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Cheng D, Ibrahim H, Luo K, Gu Y, Xie P, Xiao Y, Cai J, Wu X, Lin G, Tan Y, Hu L. Characterization of cryptic complex chromosome rearrangements in balanced chromosomal rearrangement carriers and their PGT-SR clinical outcome assessments. Sci Rep 2024; 14:20705. [PMID: 39237551 PMCID: PMC11377696 DOI: 10.1038/s41598-024-70566-5] [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: 04/05/2024] [Accepted: 08/19/2024] [Indexed: 09/07/2024] Open
Abstract
Several reports have presented that balanced chromosomal rearrangements (BCRs) carriers with normal phenotypes may be carriers of complex rearrangements. However, the incidence and PGT clinical outcomes of cryptic complex chromosome rearrangements (CCCRs) in individuals with BCRs is remain unknown. We recruited a cohort of 1,264 individuals with BCR carriers from 2016 to 2021 at the Reproductive and Genetic Hospital of CITIC Xiangya. Peripheral blood was collected for karyotyping and genomic DNA extraction and the PGT-SR clinical outcomes of CCCRs carriers were analyzed and compared with those of BCR carriers. Our findings revealed that 3.6% (45/1,264) of BCR carriers had CCCRs, involving 3-25 breakpoints on 1-3 chromosomes. Furthermore, when mate-pair sequencing was employed, 63.3% (19/30) of CCCR carriers were found to have chromosome rearrangements that were different from those identified by the MicroSeq technique. And the transferable embryo rate of CCCR carriers with 3 chromosomes was significantly lower than that of CCCR carriers with only 1-2 chromosomes. In this research, we revealed that some of the BCR carriers were actually CCCR carriers, and the prognosis of PGT in CCCR carriers with one or two chromosomes is better than that of CCCR carriers with three chromosomes.
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Affiliation(s)
- Dehua Cheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410013, Hunan, China
| | - Hebatallah Ibrahim
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Keli Luo
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410013, Hunan, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Yifan Gu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410013, Hunan, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Pingyuan Xie
- Hunan Normal University School of Medicine, Changsha, 410013, China
- Hunan Guangxiu Hospital, Changsha, 410013, Hunan, China
| | - Yanqin Xiao
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Jingpeng Cai
- Hunan Guangxiu Hospital, Changsha, 410013, Hunan, China
| | - Xianhong Wu
- Hunan Guangxiu Hospital, Changsha, 410013, Hunan, China
| | - Ge Lin
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410013, Hunan, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Yueqiu Tan
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410013, Hunan, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
| | - Liang Hu
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410013, Hunan, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
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Sund KL, Liu J, Lee J, Garbe J, Abdelhamed Z, Maag C, Hallinan B, Wu SW, Sperry E, Deshpande A, Stottmann R, Smolarek TA, Dyer LM, Hestand MS. Long-read sequencing and optical genome mapping identify causative gene disruptions in noncoding sequence in two patients with neurologic disease and known chromosome abnormalities. Am J Med Genet A 2024:e63818. [PMID: 39041659 DOI: 10.1002/ajmg.a.63818] [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: 03/07/2024] [Revised: 06/12/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024]
Abstract
Despite advances in next generation sequencing (NGS), genetic diagnoses remain elusive for many patients with neurologic syndromes. Long-read sequencing (LRS) and optical genome mapping (OGM) technologies improve upon existing capabilities in the detection and interpretation of structural variation in repetitive DNA, on a single haplotype, while also providing enhanced breakpoint resolution. We performed LRS and OGM on two patients with known chromosomal rearrangements and inconclusive Sanger or NGS. The first patient, who had epilepsy and developmental delay, had a complex translocation between two chromosomes that included insertion and inversion events. The second patient, who had a movement disorder, had an inversion on a single chromosome disrupted by multiple smaller inversions and insertions. Sequence level resolution of the rearrangements identified pathogenic breaks in noncoding sequence in or near known disease-causing genes with relevant neurologic phenotypes (MBD5, NKX2-1). These specific variants have not been reported previously, but expected molecular consequences are consistent with previously reported cases. As the use of LRS and OGM technologies for clinical testing increases and data analyses become more standardized, these methods along with multiomic data to validate noncoding variation effects will improve diagnostic yield and increase the proportion of probands with detectable pathogenic variants for known genes implicated in neurogenetic disease.
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Affiliation(s)
- Kristen L Sund
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, California, USA
| | - John Garbe
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Zakia Abdelhamed
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Chelsey Maag
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Barbara Hallinan
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Steven W Wu
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ethan Sperry
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Archana Deshpande
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rolf Stottmann
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Lisa M Dyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Matthew S Hestand
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
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3
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Lombardo A, Sinibaldi L, Genovese S, Catino G, Mei V, Pompili D, Sallicandro E, Falasca R, Liambo MT, Faggiano MV, Roberti MC, Di Donato M, Vitelli A, Russo S, Giannini R, Micalizzi A, Pietrafusa N, Digilio MC, Novelli A, Fusco L, Alesi V. A Case of CDKL5 Deficiency Due to an X Chromosome Pericentric Inversion: Delineation of Structural Rearrangements as an Overlooked Recurrent Pathological Mechanism. Int J Mol Sci 2024; 25:6912. [PMID: 39000022 PMCID: PMC11241409 DOI: 10.3390/ijms25136912] [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: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/14/2024] Open
Abstract
CDKL5 deficiency disorder (CDD) is an X-linked dominant epileptic encephalopathy, characterized by early-onset and drug-resistant seizures, psychomotor delay, and slight facial features. Genomic variants inactivating CDKL5 or impairing its protein product kinase activity have been reported, making next-generation sequencing (NGS) and chromosomal microarray analysis (CMA) the standard diagnostic tests. We report a suspicious case of CDD in a female child who tested negative upon NGS and CMA and harbored an X chromosome de novo pericentric inversion. The use of recently developed genomic techniques (optical genome mapping and whole-genome sequencing) allowed us to finely characterize the breakpoints, with one of them interrupting CDKL5 at intron 1. This is the fifth case of CDD reported in the scientific literature harboring a structural rearrangement on the X chromosome, providing evidence for the hypothesis that this type of anomaly can represent a recurrent pathogenic mechanism, whose frequency is likely underestimated, with it being overlooked by standard techniques. The identification of the molecular etiology of the disorder is extremely important in evaluating the pathological outcome and to better investigate the mechanisms associated with drug resistance, paving the way for the development of specific therapies. Karyotype and genomic techniques should be considered in all cases presenting with CDD without molecular confirmation.
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Affiliation(s)
- Antonietta Lombardo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Lorenzo Sinibaldi
- Medical Genetics Unit, IRCCS Bambino Gesù Children Hospital, 00165 Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Giorgia Catino
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Valerio Mei
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Daniele Pompili
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Ester Sallicandro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Roberto Falasca
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Teresa Liambo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Vittoria Faggiano
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maria Cristina Roberti
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Maddalena Di Donato
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Anna Vitelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Serena Russo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Rosalinda Giannini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Alessia Micalizzi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Medical Genetics Unit, San Pietro Fatebenefratelli Hospital, 00189 Rome, Italy
| | - Nicola Pietrafusa
- Neurology, Epilepsy and Movement Disorders Unit, Bambino Gesù, IRCCS Children’s Hospital, 00165 Rome, Italy
| | | | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Lucia Fusco
- Neurology, Epilepsy and Movement Disorders Unit, Bambino Gesù, IRCCS Children’s Hospital, 00165 Rome, Italy
| | - Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
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Xiao Y, Cheng D, Luo K, Li M, Tan Y, Lin G, Hu L. Evaluation of genetic risk of apparently balanced chromosomal rearrangement carriers by breakpoint characterization. J Assist Reprod Genet 2024; 41:147-159. [PMID: 37993578 PMCID: PMC10789712 DOI: 10.1007/s10815-023-02986-7] [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: 08/03/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE To report genetic characteristics and associated risk of chromosomal breaks due to chromosomal rearrangements in large samples. METHODS MicroSeq, a technique that combines chromosome microdissection and next-generation sequencing, was used to identify chromosomal breakpoints. Long-range PCR and Sanger sequencing were used to precisely characterize 100 breakpoints in 50 ABCR carriers. RESULTS In addition to the recurrent regions of balanced rearrangement breaks in 8q24.13, 11q11.23, and 22q11.21 that had been documented, we have discovered a 10-Mb region of 12q24.13-q24.3 that could potentially be a sparse region of balanced rearrangement breaks. We found that 898 breakpoints caused gene disruption and a total of 188 breakpoints interrupted genes recorded in OMIM. The percentage of breakpoints that disrupted autosomal dominant genes recorded in OMIM was 25.53% (48/188). Fifty-four of the precisely characterized breakpoints had 1-8-bp microhomologous sequences. CONCLUSION Our findings provide a reference for the evaluation of the pathogenicity of mutations in related genes that cause protein truncation in clinical practice. According to the characteristics of breakpoints, non-homologous end joining and microhomology-mediated break-induced replication may be the main mechanism for ABCRs formation.
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Affiliation(s)
- Yanqin Xiao
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
| | - Dehua Cheng
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Keli Luo
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Mengge Li
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China
- Hunan Guangxiu Hospital, Changsha, 410023, Hunan, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, 410008, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410023, Hunan, China.
- National Engineering and Research Center of Human Stem Cells, Changsha, 410023, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, Changsha, 410008, Hunan, China.
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5
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Goumy C, Guy Ouedraogo Z, Soler G, Eymard-Pierre E, Laurichesse H, Delabaere A, Gallot D, Bouchet P, Perthus I, Pebrel-Richard C, Gouas L, Salaun G, Salse J, Véronèse L, Tchirkov A. Optical genome mapping for prenatal diagnosis: A prospective study. Clin Chim Acta 2023; 551:117594. [PMID: 37832906 DOI: 10.1016/j.cca.2023.117594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
PURPOSE Cytogenetic analysis provides important information for prenatal decision-making and genetic counseling. Optical genome mapping (OGM) has demonstrated its performances in retrospective studies. In our prospective study, we assessed the quality of DNA obtained from cultures of amniotic fluid (AF) and chorionic villi (CV) and evaluated the ability of OGM to detect all clinically relevant aberrations identified by standard methods. METHODS A total of 37 prenatal samples from pregnancies with a fetal anomaly on ultrasound were analyzed prospectively by OGM between January 1, 2021 and June 31, 2022. OGM results were interpreted blindly and compared to the results obtained by standard techniques. RESULTS OGM results were interpretable in 92% of samples. We observed 100% concordance between OGM and karyotype and/or chromosomal microarray results. In addition, OGM identified a median of 30 small (<100 kb) structural variations per case with the involvement of 12 OMIM genes, of which 3 were OMIM morbid genes. CONCLUSION This prospective study showed OGM performed well in detecting genomic alterations in cell cultures from prenatal samples. The place of OGM in relation to CMA or exome sequencing remains to be defined in order to optimize the prenatal diagnostic procedure.
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Affiliation(s)
- Carole Goumy
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France.
| | - Zangbéwendé Guy Ouedraogo
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; Service de Biochimie et Génétique Moléculaire, CHU Clermont-Ferrand, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Inserm, GReD, 63001 Clermont-Ferrand, France
| | - Gwendoline Soler
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Eleonore Eymard-Pierre
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France
| | - Hélène Laurichesse
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Amélie Delabaere
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Denis Gallot
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, CNRS, Inserm, GReD, 63001 Clermont-Ferrand, France
| | - Pamela Bouchet
- Unité de Médecine Fœtale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Isabelle Perthus
- Service de Génétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Céline Pebrel-Richard
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Laetitia Gouas
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; INSERM U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont Ferrand, France
| | - Gaëlle Salaun
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France
| | - Jérôme Salse
- UMR 1095 INRAE/UCA Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Genotyping and Sequencing Plateform Gentyane, Clermont-Ferrand, France
| | - Lauren Véronèse
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; EA7453 CHELTER « Clonal Heterogeneity, Leukemic Environment, Therapy Resistance of Chronic Leukemias », Université Clermont Auvergne, Clermont-Ferrand, France
| | - Andrei Tchirkov
- Cytogénétique Médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand, France; EA7453 CHELTER « Clonal Heterogeneity, Leukemic Environment, Therapy Resistance of Chronic Leukemias », Université Clermont Auvergne, Clermont-Ferrand, France
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Bonaglia MC, Salvo E, Sironi M, Bertuzzo S, Errichiello E, Mattina T, Zuffardi O. Case Report: Decrypting an interchromosomal insertion associated with Marfan's syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants. Front Genet 2023; 14:1244983. [PMID: 37811140 PMCID: PMC10551147 DOI: 10.3389/fgene.2023.1244983] [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: 06/23/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient's neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.
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Affiliation(s)
| | - Eliana Salvo
- Cytogenetics Laboratory, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute, IRCCS E. Medea, Lecco, Italy
| | - Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Teresa Mattina
- Medical Genetics Unit, University of Catania, Catania, Italy
- Clinic G.B. Morgagni, Catania, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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7
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Lowther C, Valkanas E, Giordano JL, Wang HZ, Currall BB, O'Keefe K, Pierce-Hoffman E, Kurtas NE, Whelan CW, Hao SP, Weisburd B, Jalili V, Fu J, Wong I, Collins RL, Zhao X, Austin-Tse CA, Evangelista E, Lemire G, Aggarwal VS, Lucente D, Gauthier LD, Tolonen C, Sahakian N, Stevens C, An JY, Dong S, Norton ME, MacKenzie TC, Devlin B, Gilmore K, Powell BC, Brandt A, Vetrini F, DiVito M, Sanders SJ, MacArthur DG, Hodge JC, O'Donnell-Luria A, Rehm HL, Vora NL, Levy B, Brand H, Wapner RJ, Talkowski ME. Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies. Am J Hum Genet 2023; 110:1454-1469. [PMID: 37595579 PMCID: PMC10502737 DOI: 10.1016/j.ajhg.2023.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023] Open
Abstract
Short-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.
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Affiliation(s)
- Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Elise Valkanas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Jessica L Giordano
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Harold Z Wang
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emma Pierce-Hoffman
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nehir E Kurtas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ben Weisburd
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vahid Jalili
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Isaac Wong
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Emily Evangelista
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Laura D Gauthier
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlotte Tolonen
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nareh Sahakian
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Stevens
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Norton
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michelle DiVito
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel G MacArthur
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Anne O'Donnell-Luria
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ronald J Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
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8
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Zhang Q, Wang Y, Xu Y, Zhou R, Huang M, Qiao F, Meng L, Liu A, Zhou J, Li L, Ji X, Xu Z, Hu P. Optical genome mapping for detection of chromosomal aberrations in prenatal diagnosis. Acta Obstet Gynecol Scand 2023. [PMID: 37366235 PMCID: PMC10378017 DOI: 10.1111/aogs.14613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION Chromosomal aberrations are the most important etiological factors for birth defects. Optical genome mapping is a novel cytogenetic tool for detecting a broad range of chromosomal aberrations in a single assay, but relevant clinical feasibility studies of optical genome mapping in prenatal diagnosis are limited. MATERIAL AND METHODS We retrospectively performed optical genome mapping analysis of amniotic fluid samples from 34 fetuses with various clinical indications and chromosomal aberrations detected through standard-of-care technologies, including karyotyping, fluorescence in situ hybridization, and/or chromosomal microarray analysis. RESULTS In total, we analyzed 46 chromosomal aberrations from 34 amniotic fluid samples, including 5 aneuploidies, 10 large copy number variations, 27 microdeletions/microduplications, 2 translocations, 1 isochromosome, and 1 region of homozygosity. Overall, 45 chromosomal aberrations could be confirmed by our customized analysis strategy. Optical genome mapping reached 97.8% concordant clinical diagnosis with standard-of-care methods for all chromosomal aberrations in a blinded fashion. Compared with the widely used chromosomal microarray analysis, optical genome mapping additionally determined the relative orientation and position of repetitive segments for seven cases with duplications or triplications. The additional information provided by optical genome mapping will be conducive to characterizing complex chromosomal rearrangements and allowing us to propose mechanisms to explain rearrangements and predict the genetic recurrence risk. CONCLUSIONS Our study highlights that optical genome mapping can provide comprehensive and accurate information on chromosomal aberrations in a single test, suggesting that optical genome mapping has the potential to become a promising cytogenetic tool for prenatal diagnosis.
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Affiliation(s)
- Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - An Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jing Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Li Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiuqing Ji
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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9
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Zhang S, Pei Z, Lei C, Zhu S, Deng K, Zhou J, Yang J, Lu D, Sun X, Xu C, Xu C. Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping. J Med Genet 2023; 60:274-284. [PMID: 35710108 DOI: 10.1136/jmedgenet-2022-108553] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Chromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and the risk of miscarriage or delivering abnormal offspring with congenital malformations in carrier couples is significantly increased. In the present study, we aimed to investigate the potential of single-molecule optical genome mapping (OGM) in unravelling cryptic chromosomal rearrangements. METHODS Eleven couples with normal karyotypes that had abortions/affected offspring with unbalanced rearrangements were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells and processed via OGM. The genome assembly was performed followed by variant calling and annotation. Meanwhile, multiple detection strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing and Sanger sequencing were implemented to confirm the results obtained from OGM. RESULTS High-resolution OGM successfully detected cryptic reciprocal translocation in all recruited couples, which was consistent with the results of FISH and sequencing. All high-confidence cryptic chromosomal translocations detected by OGM were confirmed by sequencing analysis of rearrangement breakpoints. Moreover, OGM revealed additional complex rearrangement events such as inverted aberrations, further refining potential genetic interpretation. CONCLUSION To the best of our knowledge, this is the first study wherein OGM facilitate the rapid and robust detection of cryptic chromosomal reciprocal translocations in clinical practice. With the excellent performance, our findings suggest that OGM is well qualified as an accurate, comprehensive and first-line method for detecting cryptic BCRs in routine clinical testing.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhenle Pei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ke Deng
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jingmin Yang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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10
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Exploring the Genetic Causality of Discordant Phenotypes in Familial Apparently Balanced Translocation Cases Using Whole Exome Sequencing. Genes (Basel) 2022; 14:genes14010082. [PMID: 36672823 PMCID: PMC9859009 DOI: 10.3390/genes14010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Familial apparently balanced translocations (ABTs) are usually not associated with a phenotype; however, rarely, ABTs segregate with discordant phenotypes in family members carrying identical rearrangements. The current study was a follow-up investigation of four familial ABTs, where whole exome sequencing (WES) was implemented as a diagnostic tool to identify the underlying genetic aetiology of the patients' phenotypes. Data were analysed using an in-house bioinformatics pipeline alongside VarSome Clinical. WES findings were validated with Sanger sequencing, while the impact of splicing and missense variants was assessed by reverse-transcription PCR and in silico tools, respectively. Novel candidate variants were identified in three families. In family 1, it was shown that the de novo pathogenic STXBP1 variant (NM_003165.6:c.1110+2T>G) affected splicing and segregated with the patient's phenotype. In family 2, a likely pathogenic TUBA1A variant (NM_006009.4:c.875C>T, NP_006000.2:p.(Thr292Ile)) could explain the patient's symptoms. In family 3, an SCN1A variant of uncertain significance (NM_006920.6:c.5060A>G, NP_008851.3:p.(Glu1687Gly)) required additional evidence to sufficiently support causality. This first report of WES application in familial ABT carriers with discordant phenotypes supported our previous findings describing such rearrangements as coincidental. Thus, WES can be recommended as a complementary test to find the monogenic cause of aberrant phenotypes in familial ABT carriers.
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11
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Demirhan O, Hergüner Ö, Tunç E. A Cytogenetic Study of Turkish Children with Global Developmental Delay. J Pediatr Genet 2022. [DOI: 10.1055/s-0042-1758872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractGlobal developmental delay (GDD)/intellectual disability (ID) is common in children and its etiology is unknown in many cases. Chromosomal abnormalities are predominant genetic causes of GDD/ID. The aim of this study is to determine the genetic risk factors that may be involved in the etiology of GDD/ID. In this study, 810 children with moderate to severe, clinically unexplained GDD/ID for whom cytogenetic analysis were performed were retrospectively rescreened. The results showed that GDD/ID affected more females than males (2 girls:1 boy). A total of 54 children (6.7%) with GDD showed chromosomal aberrations (CAs): 59.3% of these CAs were structural aberrations, and the rest were numerical aberrations (40.7%). Specifically, inversions, deletions, and reciprocal and robertsonian translocations, which were detected in 1, 0.7, 0.8, and 0.4% of the children, respectively, constituted important categories of structural CAs. Among numerical CAs, classic Turner and mosaics were detected in 1.2% of all children. Trisomy 21 and mosaic trisomy 21 were detected in 1% of the children. Marker chromosomes and 47,XXY karyotypes were found in two children each. Our results suggest that female sex is more affected by CAs among GDD/ID cases, and cytogenetic analysis is useful in the etiological diagnosis of GDD/ID.
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Affiliation(s)
- Osman Demirhan
- Department of Medical Biology and Genetics, Faculty of Medicine, Çukurova University, Balcali-Adana, Turkey
| | - Özlem Hergüner
- Department of Child Neurology, Faculty of Medicine, Çukurova University, Balcali-Adana, Turkey
| | - Erdal Tunç
- Department of Medical Biology and Genetics, Faculty of Medicine, Çukurova University, Balcali-Adana, Turkey
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12
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Fino J, Marques B, Dong Z, David D. SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants. Front Genet 2021; 12:757170. [PMID: 34925449 PMCID: PMC8671832 DOI: 10.3389/fgene.2021.757170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
With the advent of genomic sequencing, a number of balanced and unbalanced structural variants (SVs) can be detected per individual. Mainly due to incompleteness and the scattered nature of the available annotation data of the human genome, manual interpretation of the SV's clinical significance is laborious and cumbersome. Since bioinformatic tools developed for this task are limited, a comprehensive tool to assist clinical outcome prediction of SVs is warranted. Herein, we present SVInterpreter, a free Web application, which analyzes both balanced and unbalanced SVs using topologically associated domains (TADs) as genome units. Among others, gene-associated data (as function and dosage sensitivity), phenotype similarity scores, and copy number variants (CNVs) scoring metrics are retrieved for an informed SV interpretation. For evaluation, we retrospectively applied SVInterpreter to 97 balanced (translocations and inversions) and 125 unbalanced (deletions, duplications, and insertions) previously published SVs, and 145 SVs identified from 20 clinical samples. Our results showed the ability of SVInterpreter to support the evaluation of SVs by (1) confirming more than half of the predictions of the original studies, (2) decreasing 40% of the variants of uncertain significance, and (3) indicating several potential position effect events. To our knowledge, SVInterpreter is the most comprehensive TAD-based tool to identify the possible disease-causing candidate genes and to assist prediction of the clinical outcome of SVs. SVInterpreter is available at http://dgrctools-insa.min-saude.pt/cgi-bin/SVInterpreter.py.
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Affiliation(s)
- Joana Fino
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
| | - Bárbara Marques
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Dezső David
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
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13
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Reproductive outcomes in individuals with chromosomal reciprocal translocations. Genet Med 2021; 23:1753-1760. [PMID: 33972719 DOI: 10.1038/s41436-021-01195-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Patients with reciprocal balanced translocations (RBT) have a risk for recurrent pregnancy losses (RPL), affected child, and infertility. Currently, genetic counseling is based on karyotypes found among the products of conception (POC), although factors influencing the success of assisted reproductive technologies (ART) in RBT couples are not established. METHODS Cytogenetic results from 261 POC and offspring of the parents (113 women and 90 men) with RBT were evaluated. Chromosome segregation modes and number of euploid embryos were assessed in couples undergoing in vitro fertilization. RESULTS Patients with translocations involving an acrocentric chromosome have a higher risk of unbalanced gametes caused by a 3:1 segregation. Female RBT patients have a statistically higher risk of aneuploidy due to an interchromosomal effect. The rate of euploid embryos is low due to meiosis I malsegregation of RBT, meiosis II nondisjunction, additional whole chromosome or segmental aneusomies. RBT patients with RPL have a higher rate of miscarriage of euploid fetuses with RBT. CONCLUSION Chromosome-specific factors, female gender, age, and history of RPL are the risk elements influencing pregnancy and in vitro fertilization success in RBT patients. Chromosomal microarray analysis of POC is necessary to provide an accurate and timely diagnosis for patients with adverse reproductive outcomes.
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14
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Shimokawa O, Takeda M, Ohashi H, Shono-Ota A, Kumagai M, Matsushika R, Masuda C, Uenishi K, Kimata Pooh R. D-karyo-A New Prenatal Rapid Screening Test Detecting Submicroscopic CNVs and Mosaicism. Diagnostics (Basel) 2021; 11:diagnostics11020337. [PMID: 33670620 PMCID: PMC7922406 DOI: 10.3390/diagnostics11020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosomal microarray analysis (CMA), recently introduced following conventional cytogenetic technology, can detect submicroscopic copy-number variations (CNVs) in cases previously diagnosed as "cytogenetically benign". At present, rapid and accurate chromosomal analysis is required in prenatal diagnostics, but prenatal CMA is not widely used due to its high price and long turnaround time. We introduced a new prenatal screening method named digital karyotyping (D-karyo), which utilizes a preimplantation genetic test for the aneuploidy (PGT-A) platform. First, we conducted a preliminary experiment to compare the original PGT-A method to our modified method. Based on the preliminary results, we decided to implement the modified strategy without whole-genome amplification (WGA) and combined it with three analytical software packages. Next, we conducted a prospective study with 824 samples. According to the indication for invasive tests, the D-karyo positive rates were 2.5% and 5.0%, respectively, in the screening positive group with NT ≥ 3.5 mm and the group with fetal abnormalities by ultrasound. D-karyo is a breakthrough modality that can detect submicroscopic CNVs ≥ 1.0 Mb accurately in only 10.5 h for 24 samples at a low cost. Implementing D-karyo as a prenatal rapid screening test will reduce unnecessary CMA and achieve more accurate prenatal genetic testing than G-banding.
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15
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Yu MHC, Chau JFT, Au SLK, Lo HM, Yeung KS, Fung JLF, Mak CCY, Chung CCY, Chan KYK, Chung BHY, Kan ASY. Evaluating the Clinical Utility of Genome Sequencing for Cytogenetically Balanced Chromosomal Abnormalities in Prenatal Diagnosis. Front Genet 2021; 11:620162. [PMID: 33584815 PMCID: PMC7873444 DOI: 10.3389/fgene.2020.620162] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Balanced chromosomal abnormalities (BCAs) are changes in the localization or orientation of a chromosomal segment without visible gain or loss of genetic material. BCAs occur at a frequency of 1 in 500 newborns and are associated with an increased risk of multiple congenital anomalies and/or neurodevelopmental disorders, especially if it is a de novo mutation. In this pilot project, we used short read genome sequencing (GS) to retrospectively re-sequence ten prenatal subjects with de novo BCAs and compared the performance of GS with the original karyotyping. GS characterized all BCAs found by conventional karyotyping with the added benefit of precise sub-band delineation. By identifying BCA breakpoints at the nucleotide level using GS, we found disruption of OMIM genes in three cases and identified cryptic gain/loss at the breakpoints in two cases. Of these five cases, four cases reached a definitive genetic diagnosis while the other one case had a BCA interpreted as unknown clinical significance. The additional information gained from GS can change the interpretation of the BCAs and has the potential to improve the genetic counseling and perinatal management by providing a more specific genetic diagnosis. This demonstrates the added clinical utility of using GS for the diagnosis of BCAs.
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Affiliation(s)
- Mullin Ho Chung Yu
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jeffrey Fong Ting Chau
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Sandy Leung Kuen Au
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China
| | - Hei Man Lo
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China
| | - Kit San Yeung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jasmine Lee Fong Fung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher Chun Yu Mak
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Claudia Ching Yan Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kelvin Yuen Kwong Chan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China.,Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong, China.,Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong, China
| | - Brian Hon Yin Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anita Sik Yau Kan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Hong Kong, China.,Department of Obstetrics and Gynaecology, Queen Mary Hospital, Hong Kong, China.,Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Hong Kong, China
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16
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Wallis M, Pope-Couston R, Mansour J, Amor DJ, Tang P, Stock-Myer S. Lymphedema distichiasis syndrome may be caused by FOXC2 promoter-enhancer dissociation and disruption of a topological associated domain. Am J Med Genet A 2020; 185:150-156. [PMID: 33107170 DOI: 10.1002/ajmg.a.61935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 01/05/2023]
Abstract
Lymphedema distichiasis syndrome (LDS) is a rare autosomal dominant condition characterized by lower limb lymphedema, distichiasis, and variable additional features. LDS is usually caused by heterozygous sequence variants in the FOXC2 gene located at 16q24, but in one previous instance LDS has resulted from a balanced reciprocal translocation with a breakpoint at 16q24, 120 kb distal to the FOXC2 gene suggesting a position effect. Here, we describe a second family with LDS caused by a translocation involving 16q24. The family were ascertained after detection of a paternally inherited balanced reciprocal translocation t(16;22)(q24;q13.1) in a pregnancy complicated by severe fetal hydrops. There was a past history of multiple miscarriages in the father's family, and a personal and family history of lymphedema and distichiasis, consistent with the diagnosis of LDS. Using whole genome amplified DNA from single sperm of the male proband, bead array analysis demonstrated that the FOXC2 gene was intact and the chromosome 16 breakpoint mapped to the same region 120Kb distal to the FOXC2 gene. This case highlights the clinical consequences that can arise from a translocation of genomic material without dosage imbalance, and that it is increasingly feasible to predict and characterize possible effects with improved access to molecular techniques.
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Affiliation(s)
- Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, C/- The Royal Hobart Hospital, Hobart, Tasmania, Australia.,School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rachel Pope-Couston
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, C/- The Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Julia Mansour
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, C/- The Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - David J Amor
- Department of Pediatrics, University of Melbourne.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Paisu Tang
- Virtus Diagnostics, East Melbourne, Victoria, Australia
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17
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Madjunkova S, Sundaravadanam Y, Antes R, Abramov R, Chen S, Yin Y, Zuzarte PC, Moskovtsev SI, Jorgensen LGT, Baratz A, Simpson JT, Librach C. Detection of Structural Rearrangements in Embryos. N Engl J Med 2020; 382:2472-2474. [PMID: 32558475 DOI: 10.1056/nejmc1913370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Ran Antes
- CReATe Fertility Centre, Toronto, ON, Canada
| | | | - Siwei Chen
- CReATe Fertility Centre, Toronto, ON, Canada
| | - Yin Yin
- CReATe Fertility Centre, Toronto, ON, Canada
| | | | | | | | - Ari Baratz
- University of Toronto, Toronto, ON, Canada
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18
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Bonaglia MC, Bertuzzo S, Ciaschini AM, Discepoli G, Castiglia L, Romaniello R, Zuffardi O, Fichera M. Targeted next-generation sequencing identifies the disruption of the SHANK3 and RYR2 genes in a patient carrying a de novo t(1;22)(q43;q13.3) associated with signs of Phelan-McDermid syndrome. Mol Cytogenet 2020; 13:22. [PMID: 32536973 PMCID: PMC7291734 DOI: 10.1186/s13039-020-00490-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/26/2020] [Indexed: 11/10/2022] Open
Abstract
Background It has been known for more than 30 years that balanced translocations, especially if de novo, can associate with congenital malformations and / or neurodevelopmental disorders, following the disruption of a disease gene or its cis-regulatory elements at one or both breakpoints. Case presentation We describe a 10-year-old girl with a non-specific neurodevelopmental disorder characterized by moderate intellectual disability (ID), gross motor clumsiness, social and communication deficits. She carries a de novo reciprocal translocation between chromosomes 1q43 and 22q13.3, the latter suggesting the involvement of SHANK3. Indeed, its haploinsufficiency associates with Phelan-McDermid Syndrome, whose main symptoms are characterized by global developmental delay and absent or severely delayed expressive speech. A deep molecular approach, including next-generation sequencing of SHANK3 locus, allowed demonstrating the breakage of RYR2 and SHANK3 on the derivative chromosomes 1 and 22 respectively, and the formation of two fusion genes SHANK3-RYR2 and RYR2-SHANK3 with concomitant cryptic deletion of 3.6 and 4.1 kilobases at translocation junction of both derivatives chromosomes 22 and 1, respectively. Conclusions Although the interruption of SHANK3 accounts for the patient’s psychomotor retardation and autism-like behavior, we do not exclude that the interruption of RYR2 may also have a role on her disorder, or result in further pathogenicity in the future. Indeed, RYR2 that has a well-established role in the etiology of two autosomal dominant adulthood cardiac disorders (#600996 and #604772) is also expressed in the brain (cerebellum, hippocampus, and cerebral cortex) and about half of RYR2 mutation carriers present late onset primary generalized epilepsy without cardiac arrhythmogenic disorders. Moreover, RYR2 variants have also been sporadically reported in individuals with early onset schizophrenia or ID, and its constraint values suggest intolerance to loss-of-function. This study not only confirms the usefulness of the molecular mapping of de novo balanced rearrangements in symptomatic individuals, but also underscores the need for long-term clinical evaluation of the patients, for better evaluating the pathogenicity of the chromosomal breakpoints.
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Affiliation(s)
- Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Sara Bertuzzo
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Anna Maria Ciaschini
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | - Giancarlo Discepoli
- Lab. di Genetica Medica SOS Malattie Rare, AOU Ospedali Riuniti Umberto I-G.M.Lancisi-G.Salesi, Ancona, Italy
| | | | - Romina Romaniello
- Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, 23842 Lecco, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Marco Fichera
- Oasi Research Institute-IRCCS, Troina, Italy.,Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
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19
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Murcia Pienkowski V, Kucharczyk M, Rydzanicz M, Poszewiecka B, Pachota K, Młynek M, Stawiński P, Pollak A, Kosińska J, Wojciechowska K, Lejman M, Cieślikowska A, Wicher D, Stembalska A, Matuszewska K, Materna-Kiryluk A, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype. J Clin Med 2020; 9:jcm9051245. [PMID: 32344861 PMCID: PMC7287862 DOI: 10.3390/jcm9051245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
De novo balanced chromosomal aberrations (BCAs), such as reciprocal translocations and inversions, are genomic aberrations that, in approximately 25% of cases, affect the human phenotype. Delineation of the exact structure of BCAs may provide a precise diagnosis and/or point to new disease loci. We report on six patients with de novo balanced chromosomal translocations (BCTs) and one patient with a de novo inversion, in whom we mapped breakpoints to a resolution of 1 bp, using shallow whole-genome mate pair sequencing. In all seven cases, a disruption of at least one gene was found. In two patients, the phenotypic impact of the disrupted genes is well known (NFIA, ATP7A). In five patients, the aberration damaged genes: PARD3, EPHA6, KLF13, STK24, UBR3, MLLT10 and TLE3, whose influence on the human phenotype is poorly understood. In particular, our results suggest novel candidate genes for retinal degeneration with anophthalmia (EPHA6), developmental delay with speech impairment (KLF13), and developmental delay with brain dysembryoplastic neuroepithelial tumor (UBR3). In conclusion, identification of the exact structure of symptomatic BCTs using next generation sequencing is a viable method for both diagnosis and finding novel disease candidate genes in humans.
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Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Barbara Poszewiecka
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Katarzyna Pachota
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Marlena Młynek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Katarzyna Wojciechowska
- Department of Pediatric Hematology Oncology and Transplantology, University Children’s Hospital, 20-093 Lublin, Poland;
| | - Monika Lejman
- Department of Pediatric Hematology Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Agata Cieślikowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Dorota Wicher
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | | | - Karolina Matuszewska
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Gambin
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Krajewska-Walasek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
- Correspondence: ; Tel.: +48-22-572-06-95; Fax: +48-22-572-06-96
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20
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David D, Freixo JP, Fino J, Carvalho I, Marques M, Cardoso M, Piña-Aguilar RE, Morton CC. Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscape. Hum Genet 2020; 139:531-543. [PMID: 32030560 PMCID: PMC10501484 DOI: 10.1007/s00439-020-02121-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/27/2022]
Abstract
We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints. Identification of autosomal dominant disease due to the disruption of ANKS1B and WDR26 by t(12;17)(q23.1;q21.33)dn and t(1;3)(q24.11;p25.3)dn breakpoints, respectively, substantiated the proposed workflow. We then applied this workflow to two ongoing prenatal cases with apparently balanced dnBCAs: 46,XX,t(16;17)(q24;q21.3)dn referred for increased risk on combined first trimester screening and 46,XY,t(2;19)(p13;q13.1)dn referred due to a previous trisomy 21 pregnancy. Translocation breakpoints in the t(16;17) involve ANKRD11 and WNT3 and disruption of ANKRD11 resulted in KBG syndrome confirmed in postnatal follow-up. Breakpoints in the t(2;19) are within ATP6V1B1 and the 3' UTR of CEP89, and are not interpreted to cause disease. Genotype-phenotype correlation confirms the causative role of WDR26 in the Skraban-Deardorff and 1q41q42 microdeletion phenocopy syndromes, and that disruption of ANKS1B causes ANKS1B haploinsufficiency syndrome. In sum, we show that an liGS-based approach can be realized in PND care providing additional information concerning clinical outcomes of dnBCAs in patients with such rearrangements.
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Affiliation(s)
- Dezső David
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - João P Freixo
- Department of Medical Genetics, Central Lisbon Hospital Center (CHLC), Lisbon, Portugal
| | - Joana Fino
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Inês Carvalho
- Department of Medical Genetics, Central Lisbon Hospital Center (CHLC), Lisbon, Portugal
| | - Mariana Marques
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Manuela Cardoso
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Raul E Piña-Aguilar
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Cynthia C Morton
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Manchester Academic Health Science Center, University of Manchester, Manchester, UK
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21
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Cost-effectiveness analysis of chromosomal microarray as a primary test for prenatal diagnosis in Hong Kong. BMC Pregnancy Childbirth 2020; 20:109. [PMID: 32059709 PMCID: PMC7023733 DOI: 10.1186/s12884-020-2772-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 01/27/2020] [Indexed: 11/10/2022] Open
Abstract
Background Chromosomal microarray (CMA) has been shown to be cost-effective over karyotyping in invasive prenatal diagnosis for pregnancies with fetal ultrasound anomalies. Yet, information regarding preceding and subsequent tests must be considered as a whole before the true cost-effectiveness can emerge. Currently in Hong Kong, karyotyping is offered free as the standard prenatal test while genome-wide array comparative genome hybridization (aCGH), a form of CMA, is self-financed. A new algorithm was proposed to use aCGH following quantitative fluorescent polymerase chain reaction (QF-PCR) as primary test instead of karyotyping. This study aims to evaluate the cost-effectiveness of the proposed algorithm versus the current algorithm for prenatal diagnosis in Hong Kong. Methods Between November 2014 and February 2016, 129 pregnant women who required invasive prenatal diagnosis at two public hospitals in Hong Kong were prospectively recruited. The proposed algorithm was performed for all participants in this demonstration study. For the cost-effectiveness analysis, cost and outcome (diagnostic rate) data were compared with that of a hypothetical scenario representing the current algorithm. Further analysis was performed to incorporate women’s willingness-to-pay for the aCGH test. Impact of government subsidies on the aCGH test was explored as a sensitivity analysis. Results The proposed algorithm dominated the current algorithm for prenatal diagnosis. Both algorithms were equally effective but the proposed algorithm was significantly cheaper (p ≤ 0.05). Taking into account women’s willingness-to-pay for an aCGH test, the proposed algorithm was more effective and less costly than the current algorithm. When the government subsidy reaches 100%, the maximum number of diagnoses could be made. Conclusion By switching to the proposed algorithm, cost saving can be achieved whilst maximizing the diagnostic rate for invasive prenatal diagnosis. It is recommended to implement aCGH as a primary test following QF-PCR to replace the majority of karyotyping for prenatal diagnosis in Hong Kong.
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22
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Uguen K, Jubin C, Duffourd Y, Bardel C, Malan V, Dupont JM, El Khattabi L, Chatron N, Vitobello A, Rollat-Farnier PA, Baulard C, Lelorch M, Leduc A, Tisserant E, Tran Mau-Them F, Danjean V, Delepine M, Till M, Meyer V, Lyonnet S, Mosca-Boidron AL, Thevenon J, Faivre L, Thauvin-Robinet C, Schluth-Bolard C, Boland A, Olaso R, Callier P, Romana S, Deleuze JF, Sanlaville D. Genome sequencing in cytogenetics: Comparison of short-read and linked-read approaches for germline structural variant detection and characterization. Mol Genet Genomic Med 2020; 8:e1114. [PMID: 31985172 PMCID: PMC7057128 DOI: 10.1002/mgg3.1114] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base-pair resolution, but the use of short-read sequencing is limited by repetitive sequences, and long-read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked-reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short-read to linked-read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short-read WGS. METHODS We included 13 patients carrying various SVs. Whole genome analyses were performed using paired-end HiSeq X sequencing with (linked-read strategy) or without (short-read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short-read strategy and LongRanger for long-read strategy. Variant interpretations were first blinded. RESULTS The short-read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked-read strategy identified 10/13 SVs, including one (patient 7) missed by the short-read strategy. CONCLUSION In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV.
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Affiliation(s)
- Kévin Uguen
- Service de Génétique Médicale, CHRU de Brest, Brest, France.,HCL, Service de Génétique, BRON Cedex, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Yannis Duffourd
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Claire Bardel
- HCL, Cellule bioinformatique de la plateforme NGS du CHU Lyon, BRON Cedex, France.,Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Villeurbanne, France
| | - Valérie Malan
- Service de Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Jean-Michel Dupont
- Institut Cochin, INSERM U1016, Université Paris Descartes, Faculté de Médecine, APHP, HUPC, site Cochin, Laboratoire de Cytogénétique, Paris, France
| | - Laila El Khattabi
- Institut Cochin, INSERM U1016, Université Paris Descartes, Faculté de Médecine, APHP, HUPC, site Cochin, Laboratoire de Cytogénétique, Paris, France
| | | | - Antonio Vitobello
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Céline Baulard
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Marc Lelorch
- Service de Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Aurélie Leduc
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Emilie Tisserant
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Frédéric Tran Mau-Them
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Vincent Danjean
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LIG, Grenoble, France
| | - Marc Delepine
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | | | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Stanislas Lyonnet
- Fédération de Génétique et Institut Imagine, UMR-1163, Université de Paris, Hôpital Necker-Enfants Malades, APHP Paris, France
| | - Anne-Laure Mosca-Boidron
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Laboratoire de génétique chromosomique et moléculaire, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- Centre de génétique, Hôpital Couple-Enfant, CHU Grenoble Alpes, La Tronche, Grenoble, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
| | - Patrick Callier
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Laboratoire de génétique chromosomique et moléculaire, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Serge Romana
- Service de Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France.,Labex GenMed, Evry, France
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Méndez-Rosado LA, Lardoeyt-Ferrer R. High risk for carriers of de novo balanced structural chromosomal aberrations in prenatal diagnosis: Latin America data. Prenat Diagn 2019; 40:274-275. [PMID: 31697842 DOI: 10.1002/pd.5600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 10/20/2019] [Indexed: 11/11/2022]
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Duba HC, Arzt W. Pränataldiagnostik – klassische Analytik mittels Chorionzottenbiopsie und Amniocentese. MED GENET-BERLIN 2019. [DOI: 10.1007/s11825-019-00253-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
In diesem Artikel werden die Methoden der klassischen invasiven Pränataldiagnostik und die häufigsten, mittels konventioneller Zytogenetik diagnostizierten Chromosomenaberrationen beschrieben, um ihren, trotz der in anderen Beiträgen abgehandelten neuen Methoden, nach wie vor wichtigen Stellenwert herauszuheben.
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Affiliation(s)
- Hans-Christoph Duba
- 1 grid.473675.4 Institut für Medizinische Genetik, Med Campus IV Kepler Universitätsklinikum Linz Krankenhausstraße 26–30 4020 Linz Österreich
| | - Wolfgang Arzt
- 2 grid.473675.4 Institut für Pränatalmedizin, Med Campus IV Kepler Universitätsklinikum Linz Krankenhausstraße 26–30 4020 Linz Österreich
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25
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Hashiloni-Dolev Y, Nov-Klaiman T, Raz A. Pandora's pregnancy: NIPT, CMA, and genome sequencing-A new era for prenatal genetic testing. Prenat Diagn 2019; 39:859-865. [PMID: 31161621 DOI: 10.1002/pd.5495] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/06/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVES We delineate in this article a shift from the "traditional" technologies of karyotyping in PND to the current phase of advanced genetic technologies including noninvasive prenatal testing (NIPT), chromosomal microarray analysis (CMA), and whole-exome sequencing (WES) with their higher detection rate and related abundance of uncertain data. METHODS Conceptual analysis based on seminal works that shaped the socioethical discourse surrounding the experiences of parents as well as professionals with prenatal diagnosis in the last 30 years. RESULTS We consider the implications of this new era of PND for patients and health professionals by drawing on previous studies documenting how probability and uncertainty affect informed consent/choice, health risks communication, customer satisfaction and decision making, and parent-child bonding. CONCLUSIONS We argue that these changes move us beyond the idioms and realities of the tentative pregnancy and moral pioneering, to uncertainty, probability-based counseling, and moral/translational gambling. We conclude by discussing what is needed to maintain hope in the era of Pandora's pregnancy.
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Affiliation(s)
- Yael Hashiloni-Dolev
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Tamar Nov-Klaiman
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Aviad Raz
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beersheba, Israel
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26
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Schluth-Bolard C, Diguet F, Chatron N, Rollat-Farnier PA, Bardel C, Afenjar A, Amblard F, Amiel J, Blesson S, Callier P, Capri Y, Collignon P, Cordier MP, Coubes C, Demeer B, Chaussenot A, Demurger F, Devillard F, Doco-Fenzy M, Dupont C, Dupont JM, Dupuis-Girod S, Faivre L, Gilbert-Dussardier B, Guerrot AM, Houlier M, Isidor B, Jaillard S, Joly-Hélas G, Kremer V, Lacombe D, Le Caignec C, Lebbar A, Lebrun M, Lesca G, Lespinasse J, Levy J, Malan V, Mathieu-Dramard M, Masson J, Masurel-Paulet A, Mignot C, Missirian C, Morice-Picard F, Moutton S, Nadeau G, Pebrel-Richard C, Odent S, Paquis-Flucklinger V, Pasquier L, Philip N, Plutino M, Pons L, Portnoï MF, Prieur F, Puechberty J, Putoux A, Rio M, Rooryck-Thambo C, Rossi M, Sarret C, Satre V, Siffroi JP, Till M, Touraine R, Toutain A, Toutain J, Valence S, Verloes A, Whalen S, Edery P, Tabet AC, Sanlaville D. Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with developmental disorders. J Med Genet 2019; 56:526-535. [PMID: 30923172 DOI: 10.1136/jmedgenet-2018-105778] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/30/2019] [Accepted: 02/20/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Balanced chromosomal rearrangements associated with abnormal phenotype are rare events, but may be challenging for genetic counselling, since molecular characterisation of breakpoints is not performed routinely. We used next-generation sequencing to characterise breakpoints of balanced chromosomal rearrangements at the molecular level in patients with intellectual disability and/or congenital anomalies. METHODS Breakpoints were characterised by a paired-end low depth whole genome sequencing (WGS) strategy and validated by Sanger sequencing. Expression study of disrupted and neighbouring genes was performed by RT-qPCR from blood or lymphoblastoid cell line RNA. RESULTS Among the 55 patients included (41 reciprocal translocations, 4 inversions, 2 insertions and 8 complex chromosomal rearrangements), we were able to detect 89% of chromosomal rearrangements (49/55). Molecular signatures at the breakpoints suggested that DNA breaks arose randomly and that there was no major influence of repeated elements. Non-homologous end-joining appeared as the main mechanism of repair (55% of rearrangements). A diagnosis could be established in 22/49 patients (44.8%), 15 by gene disruption (KANSL1, FOXP1, SPRED1, TLK2, MBD5, DMD, AUTS2, MEIS2, MEF2C, NRXN1, NFIX, SYNGAP1, GHR, ZMIZ1) and 7 by position effect (DLX5, MEF2C, BCL11B, SATB2, ZMIZ1). In addition, 16 new candidate genes were identified. Systematic gene expression studies further supported these results. We also showed the contribution of topologically associated domain maps to WGS data interpretation. CONCLUSION Paired-end WGS is a valid strategy and may be used for structural variation characterisation in a clinical setting.
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Affiliation(s)
- Caroline Schluth-Bolard
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Flavie Diguet
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | | | - Claire Bardel
- Cellule bioinformatique de la plateforme NGS, Hospices Civils de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Lyon 1 University, Bron, France
| | - Alexandra Afenjar
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France.,GRC n°19, pathologies Congénitales du Cervelet-LeucoDystrophies, AP-HP, Hôpital Armand Trousseau, Sorbonne Université, Paris, France
| | - Florence Amblard
- Laboratoire de Génétique Chromosomique, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France
| | - Jeanne Amiel
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Paris, France
| | | | | | - Yline Capri
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | | | | | - Christine Coubes
- Service de Génétique, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Benedicte Demeer
- Centre d'activité de génétique clinique, CLAD nord de France, CHU Amiens, Amiens, France
| | | | | | - Françoise Devillard
- Laboratoire de Génétique Chromosomique, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France
| | | | - Céline Dupont
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Jean-Michel Dupont
- Laboratoire de Cytogénétique Constitutionnelle, APHP-HUPC site Cochin, Paris, France
| | | | - Laurence Faivre
- Centre de référence anomalies du développement et syndromes malformatifs, FHU TRANSLAD et équipe GAD INSERM UMR1231, CHU Dijon-Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | | | | | - Marine Houlier
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Sylvie Jaillard
- Laboratoire de Cytogénétique et de Biologie Cellulaire, CHU Pontchaillou, Rennes, France
| | | | - Valérie Kremer
- Laboratoire de Cytogénétique, CHU Strasbourg, Strasbourg, France
| | - Didier Lacombe
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | | | - Aziza Lebbar
- Laboratoire de Cytogénétique Constitutionnelle, APHP-HUPC site Cochin, Paris, France
| | - Marine Lebrun
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - James Lespinasse
- Laboratoire de Génétique Chromosomique, CH Général, Chambéry, France
| | - Jonathan Levy
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Valérie Malan
- Service de Cytogénétique, Hôpital Necker Enfants Malades, Paris, France
| | | | - Julie Masson
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Alice Masurel-Paulet
- Centre de référence anomalies du développement et syndromes malformatifs, FHU TRANSLAD et équipe GAD INSERM UMR1231, CHU Dijon-Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Cyril Mignot
- Département de Génétique; Centre de Référence Déficience Intellectuelle de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière, APHP, Paris, France
| | - Chantal Missirian
- Laboratoire de Génétique Chromosomique, Département de Génétique Médicale, AP-HM, Marseille, France
| | - Fanny Morice-Picard
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Sébastien Moutton
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Gwenaël Nadeau
- Laboratoire de Génétique Chromosomique, CH Général, Chambéry, France.,Service de Cytogénétique, CH Valence, Valence, France
| | - Céline Pebrel-Richard
- Service de Cytogénétique Médicale, Hôpital Estaing, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Sylvie Odent
- Service de Génétique Clinique, CHU Rennes, Rennes, France.,CNRS, IGDR (Institut de Génétique et Développement de Rennes) UMR 6290, Université de Rennes, Rennes, France
| | | | | | - Nicole Philip
- Département de Génétique Médicale, Unité de Génétique Clinique, AP-HM, Marseille, France
| | | | - Linda Pons
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Marie-France Portnoï
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France
| | - Fabienne Prieur
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | | | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Marlène Rio
- Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Paris, France
| | - Caroline Rooryck-Thambo
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Massimiliano Rossi
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | - Catherine Sarret
- Service de Génétique Médicale, Hôpital Estaing, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Véronique Satre
- Laboratoire de Génétique Chromosomique, Hôpital Couple Enfant, CHU Grenoble, Grenoble, France.,Equipe Génétique, Epigénétique et Thérapies de l'Infertilité, IAB, INSERM 1209, CNRS UMR5309, Grenoble, France
| | - Jean-Pierre Siffroi
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France
| | - Marianne Till
- Service de Génétique, Hospices Civils de Lyon, Bron, France
| | - Renaud Touraine
- Service de Génétique Clinique, Chromosomique et Moléculaire, CHU Hôpital Nord, Saint-Etienne, France
| | | | - Jérome Toutain
- Service de Génétique Médicale, Hôpital Pellegrin, Université de Bordeaux, MRGM INSERM U1211, CHU Bordeaux, Bordeaux, France
| | - Stéphanie Valence
- GRC n°19, pathologies Congénitales du Cervelet-LeucoDystrophies, AP-HP, Hôpital Armand Trousseau, Sorbonne Université, Paris, France.,Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP, GHUEP, Paris, France
| | - Alain Verloes
- Département de Génétique, Hôpital Robert Debré, Paris, France
| | - Sandra Whalen
- Département de génétique et embryologie médicale, Centre de référence des déficiences intellectuelles de causes rares, AP-HP, Hôpital Armand Trousseau, Paris, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
| | | | - Damien Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, UCBL1, GENDEV Team, Neurosciences Research Center of Lyon, Bron, France
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27
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Kurtas NE, Xumerle L, Giussani U, Pansa A, Cardarelli L, Bertini V, Valetto A, Liehr T, Clara Bonaglia M, Errichiello E, Delledonne M, Zuffardi O. Insertional translocation involving an additional nonchromothriptic chromosome in constitutional chromothripsis: Rule or exception? Mol Genet Genomic Med 2018; 7:e00496. [PMID: 30565424 PMCID: PMC6393660 DOI: 10.1002/mgg3.496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/06/2018] [Accepted: 10/02/2018] [Indexed: 01/17/2023] Open
Abstract
Background Chromothripsis, which is the local massive shattering of one or more chromosomes and their reassembly in a disordered array with frequent loss of some fragments, has been mainly reported in association with abnormal phenotypes. We report three unrelated healthy persons, two of which parenting a child with some degree of intellectual disability, carrying a chromothripsis involving respectively one, two, and three chromosomes, which was detected only after whole‐genome sequencing. Unexpectedly, in all three cases a fragment from one of the chromothripsed chromosomes resulted to be inserted within a nonchromothripsed one. Methods Conventional cytogenetic techniques, paired‐end whole‐genome sequencing, polymerase chain reaction, and Sanger sequencing were used to characterize complex rearrangements, copy‐number variations, and breakpoint sequences in all three families. Results In two families, one parent was carrier of a balanced chromothripsis causing in the index case a deletion and a noncontiguous duplication at 3q in case 1, and a t(6;14) translocation associated with interstitial 14q deletion in case 2. In the third family, an unbalanced chromothripsis involving chromosomes 6, 7, and 15 was inherited to the proband by the mosaic parent. In all three parents, the chromothripsis was concurrent with an insertional translocation of a portion of one of the chromothriptic chromosomes within a further chromosome that was not involved in the chromothripsis event. Conclusion Our findings show that (a) both simple and complex unbalanced rearrangements may result by the recombination of a cryptic parental balanced chromothripsis and that (b) insertional translocations are the spy of more complex rearrangements and not simply a three‐breakpoint event.
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Affiliation(s)
| | - Luciano Xumerle
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | | | | | | | | | | | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Lecco, Italy
| | | | - Massimo Delledonne
- Personal Genomics srl, Department of Biotechnologies, University of Verona, Verona, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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28
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Murcia Pienkowski V, Kucharczyk M, Młynek M, Szczałuba K, Rydzanicz M, Poszewiecka B, Skórka A, Sykulski M, Biernacka A, Koppolu AA, Posmyk R, Walczak A, Kosińska J, Krajewski P, Castaneda J, Obersztyn E, Jurkiewicz E, Śmigiel R, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Mapping of breakpoints in balanced chromosomal translocations by shallow whole-genome sequencing points to EFNA5, BAHD1 and PPP2R5E as novel candidates for genes causing human Mendelian disorders. J Med Genet 2018; 56:104-112. [PMID: 30352868 DOI: 10.1136/jmedgenet-2018-105527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mapping the breakpoints in de novo balanced chromosomal translocations (BCT) in symptomatic individuals provides a unique opportunity to identify in an unbiased way the likely causative genetic defect and thus find novel human disease candidate genes. Our aim was to fine-map breakpoints of de novo BCTs in a case series of nine patients. METHODS Shallow whole-genome mate pair sequencing (SGMPS) together with long-range PCR and Sanger sequencing. In one case (BCT disrupting BAHD1 and RET) cDNA analysis was used to verify expression of a fusion transcript in cultured fibroblasts. RESULTS In all nine probands 11 disrupted genes were found, that is, EFNA5, EBF3, LARGE, PPP2R5E, TXNDC5, ZNF423, NIPBL, BAHD1, RET, TRPS1 and SLC4A10. Five subjects had translocations that disrupted genes with so far unknown (EFNA5, BAHD1, PPP2R5E, TXNDC5) or poorly delineated impact on the phenotype (SLC4A10, two previous reports of BCT disrupting the gene). The four genes with no previous disease associations (EFNA5, BAHD1, PPP2R5E, TXNDC5), when compared with all human genes by a bootstrap test, had significantly higher pLI (p<0.017) and DOMINO (p<0.02) scores indicating enrichment in genes likely to be intolerant to single copy damage. Inspection of individual pLI and DOMINO scores, and local topologically associating domain structure suggested that EFNA5, BAHD1 and PPP2R5E were particularly good candidates for novel disease loci. The pathomechanism for BAHD1 may involve deregulation of expression due to fusion with RET promoter. CONCLUSION SGMPS in symptomatic carriers of BCTs is a powerful approach to delineate novel human gene-disease associations.
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Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marlena Młynek
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Barbara Poszewiecka
- Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Agata Skórka
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland.,Department of Pediatrics, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Sykulski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,genXone, Poznan, Poland
| | - Anna Biernacka
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Anna Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Renata Posmyk
- Department of Clinical Genetics, Podlaskie Medical Center, Bialystok, Poland.,Department of Perinatology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Jennifer Castaneda
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Diagnostic Imaging, The Children's Memorial Health Institute, Warsaw, Poland
| | - Robert Śmigiel
- Department of Pediatrics and Rare Disorder, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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29
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Aristidou C, Theodosiou A, Bak M, Mehrjouy MM, Constantinou E, Alexandrou A, Papaevripidou I, Christophidou-Anastasiadou V, Skordis N, Kitsiou-Tzeli S, Tommerup N, Sismani C. Position effect, cryptic complexity, and direct gene disruption as disease mechanisms in de novo apparently balanced translocation cases. PLoS One 2018; 13:e0205298. [PMID: 30289920 PMCID: PMC6173455 DOI: 10.1371/journal.pone.0205298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/21/2018] [Indexed: 12/03/2022] Open
Abstract
The majority of apparently balanced translocation (ABT) carriers are phenotypically normal. However, several mechanisms were proposed to underlie phenotypes in affected ABT cases. In the current study, whole-genome mate-pair sequencing (WG-MPS) followed by Sanger sequencing was applied to further characterize de novo ABTs in three affected individuals. WG-MPS precisely mapped all ABT breakpoints and revealed three possible underlying molecular mechanisms. Firstly, in a t(X;1) carrier with hearing loss, a highly skewed X-inactivation pattern was observed and the der(X) breakpoint mapped ~87kb upstream an X-linked deafness gene namely POU3F4, thus suggesting an underlying long-range position effect mechanism. Secondly, cryptic complexity and a chromothripsis rearrangement was identified in a t(6;7;8;12) carrier with intellectual disability. Two translocations and a heterozygous deletion disrupted SOX5; a dominant nervous system development gene previously reported in similar patients. Finally, a direct gene disruption mechanism was proposed in a t(4;9) carrier with dysmorphic facial features and speech delay. In this case, the der(9) breakpoint directly disrupted NFIB, a gene involved in lung maturation and development of the pons with important functions in main speech processes. To conclude, in contrast to familial ABT cases with identical rearrangements and discordant phenotypes, where translocations are considered coincidental, translocations seem to be associated with phenotype presentation in affected de novo ABT cases. In addition, this study highlights the importance of investigating both coding and non-coding regions to decipher the underlying pathogenic mechanisms in these patients, and supports the potential introduction of low coverage WG-MPS in the clinical investigation of de novo ABTs.
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Affiliation(s)
- Constantia Aristidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Athina Theodosiou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N., Denmark
| | - Mana M. Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N., Denmark
| | - Efthymia Constantinou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Nicos Skordis
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- St George’s University of London Medical School at the University of Nicosia, Nicosia, Cyprus
| | - Sophia Kitsiou-Tzeli
- Department of Medical Genetics, Medical School, University of Athens, Athens, Greece
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N., Denmark
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- * E-mail:
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