Biology subjects

Charles Y Chiu

Publications and source records attributed to Charles Y Chiu.

4 recordsLinked to original sources

bioRxiv2016

Nanopore DNA Sequencing and Genome Assembly on the International Space Station

The emergence of nanopore-based sequencers greatly expands the reach of sequencing into low-resource field environments, enabling in situ molecular analysis. In this work, we evaluated the performance of the MinION DNA sequencer (Oxford Nanopore Technologies) in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained mixtures of genomic DNA extracted from lambda bacteriophage, Escherichia coli (strain K12) and Mus musculus (BALB/c). The in-flight sequencing experiments generated more than 80,000 total reads with mean 2D accuracies of 85 - 90%, mean 1D accuracies of 75 - 80%, and median read lengths of approximately 6,000 bases. We were able to construct directed assemblies of the ~4.7 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% pairwise identity, respectively, and de novo assemblies of the lambda and E. coli genomes generated solely from nanopore reads yielded 100% and 99.8% genome coverage, respectively, at 100% and 98.5% pairwise identity. Across all surveyed metrics (base quality, throughput, stays/base, skips/base), no observable decrease in MinION performance was observed while sequencing DNA in space. Simulated runs of in-flight nanopore data using an automated bioinformatic pipeline and cloud or laptop based genomic assembly demonstrated the feasibility of real-time sequencing analysis and direct microbial identification in space. Applications of sequencing for space exploration include infectious disease diagnosis, environmental monitoring, evaluating biological responses to spaceflight, and even potentially the detection of extraterrestrial life on other planetary bodies.

Genomics↗

bioRxiv2016

Discovery of a persistent Zika virus lineage in Bahia, Brazil

Metagenomic next-generation sequencing coupled with capture probe enrichment was used to recover 11 whole and partial Zika virus (ZIKV) genomes from patients in Bahia, Brazil from April 2015 to January 2016, where the majority of suspected Brazilian ZIKV cases have been reported. Phylogenetic reconstructions and molecular clock analyses using the newly generated data uncovered the existence of a Bahia-specific ZIKV lineage sharing a common ancestor in mid-2014, indicating sustained circulation of this strain in Bahia since that date.

Epidemiology↗

bioRxiv2015

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the critical need for reference strain sequencing

Primary amoebic meningoencephalitis (PAM) is a rare, often lethal cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes. In this study, we present the first draft assembly of the Balamuthia mandrillaris genome recovered from a rare survivor of PAM, in total comprising 49 Mb of sequence. Comparative analysis of the mitochondrial genome and high-copy number genes from 6 additional Balamuthia mandrillaris strains demonstrated remarkable sequence variation, with the closest homologs corresponding to other amoebae, hydroids, algae, slime molds, and peat moss. We also describe the use of unbiased metagenomic next-generation sequencing (NGS) and SURPI bioinformatics analysis to diagnose an ultimately fatal case of Balamuthia mandrillaris encephalitis in a 15-year old girl. Real-time NGS testing of a hospital day 6 CSF sample detected Balamuthia on the basis of high-quality hits to 16S and 18S ribosomal RNA sequences present in the National Center for Biotechnology Information (NCBI) nt reference database. Retrospective analysis of a day 1 CSF sample revealed that more timely identification of Balamuthia by metagenomic NGS, potentially resulting in a better outcome, would have required availability of the complete genome sequence. These results underscore the diverse evolutionary origins underpinning this eukaryotic pathogen, and the critical importance of whole-genome reference sequences for microbial detection by NGS.

Genomics↗

bioRxiv2015

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). At titers ranging from 107-108 copies per milliliter, reads to EBOV from two patients with acute hemorrhagic fever and CHIKV from an asymptomatic blood donor were detected within 4 to 10 minutes of data acquisition, while lower titer HCV virus (1x105 copies per milliliter) was detected within 40 minutes. Analysis of mapped nanopore reads alone, despite an average individual error rate of 24% [range 8-49%], permitted identification of the correct viral strain in all 4 isolates, and 90% of the genome of CHIKV was recovered with >98% accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hours sample-to-answer turnaround time and in a timeframe amenable for actionable clinical and public health diagnostics.

Genomics↗