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  • Genomics
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  • 1
    Language: English
    In: PLoS ONE, 2012, Vol.7(4), p.e35591
    Description: The genetic architecture of ischemic stroke is complex and is likely to include rare or low frequency variants with high penetrance and large effect sizes. Such variants are likely to provide important insights into disease pathogenesis compared to common variants with small effect sizes. Because a significant portion of human functional variation may derive from the protein-coding portion of genes we undertook a pilot study to identify variation across the human exome (i.e., the coding exons across the entire human genome) in 10 ischemic stroke cases. Our efforts focused on evaluating the feasibility and identifying the difficulties in this type of research as it applies to ischemic stroke. The cases included 8 African-Americans and 2 Caucasians selected on the basis of similar stroke subtypes and by implementing a case selection algorithm that emphasized the genetic contribution of stroke risk. Following construction of paired-end sequencing libraries, all predicted human exons in each sample were captured and sequenced. Sequencing generated an average of 25.5 million read pairs (75 bp×2) and 3.8 Gbp per sample. After passing quality filters, screening the exomes against dbSNP demonstrated an average of 2839 novel SNPs among African-Americans and 1105 among Caucasians. In an aggregate analysis, 48 genes were identified to have at least one rare variant across all stroke cases. One gene, CSN3 , identified by screening our prior GWAS results in conjunction with our exome results, was found to contain an interesting coding polymorphism as well as containing excess rare variation as compared with the other genes evaluated. In conclusion, while rare coding variants may predispose to the risk of ischemic stroke, this fact has yet to be definitively proven. Our study demonstrates the complexities of such research and highlights that while exome data can be obtained, the optimal analytical methods have yet to be determined.
    Keywords: Research Article ; Biology ; Computer Science ; Medicine ; Genetics And Genomics ; Public Health And Epidemiology ; Computational Biology ; Computer Science ; Neurological Disorders
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Science (New York, N.Y.), 24 December 2010, Vol.330(6012), pp.1775-87
    Description: We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
    Keywords: Chromosomes ; Gene Expression Profiling ; Gene Expression Regulation ; Genome, Helminth ; Molecular Sequence Annotation ; Caenorhabditis Elegans -- Genetics
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 3
    In: Proceedings of the National Academy of Sciences of the United States of America, 2017, Vol.114(51), p.13531-13536
    Description: Significance The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science program is an inclusive Research Education Community with centralized programmatic and scientific support, in which broad student engagement in authentic science is linked to increased accessibility to research experiences for students; increased persistence of these students in science, technology, engineering, and mathematics; and increased scientific productivity for students and faculty alike. Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking.
    Keywords: Biological Sciences ; Bacteriophage ; Genomics ; Science Education ; Evolution ; Assessment
    ISSN: 0027-8424
    E-ISSN: 1091-6490
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  • 4
    Language: English
    In: Neuron, 07 February 2018, Vol.97(3), pp.488-493
    Description: The Simons Foundation Autism Research Initiative (SFARI) has launched , a dynamic platform that is engaging thousands of individuals with autism spectrum disorder (ASD) and connecting them to researchers. By making all data accessible, SPARK seeks to increase our understanding of ASD and accelerate new supports and treatments for ASD. The Simons Foundation Autism Research Initiative (SFARI) has launched , a dynamic platform that is engaging thousands of individuals with autism spectrum disorder (ASD) and connecting them to researchers. By making all data accessible, SPARK seeks to increase our understanding of ASD and accelerate new supports and treatments for ASD.
    Keywords: Biology ; Anatomy & Physiology
    ISSN: 0896-6273
    E-ISSN: 1097-4199
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  • 5
    Language: English
    In: Human Mutation, July 2019, Vol.40(7), pp.893-898
    Description: Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh‐like syndrome identified homozygous protein‐truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor (NP_057673.2:p.(Arg225*)). The variant was predicted to truncate 61 amino acids at the C‐terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same defect. Our data suggest that the hypomorphic effect of the protein‐truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C‐terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.
    Keywords: Acmg Guidelines ; Complex I ; Leigh Syndrome ; Protein Truncation ; Timmdc1
    ISSN: 1059-7794
    E-ISSN: 1098-1004
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  • 6
    Language: English
    In: Molecular Psychiatry, 2016, Vol.21(2), pp.189-197
    Description: textabstractTo identify common variants contributing to normal variation in two specific domains of cognitive functioning, we conducted a genome-wide association study (GWAS) of executive functioning and information processing speed in non-demented older adults from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) consortium. Neuropsychological testing was available for 5429-32 070 subjects of European ancestry aged 45 years or older, free of dementia and clinical stroke at the time of cognitive testing from 20 cohorts in the discovery phase. We analyzed performance on the Trail Making Test parts A and B, the Letter Digit Substitution Test (LDST), the Digit Symbol Substitution Task (DSST), semantic and phonemic fluency tests, and the Stroop Color and Word Test. Replication was sought in 1311-21860 subjects from 20 independent cohorts. A significant association was observed in the discovery cohorts for the single-nucleotide polymorphism (SNP) rs17518584 (discovery P-value=3.12 × 10 -8) and in the joint discovery and replication meta-analysis (P-value=3.28 × 10 -9 after adjustment for age, gender and education) in an intron of the gene cell adhesion molecule 2 (CADM2) for performance on the LDST/DSST. Rs17518584 is located about 170 kb upstream of the transcription start site of the major transcript for the CADM2 gene, but is within an intron of a variant transcript that includes an alternative first exon. The variant is associated with expression of CADM2 in the cingulate cortex (P-value=4 × 10 -4). The protein encoded by CADM2 is involved in glutamate signaling (P-value=7.22 × 10 -15), gamma-aminobutyric acid (GABA) transport (P-value=1.36 × 10 -11) and neuron cell-cell adhesion (P-value=1.48 × 10 -13). Our findings suggest that genetic variation in the CADM2 gene is associated with individual differences in information processing speed.
    Keywords: Single Nucleotide Polymorphisms -- Research ; Dementia -- Diagnosis ; Dementia -- Genetic Aspects ; Dementia -- Research ; Gaba -- Physiological Aspects ; Gaba -- Genetic Aspects ; Gaba -- Research;
    ISSN: 13594184
    E-ISSN: 14765578
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  • 7
    Language: English
    In: G3 (Bethesda, Md.), 04 March 2015, Vol.5(5), pp.719-40
    Description: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Keywords: Codon Bias ; Evolution of Heterochromatin ; Gene Size ; Melting Characteristics ; Transposons ; Evolution, Molecular ; Genome ; Genomics ; Drosophila -- Genetics ; Drosophila Proteins -- Genetics
    E-ISSN: 2160-1836
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