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Wils G, Helsmoortel C, Volders PJ, Vereecke I, Milazzo M, Vandesompele J, Coppieters F, De Leeneer K, Lefever S. Performance Evaluation of Three DNA Sample Tracking Tools in a Whole Exome Sequencing Workflow. Mol Diagn Ther 2022; 26:411-419. [PMID: 35633488 DOI: 10.1007/s40291-022-00585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2022] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Next-generation sequencing applications are becoming indispensable for clinical diagnostics. These experiments require numerous wet- and dry-laboratory steps, each one increasing the probability of a sample swap or contamination. Therefore, identity confirmation at the end of the process is recommended to ensure the right data are used for each patient. METHODS We tested three commercially available, single nucleotide polymorphism (SNP)-based sample tracking kits in a diagnostic workflow to evaluate their ease of use and performance. The coverage uniformity, on-target specificity, sample identification, and genotyping performance were determined to assess the reliability and cost effectiveness of each kit. RESULTS AND DISCUSSION Hands-on time and manual steps are almost identical for the kits from pxlence and Nimagen. The Swift kit has an extra purification step, making it the longest and most demanding protocol. Furthermore, the Swift kit failed to correctly genotype 26 of the 46 samples. The Nimagen kit identified all but one sample and the pxlence kit unambiguously identified all samples, making it the most reliable and robust kit of this evaluation. The Nimagen kit showed poor on-target mapping rates, resulting in deeper sequencing needs and higher sequencing costs compared with the other two kits. CONCLUSION Our conclusion is that the Human Sample ID kit from pxlence is the most cost effective of the three tested tools for DNA sample tracking and identification.
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Affiliation(s)
| | - Céline Helsmoortel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | | | - Inge Vereecke
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Mauro Milazzo
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- pxlence BVBA, Dendermonde, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- pxlence BVBA, Dendermonde, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kim De Leeneer
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
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Kalve S, Sizani BL, Markakis MN, Helsmoortel C, Vandeweyer G, Laukens K, Sommen M, Naulaerts S, Vissenberg K, Prinsen E, Beemster GTS. Osmotic stress inhibits leaf growth of Arabidopsis thaliana by enhancing ARF-mediated auxin responses. New Phytol 2020; 226:1766-1780. [PMID: 32077108 DOI: 10.1111/nph.16490] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/11/2020] [Indexed: 05/18/2023]
Abstract
We investigated the interaction between osmotic stress and auxin signaling in leaf growth regulation. Therefore, we grew Arabidopsis thaliana seedlings on agar media supplemented with mannitol to impose osmotic stress and 1-naphthaleneacetic acid (NAA), a synthetic auxin. We performed kinematic analysis and flow-cytometry to quantify the effects on cell division and expansion in the first leaf pair, determined the effects on auxin homeostasis and response (DR5::β-glucuronidase), performed a next-generation sequencing transcriptome analysis and investigated the response of auxin-related mutants. Mannitol inhibited cell division and expansion. NAA increased the effect of mannitol on cell division, but ameliorated its effect on expansion. In proliferating cells, NAA and mannitol increased free IAA concentrations at the cost of conjugated IAA and stimulated DR5 promotor activity. Transcriptome analysis shows a large overlap between NAA and osmotic stress-induced changes, including upregulation of auxin synthesis, conjugation, transport and TRANSPORT INHIBITOR RESPONSE1 (TIR1) and AUXIN RESPONSE FACTOR (ARF) response genes, but downregulation of Aux/IAA response inhibitors. Consistently, arf7/19 double mutant lack the growth response to auxin and show a significantly reduced sensitivity to osmotic stress. Our results show that osmotic stress inhibits cell division during leaf growth of A. thaliana at least partly by inducing the auxin transcriptional response.
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Affiliation(s)
- Shweta Kalve
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Center Antwerp (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Biomedical Informatics Research Center Antwerp (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Stefan Naulaerts
- Biomedical Informatics Research Center Antwerp (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kris Vissenberg
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Els Prinsen
- Department of Biology, University of Antwerp, Antwerp, Belgium
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Slembrouck L, Darrigues L, Laurent C, Mittempergher L, Delahaye LJ, Vanden Bempt I, Vander Borght S, Vliegen L, Sintubin P, Raynal V, Bohec M, Reyes C, Rapinat A, Helsmoortel C, Jongen L, Hoste G, Neven P, Wildiers H, Smeets A, Nevelsteen I, Punie K, Van Nieuwenhuysen E, Han S, Vincent Salomon A, Laas Faron E, Cynober T, Gentien D, Baulande S, Snel MH, Witteveen AT, Neijenhuis S, Glas AM, Reyal F, Floris G. Decentralization of Next-Generation RNA Sequencing-Based MammaPrint® and BluePrint® Kit at University Hospitals Leuven and Curie Institute Paris. Transl Oncol 2019; 12:1557-1565. [PMID: 31513983 PMCID: PMC6742807 DOI: 10.1016/j.tranon.2019.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
A previously developed and centrally validated MammaPrint® (MP) and BluePrint® (BP) targeted RNA next-generation sequencing (NGS) kit was implemented and validated in two large academic European hospitals. Additionally, breast cancer molecular subtypes by MP and BP RNA sequencing were compared with immunohistochemistry (IHC). Patients with early breast cancer diagnosed at University Hospitals Leuven and Curie Institute Paris were prospectively included between September 2017 and January 2018. Formalin-fixed paraffin-embedded tissue sections were analyzed with MP and BP NGS technology at the beta sites and with both NGS and microarray technology at Agendia. Raw NGS data generated on Illumina MiSeq instruments at the beta sites were interpreted and compared with NGS and microarray data at Agendia. MP and BP NGS molecular subtypes were compared to surrogate IHC breast cancer subtypes. Equivalence of MP and BP indices was determined by Pearson's correlation coefficient. Acceptable limits were defined a priori, based on microarray data generated at Agendia between 2012 and 2016. The concordance, the Negative Percent Agreement and the Positive Percent Agreement were calculated based on the contingency tables and had to be equal to or higher than 90%. Out of 124 included samples, 48% were MP Low and 52% High Risk with microarray. Molecular subtypes were BP luminal, HER2 or basal in 82%, 8% and 10% respectively. Concordance between MP microarray at Agendia and MP NGS at the beta sites was 91.1%. Concordance of MP High and Low Risk classification between NGS at the beta sites and NGS at Agendia was 93.9%. Concordance of MP and BP molecular subtyping using NGS at the beta sites and microarray at Agendia was 89.5%. Concordance between MP and BP NGS subtyping, and IHC was 71.8% and 76.6%, for two IHC surrogate models. The MP/BP NGS kit was successfully validated in a decentralized setting.
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Affiliation(s)
- Laurence Slembrouck
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium.
| | - Lauren Darrigues
- Curie Institute, Department of Surgery, Paris Descartes University, F-75248, France
| | - Cecile Laurent
- Curie Institute, Residual Tumor & Response to Treatment Laboratory, RT2Lab, Paris Descartes University, INSERM, U932 Immunity and Cancer, Paris, F-75248, France
| | - Lorenza Mittempergher
- Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands
| | - Leonie Jmj Delahaye
- Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands
| | - Isabelle Vanden Bempt
- KU Leuven - University of Leuven, University Hospitals Leuven, Department of Human Genetics, B-3000 Leuven, Belgium
| | - Sara Vander Borght
- KU Leuven - University of Leuven, University Hospitals Leuven, Department of Human Genetics, B-3000 Leuven, Belgium; KU Leuven - University Hospitals Leuven, Department of Pathology, B-3000 Leuven, Belgium
| | - Liesbet Vliegen
- KU Leuven - University of Leuven, University Hospitals Leuven, Department of Human Genetics, B-3000 Leuven, Belgium
| | - Petra Sintubin
- KU Leuven - University of Leuven, University Hospitals Leuven, Department of Human Genetics, B-3000 Leuven, Belgium
| | - Virginie Raynal
- Curie Institute, PSL Research University, Genomics of Excellence (ICGex) Platform, Paris, F-75248, France
| | - Mylene Bohec
- Curie Institute, PSL Research University, Genomics of Excellence (ICGex) Platform, Paris, F-75248, France
| | - Cécile Reyes
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, F-75248, France
| | - Audrey Rapinat
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, F-75248, France
| | - Céline Helsmoortel
- KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, B-3000 Leuven, Belgium
| | - Lynn Jongen
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium
| | - Griet Hoste
- KU Leuven - University of Leuven, University Hospitals Leuven, Department of Gynaecology and Obstetrics, B-3000 Leuven, Belgium
| | - Patrick Neven
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Gynaecology and Obstetrics, B-3000 Leuven, Belgium
| | - Hans Wildiers
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of General Medical Oncology, B-3000 Leuven, Belgium
| | - Ann Smeets
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Surgical Oncology, B-3000 Leuven, Belgium
| | - Ines Nevelsteen
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Surgical Oncology, B-3000 Leuven, Belgium
| | - Kevin Punie
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of General Medical Oncology, B-3000 Leuven, Belgium
| | - Els Van Nieuwenhuysen
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Gynaecology and Obstetrics, B-3000 Leuven, Belgium
| | - Sileny Han
- KU Leuven - University of Leuven, Department of Oncology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, University Hospitals Leuven, Department of Gynaecology and Obstetrics, B-3000 Leuven, Belgium
| | | | - Enora Laas Faron
- Curie Institute, Department of Surgery, Paris Descartes University, F-75248, France
| | - Timothé Cynober
- Curie Institute, Administration and General Services, Paris, F-75248, France
| | - David Gentien
- Curie Institute, PSL Research University, Translational Research Department, Genomics Platform, Paris, F-75248, France
| | - Sylvain Baulande
- Curie Institute, PSL Research University, Genomics of Excellence (ICGex) Platform, Paris, F-75248, France
| | - Mireille Hj Snel
- Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands
| | - Anke T Witteveen
- Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands
| | - Sari Neijenhuis
- Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands
| | - Annuska M Glas
- Agendia, Department of Research and Development, Medical Affairs, Amsterdam, The Netherlands
| | - Fabien Reyal
- Curie Institute, Department of Surgery, Paris Descartes University, F-75248, France; Curie Institute, Residual Tumor & Response to Treatment Laboratory, RT2Lab, Paris Descartes University, INSERM, U932 Immunity and Cancer, Paris, F-75248, France
| | - Giuseppe Floris
- KU Leuven - University Hospitals Leuven, Department of Pathology, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research
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Darrigues L, Slembrouck L, Mittempergher L, Delahaye LJ, Vanden Bempt I, Vander Borght S, Vliegen L, Sintubin P, Raynal V, Bohec M, Reyes C, Rapinat A, Helsmoortel C, Jongen L, Hoste G, Neven P, Wildiers H, Smeets A, Nevelsteen I, Punie K, Van Nieuwenhuysen E, Han S, Laurent C, Vincent-Salomon A, Laas-Faron E, Witteveen AT, Neijenhuis S, Glas AM, Floris G, Reyal F. Abstract P4-02-07: Comparison of breast cancer molecular subtyping by Immunohistochemistry and by BluePrint® next generation RNA sequencing-based test at University Hospitals Leuven and Curie Institute Paris. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-02-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
MammaPrint® (MP) and BluePrint® (BP) are microarray-based tests with MP being prognostic for distant recurrence and BP enabling stratification into breast cancer molecular subtypes (Luminal, HER2, Basal-type). Recently, a CE marked MP and BP targeted RNA Next Generation Sequencing (NGS)-based kit was developed at Agendia and validated at University Hospitals Leuven and Curie Institute Paris. Here we compare breast cancer molecular subtype stratification defined by immunohistochemistry (IHC) and by MP and BP NGS- and microarray- based tests.
Patients and Methods
In this study, 124 primary operable invasive breast cancer patients were included at University Hospitals Leuven and at Curie Institute (n=80 Leuven; n=44 Curie) with the following histological subtypes: ductal-NOS (n=100), lobular (n=16), mucinous (n=3), tubular (n=2), others (n=3). Patients with bilateral breast cancer or with >3 positive lymph nodes were excluded. Surrogate breast cancer subtypes based on IHC were defined as follows: luminal if ≥10% estrogen receptor (ER) expression; triple negative if <10% ER and progesterone receptor (PR) expression and HER2 stained negative by IHC and/or FISH; HER2+ if HER2 receptor stained positive (2+ or 3+) by IHC and/or FISH. Luminal subtypes were further stratified into Luminal A-like (HER2 negative, Ki-67<14%, PR≥20%) and Luminal B-like (HER2 negative or positive, Ki-67 ≥14%, PR<20%). When Ki-67% was not available, tumors with grade 1 or 2 were classified as Luminal A-like and with grade 3 as Luminal B-like. IHC subtypes were compared to the BP NGS and microarray molecular subtypes (Luminal-, HER2- and Basal-type). To further stratify BP luminal type tumors, MP test was used as follows: Luminal A (BP Luminal and MP low risk) and Luminal B (BP Luminal and MP high risk).
Results
Concordance between IHC and MP/BP NGS subtyping was 75.0% (93/124), while concordance between MP/BP on NGS and microarray was 89.5% (111/124). MP/BP NGS subtyping identified more low risk Luminal A tumors compared to IHC (54.0%, (67/124) vs 44.3% (55/124)). Notably, concordance was excellent for triple-negative and, to less extent for HER2 driven tumors (Luminal B-like-HER2 positive and HER2+).
IHC vs. MP/BP NGS molecular subtyping (n=124) MP/BP NGSIHCLuminal ALuminal BHER2-positiveBasalTotalLuminal A-like4690055Luminal B-like, HER2-negative16210037Luminal B-like, HER2-positive565016HER2-positive00303Triple negative0101213Total6737812124Microarray vs MP/BP NGS molecular subtyping (n=124) MP/BP NGSMicroarrayLuminal ALuminal BHER2 positiveBasalTotalLuminal A6040064Luminal B7310038HER2-positive028010Basal0001212Total6737812124
Conclusion
This study shows a discordance of 25.0% between IHC and BP/MP NGS subtyping. This is in line with previous findings where IHC was compared to molecular subtyping based on microarray (Viale 2017, Whitworth 2014) underlining the complementarity of genomic testing in early stage breast cancer. Moreover, we observed a high concordance between NGS and microarray molecular subtyping, which suggests a successful translation of the MP/BP microarray test to a MP/BP NGS test.
Citation Format: Darrigues L, Slembrouck L, Mittempergher L, Delahaye LJ, Vanden Bempt I, Vander Borght S, Vliegen L, Sintubin P, Raynal V, Bohec M, Reyes C, Rapinat A, Helsmoortel C, Jongen L, Hoste G, Neven P, Wildiers H, Smeets A, Nevelsteen I, Punie K, Van Nieuwenhuysen E, Han S, Laurent C, Vincent-Salomon A, Laas-Faron E, Witteveen AT, Neijenhuis S, Glas AM, Floris G, Reyal F. Comparison of breast cancer molecular subtyping by Immunohistochemistry and by BluePrint® next generation RNA sequencing-based test at University Hospitals Leuven and Curie Institute Paris [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-02-07.
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Affiliation(s)
- L Darrigues
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Slembrouck
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Mittempergher
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - LJ Delahaye
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - I Vanden Bempt
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - S Vander Borght
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Vliegen
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - P Sintubin
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - V Raynal
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - M Bohec
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - C Reyes
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - A Rapinat
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - C Helsmoortel
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Jongen
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - G Hoste
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - P Neven
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - H Wildiers
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - A Smeets
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - I Nevelsteen
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - K Punie
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - E Van Nieuwenhuysen
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - S Han
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - C Laurent
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - A Vincent-Salomon
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - E Laas-Faron
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - AT Witteveen
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - S Neijenhuis
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - AM Glas
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - G Floris
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - F Reyal
- Curie Institute, Paris, France; KU Leuven - University of Leuven, Leuven, Belgium; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven – University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Next Generation Sequencing Platform, Genomics Platform, Curie Institute, Paris, France; KU Leuven – University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Curie Institute, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
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Slembrouck L, Laurent C, Delahaye LJ, Mittempergher L, Vanden Bempt I, Vander Borght S, Darrigues L, Vliegen L, Sintubin P, Raynal V, Bohec M, Reyes C, Rapinat A, Helsmoortel C, Jongen L, Hoste G, Neven P, Wildiers H, Smeets A, Nevelsteen I, Punie K, Van Nieuwenhuysen E, Han S, Salomon AV, Faron EL, Cynober T, Witteveen AT, Neijenhuis S, Glas AM, Reyal F, Floris G. Abstract P4-08-25: Decentralized beta testing of MammaPrint and BluePrint NGS kit at University Hospitals Leuven and Curie Institute Paris. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-08-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Many countries restrict patient material exchange to central diagnostic laboratories abroad, limiting access to assays like MammaPrint® (MP) and BluePrint® (BP). Both assays are microarray-based, with MP being prognostic for distant recurrence and BP for molecular subtyping of breast cancer (Luminal-, HER2-, and Basal-type). To increase accessibility, decentralization is required with Next Generation Sequencing (NGS) being the preferred testing platform given that most diagnostic laboratories have the technology in place. The aim of this beta testing study is to validate a previously developed and centrally validated MP and BP NGS kit for RNA samples in two large tertiary academic hospitals in Europe.
Patients and Methods
Patients with early breast cancer diagnosed at the Multidisciplinary Breast Center at University Hospitals Leuven and Curie Institute Paris were prospectively included between September 2017 and January 2018. Patients with bilateral breast cancer or presenting with more than 3 positive lymph nodes were excluded. Only patients with invasive ductal and invasive lobular carcinoma were included. Twenty tissue sections were cut from formalin-fixed, paraffin-embedded (FFPE) blocks; 10 tissue sections were analyzed at the local site using the MP and BP NGS kit, and 10 tissue sections were analyzed at Agendia using the same kit and procedure, as well as with the golden standard method (gene expression microarrays). Targeted RNA sequencing of the 70 MP and 80 BP signature genes was performed on Illumina MiSeq instruments. The raw NGS data generated at the local test sites was sent through a secure file transfer protocol server to Agendia for interpretation and comparison with microarray and NGS performed in the Agendia laboratories. We aimed for a minimum concordance rate between MP and BP outcome of 90% between each local site and Agendia's centralized site.
Results
In this study, 116 early breast cancer patients were included (73 from University Hospitals Leuven and 43 from Curie Institute). Out of these patients, 52% were MP Low Risk and 48% MP High Risk according to microarray. The patients had a BP luminal, HER2 or basal subtype in respectively 83%, 9% and 8%. Concordance between MP microarray obtained from Agendia and MP NGS obtained from the local sites was 91.4%. Concordance between MP High and Low Risk classification between NGS Leuven versus NGS Agendia was 92.1% and between NGS Curie versus NGS Agendia 95.3%. For BP subtype outcomes, the results from microarray versus NGS for all patients combined from both local sites gave a 98.3% concordance and NGS Agendia versus NGS from each local site gave a 100% concordance.
Conclusion
The MP and BP NGS kit was successfully validated in a decentralized setting, showing high concordance between results obtained at three different sites. There was a clear benefit of having well-trained NGS experienced diagnostic technical teams. The MP and BP NGS kit the first FFPE targeted RNA sequencing based multigene signature for breast cancer care, will provide a high and equal standard of MP and BP gene expression testing for breast cancer in a decentralized setting.
Citation Format: Slembrouck L, Laurent C, Delahaye LJ, Mittempergher L, Vanden Bempt I, Vander Borght S, Darrigues L, Vliegen L, Sintubin P, Raynal V, Bohec M, Reyes C, Rapinat A, Helsmoortel C, Jongen L, Hoste G, Neven P, Wildiers H, Smeets A, Nevelsteen I, Punie K, Van Nieuwenhuysen E, Han S, Salomon AV, Faron EL, Cynober T, Witteveen AT, Neijenhuis S, Glas AM, Reyal F, Floris G. Decentralized beta testing of MammaPrint and BluePrint NGS kit at University Hospitals Leuven and Curie Institute Paris [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-25.
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Affiliation(s)
- L Slembrouck
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - C Laurent
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - LJ Delahaye
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Mittempergher
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - I Vanden Bempt
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - S Vander Borght
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Darrigues
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Vliegen
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - P Sintubin
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - V Raynal
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - M Bohec
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - C Reyes
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - A Rapinat
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - C Helsmoortel
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - L Jongen
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - G Hoste
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - P Neven
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - H Wildiers
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - A Smeets
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - I Nevelsteen
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - K Punie
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - E Van Nieuwenhuysen
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - S Han
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - AV Salomon
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - EL Faron
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - T Cynober
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - AT Witteveen
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - S Neijenhuis
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - AM Glas
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - F Reyal
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
| | - G Floris
- KU Leuven - University of Leuven, Leuven, Belgium; Residual Tumor & Response to Treatment Laboratory, RT2Lab, PSL Research University, INSERM, U932 Immunity and Cancer, Institut Curie, Paris, France; Medical Affairs, Agendia, Amsterdam, Netherlands; KU Leuven - University of Leuven, University Hospitals Leuven, Leuven, Belgium; KU Leuven - University Hospitals Leuven, Leuven, Belgium; Institut Curie, Paris, France; Next Generation Sequencing Platform, Genomics Platform, Institut Curie, Paris, France; KU Leuven - University of Leuven, University Hospitals Leuven, Genomics Core, Leuven, Belgium; Administration and General Services, Institut Curie, Paris, France; KU Leuven - University of Leuven, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, Leuven, Belgium
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6
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van der Werf IM, Van Dijck A, Reyniers E, Helsmoortel C, Kumar AA, Kalscheuer VM, de Brouwer AP, Kleefstra T, van Bokhoven H, Mortier G, Janssens S, Vandeweyer G, Kooy RF. Mutations in two large pedigrees highlight the role of ZNF711 in X-linked intellectual disability. Gene 2016; 605:92-98. [PMID: 27993705 DOI: 10.1016/j.gene.2016.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/02/2016] [Accepted: 12/14/2016] [Indexed: 02/04/2023]
Abstract
Intellectual disability (ID) affects approximately 1-2% of the general population and is characterized by impaired cognitive abilities. ID is both clinically as well as genetically heterogeneous, up to 2000 genes are estimated to be involved in the emergence of the disease with various clinical presentations. For many genes, only a few patients have been reported and causality of some genes has been questioned upon the discovery of apparent loss-of-function mutations in healthy controls. Description of additional patients strengthens the evidence for the involvement of a gene in the disease and can clarify the clinical phenotype associated with mutations in a particular gene. Here, we present two large four-generation families with a total of 11 males affected with ID caused by mutations in ZNF711, thereby expanding the total number of families with ID and a ZNF711 mutation to four. Patients with mutations in ZNF711 all present with mild to moderate ID and poor speech accompanied by additional features in some patients, including autistic features and mild facial dysmorphisms, suggesting that ZNF711 mutations cause non-syndromic ID.
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Affiliation(s)
- Ilse M van der Werf
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Edwin Reyniers
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Céline Helsmoortel
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Ajay Anand Kumar
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Arjan Pm de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium.
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7
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Helsmoortel C, Swagemakers SMA, Vandeweyer G, Stubbs AP, Palli I, Mortier G, Kooy RF, van der Spek PJ. Whole genome sequencing of a dizygotic twin suggests a role for the serotonin receptor HTR7 in autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1049-1056. [PMID: 27380831 DOI: 10.1002/ajmg.b.32473] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/24/2016] [Indexed: 01/18/2023]
Abstract
Whole genome sequencing of a severely affected dizygotic twin with an autism spectrum disorder and intellectual disability revealed a compound heterozygous mutation in the HTR7 gene as the only variation not detected in control databases. Each parent carries one allele of the mutation, which is not present in an unaffected stepsister. The HTR7 gene encodes the 5-HT7 serotonin receptor that is involved in brain development, synaptic transmission, and plasticity. The paternally inherited p.W60C variant is situated at an evolutionary conserved nucleotide and predicted damaging by Polyphen2. A mutation akin to the maternally inherited pV286I mutation has been reported to significantly affect the binding characteristics of the receptor. Therefore, the observed sequence alterations provide a first suggestive link between a genetic abnormality in the HTR7 gene and a neurodevelopmental disorder. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Céline Helsmoortel
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | | | - Geert Vandeweyer
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
| | - Ivo Palli
- Department of Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
| | - Geert Mortier
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
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8
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Helsmoortel C, Kooy RF, Vandeweyer G. Multiplexed High Resolution Melting Assay for Versatile Sample Tracking in a Diagnostic and Research Setting. J Mol Diagn 2015; 18:32-8. [PMID: 26614051 DOI: 10.1016/j.jmoldx.2015.06.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/27/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022] Open
Abstract
Modern experimental procedures in molecular genetics, such as next-generation sequencing experiments, require that samples are taken along a whole series of wet- and dry-laboratory steps. It generally is accepted that by increasing the complexity and number of steps in the experimental pipeline, the risk of sample swaps increases. It therefore is recommended to confirm the identity of each individual sample at the end of any pipeline. Here, we present a versatile assay to determine the identity of samples rapidly and efficiently by genotyping 21 single-nucleotide polymorphisms (SNPs) using multiplex high resolution melting. The selected SNPs also are present in whole-exome sequencing data, and comparison of the differentially obtained genotypes allows reliable identification of individual samples. In this assay, we combined primers interrogating two to three SNPs per high resolution melting reaction, enabling the generation of the SNP genotype profile in only eight reactions per sample, limiting the hands-on time and minimizing the amount of reagents. This SNP profiling approach also can be used to track samples in custom next-generation sequencing enrichment panels by including these 21 SNPs in the target region, allowing for the often-required independent validation of sample identity in both clinical and research settings.
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Affiliation(s)
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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9
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Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders M, Venselaar H, Helsmoortel C, Cho M, Hoischen A, Vissers LE, Koemans T, Wissink-Lindhout W, Eichler E, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon B, Shaw M, Gecz J, Haan E, Bienek M, Jensen C, Loeys B, Van Dijck A, Innes A, Racher H, Vermeer S, Di Donato N, Rump A, Tatton-Brown K, Parker M, Henderson A, Lynch S, Fryer A, Ross A, Vasudevan P, Kini U, Newbury-Ecob R, Chandler K, Male A, Dijkstra S, Schieving J, Giltay J, van Gassen K, Schuurs-Hoeijmakers J, Tan P, Pediaditakis I, Haas S, Retterer K, Reed P, Monaghan K, Haverfield E, Natowicz M, Myers A, Kruer M, Stein Q, Strauss K, Brigatti K, Keating K, Burton B, Kim K, Charrow J, Norman J, Foster-Barber A, Kline A, Kimball A, Zackai E, Harr M, Fox J, McLaughlin J, Lindstrom K, Haude K, van Roozendaal K, Brunner H, Chung W, Kooy R, Pfundt R, Kalscheuer V, Mehta S, Katsanis N, Kleefstra T, Kleefstra T. Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling. Am J Hum Genet 2015; 97:343-52. [PMID: 26235985 DOI: 10.1016/j.ajhg.2015.07.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/13/2015] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) affects approximately 1%-3% of humans with a gender bias toward males. Previous studies have identified mutations in more than 100 genes on the X chromosome in males with ID, but there is less evidence for de novo mutations on the X chromosome causing ID in females. In this study we present 35 unique deleterious de novo mutations in DDX3X identified by whole exome sequencing in 38 females with ID and various other features including hypotonia, movement disorders, behavior problems, corpus callosum hypoplasia, and epilepsy. Based on our findings, mutations in DDX3X are one of the more common causes of ID, accounting for 1%-3% of unexplained ID in females. Although no de novo DDX3X mutations were identified in males, we present three families with segregating missense mutations in DDX3X, suggestive of an X-linked recessive inheritance pattern. In these families, all males with the DDX3X variant had ID, whereas carrier females were unaffected. To explore the pathogenic mechanisms accounting for the differences in disease transmission and phenotype between affected females and affected males with DDX3X missense variants, we used canonical Wnt defects in zebrafish as a surrogate measure of DDX3X function in vivo. We demonstrate a consistent loss-of-function effect of all tested de novo mutations on the Wnt pathway, and we further show a differential effect by gender. The differential activity possibly reflects a dose-dependent effect of DDX3X expression in the context of functional mosaic females versus one-copy males, which reflects the complex biological nature of DDX3X mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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10
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Helsmoortel C, Vandeweyer G, Ordoukhanian P, Van Nieuwerburgh F, Van der Aa N, Kooy RF. Challenges and opportunities in the investigation of unexplained intellectual disability using family-based whole-exome sequencing. Clin Genet 2014; 88:140-8. [PMID: 25081361 DOI: 10.1111/cge.12470] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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: 05/29/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 12/25/2022]
Abstract
Intellectual disability (ID), characterized by an intellectual performance of at least 2 SD (standard deviations) below average is a frequent, lifelong disorder with a prevalence of 2-3%. Today, only for at most half of patients a diagnosis is made. Knowing the cause of the ID is important for patients and their relatives, as it allows for appropriate medical care, prognosis on further development of the disorder, familial counselling or access to support groups. Whole-exome sequencing (WES) now offers the possibility to identify the genetic cause for patients for which all previously available genetic tests, including karyotyping, specific gene analysis, or microarray analysis did not reveal causative abnormalities. However, data analysis of WES experiments is challenging. Here we present an analysis workflow implementable in any laboratory, requiring no bioinformatics knowledge. We demonstrated its feasibility on a cohort of 10 patients, in which we found a conclusive diagnosis in 3 and a likely diagnosis in 2 more patients. Of the three conclusive diagnoses, one was a clinically suspected mutation missed by Sanger sequencing, and one was an atypical presentation of a known monogenic disorder, highlighting two essential strengths of WES-based diagnostics.
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Affiliation(s)
- C Helsmoortel
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - G Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Center Antwerpen (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - P Ordoukhanian
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA, USA
| | - F Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - N Van der Aa
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Department of Medical Genetics, University Hospital Antwerp, Antwerp, Belgium
| | - R F Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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11
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Vandeweyer G, Helsmoortel C, Van Dijck A, Vulto-van Silfhout AT, Coe BP, Bernier R, Gerdts J, Rooms L, van den Ende J, Bakshi M, Wilson M, Nordgren A, Hendon LG, Abdulrahman OA, Romano C, de Vries BBA, Kleefstra T, Eichler EE, Van der Aa N, Kooy RF. The transcriptional regulator ADNP links the BAF (SWI/SNF) complexes with autism. Am J Med Genet C Semin Med Genet 2014; 166C:315-26. [PMID: 25169753 DOI: 10.1002/ajmg.c.31413] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mutations in ADNP were recently identified as a frequent cause of syndromic autism, characterized by deficits in social communication and interaction and restricted, repetitive behavioral patterns. Based on its functional domains, ADNP is a presumed transcription factor. The gene interacts closely with the SWI/SNF complex by direct and experimentally verified binding of its C-terminus to three of its core components. A detailed and systematic clinical assessment of the symptoms observed in our patients allows a detailed comparison with the symptoms observed in other SWI/SNF disorders. While the mutational mechanism of the first 10 patients identified suggested a gain of function mechanism, an 11th patient reported here is predicted haploinsufficient. The latter observation may raise hope for therapy, as addition of NAP, a neuroprotective octapeptide named after the first three amino acids of the sequence NAPVSPIQ, has been reported by others to ameliorate some of the cognitive abnormalities observed in a knockout mouse model. It is concluded that detailed clinical and molecular studies on larger cohorts of patients are necessary to establish a better insight in the genotype phenotype correlation and in the mutational mechanism.
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12
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Helsmoortel C, Vulto-van Silfhout AT, Coe BP, Vandeweyer G, Rooms L, van den Ende J, Schuurs-Hoeijmakers JHM, Marcelis CL, Willemsen MH, Vissers LELM, Yntema HG, Bakshi M, Wilson M, Witherspoon KT, Malmgren H, Nordgren A, Annerén G, Fichera M, Bosco P, Romano C, de Vries BBA, Kleefstra T, Kooy RF, Eichler EE, Van der Aa N. A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP. Nat Genet 2014; 46:380-4. [PMID: 24531329 PMCID: PMC3990853 DOI: 10.1038/ng.2899] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/23/2014] [Indexed: 12/11/2022]
Abstract
Despite a high heritability, a genetic diagnosis can only be established in a minority of patients with autism spectrum disorder (ASD), characterized by persistent deficits in social communication and interaction and restricted, repetitive patterns of behavior, interests or activities1. Known genetic causes include chromosomal aberrations, such as the duplication of the 15q11-13 region, and monogenic causes, such as the Rett and Fragile X syndromes. The genetic heterogeneity within ASD is striking, with even the most frequent causes responsible for only 1% of cases at the most. Even with the recent developments in next generation sequencing, for the large majority of cases no molecular diagnosis can be established 2-7. Here, we report 10 patients with ASD and other shared clinical characteristics, including intellectual disability and facial dysmorphisms caused by a mutation in ADNP, a transcription factor involved in the SWI/SNF remodeling complex. We estimate this gene to be mutated in at least 0.17% of ASD cases, making it one of the most frequent ASD genes known to date.
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Affiliation(s)
| | - Anneke T Vulto-van Silfhout
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands. [2]
| | - Bradley P Coe
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA. [3]
| | - Geert Vandeweyer
- 1] Department of Medical Genetics, University of Antwerp, Antwerp, Belgium. [2] Biomedical informatics research center Antwerpen (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Edegem, Belgium
| | - Liesbeth Rooms
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | - Janneke H M Schuurs-Hoeijmakers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carlo L Marcelis
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Madhura Bakshi
- Department of Genetic Medicine, Westmead Hospital, Sydney, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Westmead, Australia
| | - Kali T Witherspoon
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Helena Malmgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Göran Annerén
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Marco Fichera
- 1] Unit of Neurology, I.R.C.C.S. Associazione Oasi Maria Santissima, Troina, Italy. [2] Medical Genetics, University of Catania, Catania, Italy
| | - Paolo Bosco
- Laboratory of Cytogenetics, I.R.C.C.S. Associazione Oasi Maria Santissima, Troina, Italy
| | - Corrado Romano
- Unit of Pediatrics and Medical Genetics, I.R.C.C.S. Associazione Oasi Maria Santissima, Troina, Italy
| | - Bert B A de Vries
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands. [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- 1] Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands. [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Nathalie Van der Aa
- 1] Department of Medical Genetics, University of Antwerp, Antwerp, Belgium. [2] University Hospital Antwerp, Antwerp, Belgium
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13
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Iqbal Z, Vandeweyer G, van der Voet M, Waryah AM, Zahoor MY, Besseling JA, Roca LT, Vulto-van Silfhout AT, Nijhof B, Kramer JM, Van der Aa N, Ansar M, Peeters H, Helsmoortel C, Gilissen C, Vissers LELM, Veltman JA, de Brouwer APM, Frank Kooy R, Riazuddin S, Schenck A, van Bokhoven H, Rooms L. Homozygous and heterozygous disruptions of ANK3: at the crossroads of neurodevelopmental and psychiatric disorders. Hum Mol Genet 2013; 22:1960-70. [PMID: 23390136 DOI: 10.1093/hmg/ddt043] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AnkyrinG, encoded by the ANK3 gene, is involved in neuronal development and signaling. It has previously been implicated in bipolar disorder and schizophrenia by association studies. Most recently, de novo missense mutations in this gene were identified in autistic patients. However, the causative nature of these mutations remained controversial. Here, we report inactivating mutations in the Ankyrin 3 (ANK3) gene in patients with severe cognitive deficits. In a patient with a borderline intelligence, severe attention deficit hyperactivity disorder (ADHD), autism and sleeping problems, all isoforms of the ANK3 gene, were disrupted by a balanced translocation. Furthermore, in a consanguineous family with moderate intellectual disability (ID), an ADHD-like phenotype and behavioral problems, we identified a homozygous truncating frameshift mutation in the longest isoform of the same gene, which represents the first reported familial mutation in the ANK3 gene. The causality of ANK3 mutations in the two families and the role of the gene in cognitive function were supported by memory defects in a Drosophila knockdown model. Thus we demonstrated that ANK3 plays a role in intellectual functioning. In addition, our findings support the suggested association of ANK3 with various neuropsychiatric disorders and illustrate the genetic and molecular relation between a wide range of neurodevelopmental disorders.
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Affiliation(s)
- Zafar Iqbal
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognitionand Behaviour, Radboud University Medical Centre, Nijmegen, TheNetherlands
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14
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Abstract
Over the last decade, the detection of chromosomal abnormalities has shifted from conventional karyotyping under a light microscope to molecular detection using microarrays. The latter technology identified copy number variation as a major source of variation in the human genome; moreover, copy number variants were found responsible for 10-20% of cases of intellectual disability. Recent technological advances in microarray technology have also enabled the detection of very small local chromosomal rearrangements, sometimes affecting the function of only a single gene. Here, we illustrate how high resolution microarray analysis has led to increased insights into the contribution of specific genes in disease.
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Affiliation(s)
- Céline Helsmoortel
- Cognitive Genetics, Department of Medical Genetics, University of Antwerp Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
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