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Lumaka A, Fasquelle C, Debray FG, Alkan S, Jacquinet A, Harvengt J, Boemer F, Mulder A, Vaessen S, Viellevoye R, Palmeira L, Charloteaux B, Brysse A, Bulk S, Rigo V, Bours V. Rapid Whole Genome Sequencing Diagnoses and Guides Treatment in Critically Ill Children in Belgium in Less than 40 Hours. Int J Mol Sci 2023; 24:4003. [PMID: 36835410 PMCID: PMC9967120 DOI: 10.3390/ijms24044003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/05/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Rapid Whole Genome Sequencing (rWGS) represents a valuable exploration in critically ill pediatric patients. Early diagnosis allows care to be adjusted. We evaluated the feasibility, turnaround time (TAT), yield, and utility of rWGS in Belgium. Twenty-one unrelated critically ill patients were recruited from the neonatal intensive care units, the pediatric intensive care unit, and the neuropediatric unit, and offered rWGS as a first tier test. Libraries were prepared in the laboratory of human genetics of the University of Liège using Illumina DNA PCR-free protocol. Sequencing was performed on a NovaSeq 6000 in trio for 19 and in duo for two probands. The TAT was calculated from the sample reception to the validation of results. Clinical utility data were provided by treating physicians. A definite diagnosis was reached in twelve (57.5%) patients in 39.80 h on average (range: 37.05-43.7). An unsuspected diagnosis was identified in seven patients. rWGS guided care adjustments in diagnosed patients, including a gene therapy, an off-label drug trial and two condition-specific treatments. We successfully implemented the fastest rWGS platform in Europe and obtained one of the highest rWGS yields. This study establishes the path for a nationwide semi-centered rWGS network in Belgium.
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Affiliation(s)
- Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | | | - Serpil Alkan
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Julie Harvengt
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - François Boemer
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - André Mulder
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, CHC Mont-Légia, 4000 Liège, Belgium
| | - Sandrine Vaessen
- Neuropediatric Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Renaud Viellevoye
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Leonor Palmeira
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Benoit Charloteaux
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Anne Brysse
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Saskia Bulk
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
| | - Vincent Rigo
- Neonatology Division, CHU de Liège—CHR de la Citadelle, University of Liège, 4000 Liège, Belgium
| | - Vincent Bours
- Human Genetic Laboratory, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Center for Human Genetics, Centre Hospitalier Universitaire, 4032 Liège, Belgium
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2
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Harvengt J, Lumaka A, Fasquelle C, Caberg JH, Mastouri M, Janssen A, Palmeira L, Bours V. HIDEA syndrome: A new case report highlighting similarities with ROHHAD syndrome. Front Genet 2023; 14:1137767. [PMID: 37035730 PMCID: PMC10073441 DOI: 10.3389/fgene.2023.1137767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Context: ROHHAD syndrome presents a significant resemblance to HIDEA syndrome. The latter is caused by biallelic loss-of-function variants in the P4HTM gene and encompasses hypotonia, intellectual disabilities, eye abnormalities, hypoventilation, and dysautonomia. We report the first patient identified with HIDEA syndrome from our ROHHAD cohort. Clinical case: Our patient was a 21-month-old girl who had a history of severe respiratory infections requiring intensive care, hypotonia, abnormal eye movements, and rapid weight gain. Polysomnography identified severe central hypoventilation. During her follow-up, a significant psychomotor delay and the absence of language were gradually observed. The prolactin levels were initially increased. Hypothermia was reported at 4 years. Exome sequencing identified a new homozygous truncating P4HTM variant. Discussion: Our patient met the diagnosis criteria for ROHHAD, which included rapid weight gain, central hypoventilation appearing after 1.5 years of age, hyperprolactinemia suggesting hypothalamic dysfunction, and autonomic dysfunction manifesting as strabismus and hypothermia. However, she also presented with severe neurodevelopmental delay, which is not a classic feature of ROHHAD syndrome. HIDEA syndrome presents similarities with ROHHAD, including hypoventilation, obesity, and dysautonomia. To date, only 14% of endocrinological disturbances have been reported in HIDEA patients. Better delineation of both syndromes is required to investigate the eventual involvement of P4HTM, a regulator of calcium dynamics and gliotransmission, in ROHHAD patients. Conclusion: In the case of clinical evidence of ROHHAD in a child with abnormal neurological development or eye abnormalities, we suggest that the P4HTM gene be systematically interrogated in addition to the analysis of the PHOX2B gene. A better delineation of the natural history of HIDEA is required to allow further comparisons between features of HIDEA and ROHHAD. The clinical similarities could potentially orient some molecular hypotheses in the field of ROHHAD research.
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Affiliation(s)
- J. Harvengt
- Human Genetics Department, CHU of Liège, Liège, Belgium
- GIGA Research, University of Liège, Liège, Belgium
- *Correspondence: J. Harvengt,
| | - A. Lumaka
- Human Genetics Department, CHU of Liège, Liège, Belgium
- GIGA Research, University of Liège, Liège, Belgium
| | - C. Fasquelle
- Human Genetics Department, CHU of Liège, Liège, Belgium
- GIGA Research, University of Liège, Liège, Belgium
| | - J. H. Caberg
- Human Genetics Department, CHU of Liège, Liège, Belgium
| | - M. Mastouri
- Pediatric Department, Hospital Center of Luxembourg, Luxembourg City, Luxembourg
| | - A. Janssen
- Pediatric Department, CHU of Liège, Liège, Belgium
| | - L. Palmeira
- Human Genetics Department, CHU of Liège, Liège, Belgium
- GIGA Research, University of Liège, Liège, Belgium
| | - V. Bours
- Human Genetics Department, CHU of Liège, Liège, Belgium
- GIGA Research, University of Liège, Liège, Belgium
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3
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Freire MV, Martin M, Thissen R, Van Marcke C, Segers K, Sépulchre E, Leroi N, Lété C, Fasquelle C, Radermacher J, Gokburun Y, Collignon J, Sacré A, Josse C, Palmeira L, Bours V. Case Report Series: Aggressive HR Deficient Colorectal Cancers Related to BRCA1 Pathogenic Germline Variants. Front Oncol 2022; 12:835581. [PMID: 35280729 PMCID: PMC8911702 DOI: 10.3389/fonc.2022.835581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/01/2022] [Indexed: 12/31/2022] Open
Abstract
Objective The link between BRCA1 and homologous recombination deficiency (HRD) in cancer has gained importance with the emergence of new targeted cancer treatments, while the available data on the role of the gene in colorectal cancer (CRC) remain contradictory. The aim of this case series was to elucidate the role of known pathogenic BRCA1 variants in the development of early-onset CRC. Design Patients were evaluated using targeted next generation sequencing, exome sequencing and chromosomal microarray analysis of the paired germline and tumor samples. These results were used to calculate the HRD score and the frequency of mutational signatures in the tumors. Results Three patients with metastatic CRC were heterozygous for a previously known BRCA1 nonsense variant. All tumors showed remarkably high HRD scores, and the HRD-related signature 3 had the second highest contribution to the somatic pattern of variant accumulation in the samples (23% in 1 and 2, and 13% in sample 3). Conclusions A BRCA1 germline pathogenic variant can be involved in CRC development through HRD. Thus, BRCA1 testing should be considered in young patients with a personal history of microsatellite stable CRC as this could further allow a personalized treatment approach.
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Affiliation(s)
- Maria Valeria Freire
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Marie Martin
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Romain Thissen
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Cédric Van Marcke
- Institute for Experimental and Clinical Research (Institut de Recherche Expérimentale et Clinique (IREC), Pôle Molecular Imaging, Radiotherapy and Oncology (MIRO)), Université Catholique de Louvain (UCLouvain), Brussels, Belgium.,Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Karin Segers
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Edith Sépulchre
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Natacha Leroi
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Céline Lété
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Corinne Fasquelle
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Jean Radermacher
- Department of Pathology, Institut de Pathologie et de Génétique, Charleroi, Belgium
| | - Yeter Gokburun
- Department of Gastroenterology, Centre Hospitalier Régional Sambre et Meuse, Namur, Belgium
| | - Joelle Collignon
- Department of Medical Oncology, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Anne Sacré
- Onco-Hematology Department, Centre Hospitalier Régional (CHR) Verviers, Verviers, Belgium
| | - Claire Josse
- Department of Medical Oncology, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Leonor Palmeira
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
| | - Vincent Bours
- Department of Human Genetics, GIGA Research Center - University of Liège and Centre Hospitalier Universitaire (CHU) Liège, Liège, Belgium
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4
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Uyisenga JP, Segers K, Lumaka AZ, Mugenzi P, Fasquelle C, Boujemila B, Josse C, Mutesa L, Bours V. Screening of germline mutations in young Rwandan patients with breast cancers. Mol Genet Genomic Med 2020; 8:e1500. [PMID: 32959997 PMCID: PMC7667342 DOI: 10.1002/mgg3.1500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
Background In Sub‐Saharan Africa breast cancer is commonly detected at younger age and the profile is more aggressive with a high mortality rate compared to the European countries. It is suggested that African‐specific genetic background plays a key role in this matter. The present study aimed at understanding the role of genetic factors in breast cancer development in young Rwandan. Methods We performed a massive parallel sequencing on Illumina MiSeq NGS system for the screening of 26 genes associated with hereditary breast cancer from 40 patients under 35 years old from two University Teaching Hospitals in Kigali, Rwanda. Sanger sequencing was used to confirm pathogenic and likely pathogenic mutations. Results Five patients out of 40 (12.5%) presented with pathogenic mutations including four patients (10%) carrying BRCA1 or BRCA2 pathogenic variants. One patient showed a missense likely pathogenic TP53 variant. We have also detected additional missense, intronic, and 3’UTR variants of unknown significance in all study participants. Conclusion This preliminary study suggests that the frequency of germline mutations in young Rwandan patients with breast cancer is similar to the observations made in Caucasians. However, further large studies including patients and controls are needed to better understand the impact of genetic factors as well as the environmental risk factors in the development of breast cancer in young Rwandans. Screening of germline mutations in Rwandan young patients with breast cancer. The next generation sequencing detected pathogenic BRCA 1 and 2 mutations in 6 patients. We have also detected additional missense, intronic, and 3’UTR variants of unknown significance in all study participants.
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Affiliation(s)
- Jeanne P Uyisenga
- Laboratory of Human Genetics, GIGA Research Institute, University of Liège, Liège, Belgium.,Department of Biology, College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Karin Segers
- Department of Human Genetics, University Hospital of Liège CHU Liège, Liège, Belgium
| | - Aimé Z Lumaka
- Laboratory of Human Genetics, GIGA Research Institute, University of Liège, Liège, Belgium
| | | | - Corinne Fasquelle
- Laboratory of Human Genetics, GIGA Research Institute, University of Liège, Liège, Belgium
| | - Bouchra Boujemila
- Laboratory of Human Genetics, GIGA Research Institute, University of Liège, Liège, Belgium
| | - Claire Josse
- Laboratory of Human Genetics, GIGA Research Institute, University of Liège, Liège, Belgium.,Department of Medical Oncology, University Hospital of Liège CHU Liège, Liège, Belgium
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA Research Institute, University of Liège, Liège, Belgium.,Department of Human Genetics, University Hospital of Liège CHU Liège, Liège, Belgium
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5
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Jacquinet A, Boujemla B, Fasquelle C, Thiry J, Josse C, Lumaka A, Brischoux-Boucher E, Dubourg C, David V, Pasquier L, Lehman A, Morcel K, Guerrier D, Bours V. GREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer-Rokitansky-Kuster-Hauser syndrome. Clin Genet 2020; 98:126-137. [PMID: 32378186 DOI: 10.1111/cge.13769] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance.
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Affiliation(s)
- Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Bouchra Boujemla
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium
| | - Jerôme Thiry
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Claire Josse
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium.,Medical Oncology, Centre Hospitalier Universitaire CHU Liege, Liège, Belgium
| | - Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Christèle Dubourg
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Véronique David
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Laurent Pasquier
- Department of Medical Genetics, CLAD Ouest, Université de Rennes, CHU Rennes, Rennes, France
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, BC Children's Hospital and BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Karine Morcel
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Daniel Guerrier
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Vincent Bours
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
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6
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Wenric S, ElGuendi S, Caberg JH, Bezzaou W, Fasquelle C, Charloteaux B, Karim L, Hennuy B, Frères P, Collignon J, Boukerroucha M, Schroeder H, Olivier F, Jossa V, Jerusalem G, Josse C, Bours V. Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer. Sci Rep 2017; 7:17452. [PMID: 29234122 PMCID: PMC5727077 DOI: 10.1038/s41598-017-17811-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023] Open
Abstract
Non-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% of the genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense transcripts (ncNAT) are RNA sequences that are complementary and overlapping to those of either protein-coding (PCT) or non-coding transcripts. Several ncNATs were described as regulating protein coding gene expression on the same loci, and they are expected to act more frequently in cis compared to other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired adjacent non-malignant tissues were analyzed by strand-specific RNA sequencing. To highlight ncNATs potentially playing a role in protein coding gene regulations that occur in breast cancer, three different data analysis methods were used: differential expression analysis of ncNATs between tumor and non-malignant tissues, differential correlation analysis of paired ncNAT/PCT between tumor and non-malignant tissues, and ncNAT/PCT read count ratio variation between tumor and non-malignant tissues. Each of these methods yielded lists of ncNAT/PCT pairs that were enriched in survival-associated genes. This work highlights ncNAT lists that display potential to affect the expression of protein-coding genes involved in breast cancer pathology.
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Affiliation(s)
- Stephane Wenric
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium.,University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Sonia ElGuendi
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium
| | | | - Warda Bezzaou
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium
| | - Corinne Fasquelle
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium
| | | | - Latifa Karim
- University of Liège, GIGA-Genomics Platform, Liege, Belgium
| | - Benoit Hennuy
- University of Liège, GIGA-Genomics Platform, Liege, Belgium
| | - Pierre Frères
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Joëlle Collignon
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | | | - Hélène Schroeder
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Fabrice Olivier
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Véronique Jossa
- Clinique Saint-Vincent (CHC), Department of Pathology, Liege, Belgium
| | - Guy Jerusalem
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Claire Josse
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium. .,University Hospital (CHU), Department of Medical Oncology, Liege, Belgium.
| | - Vincent Bours
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium.,University Hospital (CHU), Center of Genetics, Liege, Belgium
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7
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Frères P, Wenric S, Boukerroucha M, Fasquelle C, Thiry J, Bovy N, Struman I, Geurts P, Collignon J, Schroeder H, Kridelka F, Lifrange E, Jossa V, Bours V, Josse C, Jerusalem G. Circulating microRNA-based screening tool for breast cancer. Oncotarget 2016; 7:5416-28. [PMID: 26734993 PMCID: PMC4868695 DOI: 10.18632/oncotarget.6786] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/05/2015] [Indexed: 12/20/2022] Open
Abstract
Circulating microRNAs (miRNAs) are increasingly recognized as powerful biomarkers in several pathologies, including breast cancer. Here, their plasmatic levels were measured to be used as an alternative screening procedure to mammography for breast cancer diagnosis. A plasma miRNA profile was determined by RT-qPCR in a cohort of 378 women. A diagnostic model was designed based on the expression of 8 miRNAs measured first in a profiling cohort composed of 41 primary breast cancers and 45 controls, and further validated in diverse cohorts composed of 108 primary breast cancers, 88 controls, 35 breast cancers in remission, 31 metastatic breast cancers and 30 gynecologic tumors. A receiver operating characteristic curve derived from the 8-miRNA random forest based diagnostic tool exhibited an area under the curve of 0.81. The accuracy of the diagnostic tool remained unchanged considering age and tumor stage. The miRNA signature correctly identified patients with metastatic breast cancer. The use of the classification model on cohorts of patients with breast cancers in remission and with gynecologic cancers yielded prediction distributions similar to that of the control group. Using a multivariate supervised learning method and a set of 8 circulating miRNAs, we designed an accurate, minimally invasive screening tool for breast cancer.
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Affiliation(s)
- Pierre Frères
- University Hospital (CHU), Department of Medical Oncology, Liège, Belgium.,University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Stéphane Wenric
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Meriem Boukerroucha
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Corinne Fasquelle
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Jérôme Thiry
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Nicolas Bovy
- University of Liège, GIGA-Research, Laboratory of Molecular Angiogenesis, Liège, Belgium
| | - Ingrid Struman
- University of Liège, GIGA-Research, Laboratory of Molecular Angiogenesis, Liège, Belgium
| | - Pierre Geurts
- University of Liège, GIGA-Research, Department of EE and CS, Liège, Belgium
| | - Joëlle Collignon
- University Hospital (CHU), Department of Medical Oncology, Liège, Belgium
| | - Hélène Schroeder
- University Hospital (CHU), Department of Medical Oncology, Liège, Belgium
| | | | - Eric Lifrange
- University Hospital (CHU), Department of Senology, Liège, Belgium
| | - Véronique Jossa
- Clinique Saint-Vincent (CHC), Department of Pathology, Liège, Belgium
| | - Vincent Bours
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Claire Josse
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liège, Belgium
| | - Guy Jerusalem
- University Hospital (CHU), Department of Medical Oncology, Liège, Belgium
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8
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Wenric S, Sticca T, Caberg JH, Josse C, Fasquelle C, Herens C, Jamar M, Max S, Gothot A, Caers J, Bours V. Exome copy number variation detection: Use of a pool of unrelated healthy tissue as reference sample. Genet Epidemiol 2016; 41:35-40. [PMID: 27862228 DOI: 10.1002/gepi.22019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/09/2016] [Accepted: 09/21/2016] [Indexed: 11/06/2022]
Abstract
An increasing number of bioinformatic tools designed to detect CNVs (copy number variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been published in the recent years. The idea of using a pool of unrelated healthy DNA as reference has previously been formulated but not thoroughly validated. As of today, the gold standard for CNV calling is still aCGH but there is an increasing interest in detecting CNVs by exome sequencing. We propose to design a metric allowing the comparison of two CNV profiles, independently of the technique used and assessed the validity of using a pool of unrelated healthy DNA instead of a matched healthy tissue as reference in exome-based CNV detection. We compared the CNV profiles obtained with three different approaches (aCGH, exome sequencing with a matched healthy tissue as reference, exome sequencing with a pool of eight unrelated healthy tissue as reference) on three multiple myeloma samples. We show that the usual analyses performed to compare CNV profiles (deletion/amplification ratios and CNV size distribution) lack in precision when confronted with low LRR values, as they only consider the binary status of each CNV. We show that the metric-based distance constitutes a more accurate comparison of two CNV profiles. Based on these analyses, we conclude that a reliable picture of CNV alterations in multiple myeloma samples can be obtained from whole-exome sequencing in the absence of a matched healthy sample.
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Affiliation(s)
- Stephane Wenric
- Laboratory of Human Genetics, GIGA-Research, University of Liège, Liège, Belgium
| | - Tiberio Sticca
- Laboratory of Human Genetics, GIGA-Research, University of Liège, Liège, Belgium
| | | | - Claire Josse
- Laboratory of Human Genetics, GIGA-Research, University of Liège, Liège, Belgium
| | - Corinne Fasquelle
- Laboratory of Human Genetics, GIGA-Research, University of Liège, Liège, Belgium
| | - Christian Herens
- Department of Human Genetics, University Hospital (CHU), Liège, Belgium
| | - Mauricette Jamar
- Department of Human Genetics, University Hospital (CHU), Liège, Belgium
| | - Stéphanie Max
- Department of Haematology and Immuno-haematology, University Hospital (CHU), Liège, Belgium
| | - André Gothot
- Department of Haematology and Immuno-haematology, University Hospital (CHU), Liège, Belgium
| | - Jo Caers
- Laboratory of Haematology, GIGA-Research, University of Liège, Liège, Belgium.,Department of Clinical Haematology, University Hospital (CHU), Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Research, University of Liège, Liège, Belgium.,Department of Human Genetics, University Hospital (CHU), Liège, Belgium
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9
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Sartelet A, Li W, Pailhoux E, Richard C, Tamma N, Karim L, Fasquelle C, Druet T, Coppieters W, Georges M, Charlier C. Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. BMC Genomics 2015; 16:316. [PMID: 25895751 PMCID: PMC4404575 DOI: 10.1186/s12864-015-1528-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cattle populations are characterized by regular outburst of genetic defects as a result of the extensive use of elite sires. The causative genes and mutations can nowadays be rapidly identified by means of genome-wide association studies combined with next generation DNA sequencing, provided that the causative mutations are conventional loss-of-function variants. We show in this work how the combined use of next generation DNA and RNA sequencing allows for the rapid identification of otherwise difficult to identify splice-site variants. RESULTS We report the use of haplotype-based association mapping to identify a locus on bovine chromosome 10 that underlies autosomal recessive arthrogryposis in Belgian Blue Cattle. We identify 31 candidate mutations by resequencing the genome of four cases and 15 controls at ~10-fold depth. By analyzing RNA-Seq data from a carrier fetus, we observe skipping of the second exon of the PIGH gene, which we confirm by RT-PCR to be fully penetrant in tissues from affected calves. We identify - amongst the 31 candidate variants - a C-to-G transversion in the first intron of the PIGH gene (c211-10C > G) that is predicted to affect its acceptor splice-site. The resulting PIGH protein is likely to be non-functional as it lacks essential domains, and hence to cause arthrogryposis. CONCLUSIONS This work illustrates how the growing arsenal of genome exploration tools continues to accelerate the identification of an even broader range of disease causing mutations, therefore improving the management and control of genetic defects in livestock.
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Affiliation(s)
- Arnaud Sartelet
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Wanbo Li
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Eric Pailhoux
- INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Christophe Richard
- INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Nico Tamma
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Latifa Karim
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
- GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Corinne Fasquelle
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Tom Druet
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Wouter Coppieters
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
- GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Michel Georges
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Carole Charlier
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
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10
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Sartelet A, Stauber T, Coppieters W, Ludwig CF, Fasquelle C, Druet T, Zhang Z, Ahariz N, Cambisano N, Jentsch TJ, Charlier C. A missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle. Dis Model Mech 2013; 7:119-28. [PMID: 24159188 PMCID: PMC3882054 DOI: 10.1242/dmm.012500] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Chloride-proton exchange by the lysosomal anion transporter ClC-7/Ostm1 is of pivotal importance for the physiology of lysosomes and bone resorption. Mice lacking either ClC-7 or Ostm1 develop a lysosomal storage disease and mutations in either protein have been found to underlie osteopetrosis in mice and humans. Some human disease-causing CLCN7 mutations accelerate the usually slow voltage-dependent gating of ClC-7/Ostm1. However, it has remained unclear whether the fastened kinetics is indeed causative for the disease. Here we identified and characterized a new deleterious ClC-7 mutation in Belgian Blue cattle with a severe symptomatology including perinatal lethality and in most cases gingival hamartomas. By autozygosity mapping and genome-wide sequencing we found a handful of candidate variants, including a cluster of three private SNPs causing the substitution of a conserved tyrosine in the CBS2 domain of ClC-7 by glutamine. The case for ClC-7 was strengthened by subsequent examination of affected calves that revealed severe osteopetrosis. The Y750Q mutation largely preserved the lysosomal localization and assembly of ClC-7/Ostm1, but drastically accelerated its activation by membrane depolarization. These data provide first evidence that accelerated ClC-7/Ostm1 gating per se is deleterious, highlighting a physiological importance of the slow voltage-activation of ClC-7/Ostm1 in lysosomal function and bone resorption.
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Affiliation(s)
- Arnaud Sartelet
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège (B34), 1 Avenue de l'Hôpital, 4000-Liège (Sart Tilman), Belgium
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11
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Charlier C, Agerholm JS, Coppieters W, Karlskov-Mortensen P, Li W, de Jong G, Fasquelle C, Karim L, Cirera S, Cambisano N, Ahariz N, Mullaart E, Georges M, Fredholm M. A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina. PLoS One 2012; 7:e43085. [PMID: 22952632 PMCID: PMC3430679 DOI: 10.1371/journal.pone.0043085] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Fertility is one of the most important traits in dairy cattle, and has been steadily declining over the last decades. We herein use state-of-the-art genomic tools, including high-throughput SNP genotyping and next-generation sequencing, to identify a 3.3 Kb deletion in the FANCI gene causing the brachyspina syndrome (BS), a rare recessive genetic defect in Holstein dairy cattle. We determine that despite the very low incidence of BS (<1/100,000), carrier frequency is as high as 7.4% in the Holstein breed. We demonstrate that this apparent discrepancy is likely due to the fact that a large proportion of homozygous mutant calves die during pregnancy. We postulate that several other embryonic lethals may segregate in livestock and significantly compromise fertility, and propose a genotype-driven screening strategy to detect the corresponding deleterious mutations.
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Affiliation(s)
- Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- * E-mail: (CC); (MF)
| | - Jorgen Steen Agerholm
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- GIGA-R Genotranscriptomics Core Facility, University of Liège (B34), Liège, Belgium
| | - Peter Karlskov-Mortensen
- Division of Genetics and Bioinformatics, Department of Animal and Veterinary Basic Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Wanbo Li
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Corinne Fasquelle
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- GIGA-R Genotranscriptomics Core Facility, University of Liège (B34), Liège, Belgium
| | - Susanna Cirera
- Division of Genetics and Bioinformatics, Department of Animal and Veterinary Basic Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Nadine Cambisano
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Naima Ahariz
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Merete Fredholm
- Division of Genetics and Bioinformatics, Department of Animal and Veterinary Basic Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (CC); (MF)
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12
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Sartelet A, Druet T, Michaux C, Fasquelle C, Géron S, Tamma N, Zhang Z, Coppieters W, Georges M, Charlier C. A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory response. PLoS Genet 2012; 8:e1002581. [PMID: 22438830 PMCID: PMC3305398 DOI: 10.1371/journal.pgen.1002581] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 01/19/2012] [Indexed: 01/25/2023] Open
Abstract
We report association mapping of a locus on bovine chromosome 3 that underlies a Mendelian form of stunted growth in Belgian Blue Cattle (BBC). By resequencing positional candidates, we identify the causative c124-2A>G splice variant in intron 1 of the RNF11 gene, for which all affected animals are homozygous. We make the remarkable observation that 26% of healthy Belgian Blue animals carry the corresponding variant. We demonstrate in a prospective study design that approximately one third of homozygous mutants die prematurely with major inflammatory lesions, hence explaining the rarity of growth-stunted animals despite the high frequency of carriers. We provide preliminary evidence that heterozygous advantage for an as of yet unidentified phenotype may have caused a selective sweep accounting for the high frequency of the RNF11 c124-2A>G mutation in Belgian Blue Cattle. Recessive defects in livestock are common, and this is considered to result from the contraction of the effective population size that accompanies intense selection for desired traits, especially when relying heavily on artificial insemination (as males may concomitantly have a very large number of offspring). The costs of recessive defects are assumed to correspond to the loss of the affected animals. By performing a molecular genetic analysis of stunted growth in Belgian Blue Cattle (BBC), we highlight (i) that the economic impact of recessive defects may outweigh the only loss of affected animals and (ii) that some genetic defects are common for reasons other than inbreeding. We first demonstrate that a splice site variant in the RING finger protein 11 (RNF11) gene accounts for ∼40% of cases of stunted growth in BBC. We then show that a large proportion of animals that are homozygous for the corresponding RNF11 mutation die at a young age due to compromised resistance to pathogens. We finally demonstrate that carriers of the mutation benefit from a selective advantage of unidentified origin that accounts for its high frequency in BBC.
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Affiliation(s)
- Arnaud Sartelet
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Charles Michaux
- Unit of Bioinformatics, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Corinne Fasquelle
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Sarah Géron
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Nico Tamma
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Zhiyan Zhang
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R and Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- * E-mail:
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13
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Durkin K, Coppieters W, Drögemüller C, Ahariz N, Cambisano N, Druet T, Fasquelle C, Haile A, Horin P, Huang L, Kamatani Y, Karim L, Lathrop M, Moser S, Oldenbroek K, Rieder S, Sartelet A, Sölkner J, Stålhammar H, Zelenika D, Zhang Z, Leeb T, Georges M, Charlier C. Serial translocation by means of circular intermediates underlies colour sidedness in cattle. Nature 2012; 482:81-4. [PMID: 22297974 DOI: 10.1038/nature10757] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 12/05/2011] [Indexed: 11/09/2022]
Abstract
Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips. It is also referred to as 'lineback' or 'witrik' (which means white back), as colour-sided animals typically display a white band along their spine. Colour sidedness is documented at least since the Middle Ages and is presently segregating in several cattle breeds around the globe, including in Belgian blue and brown Swiss. Here we report that colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism.
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Affiliation(s)
- Keith Durkin
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000-Liège (Sart Tilman), Belgium
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14
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Sartelet A, Klingbeil P, Franklin CK, Fasquelle C, Géron S, Isacke CM, Georges M, Charlier C. Allelic heterogeneity of Crooked Tail Syndrome: result of balancing selection? Anim Genet 2012; 43:604-7. [DOI: 10.1111/j.1365-2052.2011.02311.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 11/27/2022]
Affiliation(s)
- A. Sartelet
- Unit of Animal Genomics, GIGA-R & Department of Animal Sciences; Faculty of Veterinary Medicine; University of Liège; Liège; Belgium
| | - P. Klingbeil
- Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; London; UK
| | - C. K. Franklin
- Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; London; UK
| | - C. Fasquelle
- Unit of Animal Genomics, GIGA-R & Department of Animal Sciences; Faculty of Veterinary Medicine; University of Liège; Liège; Belgium
| | - S. Géron
- Unit of Animal Genomics, GIGA-R & Department of Animal Sciences; Faculty of Veterinary Medicine; University of Liège; Liège; Belgium
| | - C. M. Isacke
- Breakthrough Breast Cancer Research Centre; The Institute of Cancer Research; London; UK
| | - M. Georges
- Unit of Animal Genomics, GIGA-R & Department of Animal Sciences; Faculty of Veterinary Medicine; University of Liège; Liège; Belgium
| | - C. Charlier
- Unit of Animal Genomics, GIGA-R & Department of Animal Sciences; Faculty of Veterinary Medicine; University of Liège; Liège; Belgium
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15
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Sartelet A, Fasquelle C, Tamma N, Coppieters W, Georges M, Charlier C. A direct link between growth retardation and inflammation? Identification of a splice mutation in the bovine RNF11 gene. N Biotechnol 2010. [DOI: 10.1016/j.nbt.2010.01.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Fasquelle C, Sartelet A, Li W, Dive M, Tamma N, Michaux C, Druet T, Huijbers IJ, Isacke CM, Coppieters W, Georges M, Charlier C. Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle. PLoS Genet 2009; 5:e1000666. [PMID: 19779552 PMCID: PMC2739430 DOI: 10.1371/journal.pgen.1000666] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 08/27/2009] [Indexed: 01/22/2023] Open
Abstract
We herein describe the positional identification of a 2-bp deletion in the open reading frame of the MRC2 receptor causing the recessive Crooked Tail Syndrome in cattle. The resulting frame-shift reveals a premature stop codon that causes nonsense-mediated decay of the mutant messenger RNA, and the virtual absence of functional Endo180 protein in affected animals. Cases exhibit skeletal anomalies thought to result from impaired extracellular matrix remodeling during ossification, and as of yet unexplained muscular symptoms. We demonstrate that carrier status is very significantly associated with desired characteristics in the general population, including enhanced muscular development, and that the resulting heterozygote advantage caused a selective sweep which explains the unexpectedly high frequency (25%) of carriers in the Belgian Blue Cattle Breed.
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Affiliation(s)
- Corinne Fasquelle
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Arnaud Sartelet
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Wanbo Li
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Marc Dive
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Nico Tamma
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Charles Michaux
- Unit of Bioinformatics, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Ivo J. Huijbers
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clare M. Isacke
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R, Department of Animal Sciences, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- * E-mail:
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