Biology subjects

Norambuena, T.

Publications and source records attributed to Norambuena, T..

3 recordsLinked to original sources

bioRxiv2022

Viroscope: plant viral diagnosis from NGS data using biologically-informed genome assembly coverage

Next-generation sequencing (NGS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care NGS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand NGS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.

microbiology↗

bioRxiv2021

Genomic insights into the recent population history of Mapuche Native Americans

The last few years have witnessed an explosive generation of genomic data from ancient and modern Native American populations. These data shed light on key demographic shifts that occurred in geographically diverse territories of South America, such as the Andean highlands, Southern Patagonia and the Amazon basin. We used genomic data to study the recent population history of the Mapuche, who are the major Native population from the Southern Cone (Chile and Argentina). We found evidence of specific shared genetic ancestry between the Mapuche and ancient populations from Southern Patagonia, Central Chile and the Argentine Pampas. Despite previous evidence of cultural influence of Inca and Tiwanaku polities over the Mapuche, we did not find evidence of specific shared ancestry between them, nor with Amazonian groups. We estimated the effective population size dynamics of the Mapuche ancestral population during the last millennia, identifying a population bottle-neck around 1650 AD, coinciding with a period of Spaniards invasions into the territory inhabited by the Mapuche. Finally, we show that admixed Chileans underwent post-admixture adaptation in their Mapuche subancestry component in genes related with lipid metabolism, suggesting adaptation to scarce food availability.

genetics↗

bioRxiv2018

Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis

Microbial community analysis can be biased by multiple technical factors, such as storage conditions, DNA extraction, or amplification conditions. In a high-throughput laboratory that relies on samples obtained from thousands of different subjects, knowledge of the extent of subject-introduced sampling and storage variation on the outcome of the inferred microbiome, as well as the effect of laboratory-introduced variation caused by reagent batches, equipment, or operator on the consistency of these processes within the laboratory is paramount. Here, we analyzed the effect of sampling from different parts of the same stool specimen or on different consecutive days, as well as short-term storage of samples at different temperatures on microbiome profiles obtained by 16S rRNA gene amplification. Each of these factors had relatively little effect on the microbial composition. In addition, replicate amplification of 44 stool samples showed reproducible results. Finally, 363 independent replicate extractions and amplifications of a single human homogenized stool (HS) specimen showed reproducible results (average Lins correlation = 0.95), with little variation introduced by HS batch, operator, extraction equipment, or DNA sequencer. In all cases, variations between replicates were significantly smaller than those between individual samples; subject identity always was the largest determinant. We propose that homogenized stool specimens could be used as quality control to routinely monitor the laboratory process and to validate new methods.

microbiology↗