title: Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma.
abstract: Suicidal behavior is a complex disorder, with evidence for genetic risk independent of other genetic risk factors including psychiatric disorders. Since 1996, over 3000 DNA samples from Utah suicide decedents have been collected and banked for research use through the Utah Medical Examiner. In addition, over 12,000 Utah suicides were identified through examination of death certificates back to 1904. By linking this data with the Utah Population Database, we have identified multiple extended pedigrees with increased risk for suicide completion. A number of medical conditions co-occur with suicide, including asthma, and this study was undertaken to identify genetic risk common to asthma and suicide. This study tests the hypothesis that a particular comorbid condition may identify a more homogeneous genetic subgroup, facilitating the identification of specific genetic risk factors in that group. From pedigrees at increased risk for suicide, we identified three pedigrees also at significantly increased familial risk for asthma. Five suicide decedents from each of these pedigrees, plus an additional three decedents not from these pedigrees with diagnosed asthma, and 10 decedents with close relatives with asthma were genotyped. Results were compared with 183 publicly available unaffected control exomes from 1000 Genomes and CEPH (Centre d'etude du polymorphisme humain) samples genotyped on the same platform. A further 432 suicide decedents were also genotyped as non-asthma suicide controls. Genotyping was done using the Infinium HumanExome BeadChip. For analysis, we used the pedigree extension of Variant Annotation, Analysis and Search Tool (pVAAST) to calculate the disease burden of each gene. The Phenotype Driven Variant Ontological Re-ranking tool (Phevor) then re-ranked our pVAAST results in context of the phenotype. Using asthma as a seed phenotype, Phevor traversed biomedical ontologies and identified genes with similar biological properties to those known to result in asthma. Our top associated genes included those related to neurodevelopment or neural signaling (brain-derived neurotrophic factor (BDNF), neutral sphingomyelinase 2 (SMPD2), homeobox b2 (HOXB2), neural cell adhesion molecule (NCAM2), heterogeneous nuclear ribonucleoprotein A0 (HNRNPA0)), inflammation (free fatty acid receptor 2 (FFAR2)) and inflammation with additional evidence of neuronal involvement (oxidized low density lipoprotein receptor 1 (OLR1), toll-like receptor 3 (TLR3)). Of particular interest, BDNF has been previously implicated in both psychiatric disorders and asthma. Our results demonstrate the utility of combining pedigree and co-occurring phenotypes to identify rare variants associated with suicide risk in conjunction with specific co-occurring conditions.
authors.affiliation: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
authors.forename: T M
authors.initials: TM
authors.lastname: Darlington
authors.affiliation: Pedigree and Population Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
authors.forename: R
authors.initials: R
authors.lastname: Pimentel
authors.affiliation: 1] Pedigree and Population Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA [2] Department of Family and Consumer Studies, University of Utah, Salt Lake City, UT, USA.
authors.forename: K
authors.initials: K
authors.lastname: Smith
authors.affiliation: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
authors.forename: A V
authors.initials: AV
authors.lastname: Bakian
authors.affiliation: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
authors.forename: L
authors.initials: L
authors.lastname: Jerominski
authors.affiliation: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
authors.forename: J
authors.initials: J
authors.lastname: Cardon
authors.affiliation: Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA.
authors.forename: N J
authors.initials: NJ
authors.lastname: Camp
authors.affiliation: Office of the Medical Examiner, Utah State Department of Health, Salt Lake City, UT, USA.
authors.forename: W B
authors.initials: WB
authors.lastname: Callor
authors.affiliation: Office of the Medical Examiner, Utah State Department of Health, Salt Lake City, UT, USA.
authors.forename: T
authors.initials: T
authors.lastname: Grey
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: M
authors.initials: M
authors.lastname: Singleton
authors.affiliation: Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
authors.forename: M
authors.initials: M
authors.lastname: Yandell
authors.affiliation: 1] Department of Psychiatry, University of Utah, Salt Lake City, UT, USA [2] Brain Institute, University of Utah, Salt Lake City, UT, USA.
authors.forename: P F
authors.initials: PF
authors.lastname: Renshaw
authors.affiliation: 1] Department of Psychiatry, University of Utah, Salt Lake City, UT, USA [2] Brain Institute, University of Utah, Salt Lake City, UT, USA.
authors.forename: D A
authors.initials: DA
authors.lastname: Yurgelun-Todd
authors.affiliation: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
authors.forename: D
authors.initials: D
authors.lastname: Gray
authors.affiliation: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
authors.forename: H
authors.initials: H
authors.lastname: Coon
mesh_terms: D000328:Adult; D001249:Asthma / Q000453:epidemiology* / Q000235:genetics*; D019208:Brain-Derived Neurotrophic Factor / Q000235:genetics; D016208:Databases, Factual; D005260:Female; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D008297:Male; D019006:Neural Cell Adhesion Molecules / Q000235:genetics; D010375:Pedigree; D010641:Phenotype; D012307:Risk Factors; D051127:Scavenger Receptors, Class E / Q000235:genetics; D013405:Suicide / Q000706:statistics & numerical data*; D051196:Toll-Like Receptor 3 / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014589:Utah / Q000453:epidemiology
chemical_list: D019208:Brain-Derived Neurotrophic Factor; C086061:HOXB2 protein, human; D018398:Homeodomain Proteins; D019006:Neural Cell Adhesion Molecules; C495137:OLR1 protein, human; D051127:Scavenger Receptors, Class E; C495344:TLR3 protein, human; D051196:Toll-Like Receptor 3; D014157:Transcription Factors