1
|
Tüysüz B, Kasap B, Uludağ Alkaya D, Alp Ünkar Z, Köseoğlu P, Geyik F, Özer E, Önal H, Gezdirici A, Ercan O. Investigation of (Epi)genetic causes in syndromic short children born small for gestational age. Eur J Med Genet 2023; 66:104854. [PMID: 37758162 DOI: 10.1016/j.ejmg.2023.104854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/08/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Intrauterine onset syndromic short stature constitutes a group of diseases that pose challenges in differential diagnosis due to their rarity and clinical as well as molecular heterogeneity. The aim of this study was to investigate the presence of (epi)genetic causes in children born small for gestational age (SGA) and manifesting clinically undiagnosed syndromic short stature. The study group comprised twenty-nine cases selected from the syndromic SGA cohort. Various analyses were performed, including chromosomal microarray (CMA), methylation-specific-multiple ligation probe amplification for chromosomes 6,14 and 20, and whole exome sequencing (WES). Pathogenic copy number variants (CNVs) on chromosomes 2q13, 22q11.3, Xp22.33, 17q21.31, 19p13.13 and 4p16.31 causing syndromic growth disturbance were detected in six patients. Maternal uniparental disomy 14 was identified in a patient. WES was performed in the remaining 22 patients, revealing pathogenic variants in nine cases; six were monoallelic (ACAN, ARID2, NIPBL, PIK3R1, SMAD4, BRIP1), two were biallelic (BRCA2, RFWD3) and one was hemizygous (HUWE1). Seven of these were novel. Craniofacial dysmorphism, which is an important clue for the diagnosis of syndromes, was very mild in all patients. This study unveiled, for the first time, that ARID2 mutatios can cause syndromic SGA. In conclusion, a high (55.2%) diagnosis rate was achieved through the utilization of CMA, epigenetic and WES analyzes; 15 rare syndromes were defined, who were born with SGA and had atypical and/or mild dysmorphic findings. This study not only drew attention to the association of some rare syndromes with SGA, but also introduced novel genes and CNVs as potential contributors to syndromic SGA.
Collapse
Affiliation(s)
- Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey.
| | - Büşra Kasap
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Zeynep Alp Ünkar
- Department of Neonatology, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Pınar Köseoğlu
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Filiz Geyik
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Emre Özer
- Department of Pediatric Genetics, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| | - Hasan Önal
- Department of Pediatric Endocrinology, University of Health Sciences Turkey, Başakşehir Çam ve Sakura City Hospital, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetic, University of Health Sciences Turkey, Başakşehir Çam ve Sakura City Hospital, Istanbul, Turkey
| | - Oya Ercan
- Department of Pediatric Endocrinology, Istanbul University-Cerrahpaşa, Cerrahpaşa Medical Faculty, Istanbul, Turkey
| |
Collapse
|
2
|
Prenatal diagnosis of mosaic trisomy 16 by amniocentesis in a pregnancy associated with abnormal first-trimester screening result (low PAPP-A and low PlGF), intrauterine growth restriction and a favorable outcome. Taiwan J Obstet Gynecol 2021; 60:1107-1111. [PMID: 34794747 DOI: 10.1016/j.tjog.2021.09.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2021] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE We present prenatal diagnosis of mosaic trisomy 16 by amniocentesis in a pregnancy associated with an abnormal first-trimester screening result, intrauterine growth restriction (IUGR) and a favorable outcome. CASE REPORT A 27-year-old woman underwent amniocentesis at 18 weeks of gestation because of an abnormal first-trimester screening result with maternal serum free β-hCG of 1.474 multiples of the median (MoM), pregnancy associated plasma protein-A (PAPP-A) of 0.122 MoM and placental growth factor (PlGF) of 0.101 MoM, and a Down syndrome risk of 1/45. Amniocentesis revealed a karyotype of 47,XY,+16 [9]/46,XY [16] and an abnormal array comparative genomic hybridization (aCGH) result of arr (16) × 3 [0.54] compatible with 54% mosaicism for trisomy 16 in uncultured amniocytes. At 24 weeks of gestation, repeat amniocentesis revealed a karyotype of 47,XY,+16 [4]/46,XY [16] and an aCGH result of arr 16p13.3q24.3 (96,766-90,567,357) × 2.25 with a log2 ratio = 0.2 compatible with 20-30% mosaicism for trisomy 16 in uncultured amniocytes. Quantitative fluorescent polymerase chain reaction (QF-PCR) excluded uniparental disomy (UPD) 16. Interphase fluorescence in situ hybridization (FISH) analysis on uncultured amniocytes revealed 19.4% (12/62 cells) mosaic trisomy 16. Prenatal ultrasound revealed IUGR. At 36 weeks of gestation, a phenotypically normal baby was delivered with a body weight of 1900 g. The cord blood had a karyotype of 46,XY. QF-PCR analysis confirmed biparentally inherited disomy 16 in the cord blood and maternal-origin of trisomy 16 in the placenta. When follow-up at age two months, FISH analysis on 101 buccal mucosal cells and 32 urinary cells revealed no signal of trisomy 16. CONCLUSION Mosaic trisomy 16 at amniocentesis can be associated with IUGR and an abnormal first-trimester screening result with low PAPP-A and low PlGF. Mosaic trisomy 16 without UPD 16 at amniocentesis can have a favorable outcome, and the abnormal triosmy 16 cell line may disappear after birth.
Collapse
|
3
|
Chen CP, Ko TM, Chern SR, Wu PS, Chen SW, Wu FT, Chen YY, Town DD, Chen LF, Wang W. Prenatal diagnosis of maternal uniparental disomy 16 associated with mosaic trisomy 16 at amniocentesis, and pericardial effusion and intrauterine growth restriction in the fetus. Taiwan J Obstet Gynecol 2021; 60:534-539. [PMID: 33966743 DOI: 10.1016/j.tjog.2021.03.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of maternal uniparental disomy (UPD) 16 associated with mosaic trisomy 16 at amniocentesis, and pericardial effusion and intrauterine growth restriction (IUGR) in the fetus. CASE REPORT A 38-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age, and the result was 47,XX,+16[2]/46,XX[54]. Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed 14% mosaicism for trisomy 16 and a paternally inherited 319-kb microdeletion of 15q11.2 encompassing the genes of TUBGCP5, CYFIP1, NIPA2 and NIPA1. Prenatal ultrasound revealed persistent left superior vena cava, pericardial effusion and severe IUGR. Cordocentesis at 23 weeks of gestation revealed a karyotype of 46,XX, but polymorphic DNA marker analysis revealed maternal UPD 16. Repeat amniocentesis was performed at 27 weeks of gestation and revealed a karyotype of 46, XX in 21/21 colonies. Molecular cytogenetic analysis on uncultured amniocytes revealed 22.4% mosaicism (26/116 cells) for trisomy 16 on interphase fluorescence in situ hybridization (FISH) analysis, and 20% mosaicism for trisomy 16 on aCGH. Polymorphic DNA marker analysis on the DNAs extracted from uncultured amniocytes and parental bloods revealed maternal UPD 16. The pregnancy was subsequently terminated, and a fetus was delivered with facial dysmorphism and severe IUGR. The umbilical cord had a karyotype of 47,XX,+16[28]/46,XX[16]. Polymorphic DNA marker analysis on placenta confirmed a maternal origin of trisomy 16. CONCLUSION Cytogenetic discrepancy between cultured amniocytes and uncultured amniocytes may present in mosaic trisomy 16 at amniocentesis. Prenatal diagnosis of mosaic trisomy 16 should alert the association of maternal UPD 16 which may be associated with congenital heart defects and severe IUGR on prenatal ultrasound.
Collapse
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yun-Yi Chen
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dai-Dyi Town
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| |
Collapse
|
4
|
Chen CP, Chen M, Wang LK, Chern SR, Wu PS, Ma GC, Chang SP, Chen SW, Wu FT, Lee CC, Chen YY, Wang W. Low-level mosaicism for trisomy 16 at amniocentesis in a pregnancy associated with intrauterine growth restriction and a favorable outcome. Taiwan J Obstet Gynecol 2021; 60:345-349. [PMID: 33678340 DOI: 10.1016/j.tjog.2021.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2020] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE We present low-level mosaicism for trisomy 16 at amniocentesis in a pregnancy associated with intrauterine growth restriction (IUGR) and a favorable outcome. CASE REPORT A 31-year-old woman underwent amniocentesis at 24 weeks of gestation because of IUGR. Amniocentesis revealed a karyotype of 47,XX,+16 [3]/46,XX [22]. Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed gene dosage increase in chromosome 16 consistent with 28% mosaicism for trisomy 16. Uniparental disomy (UPD) 7 and UPD 11 were excluded. She underwent repeat amniocentesis at 27 weeks of gestation. Repeat amniocentesis revealed a karyotype of 47,XX,+16 [1]/46,XX [24]. Simultaneous aCGH analysis on the DNA extracted from uncultured amniocytes revealed 25%-35% (log2 ratio = 0.17-0.25) mosaicism for trisomy 16. Interphase fluorescence in situ hybridization (FISH) analysis detected trisomy 16 signals in 28/100 (28%) uncultured amniocytes. Polymorphic DNA marker analysis excluded UPD 16. Level II ultrasound revealed no fetal abnormalities except symmetric IUGR. The pregnancy was continued to 37 weeks of gestation, and a 2306-g phenotypically normal baby was delivered. The cord blood had a karyotype of 46, XX in 50/50 lymphocytes. The umbilical cord had a karyotype of 47,XX,+16 [14]/46,XX [36]. Interphase FISH analysis on buccal mucosal cells and urinary cells at age three days revealed trisomy 16 signals in 3.8% (4/106) buccal mucosal cells and 6.5% (7/107) urinary cells, compared with 1% in the normal control. Polymorphic DNA marker analysis on placenta confirmed trisomy 16 in the placenta and a maternal origin of the extra chromosome 16. CONCLUSION Cytogenetic discrepancy between cultured amniocytes and uncultured amniocytes may present in mosaic trisomy 16 at amniocentesis. Low-level mosaicism for trisomy 16 at amniocentesis without maternal UPD 16 can be associated with a favorable outcome despite the presence of IUGR.
Collapse
Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| | - Ming Chen
- Department of Genomic Medicine, Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan; Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan; Department of Biomedical Science, Dayeh University, Changhua, Taiwan
| | - Liang-Kai Wang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Gwo-Chin Ma
- Department of Genomic Medicine, Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan; Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan, Taiwan; Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine, Department of Genomic Science and Technology, Changhua Christian Hospital Healthcare System, Changhua, Taiwan
| | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Chi Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yun-Yi Chen
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| |
Collapse
|
5
|
Abstract
Imprinting disorders are a group of congenital diseases caused by dysregulation of genomic imprinting, affecting prenatal and postnatal growth, neurocognitive development, metabolism and cancer predisposition. Aberrant expression of imprinted genes can be achieved through different mechanisms, classified into epigenetic - if not involving DNA sequence change - or genetic in the case of altered genomic sequence. Despite the underlying mechanism, the phenotype depends on the parental allele affected and opposite phenotypes may result depending on the involvement of the maternal or the paternal chromosome. Imprinting disorders are largely underdiagnosed because of the broad range of clinical signs, the overlap of presentation among different disorders, the presence of mild phenotypes, the mitigation of the phenotype with age and the limited availability of molecular techniques employed for diagnosis. This review briefly illustrates the currently known human imprinting disorders, highlighting endocrinological aspects of pediatric interest.
Collapse
Affiliation(s)
- Diana Carli
- University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy
| | - Evelise Riberi
- University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy
| | | | - Alessandro Mussa
- University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy,* Address for Correspondence: University of Torino, Department of Pediatric and Public Health Sciences, Torino, Italy Phone: +39-011-313-1985 E-mail:
| |
Collapse
|
6
|
ZNF597 is a maternally expressed imprinted gene in the Holstein breed. Theriogenology 2020; 143:133-138. [PMID: 31874365 DOI: 10.1016/j.theriogenology.2019.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/24/2019] [Accepted: 12/14/2019] [Indexed: 11/22/2022]
Abstract
Genomic imprinting is an epigenetic phenomenon that leads to the preferential expression of genes from either the paternal or maternal allele. Imprinted genes play important roles in mammalian growth and development and a central role in placental function. ZNF597 and NAA60 are two paternally imprinted genes in the human ZNF597-NAA60 imprinted locus, both of which show biallelic expression in the mouse, but their imprinting status in cattle is still unknown. In this study, we examined the allelic expression of ZNF597 and NAA60 in adult bovine placental and somatic tissues. By comparing the mRNA-based genotypes with the genomic DNA-based genotypes, we identified monoallelic expression of ZNF597 in the placenta and in seven other tissues, including the cerebrum, heart, liver, spleen, lung, kidney, and muscle. Nevertheless, analysis revealed biallelic expression of the NAA60 gene in these tissues. Moreover, we tested the imprinting status of ZNF597 and confirmed that the maternal allele is expressed in the bovine placenta. To determine the role of DNA methylation in regulating monoallelic/imprinted expression of bovine ZNF597, the methylation status of two CpG-enriched regions in the bovine ZNF597-NAA60 locus was analyzed using the bisulfite sequencing method. Differentially methylated regions were detected on ten CpG loci in the bovine ZNF597 promoter region. In summary, the bovine ZNF597 gene is a maternally expressed gene, and its expression is regulated by DNA methylation, whereas the NAA60 gene is not imprinted in cattle.
Collapse
|
7
|
Monteagudo-Sánchez A, Garin I, de Nanclares GP, Monk D. The Use of Methylation-Sensitive Multiplex Ligation-Dependent Probe Amplification for Quantification of Imprinted Methylation. Methods Mol Biol 2019; 1766:109-121. [PMID: 29605849 DOI: 10.1007/978-1-4939-7768-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Imprinting disorders are a group of congenital diseases that can result from multiple mechanisms affecting imprinted gene dosage including cytogenetic aberration and epigenetic anomalies. Quantification of CpG methylation and correct copy-number calling is required for molecular diagnosis. Methylation-sensitive multiplex ligation-dependent probe amplification (MS-MLPA) is a multiplex method that accurately measures both parameters in a single assay. This technique relies upon the ligation of MLPA probe oligonucleotides and digestion of the genomic DNA-probe hybrid complexes with the Hha1 methylation-sensitive restriction endonuclease prior to fluorescent PCR amplification with a single primer pair. Since each targeted probe contains stuffer sequence of varying length, each interrogated position is visualized as an amplicon of different size upon capillary electrophoresis.
Collapse
Affiliation(s)
- Ana Monteagudo-Sánchez
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran and Reynals, Barcelona, Spain
| | - Intza Garin
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, OSI Araba-Txagorritxu, Vitoria-Gasteiz, Spain
| | - Guiomar Perez de Nanclares
- Molecular (Epi)Genetics Laboratory, BioAraba National Health Institute, OSI Araba-Txagorritxu, Vitoria-Gasteiz, Spain
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran and Reynals, Barcelona, Spain.
| |
Collapse
|
8
|
Chaves TF, Oliveira LF, Ocampos M, Barbato IT, de Luca GR, Barbato Filho JH, de Camargo Pinto LL, Bernardi P, Maris AF. Long contiguous stretches of homozygosity detected by chromosomal microarrays (CMA) in patients with neurodevelopmental disorders in the South of Brazil. BMC Med Genomics 2019; 12:50. [PMID: 30866944 PMCID: PMC6417136 DOI: 10.1186/s12920-019-0496-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/28/2019] [Indexed: 01/14/2023] Open
Abstract
Background Currently, chromosomal microarrays (CMA) are recommended as first-tier test in the investigation of developmental disorders to examine copy number variations. The modern platforms also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH) also named runs of homozygosity (ROH). LCHS are chromosomal segments resulting from complete or segmental chromosomal homozygosity, which may be indicative of uniparental disomy (UPD), consanguinity, as well as replicative DNA repair events, however also are common findings in normal populations. Knowing common LCSH of a population, which probably represent ancestral haplotypes of low-recombination regions in the genome, facilitates the interpretation of LCSH found in patients, allowing to prioritize those with possible clinical significance. However, population records of ancestral haplotype derived LCSH by SNP arrays are still scarce, particularly for countries such as Brazil where even for the clinic, microarrays that include SNPs are difficult to request due to their high cost. Methods In this study, we evaluate the frequencies and implications of LCSH detected by Affymetrix CytoScan® HD or 750 K platforms in 430 patients with neurodevelopmental disorders in southern Brazil. LCSH were analyzed in the context of pathogenic significance and also explored to identify ancestral haplotype derived LCSH. The criteria for considering a region as LCSH was homozygosis ≥3 Mbp on an autosome. Results In 95% of the patients, at least one LCSH was detected, a total of 1478 LCSH in 407 patients. In 2.6%, the findings were suggestive of UPD. For about 8.5% LCSH suggest offspring from first to fifth grade, more likely to have a clinical impact. Considering recurrent LCSH found at a frequency of 5% or more, we outline 11 regions as potentially representing ancestral haplotypes in our population. The region most involved with homozygosity was 16p11.2p11.1 (49%), followed by 1q21.2q21.3 (21%), 11p11.2p11.12 (19%), 3p21.31p21.2 (16%), 15q15 1q33p32.3 (12%), 2q11.1q12.1 (9%), 1p33p32.3 (6%), 20q11.21q11.23 (6%), 10q22.1q23.31 (5%), 6p22.2p22 (5%), and 7q11.22q11.23 (5%). Conclusions In this work, we show the importance and usefulness of interpreting LCSH in the results of CMA wich incorporate SNPs.
Collapse
Affiliation(s)
- Tiago Fernando Chaves
- Biologist, PhD Student in Cell Biology and Development, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Luan Freitas Oliveira
- Biomedic, PhD Student in Cell Biology and Development, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Maristela Ocampos
- Biologist, PhD in Biotechnology and Molecular Biology, Laboratory Neurogene, Florianópolis, SC, Brazil
| | - Ingrid Tremel Barbato
- Biologist and MSc in Chemical Engineering, Laboratory Neurogene, Florianópolis, SC, Brazil
| | - Gisele Rozone de Luca
- Medical Neuropediatrist, Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil
| | | | | | - Pricila Bernardi
- Medical Geneticist, University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Biologist, PhD in Molecular Biology and Genetics, University Professor in the Department of Cell Biology, Embryology and Genetics, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| |
Collapse
|
9
|
Inoue T, Yagasaki H, Nishioka J, Nakamura A, Matsubara K, Narumi S, Nakabayashi K, Yamazawa K, Fuke T, Oka A, Ogata T, Fukami M, Kagami M. Molecular and clinical analyses of two patients with UPD(16)mat detected by screening 94 patients with Silver-Russell syndrome phenotype of unknown aetiology. J Med Genet 2018; 56:413-418. [PMID: 30242100 PMCID: PMC6582712 DOI: 10.1136/jmedgenet-2018-105463] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 01/06/2023]
Abstract
Background Recently, a patient with maternal uniparental disomy of chromosome 16 (UPD(16)mat) presenting with Silver-Russell syndrome (SRS) phenotype was reported. SRS is characterised by growth failure and dysmorphic features. Objective To clarify the prevalence of UPD(16)mat in aetiology-unknown patients with SRS phenotype and phenotypic differences between UPD(16)mat and SRS. Methods We studied 94 patients with SRS phenotype of unknown aetiology. Sixty-three satisfied the Netchine-Harbison clinical scoring system (NH-CSS) criteria, and 25 out of 63 patients showed both protruding forehead and relative macrocephaly (clinical SRS). The remaining 31 patients met only three NH-CSS criteria, but were clinically suspected as having SRS. To detect UPD(16)mat, we performed methylation analysis for the ZNF597:TSS-differentially methylated region (DMR) on chromosome 16 and subsequently performed microsatellite, SNP array and exome analyses in the patients with hypomethylated ZNF597:TSS-DMR. Results We identified two patients (2.1%) with a mixture of maternal isodisomy and heterodisomy of chromosome 16 in 94 aetiology-unknown patients with SRS phenotype. Both patients exhibited preterm birth and prenatal and postnatal growth failure. The male patient had ventricular septal defect and hypospadias. Whole-exome sequencing detected no gene mutations related to their phenotypes. Conclusion We suggest considering genetic testing for UPD(16)mat in SRS phenotypic patients without known aetiology.
Collapse
Affiliation(s)
- Takanobu Inoue
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Hideaki Yagasaki
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Chuo, Japan
| | - Junko Nishioka
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akira Oka
- Department of Pediatrics, University of Tokyo, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| |
Collapse
|
10
|
Gillessen-Kaesbach G, Albrecht B, Eggermann T, Elbracht M, Mitter D, Morlot S, van Ravenswaaij-Arts C, Schulz S, Strobl-Wildemann G, Buiting K, Beygo J. Molecular and clinical studies in 8 patients with Temple syndrome. Clin Genet 2018; 93:1179-1188. [DOI: 10.1111/cge.13244] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
| | - B. Albrecht
- Institut für Humangenetik; Universitätsklinikum Essen, Universität Duisburg-Essen; Essen Germany
| | - T. Eggermann
- Institute of Human Genetics; RWTH Aachen University; Aachen Germany
| | - M. Elbracht
- Institute of Human Genetics; RWTH Aachen University; Aachen Germany
| | - D. Mitter
- Institute of Human Genetics
- ; University of Leipzig Hospitals and Clinics; Leipzig Germany
| | - S. Morlot
- Department of Human Genetics; Hannover Medical School; Hannover Germany
| | - C.M.A. van Ravenswaaij-Arts
- Department of Genetics; University of Groningen, University Medical Centre Groningen; Groningen The Netherlands
| | - S. Schulz
- Center of Human Genetics; Jena University Hospital; Jena Germany
| | | | - K. Buiting
- Institut für Humangenetik; Universitätsklinikum Essen, Universität Duisburg-Essen; Essen Germany
| | - J. Beygo
- Institut für Humangenetik; Universitätsklinikum Essen, Universität Duisburg-Essen; Essen Germany
| |
Collapse
|
11
|
Bens S, Luedeke M, Richter T, Graf M, Kolarova J, Barbi G, Lato K, Barth TF, Siebert R. Mosaic genome-wide maternal isodiploidy: an extreme form of imprinting disorder presenting as prenatal diagnostic challenge. Clin Epigenetics 2017; 9:111. [PMID: 29046733 PMCID: PMC5640928 DOI: 10.1186/s13148-017-0410-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/25/2017] [Indexed: 11/10/2022] Open
Abstract
Background Uniparental disomy of certain chromosomes are associated with a group of well-known genetic syndromes referred to as imprinting disorders. However, the extreme form of uniparental disomy affecting the whole genome is usually not compatible with life, with the exception of very rare cases of patients with mosaic genome-wide uniparental disomy reported in the literature. Results We here report on a fetus with intrauterine growth retardation and malformations observed on prenatal ultrasound leading to invasive prenatal testing. By cytogenetic (conventional karyotyping), molecular cytogenetic (QF-PCR, FISH, array), and methylation (MS-MLPA) analyses of amniotic fluid, we detected mosaicism for one cell line with genome-wide maternal uniparental disomy and a second diploid cell line of biparental inheritance with trisomy X due to paternal isodisomy X. As expected for this constellation, we observed DNA methylation changes at all imprinted loci investigated. Conclusions This report adds new information on phenotypic outcome of mosaic genome-wide maternal uniparental disomy leading to an extreme form of multilocus imprinting disturbance. Moreover, the findings highlight the technical challenges of detecting these rare chromosome disorders prenatally. Electronic supplementary material The online version of this article (10.1186/s13148-017-0410-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Susanne Bens
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Manuel Luedeke
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Tanja Richter
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Melanie Graf
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Gotthold Barbi
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Krisztian Lato
- Department of Obstetrics and Gynecology, University of Ulm & Ulm University Hospital, Ulm, Germany
| | - Thomas F Barth
- Institute of Pathology, University of Ulm & Ulm University Hospital, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm & Ulm University Hospital, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| |
Collapse
|
12
|
Griffin NG, Cronin KD, Walley NM, Hulette CM, Grant GA, Mikati MA, LaBreche HG, Rehder CW, Allen AS, Crino PB, Heinzen EL. Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001735. [PMID: 28864461 PMCID: PMC5593155 DOI: 10.1101/mcs.a001735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome. Functional studies were performed to evaluate the molecular consequences of candidate disease-causing variants. Both HME patients evaluated were found to have likely disease-causing variants in DNA extracted from brain tissue but not in buccal swab or leukocyte DNA, consistent with a somatic mutational mechanism. In the first case, a previously identified disease-causing somatic single nucleotide in MTOR was identified. In the second case, we detected an overrepresentation of the alleles inherited from the mother on Chromosome 16 in brain tissue DNA only, indicative of somatic uniparental disomy (UPD) of the p-arm of Chromosome 16. Using methylation analyses, an imprinted locus on 16p spanning ZNF597 was identified, which results in increased expression of ZNF597 mRNA and protein in the brain tissue of the second case. Enhanced mTOR signaling was observed in tissue specimens from both patients. We speculate that overexpression of maternally expressed ZNF597 led to aberrant hemispheric development in the patient with somatic UPD of Chromosome 16p possibly through modulation of mTOR signaling.
Collapse
Affiliation(s)
- Nicole G Griffin
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Kenneth D Cronin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Nicole M Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christine M Hulette
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Neurobiology, Duke University, Durham, North Carolina 27708, USA
| | | | | | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina 27710, USA
| | - Peter B Crino
- Department of Neurology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
| |
Collapse
|
13
|
Meyer R, Soellner L, Begemann M, Dicks S, Fekete G, Rahner N, Zerres K, Elbracht M, Eggermann T. Targeted Next Generation Sequencing Approach in Patients Referred for Silver-Russell Syndrome Testing Increases the Mutation Detection Rate and Provides Decisive Information for Clinical Management. J Pediatr 2017; 187:206-212.e1. [PMID: 28529015 DOI: 10.1016/j.jpeds.2017.04.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/09/2017] [Accepted: 04/10/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To investigate the contribution of differential diagnoses to the mutation spectrum of patients referred for Silver-Russell syndrome (SRS) testing. STUDY DESIGN Forty-seven patients referred for molecular testing for SRS were examined after exclusion of one of the SRS-associated alterations. After clinical classification, a targeted next generation sequencing approach comprising 25 genes associated with other diagnoses or postulated as SRS candidate genes was performed. RESULTS By applying the Netchine-Harbinson clinical scoring system, indication for molecular testing for SRS was confirmed in 15 out of 47 patients. In 4 out of these 15 patients, disease-causing variants were found in genes associated with other diagnoses. These patients carried mutations associated with Bloom syndrome, Mulibrey nanism, KBG syndrome, or IGF1R-associated short stature. We could not detect any pathogenic mutation in patients with a negative clinical score. CONCLUSIONS Some of the differential diagnoses detected in the cohort presented here have a major impact on clinical management. Therefore, we emphasize that the molecular defects associated with these clinical pictures should be excluded before the clinical diagnosis "SRS" is made. Finally, we could show that a broad molecular approach including the differential diagnoses of SRS increases the detection rate.
Collapse
Affiliation(s)
- Robert Meyer
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany
| | - Lukas Soellner
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany
| | - Severin Dicks
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany
| | - György Fekete
- Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Nils Rahner
- University Clinic Düsseldorf, Institute of Human Genetics, Düsseldorf, Germany
| | - Klaus Zerres
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, Technical University Aachen (Rheinisch-Westfälische Technische Hochschule), Aachen, Germany.
| |
Collapse
|
14
|
Beygo J, Küchler A, Gillessen-Kaesbach G, Albrecht B, Eckle J, Eggermann T, Gellhaus A, Kanber D, Kordaß U, Lüdecke HJ, Purmann S, Rossier E, van de Nes J, van der Werf IM, Wenzel M, Wieczorek D, Horsthemke B, Buiting K. New insights into the imprinted MEG8-DMR in 14q32 and clinical and molecular description of novel patients with Temple syndrome. Eur J Hum Genet 2017. [PMID: 28635951 DOI: 10.1038/ejhg.2017.91] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The chromosomal region 14q32 contains several imprinted genes, which are expressed either from the paternal (DLK1 and RTL1) or the maternal (MEG3, RTL1as and MEG8) allele only. Imprinted expression of these genes is regulated by two differentially methylated regions (DMRs), the germline DLK1/MEG3 intergenic (IG)-DMR (MEG3/DLK1:IG-DMR) and the somatic MEG3-DMR (MEG3:TSS-DMR), which are methylated on the paternal and unmethylated on the maternal allele. Disruption of imprinting in the 14q32 region results in two clinically distinct imprinting disorders, Temple syndrome (TS14) and Kagami-Ogata syndrome (KOS14). Another DMR with a yet unknown function is located in intron 2 of MEG8 (MEG8-DMR, MEG8:Int2-DMR). In contrast to the IG-DMR and the MEG3-DMR, this somatic DMR is methylated on the maternal chromosome and unmethylated on the paternal chromosome. We have performed extensive methylation analyses by deep bisulfite sequencing of the IG-DMR, MEG3-DMR and MEG8-DMR in different prenatal tissues including amniotic fluid cells and chorionic villi. In addition, we have studied the methylation pattern of the MEG8-DMR in different postnatal tissues. We show that the MEG8-DMR is hypermethylated in each of 13 non-deletion TS14 patients (seven newly identified and six previously published patients), irrespective of the underlying molecular cause, and is always hypomethylated in the four patients with KOS14, who have different deletions not encompassing the MEG8-DMR itself. The size and the extent of the deletions and the resulting methylation pattern suggest that transcription starting from the MEG3 promoter may be necessary to establish the methylation imprint at the MEG8-DMR.
Collapse
Affiliation(s)
- Jasmin Beygo
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Küchler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | | | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Jonas Eckle
- Sozialpädiatrisches Zentrum, St. Elisabeth-Stiftung, Ravensburg, Germany
| | | | - Alexandra Gellhaus
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Essen, Essen, Germany
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Ulrike Kordaß
- MVZ für Humangenetik und Molekularpathologie Rostock, Zweigstelle Greifswald, Greifswald, Germany
| | - Hermann-Josef Lüdecke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Institut für Humangenetik, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Sabine Purmann
- Institut für Humangenetik, Universität zu Lübeck, Lübeck, Germany
| | - Eva Rossier
- Institut für Medizinische Genetik und angewandte Genomik, Universiät Tübingen, Tübingen, Germany.,Genetikum Stuttgart, Stuttgart, Germany
| | - Johannes van de Nes
- Institute of Neuropathology, Faculty of Medicine, University Duisburg-Essen, Essen, Germany.,Institute of Pathology, University of Bochum, Bochum, Germany
| | | | | | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Institut für Humangenetik, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| |
Collapse
|
15
|
Scheuvens R, Begemann M, Soellner L, Meschede D, Raabe-Meyer G, Elbracht M, Schubert R, Eggermann T. Maternal uniparental disomy of chromosome 16 [upd(16)mat]: clinical features are rather caused by (hidden) trisomy 16 mosaicism than by upd(16)mat itself. Clin Genet 2017; 92:45-51. [DOI: 10.1111/cge.12958] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 02/04/2023]
Affiliation(s)
- R. Scheuvens
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | - M. Begemann
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | - L. Soellner
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | | | | | - M. Elbracht
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| | | | - T. Eggermann
- Institute of Human Genetics; University Hospital, Technical University (RWTH) Aachen; Aachen Germany
| |
Collapse
|
16
|
Kagami M, Matsubara K, Nakabayashi K, Nakamura A, Sano S, Okamura K, Hata K, Fukami M, Ogata T. Genome-wide multilocus imprinting disturbance analysis in Temple syndrome and Kagami-Ogata syndrome. Genet Med 2016; 19:476-482. [PMID: 27632690 PMCID: PMC5392596 DOI: 10.1038/gim.2016.123] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 07/12/2016] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Recent studies have identified multilocus imprinting disturbances (MLIDs) in a subset of patients with imprinting diseases (IDs) caused by epimutations. We examined MLIDs in patients with Temple syndrome (TS14) and Kagami-Ogata syndrome (KOS14). METHODS We studied four TS14 patients (patients 1-4) and five KOS14 patients (patients 5-9) with epimutations. We performed HumanMethylation450 BeadChip (HM450k) analysis for 43 differentially methylated regions (DMRs) (753 CpG sites) and pyrosequencing for 12 DMRs (62 CpG sites) using leukocyte genomic DNA (Leu-gDNA) of patients 1-9, and performed HM450k analysis for 43 DMRs (a slightly different set of 753 CpG sites) using buccal cell gDNA (Buc-gDNA) of patients 1, 3, and 4. We also performed mutation analysis for six causative and candidate genes for MLIDs and quantitative expression analysis using immortalized lymphocytes in MLID-positive patients. RESULTS Methylation analysis showed hypermethylated ZDBF2-DMR and ZNF597/NAA60-DMR, hypomethylated ZNF597-DMR in both Leu-gDNA and Buc-gDNA, and hypomethylated PPIEL-DMR in Buc-gDNA of patient 1, and hypermethylated GNAS-A/B-DMR in Leu-gDNA of patient 3. No mutations were detected in the six genes for MLIDs. Expression patterns of ZDBF2, ZNF597, and GNAS-A/B were consistent with the identified MLIDs. CONCLUSION This study indicates the presence of MLIDs in TS14 patients but not in KOS14 patients.Genet Med 19 4, 476-482.
Collapse
Affiliation(s)
- Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| |
Collapse
|