Study published today by investigators with TGen’s Dorrance Center for Rare Childhood Disorders.
Using a basic genetic difference between men and women, the Translational Genomics Research Institute (TGen) has uncovered a way to track down the source of a neurological disorder in a young girl.
TGen’s discovery relies on a simple genetic fact: Men have one X and one Y chromosome, while women have two X chromosomes. This women-only factor was leveraged by TGen investigators to develop a highly accurate method of tracking down a previously unrecognized disorder of the X-chromosome.
The study of a pre-teen girl, who went years with an undiagnosed neurobehavioral condition, was published today in the scientific journal PLOS ONE.
TGen’s findings were made within its Dorrance Center for Rare Childhood Disorders, where investigators and clinicians apply the latest tools of genomic medicine to provide answers for parents seeking to identify the disease or disorder affecting their child.
The scientists sequenced, or spelled out in order, the complete genetic codes of DNA and RNA of the girl. Because girls inherit an X chromosome from each of their parents (boys inherit a Y chromosome from their father), they also sequenced her mother and father. On average, about half of all X chromosomes active in a female come from the mother and the other half from the father.
“We now have the tools to significantly accelerate the diagnostic process, reducing the need for children to undergo multiple tests that can be emotionally and physically taxing for the entire family,” said Dr. David Craig, TGen’s Deputy Director of Bioinformatics, Co-Director of the Dorrance Center and the paper’s senior author.
Sequencing would reveal the proportion of X chromosomes, and if disproportionate, whether the more abundant of the two were damaged in some way, which often leads to X-linked genetic conditions.
“At the time of enrollment, we suspected the girl had a complex neurobehavioral condition, based on her attention deficit, and delays in development and learning,” said Dr. Vinodh Narayanan, Medical Director of the Dorrance Center. “Her brain MRI scans were normal. We needed to find out more — at the genetic level — about what might be causing her disorder.”
By sequencing the DNA and RNA, TGen investigators were able to precisely identify which cells contained active X chromosomes from the girl’s mother, which contained active X chromosomes from the father, in what proportions, and whether they were associated with any known disorders.
They discovered that the X chromosome from the father contained a segment shown to be associated with neurobehavioral conditions. Interestingly, however, the proportion of X chromosomes active in the girl’s cells skewed toward the normal X inherited from her mother. This skewing may have led to a milder, harder to diagnose condition undetected by conventional methods.
“This study shows the power sequencing holds when scanning for potential disease causing and disease-modifying genetic variations,” said Dr. Matt Huentelman, the other Co-Director of the Dorrance Center and an author of the PLOS ONE paper. “I’m most excited to see the pace at which TGen has pushed the genome sequencing technology to where it can help patients — today.”
TGen Research Associate Szabolcs Szelinger, the paper’s lead author, said: “With just a small bio sample, we are now able to provide a comprehensive evaluation of the effects that genetic variation has on patients, leading to highly personalized treatment options, while at the same time providing researchers with insights into the underlying molecular processes.”
Since opening in October 2013, TGen’s Dorrance Center for Rare Childhood Disorders Dorrance Center has enrolled nearly 300 families. And with the rapid decrease in sequencing costs and improved analytical methods, comprehensive, integrative sequencing approaches will likely be used more in the future.
Funding for the study came from the State of Arizona, the Stardust Foundation, and donations to the TGen Foundation.
Contact: Steve Yozwiak – The Translational Genomics Research Institute
Source: The Translational Genomics Research Institute press release
Image Source: The image is credited to OpenClips and is in the public domain
Original Research: Full open access research for “Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing” by Szabolcs Szelinger, Ivana Malenica, Jason J. Corneveaux, Ashley L. Siniard, Ahmet A. Kurdoglu, Keri M. Ramsey, Isabelle Schrauwen, Jeffrey M. Trent, Vinodh Narayanan, Matthew J. Huentelman, and David W. Craig in PLOS ONE. Published online December 12 2014 doi:10.1371/journal.pone.0113036
Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing
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.
“Characterization of X Chromosome Inactivation Using Integrated Analysis of Whole-Exome and mRNA Sequencing” by Szabolcs Szelinger, Ivana Malenica, Jason J. Corneveaux, Ashley L. Siniard, Ahmet A. Kurdoglu, Keri M. Ramsey, Isabelle Schrauwen, Jeffrey M. Trent, Vinodh Narayanan, Matthew J. Huentelman, and David W. Craig in PLOS ONE doi:10.1371/journal.pone.0113036.
