title: Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.
abstract: In females, X chromosome inactivation (XCI) is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America; Molecular and Cellular Biology Interdisciplinary Graduate Program, College of Liberal Arts and Sciences, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Szabolcs
authors.initials: S
authors.lastname: Szelinger
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Ivana
authors.initials: I
authors.lastname: Malenica
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Jason J
authors.initials: JJ
authors.lastname: Corneveaux
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Ashley L
authors.initials: AL
authors.lastname: Siniard
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Ahmet A
authors.initials: AA
authors.lastname: Kurdoglu
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Keri M
authors.initials: KM
authors.lastname: Ramsey
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Schrauwen
authors.affiliation: Genetic Basis of Human Disease Division, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Trent
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America; Neurology Research, Barrow Neurological Institute, Phoenix, Arizona, United States of America.
authors.forename: Vinodh
authors.initials: V
authors.lastname: Narayanan
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Huentelman
authors.affiliation: Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America.
authors.forename: David W
authors.initials: DW
authors.lastname: Craig
mesh_terms: D000293:Adolescent; D022981:Allelic Imbalance; D002648:Child; D041321:Chromosomes, Human, X / Q000235:genetics*; D003198:Computer Simulation; D059472:Exome; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009422:Nervous System Diseases / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis*; D017423:Sequence Analysis, RNA / Q000379:methods*; D017384:Sequence Deletion; D049951:X Chromosome Inactivation; D055815:Young Adult
chemical_list: D012333:RNA, Messenger