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Persico I, Fiscarelli I, Pelle A, Faleschini M, Pasini B, Savoia A, Bottega R. Phenotype reversion as "natural gene therapy" in Fanconi anemia by a gene conversion event. Front Genet 2023; 14:1240758. [PMID: 37790699 PMCID: PMC10544911 DOI: 10.3389/fgene.2023.1240758] [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: 06/15/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
Somatic mosaicism appears as a recurrent phenomenon among patients suffering from Fanconi anemia (FA), but its direct prognostic significance mostly remains an open question. The clinical picture of FA mosaic subjects could indeed vary from just mild features to severe hematologic failure. Here, we illustrate the case of a proband whose FA familiarity, modest signs (absence of hematological anomalies and fertility issues), and chromosome fragility test transition to negative overtime were suggestive of somatic mosaicism. In line with this hypothesis, genetic testing on patient's peripheral blood and buccal swab reported the presence of the only FANCA paternal variant (FANCA:c.2638C>T, p. Arg880*) and of both parental alleles (the additional FANCA:c.3164G>A, p. Arg1055Gln), respectively. Moreover, the SNP analysis performed on the same biological specimens allowed us to attribute the proband's mosaicism status to a possible gene conversion mechanism. Our case clearly depicts the positive association between somatic mosaicism and the proband's favorable clinical course due to the occurrence of the reversion event at the hematopoietic stem cell level. Since this condition concerns only a limited subgroup of FA individuals, the accurate evaluation of the origin and extent of clonality would be key to steer clinicians toward the most appropriate therapeutic decision for their FA mosaic patients.
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Affiliation(s)
- Ilaria Persico
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Ilaria Fiscarelli
- Dipartimento di Scienze Mediche, Università degli Studi di Torino, Torino, Italy
- SC Genetica Medica U, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Alessandra Pelle
- SC Genetica Medica U, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Barbara Pasini
- Dipartimento di Scienze Mediche, Università degli Studi di Torino, Torino, Italy
- SC Genetica Medica U, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Anna Savoia
- Department of Engineering for Innovation Medicine, University of Verona, Verona, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
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Joshi G, Arthur NBJ, Geetha TS, Datari PVR, Modak K, Roy D, Chaudhury AD, Sundaraganesan P, Priyanka S, Na F, Ramprasad V, Abraham A, Srivastava VM, Srivastava A, Kulkarni UP, George B, Velayudhan SR. Comprehensive laboratory diagnosis of Fanconi anaemia: comparison of cellular and molecular analysis. J Med Genet 2023; 60:801-809. [PMID: 36894310 PMCID: PMC10423531 DOI: 10.1136/jmg-2022-108714] [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: 05/18/2022] [Accepted: 12/03/2022] [Indexed: 03/11/2023]
Abstract
BACKGROUND Fanconi anaemia (FA) is a rare inherited bone marrow failure disease caused by germline pathogenic variants in any of the 22 genes involved in the FA-DNA interstrand crosslink (ICL) repair pathway. Accurate laboratory investigations are required for FA diagnosis for the clinical management of the patients. We performed chromosome breakage analysis (CBA), FANCD2 ubiquitination (FANCD2-Ub) analysis and exome sequencing of 142 Indian patients with FA and evaluated the efficiencies of these methods in FA diagnosis. METHODS We performed CBA and FANCD2-Ub analysis in the blood cells and fibroblasts of patients with FA. Exome sequencing with improved bioinformatics to detect the single number variants and CNV was carried out for all the patients. Functional validation of the variants with unknown significance was done by lentiviral complementation assay. RESULTS Our study showed that FANCD2-Ub analysis and CBA on peripheral blood cells could diagnose 97% and 91.5% of FA cases, respectively. Exome sequencing identified the FA genotypes consisting of 45 novel variants in 95.7% of the patients with FA. FANCA (60.2%), FANCL (19.8%) and FANCG (11.7%) were the most frequently mutated genes in the Indian population. A FANCL founder mutation c.1092G>A; p.K364=was identified at a very high frequency (~19%) in our patients. CONCLUSION We performed a comprehensive analysis of the cellular and molecular tests for the accurate diagnosis of FA. A new algorithm for rapid and cost-effective molecular diagnosis for~90% of FA cases has been established.
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Affiliation(s)
- Gaurav Joshi
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | | | | | | | - Kirti Modak
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Debanjan Roy
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | | | - Sweety Priyanka
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Fouzia Na
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | | | - Aby Abraham
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Vivi M Srivastava
- Department of Cytogenetics, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Center for Stem Cell Research, Vellore, Tamil Nadu, India
| | - Uday Prakash Kulkarni
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Biju George
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College Vellore, Vellore, Tamil Nadu, India
- Center for Stem Cell Research, Vellore, Tamil Nadu, India
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Persico I, Fontana G, Faleschini M, Zanchetta ME, Ammeti D, Cappelli E, Corsolini F, Mosa C, Guarina A, Bogliolo M, Surrallés J, Dufour C, Farruggia P, Savoia A, Bottega R. A self-repair history: compensatory effect of a de novo variant on the FANCA c.2778+83C>G splicing mutation. Front Genet 2023; 14:1209138. [PMID: 37547463 PMCID: PMC10397729 DOI: 10.3389/fgene.2023.1209138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: Fanconi anemia (FA) is a genome instability condition that drives somatic mosaicism in up to 25% of all patients, a phenomenon now acknowledged as a good prognostic factor. Herein, we describe the case of P1, a FA proband carrying a splicing variant, molecularly compensated by a de novo insertion. Methods and Results: Targeted next-generation sequencing on P1's peripheral blood DNA detected the known FANCA c.2778 + 83C > G intronic mutation and suggested the presence of a large deletion on the other allele, which was then assessed by MLPA and RT-PCR. To determine the c.2778 + 83C > G splicing effect, we performed a RT-PCR on P1's lymphoblastoid cell line (LCL) and on the LCL of another patient (P2) carrying the same variant. Although we confirmed the expected alternative spliced form with a partial intronic retention in P2, we detected no aberrant products in P1's sample. Sequencing of P1's LCL DNA allowed identification of the de novo c.2778 + 86insT variant, predicted to compensate 2778 + 83C > G impact. Albeit not found in P1's bone marrow (BM) DNA, c.2778 + 86insT was detected in a second P1's LCL established afterward, suggesting its occurrence at a low level in vivo. Minigene assay recapitulated the c.2778 + 83C > G effect on splicing and the compensatory role of c.2778 + 86insT in re-establishing the physiological mechanism. Accordingly, P1's LCL under mitomycin C selection preserved the FA pathway activity in terms of FANCD2 monoubiquitination and cell survival. Discussion: Our findings prove the role of c.2778 + 86insT as a second-site variant capable of rescuing c.2778 + 83C > G pathogenicity in vitro, which might contribute to a slow hematopoietic deterioration and a mild hematologic evolution.
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Affiliation(s)
- Ilaria Persico
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Giorgia Fontana
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | | | - Daniele Ammeti
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Enrico Cappelli
- Hematology Unit, IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Fabio Corsolini
- LABSIEM—Laboratory for the Study of Inborn Errors of Metabolism—Pediatric Clinic and Endocrinology—IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Clara Mosa
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Angela Guarina
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Massimo Bogliolo
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Jordi Surrallés
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Carlos III Health Institute, Madrid, Spain
| | - Carlo Dufour
- Hematology Unit, IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Anna Savoia
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
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4
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Park SY, Lee JM, Kim MJ, Chung NG, Lee JB, Kim Y, Kim M. Validation of Pathogenicity of Gene Variants in Fanconi Anemia Using Patient-derived Dermal Fibroblasts. Ann Lab Med 2023; 43:127-131. [PMID: 36045072 PMCID: PMC9467830 DOI: 10.3343/alm.2023.43.1.127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 08/08/2022] [Indexed: 12/31/2022] Open
Affiliation(s)
- Seon Young Park
- Research Institute of Women’s Health, College of Natural Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Jong-Mi Lee
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea,Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myung-Jin Kim
- Research Institute of Women’s Health, College of Natural Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Bok Lee
- Research Institute of Women’s Health, College of Natural Sciences, Sookmyung Women’s University, Seoul, Korea
| | - Yonghwan Kim
- Research Institute of Women’s Health, College of Natural Sciences, Sookmyung Women’s University, Seoul, Korea,Corresponding author: Yonghwan Kim Department of Biological Sciences, College of Natural Sciences, Sookmyung Women’s University, 100 Cheongpa-ro 47 gil, Yongsan-gu, Seoul 04310, Korea Tel: +82-2-710-9552, Fax: +82-2-2077-7322 E-mail:
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea,Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea,Co-corresponding author: Myungshin Kim Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine and Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea Tel: +82-2-2258-1645, Fax: +82-2-2258-1719 E-mail:
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Rao I, Crisafulli L, Paulis M, Ficara F. Hematopoietic Cells from Pluripotent Stem Cells: Hope and Promise for the Treatment of Inherited Blood Disorders. Cells 2022; 11:cells11030557. [PMID: 35159366 PMCID: PMC8834203 DOI: 10.3390/cells11030557] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Inherited blood disorders comprise a large spectrum of diseases due to germline mutations in genes with key function in the hematopoietic system; they include immunodeficiencies, anemia or metabolic diseases. For most of them the only curative treatment is bone marrow transplantation, a procedure associated to severe complications; other therapies include red blood cell and platelet transfusions, which are dependent on donor availability. An alternative option is gene therapy, in which the wild-type form of the mutated gene is delivered into autologous hematopoietic stem cells using viral vectors. A more recent therapeutic perspective is gene correction through CRISPR/Cas9-mediated gene editing, that overcomes safety concerns due to insertional mutagenesis and allows correction of base substitutions in large size genes difficult to incorporate into vectors. However, applying this technique to genomic disorders caused by large gene deletions is challenging. Chromosomal transplantation has been proposed as a solution, using a universal source of wild-type chromosomes as donor, and induced pluripotent stem cells (iPSCs) as acceptor. One of the obstacles to be addressed for translating PSC research into clinical practice is the still unsatisfactory differentiation into transplantable hematopoietic stem or mature cells. We provide an overview of the recent progresses in this field and discuss challenges and potential of iPSC-based therapies for the treatment of inherited blood disorders.
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Affiliation(s)
- Ilaria Rao
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Italy
| | - Laura Crisafulli
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy
| | - Marianna Paulis
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy
| | - Francesca Ficara
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy; (I.R.); (L.C.); (M.P.)
- UOS Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, 20138 Milan, Italy
- Correspondence:
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6
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Shahid M, Azfaralariff A, Zubair M, Abdulkareem Najm A, Khalili N, Law D, Firasat S, Fazry S. In silico study of missense variants of FANCA, FANCC and FANCG genes reveals high risk deleterious alleles predisposing to Fanconi anemia pathogenesis. Gene 2021; 812:146104. [PMID: 34864095 DOI: 10.1016/j.gene.2021.146104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Among the 22 Fanconi anemia (FA) reported genes, 90% of mutational spectra were found in three genes, namely FANCA (64%), FANCC (12%) and FANCG (8%). Therefore, this study aimed to identify the high-risk deleterious variants in three selected genes (FANCA, FANCC, and FANCG) through various computational approaches. The missense variant datasets retrieved from the UCSC genome browser were analyzed for their pathogenicity, stability, and phylogenetic conservancy. A total of 23 alterations, of which 16 in FANCA, 6 in FANCC and one variant in FANCG, were found to be highly deleterious. The native and mutant structures were generated, which demonstrated a profound impact on the respective proteins. Besides, their pathway analysis predicted many other pathways in addition to the Fanconi anemia pathway, homologous recombination, and mismatch repair pathways. Hence, this is the first comprehensive study that can be useful for understanding the genetic signatures in the development of FA.
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Affiliation(s)
- Muhammad Shahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Ahmad Azfaralariff
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Muhammad Zubair
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Pattoki Campus, Pakistan
| | - Ahmed Abdulkareem Najm
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Nahid Khalili
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Douglas Law
- Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana BBN Putra Nilai, 71800 Nilai, Negeri Sembilan
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320 Islamabad, Pakistan
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; ZACH Biotech Depot Private Limited, Cheras, 43300, Selangor, Malaysia; Tasik Chini Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
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7
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Mahmood R, Mahmood A, Khan SA, Jaffar R. An experience with 124 cases of fanconi anemia: clinical spectrum, hematological parameters and chromosomal breakage analysis. AMERICAN JOURNAL OF BLOOD RESEARCH 2021; 11:498-503. [PMID: 34824882 PMCID: PMC8610795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Fanconi anemia is an inherited bone marrow failure syndrome characterized by somatic abnormalities and an increased predisposition to malignancies. OBJECTIVE To determine the clinical spectrum and evaluate the hematological parameters as well as highlight diagnosis by chromosomal breakage analysis of Fanconi anemia patients. MATERIAL AND METHODS A total of 124 patients were diagnosed as having Fanconi anemia from August 2014 to May 2020 at Armed Forces Institute of Pathology, Rawalpindi, Pakistan. Clinical details, somatic abnormalities, radiological findings, lab parameters and result of chromosomal breakage analysis were noted and analyzed. RESULTS One hundred and twenty four (14.29%) were diagnosed as having Fanconi anemia (FA) on chromosomal breakage test. Median age was 09 years 06 months. Male to female ratio was 1.9:1. Six of these patients exhibited mosaicism and were classified as FA mosaic. Somatic abnormalities were detected in 74 (59.7%) patients; the most common being skeletal abnormalities and short stature. CONCLUSION Chromosomal breakage analysis is a cost-effective method for diagnosis of Fanconi anemia. Early diagnosis is pertinent for proper treatment and long term prognosis.
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Affiliation(s)
- Rafia Mahmood
- Armed Forces Institute of PathologyRawalpindi, Pakistan
| | - Asad Mahmood
- Armed Forces Institute of PathologyRawalpindi, Pakistan
| | | | - Raza Jaffar
- Armed Forces Institute of PathologyRawalpindi, Pakistan
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8
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Schneider KW, Suttman A, McKinney C, Giller R, Dollerschell K, Nakano TA. Incorporating genetic counseling into the evaluation of pediatric bone marrow failure. J Genet Couns 2021; 31:433-446. [PMID: 34570941 DOI: 10.1002/jgc4.1510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022]
Abstract
The timely identification of germline genetic causes of pediatric bone marrow failure (BMF) impacts medical screening practices, family counseling, therapeutic decision-making, and risk of progression to myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). At diagnosis, treatment decisions need to be made quickly to mitigate risks associated with profound cytopenias. As genetic testing options are rapidly evolving, an efficient multi-disciplinary approach and algorithm, including early involvement of a genetics team, is needed to expedite diagnosis and therapeutic decision-making. This process aids in the identification of appropriate candidates for molecular genetic testing. We present our single center experience reviewing the implementation of genetic counseling and a diagnostic and therapeutic algorithm used to guide genetic evaluation of pediatric BMF. Disease-specific next-generation sequencing (NGS) panels were most often pursued in patients who presented with a clinical phenotype consistent with a known inherited BMF syndrome and when trying to reduce incidental or uninformative results. Broader BMF NGS panels were most often utilized when unable to narrow the suspected etiology to a single disorder. Whole exome sequencing helped with optimizing treatment decision-making in higher risk children with BMF who required expedited hematopoietic stem cell transplantation. The experience has led to improvements to our process for evaluating patients with BMF.
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Affiliation(s)
- Kami Wolfe Schneider
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO, USA
| | - Alexandra Suttman
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO, USA
| | - Christopher McKinney
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO, USA
| | - Roger Giller
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO, USA
| | - Kaylee Dollerschell
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO, USA
| | - Taizo A Nakano
- Department of Pediatrics, Section of Hematology, Oncology and Bone Marrow Transplantation, University of Colorado, Aurora, CO, USA
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9
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Shafqat S, Tariq E, Parnes AD, Dasouki MJ, Ahmed SO, Hashmi SK. Role of gene therapy in Fanconi anemia: A systematic and literature review with future directions. Hematol Oncol Stem Cell Ther 2021; 14:290-301. [PMID: 33736979 DOI: 10.1016/j.hemonc.2021.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/24/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Gene therapy (GT) has been reported to improve bone marrow function in individuals with Fanconi anemia (FA); however, its clinical application is still in the initial stages. We conducted this systematic review, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, to assess the long-term safety and clinical outcomes of GT in FA patients. Electronic searches from PubMed, Web of Science, Cochrane Library, and Google Scholar were conducted and full texts of articles meeting our inclusion criteria were reviewed. Three clinical trials were included, with a total of nine patients and mean age of 10.7 ± 5.7 years. All patients had lentiviral-mediated GT. A 1-year follow-up showed stabilization in blood lineages, without any serious adverse effects from GT. A metaregression analysis could not be conducted, as very little long-term follow-up data of patients was observed, and the median survival rate could not be calculated. Thus, we can conclude that GT seems to be a safe procedure in FA; however, further research needs to be conducted on the longitudinal clinical effects of GT in FA, for a better insight into its potential to become a standard form of treatment.
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Affiliation(s)
| | - Eleze Tariq
- Medical College, Aga Khan University, Karachi, Pakistan
| | - Aric D Parnes
- Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA
| | - Majed J Dasouki
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Syed O Ahmed
- Department of Adult Hematology and Stem Cell Transplantation, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Shahrukh K Hashmi
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA.
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10
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Pruteanu DP, Olteanu DE, Cosnarovici R, Mihut E, Nagy V. Genetic predisposition in pediatric oncology. Med Pharm Rep 2020; 93:323-334. [PMID: 33225257 PMCID: PMC7664724 DOI: 10.15386/mpr-1576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/10/2020] [Accepted: 07/25/2020] [Indexed: 11/23/2022] Open
Abstract
Identifying patients with a genetic predisposition for developing malignant tumors has a significant impact on both the patient and family. Recognition of genetic predisposition, before diagnosing a malignant pathology, may lead to early diagnosis of a neoplasia. Recognition of a genetic predisposition syndrome after the diagnosis of neoplasia can result in a change of treatment plan, a specific follow-up of adverse treatment effects and, of course, a long-term follow-up focusing on the early detection of a second neoplasia. Responsible for genetic syndromes that predispose individuals to malignant pathology are germline mutations. These mutations are present in all cells of conception, they can be inherited or can occur de novo. Several mechanisms of inheritance are described: Mendelian autosomal dominant, Mendelian autosomal recessive, X-linked patterns, constitutional chromosomal abnormality and non-Mendelian inheritance. In the following review we will present the most important genetic syndromes in pediatric oncology.
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Affiliation(s)
- Doina Paula Pruteanu
- Department of Pediatric Oncology, "Prof. Dr. Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania.,Department of Radiation Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Elena Olteanu
- Department of Pediatric Oncology, "Prof. Dr. Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania
| | - Rodica Cosnarovici
- Department of Pediatric Oncology, "Prof. Dr. Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania
| | - Emilia Mihut
- Department of Pediatric Oncology, "Prof. Dr. Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania
| | - Viorica Nagy
- Department of Pediatric Oncology, "Prof. Dr. Ion Chiricuta" Oncology Institute, Cluj-Napoca, Romania.,Department of Radiation Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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11
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Nonsense Suppression Therapy: New Hypothesis for the Treatment of Inherited Bone Marrow Failure Syndromes. Int J Mol Sci 2020; 21:ijms21134672. [PMID: 32630050 PMCID: PMC7369780 DOI: 10.3390/ijms21134672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/29/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of cancer-prone genetic diseases characterized by hypocellular bone marrow with impairment in one or more hematopoietic lineages. The pathogenesis of IBMFS involves mutations in several genes which encode for proteins involved in DNA repair, telomere biology and ribosome biogenesis. The classical IBMFS include Shwachman–Diamond syndrome (SDS), Diamond–Blackfan anemia (DBA), Fanconi anemia (FA), dyskeratosis congenita (DC), and severe congenital neutropenia (SCN). IBMFS are associated with high risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and solid tumors. Unfortunately, no specific pharmacological therapies have been highly effective for IBMFS. Hematopoietic stem cell transplantation provides a cure for aplastic or myeloid neoplastic complications. However, it does not affect the risk of solid tumors. Since approximately 28% of FA, 24% of SCN, 21% of DBA, 20% of SDS, and 17% of DC patients harbor nonsense mutations in the respective IBMFS-related genes, we discuss the use of the nonsense suppression therapy in these diseases. We recently described the beneficial effect of ataluren, a nonsense suppressor drug, in SDS bone marrow hematopoietic cells ex vivo. A similar approach could be therefore designed for treating other IBMFS. In this review we explain in detail the new generation of nonsense suppressor molecules and their mechanistic roles. Furthermore, we will discuss strengths and limitations of these molecules which are emerging from preclinical and clinical studies. Finally we discuss the state-of-the-art of preclinical and clinical therapeutic studies carried out for IBMFS.
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12
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Nie D, Zhang J, Wang F, Zhang W, Liu L, Chen X, Zhang Y, Cao P, Xiong M, Wang T, Wu P, Ma X, Tian W, Wang M, Chen KN, Liu H. Comprehensive analysis on phenotype and genetic basis of Chinese Fanconi anemia patients: dismal outcomes call for nationwide studies. BMC MEDICAL GENETICS 2020; 21:118. [PMID: 32487094 PMCID: PMC7268325 DOI: 10.1186/s12881-020-01057-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/24/2020] [Indexed: 12/25/2022]
Abstract
Background Fanconi anemia (FA) is the most common inherited bone marrow failure (BMF) syndrome with 22 related genes identified. The ALDH2 rs671variant has been proved related to accelerate the progression of BMF in FA patients. The phenotype and genetic basis of Chinese FA patients have not been investigated yet. Methods We analyzed the 22 FA-related genes of 63 BMF patients suspected to be FA. Clinical manifestations, morphological and cytogenetic feathers, ALDH2 genotypes, treatment, and outcomes of the definite cases were retrospectively studied. Results A total of 21 patients were confirmed the diagnosis of FA with the median age of BMF onset was 4-year-old. The number of patients manifested as congenital malformations and growth retardation were 20/21 and 14/21, respectively. BM dysplasia and cytogenetic abnormalities were found in 13/20 and 8/19 patients. All the patients with abnormal karyotypes also manifested as BM dysplasia or had evident blasts. Thirty-five different mutations were identified involving six genes and including twenty novel mutations. FANCA mutations contributed to 66.67% of cases. Eight patients harboring ALDH2-G/A genotype have a significantly younger age of BMF onset (p = 0.025). Within the 19 patients adhering to continuous follow-up, 15 patients underwent hematopoietic stem cell transplantations (HSCTs). During the 29 months of follow-up, 8/19 patients died, seven of which were HSCT-related, and one patient who did not receive HSCT died from severe infection. Conclusions The phenotypic and genetic spectrum of Chinese FA patients is broad. Bone marrow dysplasia and cytogenetic abnormalities are prevalent and highly consistent. The overall outcome of HSCTs is disappointing. Nationwide multicenter studies are needed for the rarity and adverse outcome of this disease.
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Affiliation(s)
- Daijing Nie
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China.,Beijing Lu Daopei Institute of Hematology, Beijing, 100176, China
| | - Jing Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Fang Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Wei Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Lili Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Xue Chen
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Yang Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Panxiang Cao
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Min Xiong
- Department of Hematology, Hebei Yanda Lu Daopei Hospital, Langfang, 065201, China
| | - Tong Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Ping Wu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Xiaoli Ma
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Wenjun Tian
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250000, China
| | - Mangju Wang
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Kylan N Chen
- Beijing Lu Daopei Institute of Hematology, Beijing, 100176, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China. .,Beijing Lu Daopei Institute of Hematology, Beijing, 100176, China. .,Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, 100176, China.
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13
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Jung M, Ramanagoudr-Bhojappa R, van Twest S, Rosti RO, Murphy V, Tan W, Donovan FX, Lach FP, Kimble DC, Jiang CS, Vaughan R, Mehta PA, Pierri F, Dufour C, Auerbach AD, Deans AJ, Smogorzewska A, Chandrasekharappa SC. Association of clinical severity with FANCB variant type in Fanconi anemia. Blood 2020; 135:1588-1602. [PMID: 32106311 PMCID: PMC7193183 DOI: 10.1182/blood.2019003249] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/12/2020] [Indexed: 01/05/2023] Open
Abstract
Fanconi anemia (FA) is the most common genetic cause of bone marrow failure and is caused by inherited pathogenic variants in any of 22 genes. Of these, only FANCB is X-linked. We describe a cohort of 19 children with FANCB variants, from 16 families of the International Fanconi Anemia Registry. Those with FANCB deletion or truncation demonstrate earlier-than-average onset of bone marrow failure and more severe congenital abnormalities compared with a large series of FA individuals in published reports. This reflects the indispensable role of FANCB protein in the enzymatic activation of FANCD2 monoubiquitination, an essential step in the repair of DNA interstrand crosslinks. For FANCB missense variants, more variable severity is associated with the extent of residual FANCD2 monoubiquitination activity. We used transcript analysis, genetic complementation, and biochemical reconstitution of FANCD2 monoubiquitination to determine the pathogenicity of each variant. Aberrant splicing and transcript destabilization were associated with 2 missense variants. Individuals carrying missense variants with drastically reduced FANCD2 monoubiquitination in biochemical and/or cell-based assays tended to show earlier onset of hematologic disease and shorter survival. Conversely, variants with near-normal FANCD2 monoubiquitination were associated with more favorable outcome. Our study reveals a genotype-phenotype correlation within the FA-B complementation group of FA, where severity is associated with level of residual FANCD2 monoubiquitination.
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Affiliation(s)
- Moonjung Jung
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Sylvie van Twest
- Genome Stability Unit, St Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Rasim Ozgur Rosti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Vincent Murphy
- Genome Stability Unit, St Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Winnie Tan
- Genome Stability Unit, St Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Frank X Donovan
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Danielle C Kimble
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Caroline S Jiang
- Department of Biostatistics, The Rockefeller University Hospital, The Rockefeller University, New York, NY
| | - Roger Vaughan
- Department of Biostatistics, The Rockefeller University Hospital, The Rockefeller University, New York, NY
| | - Parinda A Mehta
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH
| | | | - Carlo Dufour
- Hematology Unit, IRCSS G. Gaslini, Genoa, Italy; and
| | - Arleen D Auerbach
- Human Genetics and Hematology Program, The Rockefeller University, New York, NY
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute of Medical Research, Melbourne, VIC, Australia
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Settara C Chandrasekharappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
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14
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Bogliolo M, Pujol R, Aza-Carmona M, Muñoz-Subirana N, Rodriguez-Santiago B, Casado JA, Rio P, Bauser C, Reina-Castillón J, Lopez-Sanchez M, Gonzalez-Quereda L, Gallano P, Catalá A, Ruiz-Llobet A, Badell I, Diaz-Heredia C, Hladun R, Senent L, Argiles B, Bergua Burgues JM, Bañez F, Arrizabalaga B, López Almaraz R, Lopez M, Figuera Á, Molinés A, Pérez de Soto I, Hernando I, Muñoz JA, del Rosario Marin M, Balmaña J, Stjepanovic N, Carrasco E, Cuesta I, Cosuelo JM, Regueiro A, Moraleda Jimenez J, Galera-Miñarro AM, Rosiñol L, Carrió A, Beléndez-Bieler C, Escudero Soto A, Cela E, de la Mata G, Fernández-Delgado R, Garcia-Pardos MC, Sáez-Villaverde R, Barragaño M, Portugal R, Lendinez F, Hernadez I, Vagace JM, Tapia M, Nieto J, Garcia M, Gonzalez M, Vicho C, Galvez E, Valiente A, Antelo ML, Ancliff P, Garcia F, Dopazo J, Sevilla J, Paprotka T, Pérez-Jurado LA, Bueren J, Surralles J. Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. J Med Genet 2019; 57:258-268. [DOI: 10.1136/jmedgenet-2019-106249] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/06/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022]
Abstract
PurposePatients with Fanconi anaemia (FA), a rare DNA repair genetic disease, exhibit chromosome fragility, bone marrow failure, malformations and cancer susceptibility. FA molecular diagnosis is challenging since FA is caused by point mutations and large deletions in 22 genes following three heritability patterns. To optimise FA patients’ characterisation, we developed a simplified but effective methodology based on whole exome sequencing (WES) and functional studies.Methods68 patients with FA were analysed by commercial WES services. Copy number variations were evaluated by sequencing data analysis with RStudio. To test FANCA missense variants, wt FANCA cDNA was cloned and variants were introduced by site-directed mutagenesis. Vectors were then tested for their ability to complement DNA repair defects of a FANCA-KO human cell line generated by TALEN technologies.ResultsWe identified 93.3% of mutated alleles including large deletions. We determined the pathogenicity of three FANCA missense variants and demonstrated that two FANCA variants reported in mutations databases as ‘affecting functions’ are SNPs. Deep analysis of sequencing data revealed patients’ true mutations, highlighting the importance of functional analysis. In one patient, no pathogenic variant could be identified in any of the 22 known FA genes, and in seven patients, only one deleterious variant could be identified (three patients each with FANCA and FANCD2 and one patient with FANCE mutations)ConclusionWES and proper bioinformatics analysis are sufficient to effectively characterise patients with FA regardless of the rarity of their complementation group, type of mutations, mosaic condition and DNA source.
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15
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Schubert S, van Luttikhuizen JL, Auber B, Schmidt G, Hofmann W, Penkert J, Davenport CF, Hille-Betz U, Wendeburg L, Bublitz J, Tauscher M, Hackmann K, Schröck E, Scholz C, Wallaschek H, Schlegelberger B, Illig T, Steinemann D. The identification of pathogenic variants in BRCA1/2 negative, high risk, hereditary breast and/or ovarian cancer patients: High frequency of FANCM pathogenic variants. Int J Cancer 2019; 144:2683-2694. [PMID: 30426508 DOI: 10.1002/ijc.31992] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 12/31/2022]
Abstract
NGS-based multiple gene panel resequencing in combination with a high resolution CGH-array was used to identify genetic risk factors for hereditary breast and/or ovarian cancer in 237 high risk patients who were previously tested negative for pathogenic BRCA1/2 variants. All patients were screened for pathogenic variants in 94 different cancer predisposing genes. We identified 32 pathogenic variants in 14 different genes (ATM, BLM, BRCA1, CDH1, CHEK2, FANCG, FANCM, FH, HRAS, PALB2, PMS2, PTEN, RAD51C and NBN) in 30 patients (12.7%). Two pathogenic BRCA1 variants that were previously undetected due to less comprehensive and sensitive methods were found. Five pathogenic variants are novel, three of which occur in genes yet unrelated to hereditary breast and/or ovarian cancer (FANCG, FH and HRAS). In our cohort we discovered a remarkably high frequency of truncating variants in FANCM (2.1%), which has recently been suggested as a susceptibility gene for hereditary breast cancer. Two patients of our cohort carried two different pathogenic variants each and 10 other patients in whom a pathogenic variant was confirmed also harbored a variant of unknown significance in a breast and ovarian cancer susceptibility gene. We were able to identify pathogenic variants predisposing for tumor formation in 12.3% of BRCA1/2 negative breast and/or ovarian cancer patients.
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Affiliation(s)
- Stephanie Schubert
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Judith Penkert
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Ursula Hille-Betz
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Lena Wendeburg
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Janin Bublitz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Marcel Tauscher
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Partner Site Dresden, Dresden, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- National Center for Tumor Diseases (NCT) Partner Site Dresden, Dresden, Germany
| | - Caroline Scholz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Hannah Wallaschek
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Thomas Illig
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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16
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Mori M, Hira A, Yoshida K, Muramatsu H, Okuno Y, Shiraishi Y, Anmae M, Yasuda J, Tadaka S, Kinoshita K, Osumi T, Noguchi Y, Adachi S, Kobayashi R, Kawabata H, Imai K, Morio T, Tamura K, Takaori-Kondo A, Yamamoto M, Miyano S, Kojima S, Ito E, Ogawa S, Matsuo K, Yabe H, Yabe M, Takata M. Pathogenic mutations identified by a multimodality approach in 117 Japanese Fanconi anemia patients. Haematologica 2019; 104:1962-1973. [PMID: 30792206 PMCID: PMC6886416 DOI: 10.3324/haematol.2018.207241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
Fanconi anemia is a rare recessive disease characterized by multiple congenital abnormalities, progressive bone marrow failure, and a predisposition to malignancies. It results from mutations in one of the 22 known FANC genes. The number of Japanese Fanconi anemia patients with a defined genetic diagnosis was relatively limited. In this study, we reveal the genetic subtyping and the characteristics of mutated FANC genes in Japan and clarify the genotype-phenotype correlations. We studied 117 Japanese patients and successfully subtyped 97% of the cases. FANCA and FANCG pathogenic variants accounted for the disease in 58% and 25% of Fanconi anemia patients, respectively. We identified one FANCA and two FANCG hot spot mutations, which are found at low percentages (0.04-0.1%) in the whole-genome reference panel of 3,554 Japanese individuals (Tohoku Medical Megabank). FANCB was the third most common complementation group and only one FANCC case was identified in our series. Based on the data from the Tohoku Medical Megabank, we estimate that approximately 2.6% of Japanese are carriers of disease-causing FANC gene variants, excluding missense mutations. This is the largest series of subtyped Japanese Fanconi anemia patients to date and the results will be useful for future clinical management.
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Affiliation(s)
- Minako Mori
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Asuka Hira
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo Japan
| | - Michiko Anmae
- Medical Genetics Laboratory, Graduate School of Science and Engineering, Kindai University, Osaka, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan.,Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Tomoo Osumi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yasushi Noguchi
- Department of Pediatrics, Japanese Red Cross Narita Hospital, Chiba, Japan
| | - Souichi Adachi
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryoji Kobayashi
- Department of Pediatrics and Adolescence, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Hiroshi Kawabata
- Department of Hematology and Immunology, Kanazawa Medical University, Uchinada-machi, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuo Tamura
- Medical Genetics Laboratory, Graduate School of Science and Engineering, Kindai University, Osaka, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hiromasa Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Miharu Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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17
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Clinical Exome Sequencing unravels new disease-causing mutations in the myeloproliferative neoplasms: A pilot study in patients from the state of Qatar. Gene 2018; 689:34-42. [PMID: 30553997 DOI: 10.1016/j.gene.2018.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/27/2018] [Accepted: 12/10/2018] [Indexed: 01/04/2023]
Abstract
Clinical Exome Sequencing (CES) has increasingly become a popular diagnostic tool in patients suffering from genetic disorders that are clinically and genetically complicated. Myeloproliferative Neoplasms (MPNs) is an example of a heterogeneous disorder. In Qatar, familial cases of MPNs are more frequently seen than described in the literature. In this study, we aimed to use CES to classify six Qatari subjects that were suspected of clinical diagnosis of MPNs, according to the WHO 2008 diagnostic criteria for hematologic malignancies, and identify variants that can potentially explain the phenotypic diversity of MPNs. We sequenced six Qatari subjects using CES, of whom, three probands were unrelated families and three members were from the same family, all probands come from consanguineous families, and had a positive family history of MPNs. CES identified 61 variants in 50 genes; of which, 13 were recurrently mutated in our patients. Ten novel variants were identified in ten known genes related to MPNs and seven variants were identified in seven novel candidate genes. The genotype of the six subjects was due to a combination of different variants in different genes. This study serves as a pilot study to investigate the complexity of the genotype of patients with MPNS in Qatar, and serves as a guide for further well-controlled genetic epidemiological studies for patients with MPNs. CES is a powerful tool to be used in the genetic clinics for differential and definitive diagnosis of patients with MPNs.
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18
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Kedar PS, Gupta V, Dongerdiye R, Chiddarwar A, Warang P, Madkaikar MR. Molecular diagnosis of unexplained haemolytic anaemia using targeted next-generation sequencing panel revealed (p.Ala337Thr) novel mutation in GPI gene in two Indian patients. J Clin Pathol 2018; 72:81-85. [PMID: 30337328 DOI: 10.1136/jclinpath-2018-205420] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 01/19/2023]
Abstract
Glucose-6-phosphate isomerase (GPI) deficiency is an autosomal recessive genetic disorder causing congenital haemolytic anaemia (CHA). Diagnosis of GPI deficiency by the biochemical method is unpredicted. Molecular diagnosis by identifying genetic mutation is the gold standard method for confirmation of disease, but causative genes involved in CHA are numerous, and identifying a gene-by-gene approach using Sanger sequencing is also cumbersome, expensive and labour intensive. Recently, next-generation targeted sequencing is more useful in the diagnosis of unexplained haemolytic anaemia. We used targeted next-generation sequencing (NGS) clinical panel for diagnosis of unexplained haemolytic anaemia in two Indian patients which were pending for a long time. All possible causes of haemolytic anaemia were found within normal limit. NGS by clinical exome panel revealed homozygous novel missense mutation in exon 12, c.1009G>A (p.Ala337Thr) in both patients. We further confirm by measuring red blood cell GPI activity in the patients and showed deficiency whereas parents were having intermediate activity. c.1009G>A mutation was also confirmed by Sanger sequencing of exon 12 of GPI gene. The structural-functional analysis by bioinformatics software like Swiss PDB, PolyPhen-2 and PyMol suggested that this pathogenic variant has a direct impact on the structural rearrangement at the region near the active site of the enzyme. This rapid and high-performance targeted NGS assay can be configured to detect specific CHA mutations unique to an individual defect, making it a potentially valuable method for diagnosis of unexplained haemolytic anaemia.
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Affiliation(s)
- Prabhakar S Kedar
- Department of Hematogenetics, National Institute of Immunohematology (Indian Council of Medical Research), Mumbai, India
| | - Vinod Gupta
- Department of Hematogenetics, National Institute of Immunohematology (Indian Council of Medical Research), Mumbai, India
| | - Rashmi Dongerdiye
- Department of Hematogenetics, National Institute of Immunohematology (Indian Council of Medical Research), Mumbai, India
| | - Ashish Chiddarwar
- Department of Hematogenetics, National Institute of Immunohematology (Indian Council of Medical Research), Mumbai, India
| | - Prashant Warang
- Department of Hematogenetics, National Institute of Immunohematology (Indian Council of Medical Research), Mumbai, India
| | - Manisha R Madkaikar
- Department of Hematogenetics, National Institute of Immunohematology (Indian Council of Medical Research), Mumbai, India
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19
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Li N, Ding L, Li B, Wang J, D'Andrea AD, Chen J. Functional analysis of Fanconi anemia mutations in China. Exp Hematol 2018; 66:32-41.e8. [PMID: 30031030 DOI: 10.1016/j.exphem.2018.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/12/2018] [Accepted: 07/14/2018] [Indexed: 10/28/2022]
Abstract
Fanconi anemia (FA) is a rare recessive disease characterized by progressive bone marrow failure, congenital abnormalities, and increased incidence of cancers. To date, mutations in 22 genes can cause FA or an FA-like phenotype. In China, in addition to clinical information, FA diagnosis primarily relies on genetic sequencing because the chromosome breakage test is rarely performed. Here, we employed multiple genetic diagnostic tools (DNA sequencing, multiplex ligation-dependent probe amplification, and chromosome microarray) and a variant-based functional assay platform to investigate the genetic cause in 25 Chinese suspected FA patients. A total of 45 distinct candidate variants were detected in six FA genes (FA-A, FA-B, FA-C, FA-D2, FA-G, and FA-J), of which 36 were novel. Eight missense variants and one indel variant were unable to restore FANCD2 mono-ubiquitination and mitomycin C resistance in a panel of FA indicator cell lines, indicating that these mutations are deleterious. Three missense variants (FANCA-L424V, FANCC-E273K, and FANCG-A153G) were harmless. Finally, 23 patients were molecularly diagnosed with FA, consistent with their clinical phenotype. In the FA-A subgroup, large deletions accounted for 14% of the disease-causing variants. We have established a comprehensive molecular diagnostic workflow for Chinese FA patients that can substitute for standard FA cytogenetic analysis.
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Affiliation(s)
- Niu Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China; Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lixia Ding
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Benshang Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Jing Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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20
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Novel Variations of FANCA Gene Provokes Fanconi Anemia: Molecular Diagnosis in a Special Chinese Family. J Pediatr Hematol Oncol 2018; 40:e299-e304. [PMID: 29702541 DOI: 10.1097/mph.0000000000001197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fanconi anemia (FA) is a rare autosomal recessive or X-linked disorder with highly variable clinical manifestations and an incidence of ∼1 to 5 in 1 million births. To date, 15 bona fide FA genes have been reported to be responsible for the known FA complementation groups and the FANCA gene accounts for almost 60%. In the present study, we report a special Chinese family, which has 2 children with classic FA characteristics. Via 2-step analysis of the whole-exome sequencing data and verification using multiplex ligation-dependent probe amplification test, one child was found to have a novel compound heterozygous mutation of a splicing variant (c.1471-1G>A) and a large intragenic deletion (exons 23-30 del) of the FANCA gene. The other child had the same splicing variant and another novel large deletion (exons 1-18 del) in the FANCA gene. Clone sequencing showed the c.1471-1G>A variant generate an altered transcript with 1 cryptic splice site in intron 15, resulting in a premature termination codon (p.Val490HisfsX6). This study not only shows the complexity of FA molecular diagnosis via comprehensively studying the FA pathogenic genes and the mutational spectrum, but also has significant reference value for the future molecular diagnosis of FA.
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21
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Shefer Averbuch N, Steinberg-Shemer O, Dgany O, Krasnov T, Noy-Lotan S, Yacobovich J, Kuperman AA, Kattamis A, Ben Barak A, Roth-Jelinek B, Chubar E, Shabad E, Dufort G, Ellis M, Wolach O, Pazgal I, Abu Quider A, Miskin H, Tamary H. Targeted next generation sequencing for the diagnosis of patients with rare congenital anemias. Eur J Haematol 2018; 101:297-304. [PMID: 29786897 DOI: 10.1111/ejh.13097] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Most patients with anemia are diagnosed through clinical phenotype and basic laboratory testing. Nonetheless, in cases of rare congenital anemias, some patients remain undiagnosed despite undergoing an exhaustive workup. Genetic testing is complicated by the large number of genes involved in rare anemias and the similarities in the clinical presentation of the different syndromes. OBJECTIVE We aimed to enhance the diagnosis of patients with congenital anemias by using targeted next-generation sequencing. METHODS Genetic diagnosis was performed by gene capture followed by next-generation sequencing of 76 genes known to cause anemia syndromes. RESULTS Genetic diagnosis was achieved in 13 out of 21 patients (62%). Six patients were diagnosed with pyruvate kinase deficiency, 4 with dehydrated hereditary stomatocytosis, 2 with sideroblastic anemia, and 1 with CDA type IV. Eight novel mutations were found. In 7 patients, the genetic diagnosis differed from the pretest presumed diagnosis. The mean lag time from presentation to diagnosis was over 13 years. CONCLUSIONS Targeted next-generation sequencing led to an accurate diagnosis in over 60% of patients with rare anemias. These patients do not need further diagnostic workup. Earlier incorporation of this method into the workup of patients with congenital anemia may improve patients' care and enable genetic counseling.
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Affiliation(s)
- Noa Shefer Averbuch
- Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Steinberg-Shemer
- Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Petach Tikva, Israel
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Petach Tikva, Israel
| | - Sharon Noy-Lotan
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Sackler School of Medicine, Tel Aviv University, Petach Tikva, Israel
| | - Joanne Yacobovich
- Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir A Kuperman
- Blood Coagulation Service and Pediatric Hematology Clinic, Galilee Medical Center, Nahariya, Israel.,Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Antonis Kattamis
- First Department of Pediatrics, National & Kapodistrian University of Athens, Athens, Greece
| | - Ayelet Ben Barak
- Pediatric Hematology/Oncology Department, Rambam Medical Center, Haifa, Israel
| | | | | | | | - Gustavo Dufort
- Pediatric Hemato-Oncology Department, Centro Hospitalario Pereira Rossell, Montevideo, Uruguay
| | - Martin Ellis
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Hematology Institute, Meir Medical Center, Kfar Saba, Israel
| | - Ofir Wolach
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Institute of Hematology, Davidoff Cancer Center, Rabin Medical Center, Petach Tikva, Israel
| | - Idit Pazgal
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Comprehensive Center of Thalassemia, Hemoglobinopathies & Rare Anemias, Institute of Hematology, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Abed Abu Quider
- Pediatric Hematology, Soroka University Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | - Hagit Miskin
- Pediatric Hematology Unit, Shaare Zedek Medical Center, Jerusalem, Israel.,Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Hannah Tamary
- Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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22
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Bottega R, Nicchia E, Cappelli E, Ravera S, De Rocco D, Faleschini M, Corsolini F, Pierri F, Calvillo M, Russo G, Casazza G, Ramenghi U, Farruggia P, Dufour C, Savoia A. Hypomorphic FANCA mutations correlate with mild mitochondrial and clinical phenotype in Fanconi anemia. Haematologica 2017; 103:417-426. [PMID: 29269525 PMCID: PMC5830397 DOI: 10.3324/haematol.2017.176131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/14/2017] [Indexed: 11/16/2022] Open
Abstract
Fanconi anemia is a rare disease characterized by congenital malformations, aplastic anemia, and predisposition to cancer. Despite the consolidated role of the Fanconi anemia proteins in DNA repair, their involvement in mitochondrial function is emerging. The purpose of this work was to assess whether the mitochondrial phenotype, independent of genomic integrity, could correlate with patient phenotype. We evaluated mitochondrial and clinical features of 11 affected individuals homozygous or compound heterozygous for p.His913Pro and p.Arg951Gln/Trp, the two residues of FANCA that are more frequently affected in our cohort of patients. Although p.His913Pro and p.Arg951Gln proteins are stably expressed in cytoplasm, they are unable to migrate in the nucleus, preventing cells from repairing DNA. In these cells, the electron transfer between respiring complex I–III is reduced and the ATP/AMP ratio is impaired with defective ATP production and AMP accumulation. These activities are intermediate between those observed in wild-type and FANCA−/− cells, suggesting that the variants at residues His913 and Arg951 are hypomorphic mutations. Consistent with these findings, the clinical phenotype of most of the patients carrying these mutations is mild. These data further support the recent finding that the Fanconi anemia proteins play a role in mitochondria, and open up possibilities for genotype/phenotype studies based on novel mitochondrial criteria.
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Affiliation(s)
- Roberta Bottega
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Elena Nicchia
- Department of Medical Sciences, University of Trieste, Genoa, Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Silvia Ravera
- Department of Pharmacy (DIFAR), Biochemistry Lab, University of Genoa, Genoa, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Fabio Corsolini
- U.O.S.D. Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Filomena Pierri
- Clinical and Experimental Hematology Unit, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Michaela Calvillo
- Clinical and Experimental Hematology Unit, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Giovanna Russo
- Oncology Hematology Pediatric Unit, "Policlinico - Vittorio Emanuele", University of Catania, Pisa, Italy
| | - Gabriella Casazza
- Pediatric Onco-Hematology, Azienda Ospedaliera/Universitaria Pisana, Pisa, Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences, University of Torino, Palermo, Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Carlo Dufour
- Clinical and Experimental Hematology Unit, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy .,Department of Medical Sciences, University of Trieste, Genoa, Italy
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23
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Pilonetto DV, Pereira NF, Bonfim CMS, Ribeiro LL, Bitencourt MA, Kerkhoven L, Floor K, Ameziane N, Joenje H, Gille JJP, Pasquini R. A strategy for molecular diagnostics of Fanconi anemia in Brazilian patients. Mol Genet Genomic Med 2017; 5:360-372. [PMID: 28717661 PMCID: PMC5511800 DOI: 10.1002/mgg3.293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/20/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fanconi anemia (FA) is a predominantly autosomal recessive disease with wide genetic heterogeneity resulting from mutations in several DNA repair pathway genes. To date, 21 genetic subtypes have been identified. We aimed to identify the FA genetic subtypes in the Brazilian population and to develop a strategy for molecular diagnosis applicable to routine clinical use. METHODS We screened 255 patients from Hospital de Clínicas, Universidade Federal do Paraná for 11 common FA gene mutations. Further analysis by multiplex ligation-dependent probe amplification (MLPA) for FANCA and Sanger sequencing of all coding exons of FANCA, -C, and -G was performed in cases who harbored a single gene mutation. RESULTS We identified biallelic mutations in 128/255 patients (50.2%): 89, 11, and 28 carried FANCA,FANCC, and FANCG mutations, respectively. Of these, 71 harbored homozygous mutations, whereas 57 had compound heterozygous mutations. In 4/57 heterozygous patients, both mutations were identified by the initial screening, in 51/57 additional analyses was required for classification, and in 2/57 the second mutation remained unidentified. We found 52 different mutations of which 22 were novel. CONCLUSION The proposed method allowed genetic subtyping of 126/255 (49.4%) patients at a significantly reduced time and cost, which makes molecular diagnosis of FA Brazilian patients feasible.
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Affiliation(s)
- Daniela V. Pilonetto
- Immunogenetics LaboratoryHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Noemi F. Pereira
- Immunogenetics LaboratoryHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Carmem M. S. Bonfim
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Lisandro L. Ribeiro
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Marco A. Bitencourt
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Lianne Kerkhoven
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Karijn Floor
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Najim Ameziane
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Hans Joenje
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Johan J. P. Gille
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Ricardo Pasquini
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
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24
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Aymun U, Iram S, Aftab I, Khaliq S, Nadir A, Nisar A, Mohsin S. Screening for mutations in two exons of FANCG gene in Pakistani population. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017. [PMID: 28627524 DOI: 10.5507/bp.2017.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Fanconi anemia is a rare autosomal recessive disorder of genetic instability. It is both molecularly and clinically, a heterogeneous disorder. Its incidence is 1 in 129,000 births and relatively high in some ethnic groups. Sixteen genes have been identified among them mutations in FANCG gene are most common after FANCA and FANCC gene mutations. OBJECTIVE To study mutations in exon 3 and 4 of FANCG gene in Pakistani population. METHODS Thirty five patients with positive Diepoxybutane test were included in the study. DNA was extracted and amplified for exons 3 and 4. Thereafter Sequencing was done and analyzed for the presence of mutations. RESULTS No mutation was detected in exon 3 whereas a carrier of known mutation c.307+1 G>T was found in exon 4 of the FANCG gene. CONCLUSION Absence of any mutation in exon 3 and only one heterozygous mutation in exon 4 of FANCG gene points to a different spectrum of FA gene pool in Pakistan that needs extensive research in this area.
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Affiliation(s)
- Ujala Aymun
- Department of Hematology, University of Health Sciences, Lahore, Pakistan.,Department of Pathology, Avicenna Medical College, Lahore, Pakistan
| | - Saima Iram
- Department of Hematology, University of Health Sciences, Lahore, Pakistan.,Department of Pathology, Bolan Medical College, Quetta, Pakistan
| | - Iram Aftab
- Department of Hematology, University of Health Sciences, Lahore, Pakistan
| | - Saba Khaliq
- Department of Physiology and Cell Biology, University of Health Sciences, Lahore, Pakistan
| | - Ali Nadir
- Department of Hematology, Armed Forces institute of Pathology, Rawalpindi, Pakistan
| | - Ahmed Nisar
- Department of Hematology, Children Hospital Lahore, Pakistan
| | - Shahida Mohsin
- Department of Hematology, University of Health Sciences, Lahore, Pakistan
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25
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Roy NBA, Wilson EA, Henderson S, Wray K, Babbs C, Okoli S, Atoyebi W, Mixon A, Cahill MR, Carey P, Cullis J, Curtin J, Dreau H, Ferguson DJP, Gibson B, Hall G, Mason J, Morgan M, Proven M, Qureshi A, Sanchez Garcia J, Sirachainan N, Teo J, Tedgård U, Higgs D, Roberts D, Roberts I, Schuh A. A novel 33-Gene targeted resequencing panel provides accurate, clinical-grade diagnosis and improves patient management for rare inherited anaemias. Br J Haematol 2016; 175:318-330. [PMID: 27432187 PMCID: PMC5132128 DOI: 10.1111/bjh.14221] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/08/2016] [Indexed: 01/21/2023]
Abstract
Accurate diagnosis of rare inherited anaemias is challenging, requiring a series of complex and expensive laboratory tests. Targeted next-generation-sequencing (NGS) has been used to investigate these disorders, but the selection of genes on individual panels has been narrow and the validation strategies used have fallen short of the standards required for clinical use. Clinical-grade validation of negative results requires the test to distinguish between lack of adequate sequencing reads at the locations of known mutations and a real absence of mutations. To achieve a clinically-reliable diagnostic test and minimize false-negative results we developed an open-source tool (CoverMi) to accurately determine base-coverage and the 'discoverability' of known mutations for every sample. We validated our 33-gene panel using Sanger sequencing and microarray. Our panel demonstrated 100% specificity and 99·7% sensitivity. We then analysed 57 clinical samples: molecular diagnoses were made in 22/57 (38·6%), corresponding to 32 mutations of which 16 were new. In all cases, accurate molecular diagnosis had a positive impact on clinical management. Using a validated NGS-based platform for routine molecular diagnosis of previously undiagnosed congenital anaemias is feasible in a clinical diagnostic setting, improves precise diagnosis and enhances management and counselling of the patient and their family.
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Affiliation(s)
- Noémi B A Roy
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Edward A Wilson
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Shirley Henderson
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Katherine Wray
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Christian Babbs
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Steven Okoli
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Wale Atoyebi
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Avery Mixon
- Division of Pediatric Hematology/Oncology, Children's Hospital at Erlanger, Chattanooga, TN, USA
| | - Mary R Cahill
- Department of Haematology, Cork University Hospital, Cork, Ireland
| | - Peter Carey
- Department of Haematology, The Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Jonathan Cullis
- Department of Haematology, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Julie Curtin
- Department of Haematology, Sydney Children's Hospitals Network, Westmead, Australia
| | - Helene Dreau
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Brenda Gibson
- Department of Paediatric Haematology/Oncology, Royal Hospital for Children, Glasgow, UK
| | - Georgina Hall
- Paediatric Haematology/Oncology Unit, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Joanne Mason
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Mary Morgan
- Department of Paediatric Haematology-Oncology, University Hospital Southampton, Southampton, UK
| | - Melanie Proven
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Amrana Qureshi
- Paediatric Haematology/Oncology Unit, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Joaquin Sanchez Garcia
- Laboratorio Diagnóstico UGC de Hematología Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Nongnuch Sirachainan
- Division of Haemato-Oncology, Department of Paediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Juliana Teo
- Department of Haematology, Sydney Children's Hospitals Network, Westmead, Australia
| | - Ulf Tedgård
- Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Doug Higgs
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - David Roberts
- NHS Blood and Transplant, NHSBT - John Radcliffe Hospital, Level 2, Oxford, UK
| | - Irene Roberts
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.
| | - Anna Schuh
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK.
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26
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Svahn J, Bagnasco F, Cappelli E, Onofrillo D, Caruso S, Corsolini F, De Rocco D, Savoia A, Longoni D, Pillon M, Marra N, Ramenghi U, Farruggia P, Locasciulli A, Addari C, Cerri C, Mastrodicasa E, Casazza G, Verzegnassi F, Riccardi F, Haupt R, Barone A, Cesaro S, Cugno C, Dufour C. Somatic, hematologic phenotype, long-term outcome, and effect of hematopoietic stem cell transplantation. An analysis of 97 Fanconi anemia patients from the Italian national database on behalf of the Marrow Failure Study Group of the AIEOP (Italian Association of Pediatric Hematology-Oncology). Am J Hematol 2016; 91:666-71. [PMID: 27013026 DOI: 10.1002/ajh.24373] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 03/11/2016] [Accepted: 03/17/2016] [Indexed: 12/24/2022]
Abstract
We analyzed 97 Fanconi anemia patients from a clinic/biological database for genotype, somatic, and hematologic phenotype, adverse hematological events, solid tumors, and treatment. Seventy-two patients belonged to complementation group A. Eighty percent of patients presented with mild/moderate somatic phenotype and most with cytopenia. No correlation was seen between somatic/hematologic phenotype and number of missense mutations of FANCA alleles. Over follow-up, 33% of patients improved or maintained mild/moderate cytopenia or normal blood count, whereas remaining worsened cytopenia. Eleven patients developed a hematological adverse event (MDS, AML, pathological cytogenetics) and three developed solid tumors. 10 years cumulative risk of death of the whole cohort was 25.6% with median follow-up 5.8 years. In patients eligible to hematopoietic stem cell transplantation because of moderate cytopenia, mortality was significantly higher in subjects transplanted from matched unrelated donor over nontransplanted subjects, whereas there was no significant difference between matched sibling donor transplants and nontransplanted patients. In patients eligible to transplant because of severe cytopenia and clonal disease, mortality risk was not significantly different in transplanted from matched unrelated versus matched sibling donor versus nontransplanted subjects. The decision to transplant should rely on various elements including, type of donor, HLA matching, patient comorbidities, impairment, and clonal evolution of hematopoiesis. Am. J. Hematol. 91:666-671, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | | | | | - Silvia Caruso
- Epidemiology and Statistics; Gaslini Institute; Genova Italy
| | - Fabio Corsolini
- Cell Repository and Bio Bank, Gaslini Institute; Genova Italy
| | | | - Anna Savoia
- Medical Genetics, Burlo Garofalo Institute; Trieste Italy
| | | | - Marta Pillon
- Pediatric Hemato-Oncology; University of Padova; Italy
| | | | - Ugo Ramenghi
- Pediatric Hematology; Regina Margherita Hospital; Torino Italy
| | - Piero Farruggia
- Pediatric Hematology-Oncology; a.R.N.A.S. Civico Fatebenefratelli; Palermo Italy
| | - Anna Locasciulli
- Pediatric Hematology; San Camillo- Forlanini Hospital; Rome Italy
| | - Carmen Addari
- Bone Marrow Transplantation Unit; Hospital of Microcytemia; Cagliari Italy
| | - Carla Cerri
- Pediatric Onco-Hematology; Hospital of Perugia; Perugia Italy
| | | | | | | | | | - Riccardo Haupt
- Epidemiology and Statistics; Gaslini Institute; Genova Italy
| | | | - Simone Cesaro
- Pediatric Onco-Hematology Hospital of Verona; Verona Italy
| | - Chiara Cugno
- Pediatric Onco-Hematology; San Matteo Hospital; Pavia Italy
| | - Carlo Dufour
- Hematology Unit; Gaslini Institute; Genova Italy
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27
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Nicchia E, Giordano P, Greco C, De Rocco D, Savoia A. Molecular diagnosis of thrombocytopenia-absent radius syndrome using next-generation sequencing. Int J Lab Hematol 2016; 38:412-8. [DOI: 10.1111/ijlh.12516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Affiliation(s)
- E. Nicchia
- Department of Medical Sciences; University of Trieste; Trieste Italy
| | | | - C. Greco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo; Trieste Italy
| | - D. De Rocco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo; Trieste Italy
| | - A. Savoia
- Department of Medical Sciences; University of Trieste; Trieste Italy
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo; Trieste Italy
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28
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Gatz SA, Salles D, Jacobsen EM, Dörk T, Rausch T, Aydin S, Surowy H, Volcic M, Vogel W, Debatin KM, Stütz AM, Schwarz K, Pannicke U, Hess T, Korbel JO, Schulz AS, Schumacher J, Wiesmüller L. MCM3AP and POMP Mutations Cause a DNA-Repair and DNA-Damage-Signaling Defect in an Immunodeficient Child. Hum Mutat 2015; 37:257-68. [PMID: 26615982 DOI: 10.1002/humu.22939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 11/17/2015] [Indexed: 01/22/2023]
Abstract
Immunodeficiency patients with DNA repair defects exhibit radiosensitivity and proneness to leukemia/lymphoma formation. Though progress has been made in identifying the underlying mutations, in most patients the genetic basis is unknown. Two de novo mutated candidate genes, MCM3AP encoding germinal center-associated nuclear protein (GANP) and POMP encoding proteasome maturation protein (POMP), were identified by whole-exome sequencing (WES) and confirmed by Sanger sequencing in a child with complex phenotype displaying immunodeficiency, genomic instability, skin changes, and myelodysplasia. GANP was previously described to promote B-cell maturation by nuclear targeting of activation-induced cytidine deaminase (AID) and to control AID-dependent hyperrecombination. POMP is required for 20S proteasome assembly and, thus, for efficient NF-κB signaling. Patient-derived cells were characterized by impaired homologous recombination, moderate radio- and cross-linker sensitivity associated with accumulation of damage, impaired DNA damage-induced NF-κB signaling, and reduced nuclear AID levels. Complementation by wild-type (WT)-GANP normalized DNA repair and WT-POMP rescued defective NF-κB signaling. In conclusion, we identified for the first time mutations in MCM3AP and POMP in an immunodeficiency patient. These mutations lead to cooperative effects on DNA recombination and damage signaling. Digenic/polygenic mutations may constitute a novel genetic basis in immunodeficiency patients with DNA repair defects.
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Affiliation(s)
- Susanne A Gatz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, D-89075, Germany
| | - Daniela Salles
- Department of Obstetrics and Gynecology, Ulm University, Ulm, D-89075, Germany
| | - Eva-Maria Jacobsen
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, D-89075, Germany
| | - Thilo Dörk
- Gynecology Research Unit, Hannover Medical School, Hannover, D-30625, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, D-69117, Germany
| | - Sevtap Aydin
- Department of Obstetrics and Gynecology, Ulm University, Ulm, D-89075, Germany
| | - Harald Surowy
- Department of Human Genetics, Ulm University, Ulm, D-89081, Germany
| | - Meta Volcic
- Department of Obstetrics and Gynecology, Ulm University, Ulm, D-89075, Germany
| | - Walther Vogel
- Department of Human Genetics, Ulm University, Ulm, D-89081, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, D-89075, Germany
| | - Adrian M Stütz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, D-69117, Germany
| | - Klaus Schwarz
- Institute of Transfusion Medicine, Ulm University and Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg - Hessen, Ulm, D-89081, Germany
| | - Ulrich Pannicke
- Institute of Transfusion Medicine, Ulm University and Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg - Hessen, Ulm, D-89081, Germany
| | - Timo Hess
- Institute of Human Genetics, Biomedical Center, University of Bonn, Bonn, D-53127, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, D-69117, Germany
| | - Ansgar S Schulz
- Department of Pediatrics and Adolescent Medicine, Ulm University, Ulm, D-89075, Germany
| | - Johannes Schumacher
- Institute of Human Genetics, Biomedical Center, University of Bonn, Bonn, D-53127, Germany
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, D-89075, Germany
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29
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Risitano AM, Marotta S, Calzone R, Grimaldi F, Zatterale A. Twenty years of the Italian Fanconi Anemia Registry: where we stand and what remains to be learned. Haematologica 2015; 101:319-27. [PMID: 26635036 DOI: 10.3324/haematol.2015.133520] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/27/2015] [Indexed: 12/17/2022] Open
Abstract
The natural history of Fanconi anemia remains hard to establish because of its rarity and its heterogeneous clinical presentation; since 1994, the Italian Fanconi Anemia Registry has collected clinical, epidemiological and genetic data of Italian Fanconi Anemia patients. This registry includes 180 patients with a confirmed diagnosis of Fanconi anemia who have either been enrolled prospectively, at diagnosis, or later on. After enrollment, follow-up data were periodically collected to assess the clinical course, possible complications and long-term survival; the median follow up was 15.6 years. The main goal of the study was to describe the natural history of Fanconi anemia, focusing on the following variables: family history, disease presentation, development of hematological manifestations, development of malignancies, occurrence of hematopoietic stem cell transplantation and survival. Typical morphological and/or hematological abnormalities and/or growth retardation were the most common manifestations at diagnosis; the majority of patients (77%) exhibited hematological abnormalities at the initial presentation, and almost all (96%) eventually developed hematological manifestations. More than half of the patients (57%) underwent a bone-marrow transplant. The occurrence of cancer was quite rare at diagnosis, whereas the cumulative incidence of malignancies at 10, 20 and 30 years was 5%, 8% and 22%, respectively, for hematological cancers and 1%, 15% and 32%, respectively, for solid tumors. Overall survival at 10, 20 and 30 years were 88%, 56% and 37%, respectively; the main causes of death were cancer, complications of the hematological presentation and complications of transplantation. These data clearly confirm the detrimental outcome of Fanconi anemia, with no major improvement in the past decades.
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Affiliation(s)
- Antonio M Risitano
- Hematology, Department of Clinical Medicine and Surgery, "Federico II" University, Italy
| | - Serena Marotta
- Hematology, Department of Clinical Medicine and Surgery, "Federico II" University, Italy
| | | | - Francesco Grimaldi
- Hematology, Department of Clinical Medicine and Surgery, "Federico II" University, Italy
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30
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Nicchia E, Greco C, De Rocco D, Pecile V, D'Eustacchio A, Cappelli E, Corti P, Marra N, Ramenghi U, Pillon M, Farruggia P, Dufour C, Pallavicini A, Torelli L, Savoia A. Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology. Mol Genet Genomic Med 2015; 3:500-12. [PMID: 26740942 PMCID: PMC4694132 DOI: 10.1002/mgg3.160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/22/2015] [Accepted: 05/27/2015] [Indexed: 12/30/2022] Open
Abstract
Fanconi anemia (FA) is a rare bone marrow failure disorder characterized by clinical and genetic heterogeneity with at least 17 genes involved, which make molecular diagnosis complex and time-consuming. Since next-generation sequencing technologies could greatly improve the genetic testing in FA, we sequenced DNA samples with known and unknown mutant alleles using the Ion PGM (™) system (IPGM). The molecular target of 74.2 kb in size covered 96% of the FA-coding exons and their flanking regions. Quality control testing revealed high coverage. Comparing the IPGM and Sanger sequencing output of FANCA,FANCC, and FANCG we found no false-positive and a few false-negative variants, which led to high sensitivity (95.58%) and specificity (100%) at least for these two most frequently mutated genes. The analysis also identified novel mutant alleles, including those in rare complementation groups FANCF and FANCL. Moreover, quantitative evaluation allowed us to characterize large intragenic deletions of FANCA and FANCD2, suggesting that IPGM is suitable for identification of not only point mutations but also copy number variations.
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Affiliation(s)
- Elena Nicchia
- Department of Medical Sciences University of Trieste Trieste Italy
| | - Chiara Greco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy
| | - Daniela De Rocco
- Department of Medical Sciences University of Trieste Trieste Italy
| | - Vanna Pecile
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy
| | - Angela D'Eustacchio
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy
| | - Paola Corti
- Pediatrics Unit San Gerardo Hospital Monza Italy
| | - Nicoletta Marra
- Pediatric Hematology Unit Santobono Pausilipon Hospital Naples Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences University of Torino Torino Italy
| | - Marta Pillon
- Pediatric Onco-Haematology Clinic University of Padua Padua Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology ARNAS Civico Hospital Palermo Italy
| | - Carlo Dufour
- Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy
| | | | - Lucio Torelli
- Department of Mathematics and Geosciences University of Trieste Trieste Italy
| | - Anna Savoia
- Department of Medical SciencesUniversity of TriesteTriesteItaly; Institute for Maternal and Child Health - IRCCS Burlo GarofoloTriesteItaly
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31
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Virts EL, Jankowska A, Mackay C, Glaas MF, Wiek C, Kelich SL, Lottmann N, Kennedy FM, Marchal C, Lehnert E, Scharf RE, Dufour C, Lanciotti M, Farruggia P, Santoro A, Savasan S, Scheckenbach K, Schipper J, Wagenmann M, Lewis T, Leffak M, Farlow JL, Foroud TM, Honisch E, Niederacher D, Chakraborty SC, Vance GH, Pruss D, Timms KM, Lanchbury JS, Alpi AF, Hanenberg H. AluY-mediated germline deletion, duplication and somatic stem cell reversion in UBE2T defines a new subtype of Fanconi anemia. Hum Mol Genet 2015; 24:5093-108. [PMID: 26085575 PMCID: PMC4550815 DOI: 10.1093/hmg/ddv227] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/12/2015] [Indexed: 01/09/2023] Open
Abstract
Fanconi anemia (FA) is a rare inherited disorder clinically characterized by congenital malformations, progressive bone marrow failure and cancer susceptibility. At the cellular level, FA is associated with hypersensitivity to DNA-crosslinking genotoxins. Eight of 17 known FA genes assemble the FA E3 ligase complex, which catalyzes monoubiquitination of FANCD2 and is essential for replicative DNA crosslink repair. Here, we identify the first FA patient with biallelic germline mutations in the ubiquitin E2 conjugase UBE2T. Both mutations were aluY-mediated: a paternal deletion and maternal duplication of exons 2-6. These loss-of-function mutations in UBE2T induced a cellular phenotype similar to biallelic defects in early FA genes with the absence of FANCD2 monoubiquitination. The maternal duplication produced a mutant mRNA that could encode a functional protein but was degraded by nonsense-mediated mRNA decay. In the patient's hematopoietic stem cells, the maternal allele with the duplication of exons 2-6 spontaneously reverted to a wild-type allele by monoallelic recombination at the duplicated aluY repeat, thereby preventing bone marrow failure. Analysis of germline DNA of 814 normal individuals and 850 breast cancer patients for deletion or duplication of UBE2T exons 2-6 identified the deletion in only two controls, suggesting aluY-mediated recombinations within the UBE2T locus are rare and not associated with an increased breast cancer risk. Finally, a loss-of-function germline mutation in UBE2T was detected in a high-risk breast cancer patient with wild-type BRCA1/2. Cumulatively, we identified UBE2T as a bona fide FA gene (FANCT) that also may be a rare cancer susceptibility gene.
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Affiliation(s)
| | | | - Craig Mackay
- Department of MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Marcel F Glaas
- Department of Otorhinolaryngology and Head/Neck Surgery (ENT) and
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery (ENT) and
| | | | - Nadine Lottmann
- Department of Otorhinolaryngology and Head/Neck Surgery (ENT) and
| | | | | | - Erik Lehnert
- Department of Experimental and Clinical Hemostasis, Hemotherapy and Transfusion Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Rüdiger E Scharf
- Department of Experimental and Clinical Hemostasis, Hemotherapy and Transfusion Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Carlo Dufour
- Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | | | - Piero Farruggia
- Pediatric Hematology and Oncology Unit, A.R.N.A.S. Ospedale Civico, Palermo, Italy
| | | | - Süreyya Savasan
- Department of Pediatrics, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI, USA
| | | | - Jörg Schipper
- Department of Otorhinolaryngology and Head/Neck Surgery (ENT) and
| | - Martin Wagenmann
- Department of Otorhinolaryngology and Head/Neck Surgery (ENT) and
| | - Todd Lewis
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Janice L Farlow
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Tatiana M Foroud
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ellen Honisch
- Department of Gynecology, Heinrich Heine University, Düsseldorf, Germany and
| | - Dieter Niederacher
- Department of Gynecology, Heinrich Heine University, Düsseldorf, Germany and
| | - Sujata C Chakraborty
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gail H Vance
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | | | | - Arno F Alpi
- Department of MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK,
| | - Helmut Hanenberg
- Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA, Department of Otorhinolaryngology and Head/Neck Surgery (ENT) and
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32
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Nicchia E, Benedicenti F, De Rocco D, Greco C, Bottega R, Inzana F, Faleschini M, Bonin S, Cappelli E, Mogni M, Stanzial F, Svahn J, Dufour C, Savoia A. Clinical aspects of Fanconi anemia individuals with the same mutation of FANCF identified by next generation sequencing. ACTA ACUST UNITED AC 2015; 103:1003-10. [PMID: 26033879 DOI: 10.1002/bdra.23388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Fanconi anemia (FA) is a rare genetic disease characterized by congenital malformations, aplastic anemia and increased risk of developing malignancies. FA is genetically heterogeneous as it is caused by at least 17 different genes. Among these, FANCA, FANCC, and FANCG account for approximately 85% of the patients whereas the remaining genes are mutated in only a small percentage of cases. For this reason, the molecular diagnostic process is complex and not always extended to all the FA genes, preventing the characterization of individuals belonging to rare groups. METHODS The FA genes were analyzed using a next generation sequencing approach in two unrelated families. RESULTS The analysis identified the same, c.484_485del, homozygous mutation of FANCF in both families. A careful examination of three electively aborted fetuses in one family and one affected girl in the other indicated an association of the FANCF loss-of-function mutation with a severe phenotype characterized by multiple malformations. CONCLUSION The systematic use of next generation sequencing will allow the recognition of individuals from rare complementation groups, a better definition of their clinical phenotypes, and consequently, an appropriate genetic counseling.
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Affiliation(s)
- Elena Nicchia
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Chiara Greco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Inzana
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Massimo Mogni
- Human Genetics Laboratory "E.O. Ospedali Galliera", Genoa, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Johanna Svahn
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Carlo Dufour
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Anna Savoia
- Department of Medical Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
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33
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Savoia A, Kunishima S, De Rocco D, Zieger B, Rand ML, Pujol-Moix N, Caliskan U, Tokgoz H, Pecci A, Noris P, Srivastava A, Ward C, Morel-Kopp MC, Alessi MC, Bellucci S, Beurrier P, de Maistre E, Favier R, Hézard N, Hurtaud-Roux MF, Latger-Cannard V, Lavenu-Bombled C, Proulle V, Meunier S, Négrier C, Nurden A, Randrianaivo H, Fabris F, Platokouki H, Rosenberg N, HadjKacem B, Heller PG, Karimi M, Balduini CL, Pastore A, Lanza F. Spectrum of the mutations in Bernard-Soulier syndrome. Hum Mutat 2014; 35:1033-45. [PMID: 24934643 DOI: 10.1002/humu.22607] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/06/2014] [Indexed: 01/05/2023]
Abstract
Bernard-Soulier syndrome (BSS) is a rare autosomal recessive bleeding disorder characterized by defects of the GPIb-IX-V complex, a platelet receptor for von Willebrand factor (VWF). Most of the mutations identified in the genes encoding for the GP1BA (GPIbα), GP1BB (GPIbβ), and GP9 (GPIX) subunits prevent expression of the complex at the platelet membrane or more rarely its interaction with VWF. As a consequence, platelets are unable to adhere to the vascular subendothelium and agglutinate in response to ristocetin. In order to collect information on BSS patients, we established an International Consortium for the study of BSS, allowing us to enrol and genotype 132 families (56 previously unreported). With 79 additional families for which molecular data were gleaned from the literature, the 211 families characterized so far have mutations in the GP1BA (28%), GP1BB (28%), or GP9 (44%) genes. There is a wide spectrum of mutations with 112 different variants, including 22 novel alterations. Consistent with the rarity of the disease, 85% of the probands carry homozygous mutations with evidence of founder effects in some geographical areas. This overview provides the first global picture of the molecular basis of BSS and will lead to improve patient diagnosis and management.
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Affiliation(s)
- Anna Savoia
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy; Department of Medical Sciences, University of Trieste, Trieste, Italy
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