The GANSSER seismological network in Bhutan

Abstract HKT-ISTP 2013 A

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia-Pacific region

The Asia-Pacific region faces formidable challenges in achieving malaria elimination by the proposed target in 2030. Molecular surveillance of Plasmodium parasites can provide important information on malaria transmission and adaptation, which can inform national malaria control programmes (NMCPs) in decision-making processes. In November 2019 a parasite genotyping workshop was held in Jakarta, Indonesia, to review molecular approaches for parasite surveillance and explore ways in which these tools can be integrated into public health systems and inform policy. The meeting was attended by 70 participants from 8 malaria-endemic countries and partners of the Asia Pacific Malaria Elimination Network. The participants acknowledged the utility of multiple use cases for parasite genotyping including: quantifying the prevalence of drug resistant parasites, predicting risks of treatment failure, identifying major routes and reservoirs of infection, monitoring imported malaria and its contribution to local transmission, characterizing the origins and dynamics of malaria outbreaks, and estimating the frequency of Plasmodium vivax relapses. However, the priority of each use case varies with different endemic settings. Although a one-size-fits-all approach to molecular surveillance is unlikely to be applicable across the Asia-Pacific region, consensus on the spectrum of added-value activities will help support data sharing across national boundaries. Knowledge exchange is needed to establish local expertise in different laboratory-based methodologies and bioinformatics processes. Collaborative research involving local and international teams will help maximize the impact of analytical outputs on the operational needs of NMCPs. Research is also needed to explore the cost-effectiveness of genetic epidemiology for different use cases to help to leverage funding for wide-scale implementation. Engagement between NMCPs and local researchers will be critical throughout this process

Comparison of functionality between several software/platforms for microsatellite data processing.

<p>Comparison of functionality between several software/platforms for microsatellite data processing.</p

Screenshot from the VivaxGEN platform illustrating the trace viewer features for visual inspection of allele peaks and manual editing of allele annotations.

<p>The top panel of the screenshot presents a trace image highlighting examples of a short artefact peak from PET-labelled primer-dimer (A), authentic alleles for each of PET, VIC and 6-FAM-labelled amplicons (B), a stutter peak from the 6-FAM-labelled amplicon (C), and peaks for the LIZ600 size standard (D). The bottom panel of the figure presents the detailed annotation provided for each peak detected by the fragment analysis scan with examples for the VIC-labelled (msp1F3) peaks. The manual edit options (E) whereby the user can change peak annotation details are highlighted.</p

VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in <i>Plasmodium vivax</i> populations - Fig 4

<p><b>MCA plots using 9 APMEN markers (panel A) and 5 APMEN markers (panel B) between Bhutan, Ethiopia, Indonesia and South Korea samples.</b> The plot uses data from VivaxGEN version 1.0.</p

Partial allele summary plot illustrating allele binning.

<p>The figure provides a zoomed in view of an allele summary plot presenting MSP1F3 alleles from an Indonesian sample batch (blue allele peaks) and an Ethiopian sample batch (green allele peaks), which were produced by different institutes on different machines. The black allele peaks at the base of the plot are a composite of both the Indonesian and Ethiopian alleles. The allele lengths in the bin defined as allele “256” (i.e. approximating 256 bp) were slightly shifted between Indonesia (A) and Ethiopia (B), highlighting the potential for the same alleles to be assigned to different bins in Indonesia (“255”) versus Ethiopia (“256”). The standardized binning within the VivaxGEN platform ensured that the ~255 bp alleles in Indonesia and the ~256 bp alleles in Ethiopia were assigned to the same allele bin defined as “256”.</p

A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs