Formation of Chimeric Genes by Copy-Number Variation as a Mutational Mechanism in Schizophrenia

Chimeric genes can be caused by structural genomic rearrangements that fuse together portions of two different genes to create a novel gene. We hypothesize that brain-expressed chimeras may contribute to schizophrenia. Individuals with schizophrenia and control individuals were screened genome wide for copy-number variants (CNVs) that disrupted two genes on the same DNA strand. Candidate events were filtered for predicted brain expression and for frequency < 0.001 in an independent series of 20,000 controls. Four of 124 affected individuals and zero of 290 control individuals harbored such events (p = 0.002); a 47 kb duplication disrupted MATK and ZFR2, a 58 kb duplication disrupted PLEKHD1 and SLC39A9, a 121 kb duplication disrupted DNAJA2 and NETO2, and a 150 kb deletion disrupted MAP3K3 and DDX42. Each fusion produced a stable protein when exogenously expressed in cultured cells. We examined whether these chimeras differed from their parent genes in localization, regulation, or function. Subcellular localizations of DNAJA2-NETO2 and MAP3K3-DDX42 differed from their parent genes. On the basis of the expression profile of the MATK promoter, MATK-ZFR2 is likely to be far more highly expressed in the brain during development than the ZFR2 parent gene. MATK-ZFR2 includes a ZFR2-derived isoform that we demonstrate localizes preferentially to neuronal dendritic branch sites. These results suggest that the formation of chimeric genes is a mechanism by which CNVs contribute to schizophrenia and that, by interfering with parent gene function, chimeras may disrupt critical brain processes, including neurogenesis, neuronal differentiation, and dendritic arborization

Identifying New Genes for Inherited Breast Cancer by Exome Sequencing

Thesis (Ph.D.)--University of Washington, 2013Breast cancer is the most common cancer among American women and family history is an important risk factor for its occurrence. More than 20 genes have been identified with inherited mutations that lead to significantly increased risk of breast cancer. However, most familial breast cancer is not explained by mutations in these genes. The goal of this project was to identify additional breast cancer genes by exome sequencing. In order to select families for gene discovery, we first screened families for mutations in all known breast cancer genes using targeted capture and massively parallel sequencing (BROCA). Families that remained unsolved after screening with BROCA were evaluated by exome sequencing. Germline DNA of 144 subjects with breast cancer from 54 high incidence families was sequenced. All truncating mutations shared by at least two affected persons in a family were genotyped in all participating members of that family in order to evaluate co-segregation with cancer. Rare truncating mutations co-segregating with breast and ovarian cancer were detected in ATR, CHEK1, and GEN1, each in one of the 54 families. ATR is recruited to sites of DNA damage; ATR phosphorylates CHEK1 in response to DNA damage, leading to a halt in cell cycle progression; GEN1 is an endonuclease that resolves Holliday junctions. Like BRCA1 and BRCA2, all three candidate genes function in biological pathways related to homologous recombination repair. In order to identify additional mutations in these three genes, unrelated women with breast cancer or ovarian cancer and controls were evaluated with high-throughput targeted sequencing approaches including BROCA custom capture and Molecular Inversion Probes (MIPs). Public databases were also reviewed. In ATR, truncating mutations were identified in 4 of 2544 cases and 3 of 7652 controls (P = 0.049). In CHEK1 truncating mutations were identified in 5 of 2544 cases and 1 of 7652 controls (P = 0.004). In GEN1, truncating mutations were identified in 2 of 1717 cases and 3 of 7652 controls (P = 0.21). This study suggests new candidate genes for inherited predisposition to breast cancer while also demonstrating the challenges facing gene discovery for this complex disease

The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome.

Coupling chromosome conformation capture to molecular enrichment for promoter-containing DNA fragments enables the systematic mapping of interactions between individual distal regulatory sequences and their target genes. In this Minireview, we describe recent progress in the application of this technique and related complementary approaches to gain insight into the lineage- and cell-type-specific dynamics of interactions between regulators and gene promoters

The Joining of Competitors: The Dual Operation of the ABI 3730xl and GE MegaBACE4500 DNA Sequence Analyzers at the DOE Joint Genome Institute

The Joining of Competitors: The Dual Operation of the ABI 3730xl &amp; GE MegaBACE4500 DNA Sequence Analyzers at the DOE Joint Genome InstituteChristopher Daum, Damon Tighe, Lena Philips, Danielle Mihalkanin, Cailyn Spurrell, Don Miller, Alex Copeland, Susan M. Lucas, JGI Sequencing Team U.S. DOE Joint Genome Institute, Walnut Creek, CA 94598At the center of the Department of Energy s (DOE) Joint Genome Institute (JGI) Production Genomics Facility (PGF), lies a highly efficient and automated production line devoted to the generation of high-quality genomic DNA sequence. The JGI utilizes a dual platform of DNA sequence analyzers: Applied Biosystems 3730xl and GE Healthcare s MegaBACE 4500. The operation of these high-throughput fluorescence-based DNA sequence analyzers at the JGI will be assessed on the strengths and benefits of each platform, instrument overviews of operation parameters and mechanical/component specifications. In addition, instrument setups for production operation, operation schedules, loading, and maintenance strategies as well as the various sequencing strategies for each platform. Throughput numbers and sequencing quality results will be presented. UCRL ABS-217110 LBNL-59101 Abs