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Grolaux R, Hardy A, Olsen C, Van Dooren S, Smits G, Defrance M. Identification of differentially methylated regions in rare diseases from a single-patient perspective. Clin Epigenetics 2022; 14:174. [PMID: 36527161 PMCID: PMC9758859 DOI: 10.1186/s13148-022-01403-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA methylation (5-mC) is being widely recognized as an alternative in the detection of sequence variants in the diagnosis of some rare neurodevelopmental and imprinting disorders. Identification of alterations in DNA methylation plays an important role in the diagnosis and understanding of the etiology of those disorders. Canonical pipelines for the detection of differentially methylated regions (DMRs) usually rely on inter-group (e.g., case versus control) comparisons. However, these tools might perform suboptimally in the context of rare diseases and multilocus imprinting disturbances due to small cohort sizes and inter-patient heterogeneity. Therefore, there is a need to provide a simple but statistically robust pipeline for scientists and clinicians to perform differential methylation analyses at the single patient level as well as to evaluate how parameter fine-tuning may affect differentially methylated region detection. RESULT We implemented an improved statistical method to detect differentially methylated regions in correlated datasets based on the Z-score and empirical Brown aggregation methods from a single-patient perspective. To accurately assess the predictive power of our method, we generated semi-simulated data using a public control population of 521 samples and investigated how the size of the control population, methylation difference, and region size affect DMR detection. In addition, we validated the detection of methylation events in patients suffering from rare multi-locus imprinting disturbance and evaluated how this method could complement existing tools in the context of clinical diagnosis. CONCLUSION In this study, we present a robust statistical method to perform differential methylation analysis at the single patient level and describe its optimal parameters to increase DMRs identification performance. Finally, we show its diagnostic utility when applied to rare disorders.
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Affiliation(s)
- Robin Grolaux
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexis Hardy
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Catharina Olsen
- grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sonia Van Dooren
- grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Guillaume Smits
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Matthieu Defrance
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
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Ochoa E, Lee S, Lan-Leung B, Dias RP, Ong KK, Radley JA, Pérez de Nanclares G, Martinez R, Clark G, Martin E, Castaño L, Bottolo L, Maher ER. ImprintSeq, a novel tool to interrogate DNA methylation at human imprinted regions and diagnose multilocus imprinting disturbance. Genet Med 2022; 24:463-474. [PMID: 34906518 DOI: 10.1016/j.gim.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
PURPOSE Disruptions of genomic imprinting are associated with congenital imprinting disorders (CIDs) and other disease states, including cancer. CIDs are most often associated with altered methylation at imprinted differentially methylated regions (iDMRs). In some cases, multiple iDMRs are affected causing multilocus imprinting disturbances (MLIDs). The availability of accurate, quantitative, and scalable high-throughput methods to interrogate multiple iDMRs simultaneously would enhance clinical diagnostics and research. METHODS We report the development of a custom targeted methylation sequencing panel that covered most relevant 63 iDMRs for CIDs and the detection of MLIDs. We tested it in 70 healthy controls and 147 individuals with CIDs. We distinguished loss and gain of methylation per differentially methylated region and classified high and moderate methylation alterations. RESULTS Across a range of CIDs with a variety of molecular mechanisms, ImprintSeq performed at 98.4% sensitivity, 99.9% specificity, and 99.9% accuracy (when compared with previous diagnostic testing). ImprintSeq was highly sensitive for detecting MLIDs and enabled diagnostic criteria for MLID to be proposed. In a child with extreme MLID profile a probable genetic cause was identified. CONCLUSION ImprintSeq provides a novel assay for clinical diagnostic and research studies of CIDs, MLIDs, and the role of disordered imprinting in human disease states.
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Affiliation(s)
- Eguzkine Ochoa
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sunwoo Lee
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benoit Lan-Leung
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Renuka P Dias
- Department of Endocrinology and Diabetes, Birmingham Children's Hospital, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom; Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom; Department of Paediatrics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jessica A Radley
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom; London North West Regional Genetics Service, St. Mark's and Northwick Park hospitals, Harrow, Middlesex, United Kingdom
| | - Gustavo Pérez de Nanclares
- Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, University of the Basque Country (UPV-EHU), Bizkaia, Spain
| | - Rosa Martinez
- Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, University of the Basque Country (UPV-EHU), Bizkaia, Spain
| | - Graeme Clark
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom; Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ezequiel Martin
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Luis Castaño
- Biocruces Bizkaia Health Research Institute, Hospital Universitario Cruces, CIBERDEM, CIBERER, Endo-ERN, University of the Basque Country (UPV-EHU), Bizkaia, Spain
| | - Leonardo Bottolo
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom; The Alan Turing Institute, London, United Kingdom; MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eamonn R Maher
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.
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Kagami M, Hara-Isono K, Matsubara K, Nakabayashi K, Narumi S, Fukami M, Ohkubo Y, Saitsu H, Takada S, Ogata T. ZNF445: a homozygous truncating variant in a patient with Temple syndrome and multilocus imprinting disturbance. Clin Epigenetics 2021; 13:119. [PMID: 34039421 PMCID: PMC8157728 DOI: 10.1186/s13148-021-01106-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022] Open
Abstract
Background ZNF445, as well as ZFP57, is involved in the postfertilization methylation maintenance of multiple imprinting-associated differentially methylated regions (iDMRs). Thus, ZNF445 pathogenic variants are predicted to cause multilocus imprinting disturbances (MLIDs), as do ZFP57 pathogenic variants. In particular, the MEG3/DLK1:IG-DMR would be affected, because the postzygotic methylation imprint of the MEG3/DLK1:IG-DMR is maintained primarily by ZNF445, whereas that of most iDMRs is preserved by both ZFP57 and ZNF445 or primarily by ZFP57. Results We searched for a ZNF445 variant(s) in six patients with various imprinting disorders (IDs) caused by epimutations and MLIDs revealed by pyrosequencing for nine iDMRs, without a selection for the original IDs. Re-analysis of the previously obtained whole exome sequencing data identified a homozygous ZNF445 variant (NM_181489.6:c.2803C>T:p.(Gln935*)) producing a truncated protein missing two of 14 zinc finger domains in a patient with Temple syndrome and MLID. In this patient, array-based genomewide methylation analysis revealed severe hypomethylation of most CpGs at the MEG3:TSS-DMR, moderate hypomethylation of roughly two-thirds of CpGs at the H19/IGF2:IG-DMR, and mild-to-moderate hypomethylation of a few CpGs at the DIRAS3:TSS-DMR, MEST:alt-TSS-DMR, IGF2:Ex9-DMR, IGF2:alt-TSS, and GNAS-AS1:TSS-DMR. Furthermore, bisulfite sequencing analysis for the MEG3/DLK1:IG-DMR delineated a markedly hypomethylated segment (CG-A). The heterozygous parents were clinically normal and had virtually no aberrant methylation pattern. Conclusions We identified a ZNF445 pathogenic variant for the first time. Since ZNF445 binds to the MEG3/DLK1:IG-DMR and other iDMRs affected in this patient, the development of Temple syndrome and MLID would primarily be explained by the ZNF445 variant. Furthermore, CG-A may be the target site for ZNF445 within the MEG3/DLK1:IG-DMR. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01106-5.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan. .,Department of Pediatrics, Shizuoka Saiseikai Hospital, Oshika 1-1-1, Suruga-ku, Shizuoka, 422-8527, Japan. .,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan. .,Department of Pediatrics, Hamamatsu Medical Center, Tomitsuka 328, Naka-ku, Hamamatsu, 432-8580, Japan.
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Brück J, Begemann M, Dey D, Elbracht M, Eggermann T. Molecular characterization of temple syndrome families with 14q32 epimutations. Eur J Med Genet 2020; 63:104077. [PMID: 33010492 DOI: 10.1016/j.ejmg.2020.104077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/19/2020] [Revised: 09/07/2020] [Accepted: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Temple Syndrome (TS14) is an imprinting disorder caused by molecular disruptions of the imprinted region in 14q32 (MEG3:TSS-DMR). The frequency of the three known TS14 subtypes (deletions, maternal uniparental disomy (upd(14)mat), loss of methylation (LOM)) is currently in discussion, and within the LOM group, the occurrence of Multilocus Imprinting Disturbances (MLID) has been identified. We present 16 TS14 patients with molecular alterations affecting the MEG3:TSS-DMR, comprising seven patients (43.8%) with LOM, six carriers with upd(14)mat (37.5%), and three cases (18.8%) with a deletion affecting the paternal MEG3:TSS-DMR. We did not find any evidence for MLID in the LOM group, including two cases in which different tissues were available. Whole exome sequencing (WES) in the MEG3:TSS-DMR LOM patients and their parents (Trio WES) did not reveal an obvious pathogenic variant which might cause aberrant methylation at imprinted loci. By summarizing our data with those from the literature, we could show that MLID affecting clinically relevant imprinted loci is rare in TS14 and therefore differs markedly from other imprinting disorders associated with MLID, e.g. Silver-Russell syndrome (SRS) and Beckwith-Wiedemann syndrome (BWS). However, consistent with the clinical overlap with TS14, in SRS patients carrying MLID the MEG3:TSS-DMR is frequently affected. Variants in the known candidate genes for maternal effect variants causing MLID and fetal MLID determinants could not be identified in TS14 patients. Thus, 14q32 epimutations probably have other molecular causes than epimutations in BWS or SRS patients.
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Affiliation(s)
- Johanna Brück
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Daniela Dey
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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Kagami M, Yanagisawa A, Ota M, Matsuoka K, Nakamura A, Matsubara K, Nakabayashi K, Takada S, Fukami M, Ogata T. Temple syndrome in a patient with variably methylated CpGs at the primary MEG3/DLK1:IG-DMR and severely hypomethylated CpGs at the secondary MEG3:TSS-DMR. Clin Epigenetics 2019; 11:42. [PMID: 30846001 PMCID: PMC6407230 DOI: 10.1186/s13148-019-0640-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/28/2019] [Indexed: 12/16/2022] Open
Abstract
Background The human chromosome 14q32.2 imprinted region harbors the primary MEG3/DLK1:IG-differentially methylated region (DMR) and secondary MEG3:TSS-DMR. The MEG3:TSS-DMR can remain unmethylated only in the presence of unmethylated MEG3/DLK1:IG-DMR in somatic tissues, but not in the placenta, because of a hierarchical regulation of the methylation pattern between the two DMRs. Methods We performed molecular studies in a 4-year-old Japanese girl with Temple syndrome (TS14). Results Pyrosequencing analysis showed extremely low methylation levels of five CpGs at the MEG3:TSS-DMR and grossly normal methylation levels of four CpGs at the MEG3/DLK1:IG-DMR in leukocytes. HumanMethylation450 BeadChip confirmed marked hypomethylation of the MEG3:TSS-DMR and revealed multilocus imprinting disturbance (MLID) including mild hypomethylation of the H19/IGF2:IG-DMR and mild hypermethylation of the GNAS A/B:TSS-DMR in leukocytes. Bisulfite sequencing showed markedly hypomethylated CpGs at the MEG3:TSS-DMR and irregularly and non-differentially methylated CpGs at the MEG3/DLK1:IG-DMR in leukocytes and apparently normal methylation patterns of the two DMRs in the placenta. Maternal uniparental disomy 14 and a deletion involving this imprinted region were excluded. Conclusions Such a methylation pattern of the MEG3/DLK1:IG-DMR has not been reported in patients with TS14. It may be possible that a certain degree of irregular hypomethylation at the MEG3/DLK1:IG-DMR has prevented methylation of the MEG3:TSS-DMR in somatic tissues and that a hypermethylation type MLID has occurred at the MEG3/DLK1:IG-DMR to yield the apparently normal methylation pattern in the placenta. Electronic supplementary material The online version of this article (10.1186/s13148-019-0640-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Atsuhiro Yanagisawa
- Department of Pediatrics, Yaizu City Hospital, 1000 Doubara, Yaizu, Shizuoka, 425-8505, Japan.,Department of Pediatrics, JR Tokyo General Hospital, 2-1-3 Yoyogi, Shibuya-ku, Tokyo, 151-8528, Japan
| | - Miyuki Ota
- Department of Pediatrics, Yaizu City Hospital, 1000 Doubara, Yaizu, Shizuoka, 425-8505, Japan
| | - Kentaro Matsuoka
- Department of Pathology, Dokkyo Medical University, Saitama Medical Center, 2-1-50 Minami-Koshigaya, Koshigaya, Saitama, 343-8555, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.,Department of Pediatrics, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan. .,Department of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
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