Nanopore DNA Sequencing and Genome Assembly on the International Space Station, bioRxiv, 2016-09-28

AbstractThe 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 (BALBc). 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, staysbase, skipsbase), 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.

biorxiv genomics 100-200-users 2016

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing, bioRxiv, 2016-09-09

AbstractExome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25-50%. Here, we explore the utility of transcriptome sequencing (RNA-seq) as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to over 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.One Sentence SummaryTranscriptome sequencing improves the diagnostic rate for Mendelian disease in patients for whom genetic analysis has not returned a diagnosis.

biorxiv genomics 100-200-users 2016

 

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