title: Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis.
abstract: Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10(-10)) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10(-27)). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.
authors.affiliation: Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Linda M
authors.initials: LM
authors.lastname: Polfus
authors.affiliation: Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Berlin-Brandenburg School for Regenerative Therapies, Charité Universitätsmedizin Berlin, Berlin 13353, Germany.
authors.forename: Rajiv K
authors.initials: RK
authors.lastname: Khajuria
authors.affiliation: The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors.forename: Ursula M
authors.initials: UM
authors.lastname: Schick
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55454, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Pankratz
authors.affiliation: Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Raha
authors.initials: R
authors.lastname: Pazoki
authors.affiliation: Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98195, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Brody
authors.affiliation: Department of Neurology, School of Medicine, Boston University, Boston, MA 02118, USA.
authors.forename: Ming-Huei
authors.initials: MH
authors.lastname: Chen
authors.affiliation: School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA.
authors.forename: Paul L
authors.initials: PL
authors.lastname: Auer
authors.affiliation: Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98195, USA.
authors.forename: James S
authors.initials: JS
authors.lastname: Floyd
authors.affiliation: Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK.
authors.forename: Jie
authors.initials: J
authors.lastname: Huang
authors.affiliation: Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Leslie
authors.initials: L
authors.lastname: Lange
authors.affiliation: Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Frank J A
authors.initials: FJ
authors.lastname: van Rooij
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Ginger
authors.initials: G
authors.lastname: Metcalf
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Muzny
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Narayanan
authors.initials: N
authors.lastname: Veeraraghavan
authors.affiliation: Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK.
authors.forename: Klaudia
authors.initials: K
authors.lastname: Walter
authors.affiliation: Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK.
authors.forename: Lu
authors.initials: L
authors.lastname: Chen
authors.affiliation: GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Yanek
authors.affiliation: GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
authors.forename: Lewis C
authors.initials: LC
authors.lastname: Becker
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Gina M
authors.initials: GM
authors.lastname: Peloso
authors.affiliation: Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Aoi
authors.initials: A
authors.lastname: Wakabayashi
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia.
authors.forename: Mart
authors.initials: M
authors.lastname: Kals
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Metspalu
authors.affiliation: Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia.
authors.forename: Tõnu
authors.initials: T
authors.lastname: Esko
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Keolu
authors.initials: K
authors.lastname: Fox
authors.affiliation: College of Public Health, the University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Wallace
authors.affiliation: Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Nora
authors.initials: N
authors.lastname: Franceschini
authors.affiliation: Department of Surgery, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Nena
authors.initials: N
authors.lastname: Matijevic
authors.affiliation: Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98195, USA.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Rice
authors.affiliation: Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98195, USA.
authors.forename: Traci M
authors.initials: TM
authors.lastname: Bartz
authors.affiliation: Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, Tampere 33520, Finland.
authors.forename: Leo-Pekka
authors.initials: LP
authors.lastname: Lyytikäinen
authors.affiliation: Department of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere 33521, Finland.
authors.forename: Mika
authors.initials: M
authors.lastname: Kähönen
authors.affiliation: Department of Clinical Chemistry, Fimlab Laboratories and University of Tampere School of Medicine, Tampere 33520, Finland.
authors.forename: Terho
authors.initials: T
authors.lastname: Lehtimäki
authors.affiliation: Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital and Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland.
authors.forename: Olli T
authors.initials: OT
authors.lastname: Raitakari
authors.affiliation: Department of Clinical Epidemiology, Leiden University Medical Center, Leiden RC 2300, the Netherlands.
authors.forename: Ruifang
authors.initials: R
authors.lastname: Li-Gao
authors.affiliation: Department of Clinical Epidemiology, Leiden University Medical Center, Leiden RC 2300, the Netherlands; Epidemiology Section, Department of Biostatistics, Epidemiology, and Scientific Computing Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211 Saudi Arabia.
authors.forename: Dennis O
authors.initials: DO
authors.lastname: Mook-Kanamori
authors.affiliation: Montreal Heart Institute and Université de Montréal, Montreal, QC H1T 1C8, Canada.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Lettre
authors.affiliation: Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Cornelia M
authors.initials: CM
authors.lastname: van Duijn
authors.affiliation: Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Oscar H
authors.initials: OH
authors.lastname: Franco
authors.affiliation: Center for Public Health Genomics, University of Virginia, Charlottesville VA 22908, USA.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Rich
authors.affiliation: Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Fernando
authors.initials: F
authors.lastname: Rivadeneira
authors.affiliation: Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Albert
authors.initials: A
authors.lastname: Hofman
authors.affiliation: Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: André G
authors.initials: AG
authors.lastname: Uitterlinden
authors.affiliation: Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson MS 39216, USA.
authors.forename: James G
authors.initials: JG
authors.lastname: Wilson
authors.affiliation: Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98195, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA.
authors.forename: Bruce M
authors.initials: BM
authors.lastname: Psaty
authors.affiliation: Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK.
authors.forename: Nicole
authors.initials: N
authors.lastname: Soranzo
authors.affiliation: Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands.
authors.forename: Abbas
authors.initials: A
authors.lastname: Dehghan
authors.affiliation: Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Boerwinkle
authors.affiliation: Departments of Medicine and Biostatistics, Schools of Medicine and Public Health, Boston University, Boston, MA 02118, USA.
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Cardiovascular Epidemiology and Human Genomics Branch, Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Johnson
authors.affiliation: Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: O'Donnell
authors.affiliation: Bloodworks Northwest, Seattle, WA 98102, USA.
authors.forename: Jill M
authors.initials: JM
authors.lastname: Johnsen
authors.affiliation: Women's Health Initiative Clinical Coordinating Center, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Reiner
authors.affiliation: Division of Cardiovascular Medicine, Departments of Internal Medicine and Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Santhi K
authors.initials: SK
authors.lastname: Ganesh
authors.affiliation: Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: sankaran@broadinstitute.org.
authors.forename: Vijay G
authors.initials: VG
authors.lastname: Sankaran
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001792:Blood Platelets / Q000166:cytology; D064113:CRISPR-Cas Systems; D004252:DNA Mutational Analysis; D059472:Exome / Q000235:genetics*; D000072669:Gene Editing; D056426:Genetic Loci / Q000235:genetics*; D006410:Hematopoiesis / Q000235:genetics*; D006412:Hematopoietic Stem Cells / Q000166:cytology; D006801:Humans; D008533:Megakaryocytes / Q000166:cytology; D010976:Platelet Count; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics*
chemical_list: C111977:GFI1B protein, human; D011518:Proto-Oncogene Proteins; D012097:Repressor Proteins