Robin Coope
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View article: Development of lesion and organ negative cast modelling technique for quality assurance and optimization of nuclear medicine images
Development of lesion and organ negative cast modelling technique for quality assurance and optimization of nuclear medicine images Open
The NCM method has potential to enable more realistic phantom studies within nuclear medicine imaging. The cost for the lymphoma tumour phantom study is less than $400 USD, making it feasible for large-scale studies.
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: 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: Development of the quantitative PET prostate phantom (Q3P) for improved quality assurance of <sup>18</sup>F‐PSMA PET imaging in metastatic prostate cancer
Development of the quantitative PET prostate phantom (Q3P) for improved quality assurance of <sup>18</sup>F‐PSMA PET imaging in metastatic prostate cancer Open
Background Phantoms are commonly used to evaluate and compare the performance of imaging systems given the known ground truth. Positron emission tomography (PET) scanners are routinely validated using the NEMA image quality phantom, in whi…
View article: P658: Detection of variant parent-of-origin in diverse hereditary cancer syndromes using only the proband’s blood sample
P658: Detection of variant parent-of-origin in diverse hereditary cancer syndromes using only the proband’s blood sample Open
Parent-of-Origin-Aware genomic analysis (POAga) using Oxford Nanopore Technologies long-read sequencing combined with Strand-seq enables assignment of any autosomal variant to either parent with 99% accuracy using only the blood sample of …
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: Reduction in Doses to Organs at Risk and Normal Tissue During Breast Radiation Therapy With a Carbon-Fiber Adjustable Reusable Accessory
Reduction in Doses to Organs at Risk and Normal Tissue During Breast Radiation Therapy With a Carbon-Fiber Adjustable Reusable Accessory Open
CARA can reduce V105%breast, lung and normal tissue dose, and remove the inframammary fold for breast patients with large or pendulous breasts and high body mass index treated in the supine position, without compromising target coverage. C…
View article: A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells Open
RNA sequencing (RNAseq) has been widely used to generate bulk gene expression measurements collected from pools of cells. Only relatively recently have single-cell RNAseq (scRNAseq) methods provided opportunities for gene expression analys…
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: Comprehensive molecular portraits of human breast tumours
Comprehensive molecular portraits of human breast tumours Open
This Article from the Cancer Genome Atlas consortium describes a multifaceted analysis of primary breast cancers in 825 people. Exome sequencing, copy number variation, DNA methylation, messenger RNA arrays, microRNA sequencing and proteom…
View article: Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure
Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure Open
Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller th…
View article: Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA
Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA Open
Next generation RNA-sequencing (RNA-seq) is a flexible approach that can be applied to a range of applications including global quantification of transcript expression, the characterization of RNA structure such as splicing patterns and pr…
View article: Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (<i>Picea sitchensis</i>), Indicates Complex Physical Structure
Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (<i>Picea sitchensis</i>), Indicates Complex Physical Structure Open
Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller th…
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: Imaging-Based 3-Dimensional Printing for Improved Maxillofacial Presurgical Planning: A Single Center Case Series
Imaging-Based 3-Dimensional Printing for Improved Maxillofacial Presurgical Planning: A Single Center Case Series Open
Purpose 3-D printing is an increasingly widespread technology that allows physical models to be constructed based on cross-sectional medical imaging data. We sought to develop a pipeline for production of 3-dimensional (3-D) models for pre…
View article: Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples
Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples Open
Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequ…
View article: Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires Open
Summary Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes …
View article: MAVIS: merging, annotation, validation, and illustration of structural variants
MAVIS: merging, annotation, validation, and illustration of structural variants Open
Summary Reliably identifying genomic rearrangements and interpreting their impact is a key step in understanding their role in human cancers and inherited genetic diseases. Many short read algorithmic approaches exist but all have apprecia…
View article: PO-222 Molecular characterisation of low grade lymphoma in northern sea otters (Enhydra lutris kenyoni)
PO-222 Molecular characterisation of low grade lymphoma in northern sea otters (Enhydra lutris kenyoni) Open
Introduction Lymphoid cancers are a biologically diverse group of neoplasms. Disease aetiology is multifactorial, implicating viral and infectious agents, immune dysfunction, and genetic factors. Lymphoid cancers affect domestic and labor…
View article: The Genome of the Northern Sea Otter (Enhydra lutris kenyoni)
The Genome of the Northern Sea Otter (Enhydra lutris kenyoni) Open
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were use…
View article: The Genome of the Beluga Whale (Delphinapterus leucas)
The Genome of the Beluga Whale (Delphinapterus leucas) Open
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microflu…