Barendregt-Smouter
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marco J. Koudijs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Ies Nijman
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - John W. J. Hinrichs
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Edwin Cuppen
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stef van Lieshout
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Robert D. Loberg
- Medical Sciences, Amgen Inc., Thousand Oaks, CA, 91320–1799, United States of America
| | - Maja de Jonge
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Emile E. Voest
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Roel A. de Weger
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Neeltje Steeghs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Marlies H. G. Langenberg
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stefan Sleijfer
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Martijn P. Lolkema
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
- * E-mail:
| |
Collapse
|
22
|
Moens LNJ, Falk-Sörqvist E, Ljungström V, Mattsson J, Sundström M, La Fleur L, Mathot L, Micke P, Nilsson M, Botling J. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples. J Mol Diagn 2015; 17:729-39. [PMID: 26354930 DOI: 10.1016/j.jmoldx.2015.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/29/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022] Open
Abstract
In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.
Collapse
Affiliation(s)
- Lotte N J Moens
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Elin Falk-Sörqvist
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Johanna Mattsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Magnus Sundström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Linnéa La Fleur
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Mats Nilsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden.
| | - Johan Botling
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden.
| |
Collapse
|