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Lehtonen J, Sulonen AM, Almusa H, Lehtokari VL, Johari M, Palva A, Hakonen AH, Wartiovaara K, Lehesjoki AE, Udd B, Wallgren-Pettersson C, Pelin K, Savarese M, Saarela J. Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield. Sci Rep 2024; 14:4306. [PMID: 38383731 PMCID: PMC10881483 DOI: 10.1038/s41598-024-54866-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 02/17/2024] [Indexed: 02/23/2024] Open
Abstract
Rare or novel missense variants in large genes such as TTN and NEB are frequent in the general population, which hampers the interpretation of putative disease-causing biallelic variants in patients with sporadic neuromuscular disorders. Often, when the first initial genetic analysis is performed, the reconstructed haplotype, i.e. phasing information of the variants is missing. Segregation analysis increases the diagnostic turnaround time and is not always possible if samples from family members are lacking. To overcome this difficulty, we investigated how well the linked-read technology succeeded to phase variants in these large genes, and whether it improved the identification of structural variants. Linked-read sequencing data of nemaline myopathy, distal myopathy, and proximal myopathy patients were analyzed for phasing, single nucleotide variants, and structural variants. Variant phasing was successful in the large muscle genes studied. The longest continuous phase blocks were gained using high-quality DNA samples with long DNA fragments. Homozygosity increased the number of phase blocks, especially in exome sequencing samples lacking intronic variation. In our cohort, linked-read sequencing added more information about the structural variation but did not lead to a molecular genetic diagnosis. The linked-read technology can support the clinical diagnosis of neuromuscular and other genetic disorders.
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Affiliation(s)
- Johanna Lehtonen
- Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna-Maija Sulonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Vilma-Lotta Lehtokari
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Aino Palva
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anna H Hakonen
- Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | | | - Anna-Elina Lehesjoki
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marco Savarese
- Folkhälsan Research Center, Folkhälsan Institute of Genetics, Helsinki, Finland
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Janna Saarela
- Centre for Molecular Medicine Norway (NCMM), University of Oslo, Oslo, Norway.
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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2
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Zenagui R, Bernicot I, Ranisavljevic N, Ferrieres-Hoa A, Puechberty J, Anahory T. Whole-genome analysis of a putative rare and complex interchromosomal reciprocal insertion: thorough investigations for a straightforward interpretation. Reprod Biomed Online 2021; 44:636-640. [DOI: 10.1016/j.rbmo.2021.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
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3
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Maroilley T, Li X, Oldach M, Jean F, Stasiuk SJ, Tarailo-Graovac M. Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing. Sci Rep 2021; 11:18258. [PMID: 34521941 PMCID: PMC8440550 DOI: 10.1038/s41598-021-97764-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.
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Affiliation(s)
- Tatiana Maroilley
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Xiao Li
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Matthew Oldach
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Francesca Jean
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Susan J Stasiuk
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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4
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Donaldson B, Villagomez DAF, King WA. Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective. Animals (Basel) 2021; 11:1257. [PMID: 33925534 PMCID: PMC8146943 DOI: 10.3390/ani11051257] [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: 03/21/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.
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Affiliation(s)
- Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | | | - W. Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Karyotekk Inc., Box 363 OVC, University of Guelph, Guelph, ON N1G 2W1, Canada
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Kumar A, Adhikari S, Kankainen M, Heckman CA. Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma. Cancers (Basel) 2021; 13:1212. [PMID: 33802025 PMCID: PMC7999337 DOI: 10.3390/cancers13061212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Linked-read sequencing was developed to aid the detection of large structural variants (SVs) from short-read sequencing efforts. We performed a systematic evaluation to determine if linked-read exome sequencing provides more comprehensive and clinically relevant information than whole-exome sequencing (WES) when applied to the same set of multiple myeloma patient samples. We report that linked-read sequencing detected a higher number of SVs (n = 18,455) than WES (n = 4065). However, linked-read predictions were dominated by inversions (92.4%), leading to poor detection of other types of SVs. In contrast, WES detected 56.3% deletions, 32.6% insertions, 6.7% translocations, 3.3% duplications and 1.2% inversions. Surprisingly, the quantitative performance assessment suggested a higher performance for WES (AUC = 0.791) compared to linked-read sequencing (AUC = 0.766) for detecting clinically validated cytogenetic alterations. We also found that linked-read sequencing detected more short variants (n = 704) compared to WES (n = 109). WES detected somatic mutations in all MM-related genes while linked-read sequencing failed to detect certain mutations. The comparison of somatic mutations detected using linked-read, WES and RNA-seq revealed that WES and RNA-seq detected more mutations than linked-read sequencing. These data indicate that WES outperforms and is more efficient than linked-read sequencing for detecting clinically relevant SVs and MM-specific short variants.
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Affiliation(s)
- Ashwini Kumar
- Institute for Molecular Medicine Finland-FIMM, HiLIFE-Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Tukholmankatu 8, 00290 Helsinki, Finland; (A.K.); (S.A.)
- iCAN Digital Precision Cancer Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Sadiksha Adhikari
- Institute for Molecular Medicine Finland-FIMM, HiLIFE-Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Tukholmankatu 8, 00290 Helsinki, Finland; (A.K.); (S.A.)
- iCAN Digital Precision Cancer Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Matti Kankainen
- iCAN Digital Precision Cancer Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Medical and Clinical Genetics, University of Helsinki, Helsinki University Hospital, 00029 Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry, University of Helsinki, 00290 Helsinki, Finland
- Hematology Research Unit Helsinki, Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland-FIMM, HiLIFE-Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Tukholmankatu 8, 00290 Helsinki, Finland; (A.K.); (S.A.)
- iCAN Digital Precision Cancer Medicine, University of Helsinki, 00014 Helsinki, Finland;
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6
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Linked-Read Whole Genome Sequencing Solves a Double DMD Gene Rearrangement. Genes (Basel) 2021; 12:genes12020133. [PMID: 33494189 PMCID: PMC7909759 DOI: 10.3390/genes12020133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 01/25/2023] Open
Abstract
Next generation sequencing (NGS) has changed our approach to diagnosis of genetic disorders. Nowadays, the most comprehensive application of NGS is whole genome sequencing (WGS) that is able to detect virtually all DNA variations. However, even after accurate WGS, many genetic conditions remain unsolved. This may be due to the current NGS protocols, based on DNA fragmentation and short reads. To overcome these limitations, we applied a linked-read sequencing technology that combines single-molecule barcoding with short-read WGS. We were able to assemble haplotypes and distinguish between alleles along the genome. As an exemplary case, we studied the case of a female carrier of X-linked muscular dystrophy with an unsolved genetic status. A deletion of exons 16–29 in DMD gene was responsible for the disease in her family, but she showed a normal dosage of these exons by Multiplex Ligation-dependent Probe Amplification (MLPA) and array CGH. This situation is usually considered compatible with a “non-carrier” status. Unexpectedly, the girl also showed an increased dosage of flanking exons 1–15 and 30–34. Using linked-read WGS, we were able to distinguish between the two X chromosomes. In the first allele, we found the 16–29 deletion, while the second allele showed a 1–34 duplication: in both cases, linked-read WGS correctly mapped the borders at single-nucleotide resolution. This duplication in trans apparently restored the normal dosage of exons 16–29 seen by quantitative assays. This had a dramatic impact in genetic counselling, by converting a non-carrier into a double carrier status prediction. We conclude that linked-read WGS should be considered as a valuable option to improve our understanding of unsolved genetic conditions.
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7
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Delvallée C, Nicaise S, Antin M, Leuvrey AS, Nourisson E, Leitch CC, Kellaris G, Stoetzel C, Geoffroy V, Scheidecker S, Keren B, Depienne C, Klar J, Dahl N, Deleuze JF, Génin E, Redon R, Demurger F, Devriendt K, Mathieu-Dramard M, Poitou-Bernert C, Odent S, Katsanis N, Mandel JL, Davis EE, Dollfus H, Muller J. A BBS1 SVA F retrotransposon insertion is a frequent cause of Bardet-Biedl syndrome. Clin Genet 2020; 99:318-324. [PMID: 33169370 DOI: 10.1111/cge.13878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinitis pigmentosa, obesity, polydactyly, cognitive impairment and renal failure. Pathogenic variants in 24 genes account for the molecular basis of >80% of cases. Toward saturated discovery of the mutational basis of the disorder, we carefully explored our cohorts and identified a hominid-specific SINE-R/VNTR/Alu type F (SVA-F) insertion in exon 13 of BBS1 in eight families. In six families, the repeat insertion was found in trans with c.1169 T > G, p.Met390Arg and in two families the insertion was found in addition to other recessive BBS loci. Whole genome sequencing, de novo assembly and SNP array analysis were performed to characterize the genomic event. This insertion is extremely rare in the general population (found in 8 alleles of 8 BBS cases but not in >10 800 control individuals from gnomAD-SV) and due to a founder effect. Its 2435 bp sequence contains hallmarks of LINE1 mediated retrotransposition. Functional studies with patient-derived cell lines confirmed that the BBS1 SVA-F is deleterious as evidenced by a significant depletion of both mRNA and protein levels. Such findings highlight the importance of dedicated bioinformatics pipelines to identify all types of variation.
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Affiliation(s)
- Clarisse Delvallée
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Samuel Nicaise
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Manuela Antin
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anne-Sophie Leuvrey
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Elsa Nourisson
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Carmen C Leitch
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Georgios Kellaris
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Sophie Scheidecker
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Boris Keren
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Christel Depienne
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, Paris, France.,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de biologie François Jacob, Evry, France
| | | | - Richard Redon
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Florence Demurger
- Service de Génétique Médicale, Centre Hospitalier Bretagne Atlantique, Vannes, France
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | | | - Christine Poitou-Bernert
- Assistance Publique Hôpitaux de Paris, Nutrition Department Pitié-Salpêtrière Hospital; Sorbonne Université, INSERM, NutriOmics Research Unit, Paris, France
| | - Sylvie Odent
- Centre de Référence Maladies Rares CLAD-Ouest, Service de Génétique Clinique, CHU Rennes, Rennes, France.,CNRS, IGDR (Institut de Génétique et Développement de Rennes) UMR 6290, Université de Rennes, Rennes, France
| | - Nicholas Katsanis
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jean-Louis Mandel
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, Dept Transl Med and Neurogenetics Illkirch, France
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France.,Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Filière SENSGENE, Centre de Référence pour les affections rares en génétique ophtalmologique, CARGO, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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8
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Bouwman AC, Derks MFL, Broekhuijse MLWJ, Harlizius B, Veerkamp RF. Using short read sequencing to characterise balanced reciprocal translocations in pigs. BMC Genomics 2020; 21:576. [PMID: 32831014 PMCID: PMC7444045 DOI: 10.1186/s12864-020-06989-x] [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: 05/12/2020] [Accepted: 08/13/2020] [Indexed: 11/15/2022] Open
Abstract
Background A balanced constitutional reciprocal translocation (RT) is a mutual exchange of terminal segments of two non-homologous chromosomes without any loss or gain of DNA in germline cells. Carriers of balanced RTs are viable individuals with no apparent phenotypical consequences. These animals produce, however, unbalanced gametes and show therefore reduced fertility and offspring with congenital abnormalities. This cytogenetic abnormality is usually detected using chromosome staining techniques. The aim of this study was to test the possibilities of using paired end short read sequencing for detection of balanced RTs in boars and investigate their breakpoints and junctions. Results Balanced RTs were recovered in a blinded analysis, using structural variant calling software DELLY, in 6 of the 7 carriers with 30 fold short read paired end sequencing. In 15 non-carriers we did not detect any RTs. Reducing the coverage to 20 fold, 15 fold and 10 fold showed that at least 20 fold coverage is required to obtain good results. One RT was not detected using the blind screening, however, a highly likely RT was discovered after unblinding. This RT was located in a repetitive region, showing the limitations of short read sequence data. The detailed analysis of the breakpoints and junctions suggested three junctions showing microhomology, three junctions with blunt-end ligation, and three micro-insertions at the breakpoint junctions. The RTs detected also showed to disrupt genes. Conclusions We conclude that paired end short read sequence data can be used to detect and characterize balanced reciprocal translocations, if sequencing depth is at least 20 fold coverage. However, translocations in repetitive areas may require large fragments or even long read sequence data.
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Affiliation(s)
- Aniek C Bouwman
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.,Topigs Norsvin Research Center, 6640 AA, Beuningen, The Netherlands
| | | | | | - Roel F Veerkamp
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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9
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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: 8] [Impact Index Per Article: 2.0] [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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