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Scholarly Works (6 results)

  • Article
  • Peer Reviewed
International Journal of Comparative Psychology, Volume 31 (2018)

Duane Rumbaugh was one of the first primatologists of the modern era (which began after WWII), to engage in comparative studies of the cognitive capacities of nonhuman primates.  In fact, it was Rumbaugh who drew the world's attention to the Order Primates and who helped initiate the International Primatological Society, IPS, the first academic society to be organized around an Order rather than a discipline. His work eventually led in two directions, first the development of the Transfer Index, a was completely new way of looking at learning. The TI seperated monkeys from apes as completely as did Gallup's mirror task.  From this arose the Primate Test Battery, a video based system to test cognitive skills across a wide range of tasks from memory to numerical skils in primates. The other direction was to look at language and its effect on cognition. Only Apes succeeded in the laguage tasks. With Lana's success arose a raft of critiques that - in the light of more recent findings about the structure of human language, are now rendered invalid. Rumbaugh's initial findings in all domains has remained sound. This includes fundamental differences between monkeys and apes in their capacity to spontaneously begin control their attention, to consciously monitor their own behavior, and then to alter it deliberately, or by their own choice. It is the ape's conscious capacity to control its attention and to conciously monitor outcomes in a cause/effect manner, that allows for the acquisition of langauge. This also allows for the creation of "personal self", as a being that exists apart from the current experience of the self. Language greatly assists the emergence of this ability in apes, as does early rearing in which the ape is carried but not seperated from its mother. This allows pointing and joint reference to appear far ahead of schedule and for the spontaneouls development of human  language in cross-species co-reared apes.  The presence of a wild-reared mother (not present in other captive environments)also allows for the emergence of a nonhuman form of vocal language. The implications of this work for future investigations of apes are discussed.

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Cover page: The Fully Conscious ApeCreative Commons 'BY' version 4.0 license
  • Article
  • Peer Reviewed
UCLA Previously Published Works (2011)
Abstract Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this article, we present an overview of the 1000 Genomes Project exome data and simulated phenotype data that were distributed to GAW17 participants for analyses, the different issues addressed by the participants, and the process of preparation of manuscripts resulting from the discussions during the workshop.
    Cover page: Identifying rare variants from exome scans: the GAW17 experience
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2008)

    Objective

    Type 2 diabetes is a common complex disorder with environmental and genetic components. We used a candidate gene-based approach to identify single nucleotide polymorphism (SNP) variants in 222 candidate genes that influence susceptibility to type 2 diabetes.

    Research design and methods

    In a case-control study of 1,161 type 2 diabetic subjects and 1,174 control Finns who are normal glucose tolerant, we genotyped 3,531 tagSNPs and annotation-based SNPs and imputed an additional 7,498 SNPs, providing 99.9% coverage of common HapMap variants in the 222 candidate genes. Selected SNPs were genotyped in an additional 1,211 type 2 diabetic case subjects and 1,259 control subjects who are normal glucose tolerant, also from Finland.

    Results

    Using SNP- and gene-based analysis methods, we replicated previously reported SNP-type 2 diabetes associations in PPARG, KCNJ11, and SLC2A2; identified significant SNPs in genes with previously reported associations (ENPP1 [rs2021966, P = 0.00026] and NRF1 [rs1882095, P = 0.00096]); and implicated novel genes, including RAPGEF1 (rs4740283, P = 0.00013) and TP53 (rs1042522, Arg72Pro, P = 0.00086), in type 2 diabetes susceptibility.

    Conclusions

    Our study provides an effective gene-based approach to association study design and analysis. One or more of the newly implicated genes may contribute to type 2 diabetes pathogenesis. Analysis of additional samples will be necessary to determine their effect on susceptibility.
      Cover page: Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes.
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2015)
      Genetic risk factors for intracranial aneurysm (IA) are not yet fully understood. Genomewide association studies have been successful at identifying common variants; however, the role of rare variation in IA susceptibility has not been fully explored. In this study, we report the use of whole exome sequencing (WES) in seven densely-affected families (45 individuals) recruited as part of the Familial Intracranial Aneurysm study. WES variants were prioritized by functional prediction, frequency, predicted pathogenicity, and segregation within families. Using these criteria, 68 variants in 68 genes were prioritized across the seven families. Of the genes that were expressed in IA tissue, one gene (TMEM132B) was differentially expressed in aneurysmal samples (n=44) as compared to control samples (n=16) (false discovery rate adjusted p-value=0.023). We demonstrate that sequencing of densely affected families permits exploration of the role of rare variants in a relatively common disease such as IA, although there are important study design considerations for applying sequencing to complex disorders. In this study, we explore methods of WES variant prioritization, including the incorporation of unaffected individuals, multipoint linkage analysis, biological pathway information, and transcriptome profiling. Further studies are needed to validate and characterize the set of variants and genes identified in this study.
        Cover page: Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm.
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2017)
        Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P < 5 × 10-8. The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.
          Cover page: Association analysis identifies 65 new breast cancer risk loci.Creative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2017)
          To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC.
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