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Hofste LS, Geerlings MJ, Kamping EJ, Kouwenhoven ND, von Rhein D, Jansen EA, Garms LM, Nagtegaal ID, van der Post RS, de Wilt JH, Klarenbeek BR, Ligtenberg MJ. Clinical Validity of Tumor-Informed Circulating Tumor DNA Analysis in Patients Undergoing Surgery of Colorectal Metastases. Dis Colon Rectum 2023; 66:796-804. [PMID: 35857852 PMCID: PMC10191207 DOI: 10.1097/dcr.0000000000002443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Accurate biomarkers to monitor tumor load and response in metastatic colorectal cancer patients undergoing surgery could optimize treatment regimens. OBJECTIVE This study aimed to explore the clinical validity of tumor-informed quantification of circulating tumor DNA in blood using ultradeep sequencing. DESIGN Resection specimens from 53 colorectal cancer patients were analyzed for tumor-specific mutations in 15 genes. These mutations were used to measure the presence of circulating tumor DNA in preoperatively collected plasma samples using hybrid capture-based sequencing. Additional postoperative measurements were performed 1 week after surgery in 16 patients. SETTINGS The study was conducted at the Radboud University Medical Center. PATIENTS A total of 53 colorectal cancer patients undergoing surgery of metastases were included. MAIN OUTCOME MEASURES The detection of circulating tumor DNA. RESULTS At least 1 tumor-specific mutation was detected in all tumor samples. In preoperative plasma samples, circulating tumor DNA was detected in 88% (37/42) of systemic treatment-naïve patients and in 55% (6/11) of patients who received preoperative chemotherapy. More specifically, circulating tumor DNA was detected in 0% (0/3) of cases with a subtotal or partial pathologic response and in 75% (6/8) of cases without a pathologic response in the resection specimen ( p = 0.06). In postoperative plasma samples, circulating tumor DNA was detected in 80% (4/5) of patients with an incomplete resection and in 0% (0/11) of those with a complete resection ( p = 0.003). LIMITATIONS The study was limited by the heterogeneity of the cohort and the small number of postoperative plasma samples. CONCLUSIONS These data indicate that tumor-informed circulating tumor DNA detection in the plasma of patients undergoing surgery for metastatic colorectal cancer is feasible and may have clinical value in response monitoring and predicting residual disease. Prospective studies are needed to establish the clinical utility of circulating tumor DNA analysis to guide treatment decisions in these patients. See Video Abstract at http://links.lww.com/DCR/B990 . VALIDEZ CLNICA DEL ANLISIS DE ADN DEL TUMOR CIRCULANTE INFORMADO POR EL TUMOR EN PACIENTES SOMETIDOS A CIRUGA DE METSTASIS COLORRECTALES ANTECEDENTES:Los biomarcadores precisos para monitorear la carga tumoral y la respuesta en pacientes con cáncer colorrectal metastásico que se someten a cirugía podrían optimizar los regímenes de tratamiento.OBJETIVO:Este estudio explora la validez clínica de la cuantificación informada por el tumor del ADN tumoral circulante en sangre mediante secuenciación ultraprofunda.DISEÑO:Se analizaron muestras de resección de 53 pacientes con cáncer colorrectal en busca de mutaciones específicas del tumor en quince genes. Estas mutaciones se usaron para medir la presencia de ADN tumoral circulante en muestras de plasma recolectadas antes de la operación usando secuenciación basada en captura híbrida. Se realizaron mediciones postoperatorias adicionales una semana después de la cirugía en dieciséis pacientes.AJUSTES:El estudio se realizó en el centro médico de la universidad de Radboud.PACIENTES:Se incluyeron un total de 53 pacientes con cáncer colorrectal sometidos a cirugía de metástasis.PRINCIPALES MEDIDAS DE RESULTADO:La detección de ADN tumoral circulante.RESULTADOS:Se detectó al menos una mutación específica de tumor en todas las muestras de tumor. En muestras de plasma preoperatorias, se detectó ADN tumoral circulante en el 88% (37/42) de los pacientes sin tratamiento sistémico previo y en el 55% (6/11) de los pacientes que recibieron quimioterapia preoperatoria. Más concretamente, en el 0% (0/3) de los casos con respuesta patológica subtotal o parcial y en el 75% (6/8) de los casos sin respuesta patológica en la pieza de resección ( p = 0,06). En muestras de plasma postoperatorio se detectó ADN tumoral circulante en el 80% (4/5) de los pacientes con una resección incompleta y en el 0% (0/11) de los que tenían resección completa ( p = 0,003).LIMITACIONES:El estudio estuvo limitado por la heterogeneidad de la cohorte y el pequeño número de muestras de plasma postoperatorias.CONCLUSIONES:Estos datos indican que la detección de ADN tumoral circulante informado por el tumor en el plasma de pacientes sometidos a cirugía por cáncer colorrectal metastásico es factible y puede tener valor clínico en el control de la respuesta y la predicción de la enfermedad residual. Se necesitan estudios prospectivos para establecer la utilidad clínica del análisis de ADN tumoral circulante para guiar las decisiones de tratamiento en estos pacientes. Consulte Video Resumen en http://links.lww.com/DCR/B990 . (Traducción-Dr. Mauricio Santamaria ).
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Affiliation(s)
- Lisa S.M. Hofste
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje J. Geerlings
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline J. Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik A.M. Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Linda M. Garms
- Department of Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D. Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | - Marjolijn J.L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
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2
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de Voer RM, Diets IJ, van der Post RS, Weren RDA, Kamping EJ, de Bitter TJJ, Elze L, Verhoeven RHA, Vink-Börger E, Eijkelenboom A, Mensenkamp A, Nagtegaal ID, Jongmans MCJ, Ligtenberg MJL. Clinical, Pathology, Genetic, and Molecular Features of Colorectal Tumors in Adolescents and Adults 25 Years or Younger. Clin Gastroenterol Hepatol 2021; 19:1642-1651.e8. [PMID: 32585361 DOI: 10.1016/j.cgh.2020.06.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Colorectal cancers (CRCs) are rare in adolescents and adults ages 25 years or younger. We analyzed clinical, pathology, and molecular features of colorectal tumors from adolescents and young adults in an effort to improve genetic counseling, surveillance, and, ultimately, treatment and outcomes. METHODS We analyzed clinical data and molecular and genetic features of colorectal tumor tissues from 139 adolescents or young adults (age, ≤25 y; median age, 23 y; 58% male), collected from 2000 through 2017; tumor tissues and clinical data were obtained from the nationwide network and registry of histopathology and cytopathology and The Netherlands Cancer Registry, respectively. DNA samples from tumors were analyzed for microsatellite instability, mutations in 56 genes, and genome-wide somatic copy number aberrations. RESULTS Mucinous and/or signet ring cell components were observed in 33% of tumor samples. A genetic tumor risk syndrome was confirmed for 39% of cases. Factors associated with shorter survival time included younger age at diagnosis, signet ring cell carcinoma, the absence of a genetic tumor risk syndrome, and diagnosis at an advanced stage of disease. Compared with colorectal tumors from patients ages 60 years or older in the Cancer Genome Atlas, higher proportions of tumors from adolescents or young adults were microsatellite stable with nearly diploid genomes, or contained somatic mutations in TP53 and POLE, whereas lower proportions contained mutations in APC. CONCLUSIONS We found clinical, molecular, and genetic features of CRCs in adolescents or young adults to differ from those of patients older than age 60 years. In 39% of patients a genetic tumor risk syndrome was identified. These findings provide insight into the pathogenesis of CRC in young patients and suggest new strategies for clinical management. Performing genetic and molecular analyses for every individual diagnosed with CRC at age 25 years or younger would aid in this optimization.
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Affiliation(s)
- Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robbert D A Weren
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tessa J J de Bitter
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisa Elze
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob H A Verhoeven
- Department of Surgery, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Research and Development, Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Elisa Vink-Börger
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D Nagtegaal
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
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3
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Geerlings MJ, Hofste LSM, Kamping EJ, Abdi Z, Tolmeijer SH, Garms LM, Klarenbeek BR, Ligtenberg MJL. Effect of Pneumatic Tube System Transport on Cell-Free DNA. Clin Chem 2020; 67:434-435. [PMID: 33280007 DOI: 10.1093/clinchem/hvaa285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Maartje J Geerlings
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lisa S M Hofste
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Zumaya Abdi
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sofie H Tolmeijer
- Department of Medical Oncology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Linda M Garms
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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4
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Pouwer AFW, VAN DEN Einden LCG, VAN DER Linden M, Hehir-Kwa JY, Yu J, Hendriks KM, Kamping EJ, Eijkelenboom A, Massuger LFAG, Bulten J, VAN Tilborg AAG, DE Hullu JA, Kuiper RP. Clonal Relationship Between Lichen Sclerosus, Differentiated Vulvar Intra-epithelial Neoplasia and Non HPV-related Vulvar Squamous Cell Carcinoma. Cancer Genomics Proteomics 2020; 17:151-160. [PMID: 32108037 DOI: 10.21873/cgp.20175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/19/2019] [Accepted: 01/10/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/AIM Differentiated vulvar intraepithelial neoplasia (dVIN) and lichen sclerosus (LS) can give rise to vulvar squamous cell carcinoma (VSCC), but genetic evidence is currently still limited. We aimed to determine genetic abnormalities in VSCC and backtrack these abnormalities in the dVIN and LS lesions. MATERIALS AND METHODS DNA from VSCC and patient-matched dVIN and LS samples of twelve patients was collected. High-resolution genome-wide copy number analysis was performed and subsequently, we sequenced TP53. RESULTS Copy number alterations were identified in all VSCC samples. One dVIN lesion presented with three copy number alterations that were preserved in the paired VSCC sample. Targeted sequencing of TP53 identified mutations in five VSCCs. All five mutations were traced back in the dVIN (n=5) or the LS (n=1) with frequencies ranging from 3-19%. CONCLUSION Our data provide genetic evidence for a clonal relationship between VSCC and dVIN or LS.
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Affiliation(s)
- Anne-Floor W Pouwer
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Loes C G VAN DEN Einden
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michelle VAN DER Linden
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jiangyan Yu
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Koen M Hendriks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leon F A G Massuger
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Johan Bulten
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Joanne A DE Hullu
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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5
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Simons M, Simmer F, Bulten J, Ligtenberg MJ, Hollema H, van Vliet S, de Voer RM, Kamping EJ, van Essen DF, Ylstra B, Schwartz LE, Wang Y, Massuger LF, Nagtegaal ID, Kurman RJ. Two types of primary mucinous ovarian tumors can be distinguished based on their origin. Mod Pathol 2020; 33:722-733. [PMID: 31695154 DOI: 10.1038/s41379-019-0401-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/07/2019] [Accepted: 10/07/2019] [Indexed: 01/09/2023]
Abstract
The origin of primary mucinous ovarian tumors is unknown. We explore the hypothesis that they originate from either Brenner tumors or teratomas and examine differences between the tumors that arise in these settings. A total of 104 Brenner tumor-associated mucinous tumors and 58 teratoma-associated mucinous tumors were analyzed. Immunohistochemistry for 21 antigens and fluorescence in situ hybridization for ERBB2 and MYC were performed. Genome-wide copy number analysis and mutation analysis for 56 cancer-related genes was carried out on a subset of mucinous ovarian tumors and their complementary Brenner tumor or teratoma. Patients with teratoma-associated mucinous tumors were significantly younger than patients with Brenner tumor-associated mucinous tumors (43 vs. 61 years). During progression from cystadenoma to atypical proliferative mucinous (borderline) tumor to carcinoma expression of typical gastrointestinal markers was increased in both Brenner tumor-associated and teratoma-associated mucinous tumors. Brenner tumor-associated mucinous tumors showed more frequently calcifications and Walthard cell nests, rarely expressed SATB2 and showed more often co-deletion of CDKN2A and MTAP. Teratoma-associated mucinous tumors were characterized by mucinous stromal dissection, SATB2 expression and RNF43 mutations. Other frequent mutations in both Brenner tumor-associated and teratoma-associated mucinous tumors were TP53 and KRAS mutations. Based on identical mutations or copy number profiles clonal relationships were indicated in two mucinous tumors and their associated Brenner tumor. Teratomas and Brenner tumors give rise to different subtypes of mucinous ovarian tumors. Subsequent progression pathways are comparable since both Brenner tumor-associated and teratoma-associated mucinous tumors develop a gastrointestinal immunophenotype during progression and show early mutations in KRAS and TP53. Teratoma-associated mucinous tumors may more closely resemble true gastrointestinal tumors, indicated by their expression of SATB2 and the presence of RNF43 mutations.
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Affiliation(s)
- Michiel Simons
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Femke Simmer
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johan Bulten
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Harry Hollema
- Department of Pathology, University Medical Center Groningen, Groningen, The Netherlands
| | - Shannon van Vliet
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dirk F van Essen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Lauren E Schwartz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Yihong Wang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Leon F Massuger
- Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert J Kurman
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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6
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Grolleman JE, de Voer RM, Elsayed FA, Nielsen M, Weren RDA, Palles C, Ligtenberg MJL, Vos JR, Ten Broeke SW, de Miranda NFCC, Kuiper RA, Kamping EJ, Jansen EAM, Vink-Börger ME, Popp I, Lang A, Spier I, Hüneburg R, James PA, Li N, Staninova M, Lindsay H, Cockburn D, Spasic-Boskovic O, Clendenning M, Sweet K, Capellá G, Sjursen W, Høberg-Vetti H, Jongmans MC, Neveling K, Geurts van Kessel A, Morreau H, Hes FJ, Sijmons RH, Schackert HK, Ruiz-Ponte C, Dymerska D, Lubinski J, Rivera B, Foulkes WD, Tomlinson IP, Valle L, Buchanan DD, Kenwrick S, Adlard J, Dimovski AJ, Campbell IG, Aretz S, Schindler D, van Wezel T, Hoogerbrugge N, Kuiper RP. Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype. Cancer Cell 2019; 35:256-266.e5. [PMID: 30753826 DOI: 10.1016/j.ccell.2018.12.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/17/2018] [Accepted: 12/26/2018] [Indexed: 01/01/2023]
Abstract
Biallelic germline mutations affecting NTHL1 predispose carriers to adenomatous polyposis and colorectal cancer, but the complete phenotype is unknown. We describe 29 individuals carrying biallelic germline NTHL1 mutations from 17 families, of which 26 developed one (n = 10) or multiple (n = 16) malignancies in 14 different tissues. An unexpected high breast cancer incidence was observed in female carriers (60%). Mutational signature analysis of 14 tumors from 7 organs revealed that NTHL1 deficiency underlies the main mutational process in all but one of the tumors (93%). These results reveal NTHL1 as a multi-tumor predisposition gene with a high lifetime risk for extracolonic cancers and a typical mutational signature observed across tumor types, which can assist in the recognition of this syndrome.
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Affiliation(s)
- Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Fadwa A Elsayed
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Robbert D A Weren
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Janet R Vos
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Renske A Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M Elisa Vink-Börger
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Isabell Popp
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Alois Lang
- Vorarlberg Cancer Registry, Agency for Preventive and Social Medicine, Bregenz 6900, Austria
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Robert Hüneburg
- Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany; Department of Internal Medicine I, University of Bonn, 53127 Bonn, Germany
| | - Paul A James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbournem, VIC 3000, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marija Staninova
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Helen Lindsay
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - David Cockburn
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | | | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Kevin Sweet
- Division of Human Genetics, Ohio State University Medical Centre, Columbus, OH 43221, USA
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs University Hospital, 7030 Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Hildegunn Høberg-Vetti
- Western Norway Familial Cancer Center, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia 15706, Spain
| | - Dagmara Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Ian P Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Sue Kenwrick
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service and University of Leeds, Leeds LS7 4SA, UK
| | - Aleksandar J Dimovski
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CT Utrecht, The Netherlands.
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7
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Ten Broek RW, Eijkelenboom A, van der Vleuten CJM, Kamping EJ, Kets M, Verhoeven BH, Grünberg K, Schultze Kool LJ, Tops BBJ, Ligtenberg MJL, Flucke U. Comprehensive molecular and clinicopathological analysis of vascular malformations: A study of 319 cases. Genes Chromosomes Cancer 2019; 58:541-550. [PMID: 30677207 PMCID: PMC6594036 DOI: 10.1002/gcc.22739] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/19/2023] Open
Abstract
Vascular malformations are part of overgrowth syndromes characterized by somatic mosaic mutations or rarely by germline mutations. Due to their similarities and diversity, clinicopathological classification can be challenging. A comprehensive targeted Next Generation Sequencing screen using Unique Molecular Identifiers with a technical sensitivity of 1% mutant alleles was performed for frequently mutated positions in ≥21 genes on 319 formalin‐fixed paraffin‐embedded samples. In 132 out of 319 cases pathogenic mosaic mutations were detected affecting genes previously linked to vascular malformations e.g. PIK3CA (n=80), TEK (TIE2) (n=11), AKT1 (n=1), GNAQ (n=7), GNA11 (n=4), IDH1 (n=3), KRAS (n=9), and NRAS (n=1). Six cases harbored a combination of mutations in PIK3CA and in GNA11 (n=2), GNAQ (n=2), or IDH1 (n=2). Aberrations in PTEN and RASA1 with a variant allele frequency approaching 50% suggestive of germline origin were identified in six out of 102 cases tested; four contained a potential second hit at a lower allele frequency. Ninety‐one of the total 142 pathogenic mutations were present at a variant allele frequency <10% illustrating the importance of sensitive molecular analysis. Clinicopathological characteristics showed a broad spectrum and overlap when correlated with molecular data. Sensitive screening of recurrently mutated genes in vascular malformations may help to confirm the diagnosis and reveals potential therapeutic options with a significant contribution of PIK3CA/mTOR and RAS‐MAPK pathway mutations. The co‐existence of two activating pathogenic mutations in parallel pathways illustrates potential treatment challenges and underlines the importance of multigene testing. Detected germline mutations have major clinical impact.
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Affiliation(s)
- Roel W Ten Broek
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carine J M van der Vleuten
- Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc Expertise Center for Hemangiomas and Congenital Vascular Anomalies Nijmegen (Hecovan), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marleen Kets
- Radboudumc Expertise Center for Hemangiomas and Congenital Vascular Anomalies Nijmegen (Hecovan), Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bas H Verhoeven
- Radboudumc Expertise Center for Hemangiomas and Congenital Vascular Anomalies Nijmegen (Hecovan), Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo J Schultze Kool
- Radboudumc Expertise Center for Hemangiomas and Congenital Vascular Anomalies Nijmegen (Hecovan), Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Uta Flucke
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboudumc Expertise Center for Hemangiomas and Congenital Vascular Anomalies Nijmegen (Hecovan), Radboud University Medical Center, Nijmegen, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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8
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van der Tuin K, de Kock L, Kamping EJ, Hannema SE, Pouwels MJM, Niedziela M, van Wezel T, Hes FJ, Jongmans MC, Foulkes WD, Morreau H. Clinical and Molecular Characteristics May Alter Treatment Strategies of Thyroid Malignancies in DICER1 Syndrome. J Clin Endocrinol Metab 2019; 104:277-284. [PMID: 30260442 DOI: 10.1210/jc.2018-00774] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/21/2018] [Indexed: 12/31/2022]
Abstract
CONTEXT DICER1 syndrome is a rare autosomal-dominantly inherited disorder that predisposes to a variety of cancerous and noncancerous tumors of mostly pediatric and adolescent onset, including differentiated thyroid carcinoma (DTC). DTC has been hypothesized to arise secondarily to the increased prevalence of thyroid hyperplastic nodules in syndromic patients. OBJECTIVE To determine somatic alterations in DICER1-associated DTC and to study patient outcomes. DESIGN Retrospective series. SETTING Tertiary referral centers. PATIENTS Ten patients with germline pathogenic DICER1 variants and early-onset DTC. METHODS Somatic DICER1 mutation analysis, extensive somatic DNA variant and gene fusion analyses were performed on all tumors. RESULTS Median age at DTC diagnosis was 13.5 years and there was no recurrent or metastatic disease (median follow-up, 8 years). All thyroid specimens showed diffuse nodular hyperplasia with at least one focus suspicious of DTC but without infiltrative growth, extrathyroidal extension, vascular invasion, or lymph node metastasis. Most of the individual nodules (benign and malignant) sampled from the 10 tumors harbored distinct DICER1 RNase IIIb hotspot mutations, indicating a polyclonal composition of each tumor. Furthermore, nine of 10 DICER1-related DTCs lacked well-known oncogenic driver DNA variants and gene rearrangements. CONCLUSION On the basis of our clinical, histological, and molecular data, we consider that most DICER1-related DTCs form a low-risk subgroup. These tumors may arise within one of multiple benign monoclonal nodules; thus, hemi-thyroidectomy or, more likely, total thyroidectomy may often be required. However, radioiodine treatment may be unnecessary given the patients' ages and the tumors' low propensity for metastases.
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Affiliation(s)
- Karin van der Tuin
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Leanne de Kock
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Eveline J Kamping
- Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Sabine E Hannema
- Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - Marie-Jose M Pouwels
- Department of Internal Medicine, Division of Endocrinology, Medical Spectrum Twente, Enschede, Netherlands
| | - Marek Niedziela
- Department of Pediatric Endocrinology and Rheumatology, Karol Jonscher's Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Marjolijn C Jongmans
- Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Medical Genetics, Utrecht University Medical Center, Utrecht, Netherlands
- Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, Netherlands
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9
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Diets IJ, Waanders E, Ligtenberg MJ, van Bladel DAG, Kamping EJ, Hoogerbrugge PM, Hopman S, Olderode-Berends MJ, Gerkes EH, Koolen DA, Marcelis C, Santen GW, van Belzen MJ, Mordaunt D, McGregor L, Thompson E, Kattamis A, Pastorczak A, Mlynarski W, Ilencikova D, van Silfhout AV, Gardeitchik T, de Bont ES, Loeffen J, Wagner A, Mensenkamp AR, Kuiper RP, Hoogerbrugge N, Jongmans MC. High Yield of Pathogenic Germline Mutations Causative or Likely Causative of the Cancer Phenotype in Selected Children with Cancer. Clin Cancer Res 2018; 24:1594-1603. [PMID: 29351919 DOI: 10.1158/1078-0432.ccr-17-1725] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/11/2017] [Accepted: 01/12/2018] [Indexed: 11/16/2022]
Abstract
Purpose: In many children with cancer and characteristics suggestive of a genetic predisposition syndrome, the genetic cause is still unknown. We studied the yield of pathogenic mutations by applying whole-exome sequencing on a selected cohort of children with cancer.Experimental Design: To identify mutations in known and novel cancer-predisposing genes, we performed trio-based whole-exome sequencing on germline DNA of 40 selected children and their parents. These children were diagnosed with cancer and had at least one of the following features: (1) intellectual disability and/or congenital anomalies, (2) multiple malignancies, (3) family history of cancer, or (4) an adult type of cancer. We first analyzed the sequence data for germline mutations in 146 known cancer-predisposing genes. If no causative mutation was found, the analysis was extended to the whole exome.Results: Four patients carried causative mutations in a known cancer-predisposing gene: TP53 and DICER1 (n = 3). In another 4 patients, exome sequencing revealed mutations causing syndromes that might have contributed to the malignancy (EP300-based Rubinstein-Taybi syndrome, ARID1A-based Coffin-Siris syndrome, ACTB-based Baraitser-Winter syndrome, and EZH2-based Weaver syndrome). In addition, we identified two genes, KDM3B and TYK2, which are possibly involved in genetic cancer predisposition.Conclusions: In our selected cohort of patients, pathogenic germline mutations causative or likely causative of the cancer phenotype were found in 8 patients, and two possible novel cancer-predisposing genes were identified. Therewith, our study shows the added value of sequencing beyond a cancer gene panel in selected patients, to recognize childhood cancer predisposition. Clin Cancer Res; 24(7); 1594-603. ©2018 AACR.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Esmé Waanders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marjolijn J Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Diede A G van Bladel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Maran J Olderode-Berends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gijs W Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Martine J van Belzen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dylan Mordaunt
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Lesley McGregor
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Elizabeth Thompson
- Department of Genetics and Molecular Pathology, SA Pathology, Women's and Children's Hospital, North Adelaide, Australia
| | - Antonis Kattamis
- First Department of Pediatrics, Athens University Medical School, Athens, Greece
| | - Agata Pastorczak
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Denisa Ilencikova
- 2nd Pediatric Department, Children's University Hospital, Comenius University, Bratislava, Slovakia
| | | | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eveline S de Bont
- Department of Pediatric Oncology and Hematology, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Loeffen
- Department of Pediatric Oncology and Hematology, Sophia Children's Hospital, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands. .,Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
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10
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Weren RDA, van der Post RS, Vogelaar IP, van Krieken JH, Spruijt L, Lubinski J, Jakubowska A, Teodorczyk U, Aalfs CM, van Hest LP, Oliveira C, Kamping EJ, Schackert HK, Ranzani GN, Gómez García EB, Hes FJ, Holinski-Feder E, Genuardi M, Ausems MGEM, Sijmons RH, Wagner A, van der Kolk LE, Cats A, Bjørnevoll I, Hoogerbrugge N, Ligtenberg MJL. Role of germline aberrations affecting CTNNA1, MAP3K6 and MYD88 in gastric cancer susceptibility. J Med Genet 2018; 55:669-674. [PMID: 29330337 PMCID: PMC6161648 DOI: 10.1136/jmedgenet-2017-104962] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/19/2017] [Accepted: 12/11/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND In approximately 10% of all gastric cancer (GC) cases, a heritable cause is suspected. A subset of these cases have a causative germline CDH1 mutation; however, in most cases the cause remains unknown. Our objective was to assess to what extent these remaining cases may be explained by germline mutations in the novel candidate GC predisposing genes CTNNA1, MAP3K6 or MYD88. METHODS We sequenced a large cohort of unexplained young and/or familial patients with GC (n=286) without a CDH1germline mutation for germline variants affecting CTNNA1, MAP3K6 and MYD88 using a targeted next-generation sequencing approach based on single-molecule molecular inversion probes. RESULTS Predicted deleterious germline variants were not encountered in MYD88, but recurrently observed in CTNNA1 (n=2) and MAP3K6 (n=3) in our cohort of patients with GC. In contrast to deleterious variants in CTNNA1, deleterious variants in MAP3K6 also occur frequently in the general population. CONCLUSIONS Based on our results MAP3K6 should no longer be considered a GC predisposition gene, whereas deleterious CTNNA1 variants are confirmed as an infrequent cause of GC susceptibility. Biallelic MYD88 germline mutations are at most a very rare cause of GC susceptibility as no additional cases were identified.
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Affiliation(s)
- Robbert D A Weren
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Ingrid P Vogelaar
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - J Han van Krieken
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Liesbeth Spruijt
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Urszula Teodorczyk
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Cora M Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Carla Oliveira
- Expression Regulation in Cancer Group, Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Department of Cancer Genetics, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Eveline J Kamping
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Encarna B Gómez García
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | - Maurizio Genuardi
- Institute of Genomic Medicine, Catholic University of the Sacred Heart, Milan, Italy
| | | | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annemieke Cats
- Department of Gastrointestinal Oncology, The Netherlands Cancer Institute/Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Inga Bjørnevoll
- Department of Medical Genetics, St Olav's Hospital, Trondheim, Norway
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
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11
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Zhang J, Wang X, de Voer RM, Hehir-Kwa JY, Kamping EJ, Weren RD, Nelen M, Hoischen A, Ligtenberg MJ, Hoogerbrugge N, Yang X, Yang Z, Fan X, Wang L, Liu H, Wang J, Kuiper RP, van Kessel AG. A molecular inversion probe-based next-generation sequencing panel to detect germline mutations in Chinese early-onset colorectal cancer patients. Oncotarget 2017; 8:24533-24547. [PMID: 28445943 PMCID: PMC5421868 DOI: 10.18632/oncotarget.15593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/12/2017] [Indexed: 02/07/2023] Open
Abstract
The currently known Mendelian colorectal cancer (CRC) predisposition syndromes account for ~5-10% of all CRC cases, and are caused by inherited germline mutations in single CRC predisposing genes. Using molecular inversion probes (MIPs), we designed a targeted next-generation sequencing panel to identify mutations in seven CRC predisposing genes: APC, MLH1, MSH2, MSH6, PMS2, MUTYH and NTHL1. From a consecutive series of 2,371 Chinese CRC patients, 140 familial and non-familial cases were selected that were diagnosed with CRC at or below the age of 35 years. Through MIP-based sequencing we identified pathogenic variants in six genes in 16 out of the 140 (11.4%) patients selected. In 10 patients, known pathogenic mutations in APC (five patients), MLH1 (three patients), or MSH2 (two patients) were identified. Three additional patients were found to carry novel, likely pathogenic truncating (n = 2) and missense (n = 1) mutations in the MSH2 gene and a concomitant loss of expression of both the MSH2 and MSH6 proteins in their respective tumor tissues. From our data, we conclude that targeted MIP-based sequencing is a reliable and cost-efficient approach to identify patients with a Mendelian CRC syndrome.
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Affiliation(s)
- Junxiao Zhang
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Xiaoyan Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jayne Y. Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Robbert D.A. Weren
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marjolijn J.L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Xiangling Yang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zihuan Yang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Xinjuan Fan
- Department of Pathology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Lei Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Huanliang Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Clinical Laboratory, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jianping Wang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Roland P. Kuiper
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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12
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Eijkelenboom A, Kamping EJ, Kastner-van Raaij AW, Hendriks-Cornelissen SJ, Neveling K, Kuiper RP, Hoischen A, Nelen MR, Ligtenberg MJ, Tops BB. Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags. J Mol Diagn 2016; 18:851-863. [DOI: 10.1016/j.jmoldx.2016.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/04/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
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13
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Waanders E, Hebeda KM, Kamping EJ, Groenen PJTA, Simons A, Hoischen A, Jongmans MCJ, Hoogerbrugge PM, van Leeuwen FN, Kuiper RP, Te Loo DMWM. Independent development of lymphoid and histiocytic malignancies from a shared early precursor. Leukemia 2015. [PMID: 26202925 DOI: 10.1038/leu.2015.193] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- E Waanders
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - K M Hebeda
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E J Kamping
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - P J T A Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Simons
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - A Hoischen
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - M C J Jongmans
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - P M Hoogerbrugge
- Princess Máxima Center for Pediatric Oncology, De Bilt, The Netherlands
| | - F N van Leeuwen
- Department of Pediatric Oncology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - R P Kuiper
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - D M W M Te Loo
- Department of Pediatric Oncology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
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14
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Weren RDA, Venkatachalam R, Cazier JB, Farin HF, Kets CM, de Voer RM, Vreede L, Verwiel ETP, van Asseldonk M, Kamping EJ, Kiemeney LA, Neveling K, Aben KKH, Carvajal-Carmona L, Nagtegaal ID, Schackert HK, Clevers H, van de Wetering M, Tomlinson IP, Ligtenberg MJL, Hoogerbrugge N, Geurts van Kessel A, Kuiper RP. Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development. J Pathol 2015; 236:155-64. [PMID: 25712196 PMCID: PMC6681464 DOI: 10.1002/path.4520] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 02/09/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022]
Abstract
Heritable genetic variants can significantly affect the lifetime risk of developing cancer, including polyposis and colorectal cancer (CRC). Variants in genes currently known to be associated with a high risk for polyposis or CRC, however, explain only a limited number of hereditary cases. The identification of additional genetic causes is, therefore, crucial to improve CRC prevention, detection and treatment. We have performed genome-wide and targeted DNA copy number profiling and resequencing in early-onset and familial polyposis/CRC patients, and show that deletions affecting the open reading frame of the tumour suppressor gene FOCAD are recurrent and significantly enriched in CRC patients compared with unaffected controls. All patients carrying FOCAD deletions exhibited a personal or family history of polyposis. RNA in situ hybridization revealed FOCAD expression in epithelial cells in the colonic crypt, the site of tumour initiation, as well as in colonic tumours and organoids. Our data suggest that monoallelic germline deletions in the tumour suppressor gene FOCAD underlie moderate genetic predisposition to the development of polyposis and CRC.
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Affiliation(s)
- Robbert D A Weren
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | | | - Henner F Farin
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | - C Marleen Kets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lilian Vreede
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Eugène T P Verwiel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Monique van Asseldonk
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
| | - Luis Carvajal-Carmona
- Genome Center and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California at Davis, CA, USA
| | - Iris D Nagtegaal
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Hans Clevers
- Hubrecht Institute, University Medical Centre Utrecht, The Netherlands
| | | | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics University of Oxford, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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15
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Stevens-Kroef MJ, Hebeda KM, Verwiel ET, Kamping EJ, van Cleef PH, Kuiper RP, Groenen PJ. Microarray-based genomic profiling and in situ hybridization on fibrotic bone marrow biopsies for the identification of numerical chromosomal abnormalities in myelodysplastic syndrome. Mol Cytogenet 2015; 8:33. [PMID: 26023320 PMCID: PMC4447009 DOI: 10.1186/s13039-015-0136-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/16/2015] [Indexed: 11/21/2022] Open
Abstract
Background Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematological malignancies. In MDS patients with a fibrotic bone marrow the aspiration of cells often fails (dry-tap), which hampers standard karyotyping. Obtaining genetic data from these fibrotic marrows is therefore challenging, and up till now in situ hybridization applied to bone marrow biopsies is the only option. The microarray-based genomic profiling technology has already proven its value for bone marrow aspirates and peripheral blood samples, but has never been applied to the technically challenging bone marrow biopsies. We describe an approach for microarray-based genomic profiling on bone marrow biopsies and demonstrate its ability to obtain clinically relevant cytogenetic aberrations. In addition the data were compared with those obtained by in situ hybridization and karyotyping. Results We have evaluated the success rate of microarray-based genomic profiling by studying twenty-one bone marrow biopsies (7 fibrotic MDS, 12 non-fibrotic MDS and 2 reactive), by microarray-based genomic profiling and in situ hybridization (12 of 21 cases). The data obtained with these techniques were compared with conventional karyotyping data on corresponding bone marrow aspirates. Of the 15 copy number aberrations that were detected by in situ hybridization, 13 were concordant with microarray-based genomic profiling and karyotyping, whereas two hybridizations were misinterpreted. In 20 of 21 patients, the data obtained by microarray-based genomic profiling and karyotyping were identical or differences could be explained by the presence of marker chromosomes, complex karyotypes, clonal heterogeneity or disease progression. Conclusions We demonstrate that genome wide microarray-based genomic profiling performed on bone marrow biopsies has a similar success rate compared to in situ hybridization, and prevents misinterpretation of chromosomal losses as observed by FISH. In addition, equal to even higher resolutions were obtained with genomic profiling compared to conventional karyotyping. Our findings indicate that microarray-based profiling, even on bone marrow biopsies, is a valid approach for the identification of genetic abnormalities. This is a valuable substitution in cases of fibrotic MDS lacking cytogenetic results.
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Affiliation(s)
- Marian Jpl Stevens-Kroef
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Konnie M Hebeda
- Department of Pathology, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Eugène T Verwiel
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Patricia H van Cleef
- Department of Pathology, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Patricia Jta Groenen
- Department of Pathology, Radboud university medical center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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16
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de Voer RM, Geurts van Kessel A, Weren RDA, Ligtenberg MJL, Smeets D, Fu L, Vreede L, Kamping EJ, Verwiel ETP, Hahn MM, Ariaans M, Spruijt L, van Essen T, Houge G, Schackert HK, Sheng JQ, Venselaar H, van Ravenswaaij-Arts CMA, van Krieken JHJM, Hoogerbrugge N, Kuiper RP. Germline mutations in the spindle assembly checkpoint genes BUB1 and BUB3 are risk factors for colorectal cancer. Gastroenterology 2013; 145:544-7. [PMID: 23747338 DOI: 10.1053/j.gastro.2013.06.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 05/31/2013] [Accepted: 06/01/2013] [Indexed: 12/14/2022]
Abstract
The spindle assembly checkpoint controls proper chromosome segregation during mitosis and prevents aneuploidy-an important feature of cancer cells. We performed genome-wide and targeted copy number and mutation analyses of germline DNA from 208 patients with familial or early-onset (40 years of age or younger) colorectal cancer; we identified haploinsufficiency or heterozygous mutations in the spindle assembly checkpoint genes BUB1 and BUB3 in 2.9% of them. Besides colorectal cancer, these patients had variegated aneuploidies in multiple tissues and variable dysmorphic features. These results indicate that mutations in BUB1 and BUB3 cause mosaic variegated aneuploidy and increase the risk of colorectal cancer at a young age.
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Affiliation(s)
- Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Centre and Research Institute for Oncology, Nijmegen, The Netherlands
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17
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Venkatachalam R, Verwiel ETP, Kamping EJ, Hoenselaar E, Görgens H, Schackert HK, van Krieken JHJM, Ligtenberg MJL, Hoogerbrugge N, van Kessel AG, Kuiper RP. Identification of candidate predisposing copy number variants in familial and early-onset colorectal cancer patients. Int J Cancer 2011; 129:1635-42. [PMID: 21128281 DOI: 10.1002/ijc.25821] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/16/2010] [Indexed: 12/21/2022]
Abstract
In the majority of colorectal cancers (CRCs) under clinical suspicion for a hereditary cause, the disease-causing genetic factors are still to be discovered. To identify such genetic factors we stringently selected a discovery cohort of 41 CRC index patients with microsatellite-stable tumors. All patients were below 40 years of age at diagnosis and/or exhibited an overt family history. We employed genome-wide copy number profiling using high-resolution SNP arrays on germline DNA, which resulted in the identification of novel copy number variants (CNVs) in six patients (15%) encompassing, among others, the cadherin gene CDH18, the bone morphogenetic protein antagonist family gene GREM1, and the breakpoint cluster region gene BCR. In addition, two genomic deletions were encountered encompassing two microRNA genes, hsa-mir-491/KIAA1797 and hsa-mir-646/AK309218. None of these CNVs has previously been reported in relation to CRC predisposition in humans, nor were they encountered in large control cohorts (>1,600 unaffected individuals). Since several of these newly identified candidate genes may be functionally linked to CRC development, our results illustrate the potential of this approach for the identification of novel candidate genes involved in CRC predisposition.
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Affiliation(s)
- Ramprasath Venkatachalam
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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18
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Venkatachalam R, Ligtenberg MJL, Hoogerbrugge N, Schackert HK, Görgens H, Hahn MM, Kamping EJ, Vreede L, Hoenselaar E, van der Looij E, Goossens M, Churchman M, Carvajal-Carmona L, Tomlinson IPM, de Bruijn DRH, Van Kessel AG, Kuiper RP. Germline epigenetic silencing of the tumor suppressor gene PTPRJ in early-onset familial colorectal cancer. Gastroenterology 2010; 139:2221-4. [PMID: 21036128 DOI: 10.1053/j.gastro.2010.08.063] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 08/26/2010] [Indexed: 01/05/2023]
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19
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Langemeijer SMC, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop M, Stevens-Linders E, van Hoogen P, van Kessel AG, Raymakers RAP, Kamping EJ, Verhoef GE, Verburgh E, Hagemeijer A, Vandenberghe P, de Witte T, van der Reijden BA, Jansen JH. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 2009; 41:838-42. [PMID: 19483684 DOI: 10.1038/ng.391] [Citation(s) in RCA: 585] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 04/17/2009] [Indexed: 02/08/2023]
Abstract
Myelodysplastic syndromes (MDS) represent a heterogeneous group of neoplastic hematopoietic disorders. Several recurrent chromosomal aberrations have been associated with MDS, but the genes affected have remained largely unknown. To identify relevant genetic lesions involved in the pathogenesis of MDS, we conducted SNP array-based genomic profiling and genomic sequencing in 102 individuals with MDS and identified acquired deletions and missense and nonsense mutations in the TET2 gene in 26% of these individuals. Using allele-specific assays, we detected TET2 mutations in most of the bone marrow cells (median 96%). In addition, the mutations were encountered in various lineages of differentiation including CD34(+) progenitor cells, suggesting that TET2 mutations occur early during disease evolution. In healthy tissues, TET2 expression was shown to be elevated in hematopoietic cells with highest expression in granulocytes, in line with a function in myelopoiesis. We conclude that TET2 is the most frequently mutated gene in MDS known so far.
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Affiliation(s)
- Saskia M C Langemeijer
- Department of Hematology and Central Hematology Laboratory, Radboud University Nijmegen Medical Centre and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
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20
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Letteboer TGW, Zewald RA, Kamping EJ, de Haas G, Mager JJ, Snijder RJ, Lindhout D, Hennekam FAM, Westermann CJJ, Ploos van Amstel JK. Hereditary hemorrhagic telangiectasia: ENG and ALK-1 mutations in Dutch patients. Hum Genet 2004; 116:8-16. [PMID: 15517393 DOI: 10.1007/s00439-004-1196-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 09/07/2004] [Indexed: 10/26/2022]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) or Rendu-Osler-Weber disease is an autosomal dominant disorder characterized by an aberrant vascular development. The resulting vascular lesions range from smaller mucocutaneous telangiectases to large visceral arteriovenous malformations, especially in the skin, lung, gastrointestinal tract and the brain. Mutations in the genes encoding endoglin (ENG, chromosome 9q34) and activin A receptor type-like kinase 1 (ALK-1, also named ACVRL1, chromosome 12q13) are associated with HHT1 and HHT2, respectively. We report here on the genetic and molecular heterogeneity found in the HHT population in the Netherlands. Probands of 104 apparently unrelated families were studied and we performed sequence analysis on both the ENG gene and ALK-1 gene. In most of the probands, we found a mutation in one of the two genes: 53% in the ENG gene and 40% in the ALK-1 gene. In 7% of the families no ENG or ALK1 mutation was found. The mutations detected were deletions, insertions, nonsense, missense and splice site mutations. The majority were novel mutations.
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Affiliation(s)
- T G W Letteboer
- DBG-Department of Medical Genetics, University Medical Center Utrecht, PO Box 85090, 3508 AB, Utrecht, The Netherlands.
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