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Mazzonetto PC, Villela D, Krepischi ACV, Pierry PM, Bonaldi A, Almeida LGD, Paula MG, Bürger MC, de Oliveira AG, Fonseca GGG, Giugliani R, Riegel-Giugliani M, Bertola D, Yamamoto GL, Passos-Bueno MR, Campos GDS, Machado ACD, Mazzeu JF, Perrone E, Zechi-Ceide RM, Kokitsu-Nakata NM, Vieira TP, Steiner CE, Gil-da-Silva-Lopes VL, Vieira DKR, Boy R, de Pina-Neto JM, Scapulatempo-Neto C, Milanezi F, Rosenberg C. Low-pass whole genome sequencing as a cost-effective alternative to chromosomal microarray analysis for low- and middle-income countries. Am J Med Genet A 2024:e63802. [PMID: 38924610 DOI: 10.1002/ajmg.a.63802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%-20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Mariluce Riegel-Giugliani
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Débora Bertola
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Gabriele da Silva Campos
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Dantas Machado
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana F Mazzeu
- Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Eduardo Perrone
- Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roseli M Zechi-Ceide
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Nancy M Kokitsu-Nakata
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Daniela Koeller Rodrigues Vieira
- Municipal Secretary of Health of Angra dos Reis, Rio de Janeiro, Brazil
- National Institute of Women, Children and Adolescents Health Fernandes Figueira/Oswaldo Cruz Foundation (IFF/FIOCRUZ), Rio de Janeiro, Brazil
| | - Raquel Boy
- State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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Kerkhof J, Rastin C, Levy MA, Relator R, McConkey H, Demain L, Dominguez-Garrido E, Kaat LD, Houge SD, DuPont BR, Fee T, Fletcher RS, Gokhale D, Haukanes BI, Henneman P, Hilton S, Hilton BA, Jenkinson S, Lee JA, Louie RJ, Motazacker MM, Rzasa J, Stevenson RE, Plomp A, van der Laan L, van der Smagt J, Walden KK, Banka S, Mannens M, Skinner SA, Friez MJ, Campbell C, Tedder ML, Alders M, Sadikovic B. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases. Genet Med 2024; 26:101075. [PMID: 38251460 DOI: 10.1016/j.gim.2024.101075] [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: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
PURPOSE This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.
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Affiliation(s)
- Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sofia Douzgou Houge
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | | | | | | | - David Gokhale
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Bjørn Ivar Haukanes
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | | | - M Mahdi Motazacker
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Astrid Plomp
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jasper van der Smagt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | | | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Marcel Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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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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Mazzonetto PC, Villela D, da Costa SS, Krepischi ACV, Milanezi F, Migliavacca MP, Pierry PM, Bonaldi A, Almeida LGD, De Souza CA, Kroll JE, Paula MG, Guarischi-Sousa R, Scapulatempo-Neto C, Rosenberg C. Low-pass whole genome sequencing is a reliable and cost-effective approach for copy number variant analysis in the clinical setting. Ann Hum Genet 2024; 88:113-125. [PMID: 37807935 DOI: 10.1111/ahg.12532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics. MATERIALS AND METHODS DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism. RESULTS All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA. DISCUSSION Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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Chaves TF, Ocampos M, Barbato IT, de Camargo Pinto LL, de Luca GR, Barbato Filho JH, Bernardi P, Costa Netto Muniz Y, Francesca Maris A. A cohort study of neurodevelopmental disorders and/or congenital anomalies using high resolution chromosomal microarrays in southern Brazil highlighting the significance of ASD. Sci Rep 2024; 14:3762. [PMID: 38355898 PMCID: PMC10867078 DOI: 10.1038/s41598-024-54385-2] [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: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 02/16/2024] Open
Abstract
Chromosomal microarray (CMA) is the reference in evaluation of copy number variations (CNVs) in individuals with neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and/or autism spectrum disorder (ASD), which affect around 3-4% of the world's population. Modern platforms for CMA, also include probes for single nucleotide polymorphisms (SNPs) that detect homozygous regions in the genome, such as long contiguous stretches of homozygosity (LCSH). These regions result from complete or segmental chromosomal homozygosis and may be indicative of uniparental disomy (UPD), inbreeding, population characteristics, as well as replicative DNA repair events. In this retrospective study, we analyzed CMA reading files requested by geneticists and neurologists for diagnostic purposes along with available clinical data. Our objectives were interpreting CNVs and assess the frequencies and implications of LCSH detected by Affymetrix CytoScan HD (41%) or 750K (59%) platforms in 1012 patients from the south of Brazil. The patients were mainly children with NDDs and/or congenital anomalies (CAs). A total of 206 CNVs, comprising 132 deletions and 74 duplications, interpreted as pathogenic, were found in 17% of the patients in the cohort and across all chromosomes. Additionally, 12% presented rare variants of uncertain clinical significance, including LPCNVs, as the only clinically relevant CNV. Within the realm of NDDs, ASD carries a particular importance, owing to its escalating prevalence and its growing repercussions for individuals, families, and communities. ASD was one clinical phenotype, if not the main reason for referral to testing, for about one-third of the cohort, and these patients were further analyzed as a sub-cohort. Considering only the patients with ASD, the diagnostic rate was 10%, within the range reported in the literature (8-21%). It was higher (16%) when associated with dysmorphic features and lower (7%) for "isolated" ASD (without ID and without dysmorphic features). In 953 CMAs of the whole cohort, LCSH (≥ 3 Mbp) were analyzed not only for their potential pathogenic significance but were also explored to identify common LCSH in the South Brazilians population. CMA revealed at least one LCSH in 91% of the patients. For about 11.5% of patients, the LCSH suggested consanguinity from the first to the fifth degree, with a greater probability of clinical impact, and in 2.8%, they revealed a putative UPD. LCSH found at a frequency of 5% or more were considered common LCSH in the general population, allowing us to delineate 10 regions as potentially representing ancestral haplotypes of neglectable clinical significance. The main referrals for CMA were developmental delay (56%), ID (33%), ASD (33%) and syndromic features (56%). Some phenotypes in this population may be predictive of a higher probability of indicating a carrier of a pathogenic CNV. Here, we present the largest report of CMA data in a cohort with NDDs and/or CAs from the South of Brazil. We characterize the rare CNVs found along with the main phenotypes presented by each patient and show the importance and usefulness of LCSH interpretation in CMA results that incorporate SNPs, as well as we illustrate the value of CMA to investigate CNV in ASD.
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Affiliation(s)
- Tiago Fernando Chaves
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
| | - Maristela Ocampos
- Laboratory Neurogene (former), Florianopolis, SC, Brazil
- Mercolab Diagnóstica (actual), Florianopolis, SC, Brazil
| | | | | | | | | | - Priscila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
| | - Yara Costa Netto Muniz
- Laboratório de Polimorfismos Genéticos (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Angelica Francesca Maris
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil.
- Children's Hospital Joana de Gusmão, Florianópolis, SC, Brazil.
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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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