Duane E. Smailus
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View article: Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs
Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs Open
The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure of transcripts with potential for end-to-end sequencing of full-length RNAs. LR methods that have been described to date incl…
View article: Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes Open
The Long-Read Personalized OncoGenomics (POG) dataset comprises a cohort of 189 patient tumors and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the POG program and the Ma…
View article: Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses
Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses Open
Background Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next-generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translatio…
View article: Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes Open
The Long-read POG dataset comprises a cohort of 189 patient tumours and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the Personalized Oncogenomics (POG) program and the M…
View article: A High-throughput Pipeline for DNA/RNA/small RNA Purification from Tissue Samples for Sequencing
A High-throughput Pipeline for DNA/RNA/small RNA Purification from Tissue Samples for Sequencing Open
High-throughput total nucleic acid (TNA) purification methods based on solid-phase reversible immobilization (SPRI) beads produce TNA suitable for both genomic and transcriptomic applications. Even so, small RNA species, including miRNA, b…
View article: Extraction-free clinical detection of SARS-CoV-2 virus from saline gargle samples using Hamilton STARlet liquid handler
Extraction-free clinical detection of SARS-CoV-2 virus from saline gargle samples using Hamilton STARlet liquid handler Open
As part of the COVID-19 pandemic, clinical laboratories have been faced with massive increases in testing, resulting in sample collection systems, reagent, and staff shortages. We utilized self-collected saline gargle samples to optimize h…
View article: Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2
Automated Library Construction and Analysis for High-Throughput Nanopore Sequencing of SARS-CoV-2 Open
Background To support the implementation of high-throughput pipelines suitable for SARS-CoV-2 sequencing and analysis in a clinical laboratory, we developed an automated sample preparation and analysis workflow. Methods We used the establi…
View article: Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents
Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents Open
The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet…
View article: Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents
Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents Open
The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet…
View article: A High-Throughput Protocol for Isolating Cell-Free Circulating Tumor DNA from Peripheral Blood
A High-Throughput Protocol for Isolating Cell-Free Circulating Tumor DNA from Peripheral Blood Open
The analysis of cell-free circulating tumor DNA (ctDNA) is potentially a less invasive, more dynamic assessment of cancer progression and treatment response than characterizing solid tumor biopsies. Standard isolation methods require separ…
View article: Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis
Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis Open
Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing ana…
View article: Additional file 5: Table S1. of Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing
Additional file 5: Table S1. of Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing Open
Alignment-based metrics for reverse transcriptase comparisons. Table S2. Alignment-based metrics for the size selection experiment. Table S3. Alignment-based metrics for the comparison of library construction kits. Table S4. Alignment-base…