It has become apparent during the previous twenty years that many neurological disease traits do not result from coding region mutations within genes, but instead manifest because of alterations of the genome. Genomic disorders are a class of conditions that result from genomic rearrangements rather than base pair changes of DNA sequence. In general, two major types of rearrangements are observed: recurrent and nonrecurrent genomic changes. Recurrent rearrangements have a common size in different patients;in which the breakpoints occur at 'fixed'genomic positions, or breakpoint cluster regions. The breakpoints cluster in paralogous segments of the human genome (also referred to as low-copy repeats, LCRs, or segmental duplications, SDs) that facilitate a non-allelic homologous recombination (NAHR) by both stimulating and mediating the rearrangement. Nonrecurrent rearrangements can be of different sizes in different patients, but usually share a """"""""smallest region of overlap"""""""" (SRO) in which the critical genomic contents and/or gene(s) reside. Genomic disorders produced by non-recurrent rearrangements provide a unique challenge for studies of genotype/phenotype correlations. The variable size and genomic content as well as the frequent co- occurrence of complex alterations (e.g. triplications and inversions) that can occur with nonrecurrent rearrangements add further complexity to interpreting the genome and gene variation in the context of each patient's clinical manifestations. We hypothesize that nonrecurrent rearrangements may occur by mechanisms that are distinct from homologous recombination mechanisms;our preliminary studies and recent publications from the first year of this stimulus grant strongly support this hypothesis. Furthermore, we suggested some nonrecurrent rearrangements may result because of specific genome architectural features causing susceptibility to such rearrangements. We plan to investigate these hypotheses in an attempt to learn """"""""the rules"""""""" for mechanisms leading to nonrecurrent rearrangements. We will investigate these hypotheses experimentally by;1) mapping breakpoints of duplication rearrangements, triplication rearrangements, and complex rearrangements. 2) performing bioinformatic analyses of the genomic region undergoing rearrangement, and 3) determining the products of recombination through direct DNA sequences of the recombinant junction;i.e. breakpoint sequencing. 4) studying marker genotypes by whole-genome arrays in trios that consist of patients with disease associated de novo complex rearrangements and their unaffected parents to surmise strand exchanges or potential template switches by the segregation of marker haplotypes. Finally, we will attempt to elucidate genes that may be important to these rearrangement processes by whole genome sequencing of personal genomes in subjects, or parents of these subjects, with multiple de novo CNV events. In this manner we will identify the substrates for recombination, gain insights into genome architecture in regions involved, and potentially infer mechanisms for the rearrangements.

Public Health Relevance

The relevance to public health is that the project will provide new insights into mechanisms for genomic changes that result from nonrecurrent rearrangements enabling better diagnostics and potential new avenues for therapy by correcting gene dosage. Such genome rearrangements cause gene copy number variations (CNV) that result in neurodevelopmental disorders such as mental retardation, behavioral disorders such as autism, psychiatric conditions such as schizophrenia, and neurodegenerative disease such as Alzheimer dementia, Parkinson disease and Charcot-Marie-Tooth disorders.

Agency
National Institute of Health (NIH)
Institute
National Institute of Neurological Disorders and Stroke (NINDS)
Type
Research Project (R01)
Project #
2R01NS058529-03
Application #
8104852
Study Section
Genetics of Health and Disease Study Section (GHD)
Program Officer
Gwinn, Katrina
Project Start
2007-04-01
Project End
2014-07-31
Budget Start
2011-08-15
Budget End
2012-07-31
Support Year
3
Fiscal Year
2011
Total Cost
$547,750
Indirect Cost
Name
Baylor College of Medicine
Department
Genetics
Type
Schools of Medicine
DUNS #
051113330
City
Houston
State
TX
Country
United States
Zip Code
77030
Posey, Jennifer E; Harel, Tamar; Liu, Pengfei et al. (2017) Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. N Engl J Med 376:21-31
Zhang, Jing; Gambin, Tomasz; Yuan, Bo et al. (2017) Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. Hum Genet 136:377-386
Zhang, Ling; Wang, Jingmin; Zhang, Cheng et al. (2017) Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders. Hum Mol Genet 26:1927-1941
Yoon, Wan Hee; Sandoval, Hector; Nagarkar-Jaiswal, Sonal et al. (2017) Loss of Nardilysin, a Mitochondrial Co-chaperone for ?-Ketoglutarate Dehydrogenase, Promotes mTORC1 Activation and Neurodegeneration. Neuron 93:115-131
Liu, Pengfei; Yuan, Bo; Carvalho, Claudia M B et al. (2017) An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell 168:830-842.e7
Vogelaar, Ingrid P; van der Post, Rachel S; van Krieken, J Han Jm et al. (2017) Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing. Eur J Hum Genet 25:1246-1252
Bayram, Yavuz; White, Janson J; Elcioglu, Nursel et al. (2017) REST Final-Exon-Truncating Mutations Cause Hereditary Gingival Fibromatosis. Am J Hum Genet 101:149-156
Tcw, Julia; Carvalho, Claudia M B; Yuan, Bo et al. (2017) Divergent Levels of Marker Chromosomes in an hiPSC-Based Model of Psychosis. Stem Cell Reports 8:519-528
Gambin, Tomasz; Yuan, Bo; Bi, Weimin et al. (2017) Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 9:83
Bekheirnia, Mir Reza; Bekheirnia, Nasim; Bainbridge, Matthew N et al. (2017) Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. Genet Med 19:412-420

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