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The Genetic Landscape of Diamond-Blackfan Anemia

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The Genetic Landscape of Diamond-Blackfan Anemia ARTICLE The Genetic Landscape of Diamond-Blackfan Anemia Jacob C. Ulirsch,1,2,3 Jeffrey M. Verboon,1,2 Shideh Kazerounian,4 Michael H. Guo,2 Daniel Yuan,4 Leif S. Ludwig,1,2 Robert E. Handsaker,2,5 Nour J. Abdulhay,1,2 Claudia Fiorini,1,2 Giulio Genovese,2 Elaine T. Lim,2 Aaron Cheng,1,2 Beryl B. Cummings,2,3 Katherine R. Chao,2 Alan H. Beggs,4 Casie A. Genetti,4 Colin A. Sieff,1 Peter E. Newburger,6 Edyta Niewiadomska,7 Michal Matysiak,7 Adrianna Vlachos,8 Jeffrey M. Lipton,8 Eva Atsidaftos,8 Bertil Glader,9 Anupama Narla,9 Pierre-Emmanuel Gleizes,10 Marie-Franc¸oise O’Donohue,10 Nathalie Montel-Lehry,10 David J. Amor,11 Steven A. McCarroll,2,5 Anne H. O’Donnell-Luria,2,4,12 Namrata Gupta,2 Stacey B. Gabriel,2 Daniel G. MacArthur,2,12 Eric S. Lander,2 Monkol Lek,2 Lydie Da Costa,13,14 David G. Nathan,1 Andrei A. Korostelev,15 Ron Do,16 Vijay G. Sankaran,1,2,17,18,* and Hanna T. Gazda2,4,18,* Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000 live births and has been associated with mutations in components of the ribosome. In order to characterize the genetic landscape of this heterogeneous disorder, we re- cruited a cohort of 472 individuals with a clinical diagnosis of DBA and performed whole-exome sequencing (WES). We identified rele- vant rare and predicted damaging mutations for 78% of individuals. The majority of mutations were singletons, absent from population databases, predicted to cause loss of function, and located in 1 of 19 previously reported ribosomal protein (RP)-encoding genes. Using exon coverage estimates, we identified and validated 31 deletions in RP genes. We also observed an enrichment for extended splice site mutations and validated their diverse effects using RNA sequencing in cell lines obtained from individuals with DBA. Leveraging the size of our cohort, we observed robust genotype-phenotype associations with congenital abnormalities and treatment outcomes. We further identified rare mutations in seven previously unreported RP genes that may cause DBA, as well as several distinct disorders that appear to phenocopy DBA, including nine individuals with biallelic CECR1 mutations that result in deficiency of ADA2. However, no new genes were identified at exome-wide significance, suggesting that there are no unidentified genes containing mutations readily identified by WES that explain >5% of DBA-affected case subjects. Overall, this report should inform not only clinical practice for DBA-affected individuals, but also the design and analysis of rare variant studies for heterogeneous Mendelian disorders. Introduction criteria are being recognized.4 Treatment with corticoste- roids can improve the anemia in 80% of case subjects, Diamond-Blackfan anemia (DBA [MIM: 105650]), origi- but individuals often become intolerant to long- nally termed congenital hypoplastic anemia, is an term corticosteroid therapy and turn to regular red inherited bone marrow failure syndrome estimated blood cell transfusions, the only available standard ther- to occur in 1 out of 100,000 to 200,000 live births.1,2 apy for the anemia.5 Currently, a hematopoietic stem A consensus clinical diagnosis for DBA suggests that cell transplant (HSCT) is the sole curative option, but individuals with this disorder should present within this procedure carries significant morbidity and is gener- the first year of life and have normochromic macrocytic ally restricted to those with a matched related donor.6 anemia, limited cytopenias of other lineages, reticulocy- Ultimately, 40% of case subjects remain dependent topenia, and a visible paucity of erythroid precursor upon corticosteroids which increase the risk of cells in the bone marrow.3 Nonetheless, an increasing heart disease, osteoporosis, and severe infections, number of cases that fall outside of these strict clinical while another 40% become dependent upon red cell 1Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; 2Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; 3Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA; 4Division of Ge- netics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA; 5Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; 6Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA; 7Department of Pediatric Hematology/Oncology, Medical University of Warsaw, Warsaw, Poland; 8Feinstein Institute for Med- ical Research, Manhasset, NY; Division of Hematology/Oncology and Stem Cell Transplantation, Cohen Children’s Medical Center, New Hyde Park, NY; Hofstra Northwell School of Medicine, Hempstead, NY 11030, USA; 9Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 02114, USA; 10Laboratory of Eukaryotic Molecular Biology, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France; 11Mur- doch Children’s Research Institute and Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia; 12Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; 13University Paris VII Denis DIDEROT, Faculte´ de Me´decine Xavier Bichat, 75019 Paris, France; 14Laboratory of Excellence for Red Cell, LABEX GR-Ex, 75015 Paris, France; 15RNA Therapeutics Institute, Department of Biochemistry and Molec- ular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; 16Department of Genetics and Genomic Sciences and The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; 17Harvard Stem Cell Institute, Cambridge, MA 02138, USA 18These authors contributed equally to this work *Correspondence: [email protected] (V.G.S.), [email protected] (H.T.G.) https://doi.org/10.1016/j.ajhg.2018.10.027. Ó 2018 American Society of Human Genetics. 930 The American Journal of Human Genetics 103, 930–947, December 6, 2018 transfusions which requires regular chelation to prevent MATERIAL AND METHODS iron overload and increases the risk of alloimmunization and transfusion reactions, both of which can be severe Diamond-Blackfan Anemia Cohort co-morbidities.2,5 From 1998 until 2018, we recruited a cohort of 472 affected indi- In contrast to many other rare, presumed monogenic or viduals with a clinical diagnosis or strong suspicion of DBA Mendelian disorders,7–9 putative causal genetic lesions (Table 1). Briefly, 112 affected individuals and their families were have now been identified in an estimated 50%–60% of recruited through the DBA registry of North America; 73 affected DBA-affected case subjects.2 In 1999, mutations in ribo- individuals and their families were recruited through the French DBA registry; and 287 affected individuals and their families somal protein S19 (RPS19), one of the proteins in the were recruited from hematological centers and clinics from the 40S small ribosomal subunit, were identified as the first USA (176), Poland (67), Turkey (16), and 13 other countries (28) causal genetic lesions for DBA that explained 25% of (Table S1). The diagnosis of DBA was based on normochromic 10 case subjects. Through the use of targeted Sanger often macrocytic anemia, reticulocytopenia, bone marrow eryth- sequencing, whole-exome sequencing (WES), and copy roblastopenia, and in some individuals, physical abnormalities number variant (CNV) assays, putatively causal haploin- and elevated erythrocyte adenosine deaminase activity. However, sufficient variants have been identified in 19 of the 79 we note that, given the international nature of this cohort, this ribosomal protein (RP) genes (RPS19 [MIM: 603474, was not uniformly assessed by any single clinician or center. 105650], RPL5 [MIM: 603364, 612561], RPS26 [MIM: The study was approved by the Institutional Review Board at 603701, 613309], RPL11 [MIM: 604175, 612562], Boston Children’s Hospital. Informed consent was obtained RPL35A [MIM: 180468, 612528], RPS10 [MIM: 603362, from affected individuals and their family members participating in the study. According to our study protocol, incidental findings 613308], RPS24 [MIM: 602412, 610629], RPS17 [MIM: that were unrelated to clinical features at presentation were not re- 180472, 612527], RPS7 [MIM: 603658, 612563], RPL26 ported. DNA from whole blood samples and individual derived [MIM: 603704, 614900], RPL15 [MIM: 604174, 615550], lymphoblastoid cell lines was obtained for 90% (427/472) and RPS29 [MIM: 603633, 615909], RPS28 [MIM: 603685, 10% (45/472) of individuals, respectively. 606164], RPL31 [MIM: 617415], RPS27 [MIM: 603702, 617409], RPL27 [MIM: 607526, 617408], RPL35, RPL18 [MIM: 604179], RPS15A [MIM: 603674]), making DBA Whole-Exome Sequencing one of the best genetically defined congenital disorders. By 2010, prior to the widespread adoption of WES, approximately In 2012, through the use of unbiased WES, mutations in 200 individual DNA samples from the cohort had been screened for mutations in 8 RP genes exclusively by Sanger sequencing. GATA1 (MIM: 305371, 300835), a hematopoietic master Starting in 2011, all previously collected and newly collected transcription factor that is both necessary for proper DNA samples
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