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Higashimoto K, Sun F, Imagawa E, Saida K, Miyake N, Hara S, Yatsuki H, Kubiura-Ichimaru M, Fujita A, Mizuguchi T, Matsumoto N, Soejima H. Whole-exome sequencing reveals causative genetic variants for several overgrowth syndromes in molecularly negative Beckwith-Wiedemann spectrum. J Med Genet 2024; 61:590-594. [PMID: 38228391 DOI: 10.1136/jmg-2023-109621] [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: 09/07/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Background Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder caused by (epi)genetic alterations at 11p15. Because approximately 20% of patients test negative via molecular testing of peripheral blood leukocytes, the concept of Beckwith-Wiedemann spectrum (BWSp) was established to encompass a broader cohort with diverse and overlapping phenotypes. The prevalence of other overgrowth syndromes concealed within molecularly negative BWSp remains unexplored. Methods We conducted whole-exome sequencing (WES) on 69 singleton patients exhibiting molecularly negative BWSp. Variants were confirmed by Sanger sequencing or quantitative genomic PCR. We compared BWSp scores and clinical features between groups with classical BWS (cBWS), atypical BWS or isolated lateralised overgrowth (aBWS+ILO) and overgrowth syndromes identified via WES. Results Ten patients, one classified as aBWS and nine as cBWS, showed causative gene variants for Simpson-Golabi-Behmel syndrome (five patients), Sotos syndrome (two), Imagawa-Matsumoto syndrome (one), glycosylphosphatidylinositol biosynthesis defect 11 (one) or 8q duplication/9p deletion (one). BWSp scores did not distinguish between cBWS and other overgrowth syndromes. Birth weight and height in other overgrowth syndromes were significantly larger than in aBWS+ILO and cBWS, with varying intergroup frequencies of clinical features. Conclusion Molecularly negative BWSp encapsulates other syndromes, and considering both WES and clinical features may facilitate accurate diagnosis.
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Affiliation(s)
- Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Feifei Sun
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, China
| | - Eri Imagawa
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Satoshi Hara
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Musashi Kubiura-Ichimaru
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan
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Navarrete-Meneses MP, Ochoa-Mellado I, Gutiérrez-Álvarez R, Martínez-Anaya D, Juárez-Figueroa U, Durán-McKinster C, Lieberman-Hernández E, Yokoyama-Rebollar E, Gómez-Carmona S, Del Castillo-Ruiz V, Pérez-Vera P, Salas-Labadía C. Cytogenomic characterization of small supernumerary marker chromosomes in patients with pigmentary mosaicism. Front Genet 2024; 15:1356786. [PMID: 38711916 PMCID: PMC11071077 DOI: 10.3389/fgene.2024.1356786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/21/2024] [Indexed: 05/08/2024] Open
Abstract
Introduction The combination of gene content on the marker chromosome, chromosomal origin, level of mosaicism, origin mechanism (chromothripsis), and uniparental disomy can influence the final characterization of sSMCs. Several chromosomal aberrations, including sSMCs, have been observed in 30%-60% of patients with pigmentary mosaicism, and in more than 80%, chromosomal abnormalities are present in the mosaic state. In patients with pigmentary mosaicism the most representative chromosomes involved in sSMCs are 3, 5, 6, 9, 10, 13, 15, 18, 20, and X. In this study, we included the complete clinical, cytogenetic, and molecular characterization of seven patients with pigmentary mosaicism associated with the presence of SMCs of different chromosomal origins. Methods The patients were diagnosed by the Genetics and Dermatology Department of three different hospitals. Cytogenetic and FISH analyses were performed on peripheral blood, light skin, and dark skin. FISH analysis was performed using different probes, depending on the marker chromosome description. Different array analysis was performed. Results To date, of the seven cases studied, the chromosomal origins of six were successfully identified by FISH or array analysis. The chromosomes involved in SMCs were 6, 9, 15, and 18, X. The most frequently found was the centric minute structure. Discussion To date, this group of seven patients constitutes the largest clinical and cytogenetically finely described study of cases with pigmentary mosaicism associated with sSMCs. Undoubtedly, analysis of the two skin types is a fundamental part of our study, as numerical differences may occur in the cell lines found in each skin type. The knowledge generated in this study will help delineate a very heterogeneous entity more accurately, and in the future, analyzing more patients with PM will likely establish a more definite association with the presence of this genetic alteration.
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Affiliation(s)
- M. P. Navarrete-Meneses
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - I. Ochoa-Mellado
- Genética Humana, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - R. Gutiérrez-Álvarez
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - D. Martínez-Anaya
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - U. Juárez-Figueroa
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - C. Durán-McKinster
- Departamento de Dermatología, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | | | - S. Gómez-Carmona
- Departamento de Genética Médica, Centro de Rehabilitación e Inclusión Infantil Teletón, Cancún, México
| | | | - P. Pérez-Vera
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
| | - C. Salas-Labadía
- Genetic and cancer Laboratory, National Institute of Pediatrics (Mexico), Mexico City, Mexico
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da Costa SS, Fishman V, Pinheiro M, Rodrigueiro A, Sanseverino MT, Zielinsky P, Carvalho CMB, Rosenberg C, Krepischi ACV. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. Chromosome Res 2024; 32:6. [PMID: 38504027 DOI: 10.1007/s10577-024-09750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, genome sequencing (GS), RNA-seq, and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined GS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints matches the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2 Mb region on chromosome 9 and a SINE element insertion at the more distal breakpoint. Interestingly, this genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by both RNA-seq and Sanger sequencing on blood samples from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype-phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p24 segregating with a familial congenital heart defect, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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Affiliation(s)
- Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Veniamin Fishman
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mara Pinheiro
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Maria Teresa Sanseverino
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- School of Medicine, Pontifícia Universidade Catolica do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Paulo Zielinsky
- Department of Pediatrics and Childcare, Federal University of the Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.
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4
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Costa SS, Fishman V, Pinheiro M, Rodrigueiro A, Sanseverino MT, Zielinsky P, Carvalho CMB, Rosenberg C, Krepischi ACV. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. RESEARCH SQUARE 2023:rs.3.rs-3740005. [PMID: 38168413 PMCID: PMC10760254 DOI: 10.21203/rs.3.rs-3740005/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis, and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, whole-genome sequencing (WGS), RNA-seq and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined WGS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints match the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2Mb region on chromosome 9 with a SINE element insertion at the more distal breakpoint. Interestingly, this hypothesized genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by RNA-seq on blood from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype-phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p segregating with a familial congenital clinical trait, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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Nguyen JP, Arthur TD, Fujita K, Salgado BM, Donovan MKR, Matsui H, Kim JH, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk. Nat Commun 2023; 14:6928. [PMID: 37903777 PMCID: PMC10616100 DOI: 10.1038/s41467-023-42560-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023] Open
Abstract
The impact of genetic regulatory variation active in early pancreatic development on adult pancreatic disease and traits is not well understood. Here, we generate a panel of 107 fetal-like iPSC-derived pancreatic progenitor cells (iPSC-PPCs) from whole genome-sequenced individuals and identify 4065 genes and 4016 isoforms whose expression and/or alternative splicing are affected by regulatory variation. We integrate eQTLs identified in adult islets and whole pancreas samples, which reveal 1805 eQTL associations that are unique to the fetal-like iPSC-PPCs and 1043 eQTLs that exhibit regulatory plasticity across the fetal-like and adult pancreas tissues. Colocalization with GWAS risk loci for pancreatic diseases and traits show that some putative causal regulatory variants are active only in the fetal-like iPSC-PPCs and likely influence disease by modulating expression of disease-associated genes in early development, while others with regulatory plasticity likely exert their effects in both the fetal and adult pancreas by modulating expression of different disease genes in the two developmental stages.
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Affiliation(s)
- Jennifer P Nguyen
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Arthur
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kyohei Fujita
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bianca M Salgado
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Hiroko Matsui
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Ji Hyun Kim
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, South Korea
| | | | - Matteo D'Antonio
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute of Genomic Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA.
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Ng JK, Turner TN. HAT: de novo variant calling for highly accurate short-read and long-read sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525940. [PMID: 36747667 PMCID: PMC9900919 DOI: 10.1101/2023.01.27.525940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Motivation de novo variant (DNV) calling is challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genetics studies (e.g., autism, epilepsy). Results HAT is a workflow to detect DNVs from short-read and long read sequencing data. This workflow begins with aligned read data (i.e., CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from short-read whole-exome sequencing, short-read whole-genome sequencing, and highly accurate long-read sequencing data.
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Affiliation(s)
- Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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