MACHADO DE ASSIS AND EUCLIDES DA CUNHA, INTERPRETERS OF AN INEXPLICABLE NATION

Abstract: The texts of the growing canon of intérpretes do Brasil are frequently seen as offering firm interpretations of national development, promoting determinate categories of analysis, defending Brazil’s virtues, and implying specific corrections for the nation’s faults. Yet some notable works of the genre seem to reject the notions that interpreting the past may usefully inform the future and that the nation may be in any substantial way explained. This article shows how “interpretations” of Brazil as disparate as Machado de Assis’s Esaú e Jacó and Euclides da Cunha’s Os Sertões arrive at a skeptical suspension of judgment about the nature, condition, and future of the nation.Keywords: Intérpretes da nação; Machado de Assis; Euclides da Cunha Resumo: Os textos do crescente cânone de intérpretes do Brasil são lidos frequentemente como oferecendo interpretações firmes do desenvolvimento national, promovendo categorias de análise fixas, defendendo as virtudes do Brasil e sugerindo correções específicas para as faltas da nação. No entanto, algumas obras notáveis do gênero parecem rejeitar as suposições de que interpretar o passado possa dar forma ao futuro e de que a nação possa ser explicada de maneira significativa. Este artigo mostra como “interpretações” do Brasil tão díspares quanto Esaú e Jacó de Machado de Assis e Os Sertões de Euclides da Cunha acabam na suspensão cética do juízo no tocante à natureza, condição e futuro da nação.Palavras-chave: Intérpretes da nação; Machado de Assis; Euclides da Cunh

The landscape of human STR variation

Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome’s representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations.American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

Clinical adoption of human genome sequencing requires methods that output genotypes with known accuracy at millions or billions of positions across a genome. Because of substantial discordance among calls made by existing sequencing methods and algorithms, there is a need for a highly accurate set of genotypes across a genome that can be used as a benchmark. Here we present methods to make high-confidence, single-nucleotide polymorphism (SNP), indel and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias toward any method by integrating and arbitrating between 14 data sets from five sequencing technologies, seven read mappers and three variant callers. We identify regions for which no confident genotype call could be made, and classify them into different categories based on reasons for uncertainty. Our genotype calls are publicly available on the Genome Comparison and Analytic Testing website to enable real-time benchmarking of any method

SEQanswers: an open access community for collaboratively decoding genomes

Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers

Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing

Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. The error profiles and read length limitations of early versions of next-generation sequencing technologies rendered them ineffective for some sequence variant types, particularly microsatellites and other tandem repeats, and fostered the general misconception that such variants are inherently inaccessible to these platforms. At the same time, tandem repeats have emerged as important sources of functional variation. Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between markers and traits. Sensitive identification of these variants in large-scale next-gen sequencing efforts will enable more comprehensive association studies capable of revealing previously invisible associations. We present a population-scale analysis of microsatellite repeats using whole-genome data from 158 inbred isolates from the Drosophila Genetics Reference Panel, a collection of over 200 extensively phenotypically characterized isolates from a single natural population, to uncover processes underlying repeat mutation and to enable associations with behavioral, morphological, and life-history traits. Analysis of repeat variation from next-generation sequence data will also enhance studies of genome stability and neurodegenerative diseases