title: Identification of Rare Variants in ATP8B4 as a Risk Factor for Systemic Sclerosis by Whole-Exome Sequencing.
abstract: OBJECTIVE
  To determine the contribution of rare variants as genetic modifiers of the expressivity, penetrance, and severity of systemic sclerosis (SSc).
  
  
  METHODS
  We performed whole-exome sequencing of 78 European American patients with SSc, including 35 patients without pulmonary arterial hypertension (PAH) and 43 patients with PAH. Association testing of case-control probability for rare variants was performed using the unified sequence kernel association test with optimal kernel weighting and small sample adjustment by comparing all SSc patients with a reference population of 3,179 controls from the Exome Sequencing Project 5,500 exome data set. Replication genotyping was performed in an independent sample of 3,263 patients (415 patients with SSc and 2,848 controls). We conducted expression profiling of messenger RNA from 61 SSc patients (19 without PAH and 42 with PAH) and 41 corresponding controls.
  
  
  RESULTS
  The ATP8B4 gene was associated with a significant increase in the risk of SSc (P = 2.77 × 10(-7)). Among the 64 ATP8B4 variants tested, a single missense variant, c.1308C>G (F436L, rs55687265), provided the most compelling evidence of association (P = 9.35 × 10(-10), odds ratio [OR] 6.11), which was confirmed in the replication cohort (P = 0.012, OR 1.86) and meta-analysis (P = 1.92 × 10(-7), OR 2.5). Genes involved in E3 ubiquitin-protein ligase complex (ASB10) and cyclic nucleotide gated channelopathies (CNGB3) as well as HLA-DRB5 and HSPB2 (heat-shock protein 27) provided additional evidence of association (P < 10(-5)). Differential ATP8B4 expression was observed among the SSc patients compared to the controls (P = 0.0005).
  
  
  CONCLUSIONS
  ATP8B4 may represent a putative genetic risk factor for SSc and pulmonary vascular complications.
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Li
authors.initials: L
authors.lastname: Gao
authors.affiliation: University of Washington, Seattle.
authors.forename: Mary J
authors.initials: MJ
authors.lastname: Emond
authors.affiliation: University of Washington, Seattle.
authors.forename: Tin
authors.initials: T
authors.lastname: Louie
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Chris
authors.initials: C
authors.lastname: Cheadle
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Alan E
authors.initials: AE
authors.lastname: Berger
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Rafaels
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Candelaria
authors.initials: C
authors.lastname: Vergara
authors.affiliation: National Human Genome Research Institute, NIH, Baltimore, Maryland.
authors.forename: Yoonhee
authors.initials: Y
authors.lastname: Kim
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Taub
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Ingo
authors.initials: I
authors.lastname: Ruczinski
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Mathai
authors.affiliation: University of Virginia, Charlottesville.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Rich
authors.affiliation: University of Washington, Seattle.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Nickerson
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Laura K
authors.initials: LK
authors.lastname: Hummers
authors.affiliation: University of Washington and Seattle Children's Hospital, Seattle.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Bamshad
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Hassoun
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Rasika A
authors.initials: RA
authors.lastname: Mathias
authors.affiliation: Johns Hopkins University, Baltimore, Maryland.
authors.forename: Kathleen C
authors.initials: KC
authors.lastname: Barnes
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics*; D000328:Adult; D000368:Aged; D016022:Case-Control Studies; D005260:Female; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D006801:Humans; D006976:Hypertension, Pulmonary / Q000209:etiology / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D016017:Odds Ratio; D012333:RNA, Messenger / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012595:Scleroderma, Systemic / Q000150:complications / Q000235:genetics*; D017422:Sequence Analysis, DNA; D044465:White People / Q000235:genetics
chemical_list: D012333:RNA, Messenger; C000607204:ATP8B4 protein, human; D000251:Adenosine Triphosphatases