title: Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation.
abstract: Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes.
  
  
  
  We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported. The phenotypic similarity between molecularly diagnosed pairs of diseases was calculated with the use of terms from the Human Phenotype Ontology.
  
  
  
  A molecular diagnosis was rendered for 2076 of 7374 patients (28.2%); among these patients, 101 (4.9%) had diagnoses that involved two or more disease loci. We also analyzed parental samples, when available, and found that de novo variants accounted for 67.8% (61 of 90) of pathogenic variants in autosomal dominant disease genes and 51.7% (15 of 29) of pathogenic variants in X-linked disease genes; both variants were de novo in 44.7% (17 of 38) of patients with two monoallelic variants. Causal copy-number variants were found in 12 patients (11.9%) with multiple diagnoses. Phenotypic similarity scores were significantly lower among patients in whom the phenotype resulted from two distinct mendelian disorders that affected different organ systems (50 patients) than among patients with disorders that had overlapping phenotypic features (30 patients) (median score, 0.21 vs. 0.36; P=1.77×10-7).
  
  
  
  In our study, we found multiple molecular diagnoses in 4.9% of cases in which whole-exome sequencing was informative. Our results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within the same pathway. (Funded by the National Institutes of Health and the Ting Tsung and Wei Fong Chao Foundation.).
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Posey
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Tamar
authors.initials: T
authors.lastname: Harel
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Liu
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Jill A
authors.initials: JA
authors.lastname: Rosenfeld
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Regis A
authors.initials: RA
authors.lastname: James
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Zeynep H
authors.initials: ZH
authors.lastname: Coban Akdemir
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Walkiewicz
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Weimin
authors.initials: W
authors.lastname: Bi
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Rui
authors.initials: R
authors.lastname: Xiao
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Yan
authors.initials: Y
authors.lastname: Ding
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Fan
authors.initials: F
authors.lastname: Xia
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Beaudet
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Eric
authors.initials: E
authors.lastname: Boerwinkle
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Eng
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: V Reid
authors.initials: VR
authors.lastname: Sutton
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Chad A
authors.initials: CA
authors.lastname: Shaw
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Sharon E
authors.initials: SE
authors.lastname: Plon
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Yang
authors.affiliation: From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston.
authors.forename: James R
authors.initials: JR
authors.lastname: Lupski
mesh_terms: D059472:Exome; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D014644:Genetic Variation; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010641:Phenotype; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA / Q000379:methods