Kevin McKernan

Kevin McKernan
Medicinal Genomics · R&D

About

114
Publications
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Introduction
Psilocybe cubensis and Cannabis sativa genomics

Publications

Publications (114)
Article
Background: Cannabis safety testing requires adequate detection of a broad class of bacteria known as Enterobacteria, from the family of Enterobacteriaceae. These organisms are responsible for many food-borne illnesses including gastroenteritis, and are common targets in the food testing industry. While all these organisms contain 16S DNA, not all...
Article
Full-text available
The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place...
Preprint
Cannabis safety testing requires adequate detection of a broad class of bacteria known as Enterobacteria from the family of Enterobacteriaceae. These organisms are responsible for many food-borne illnesses including gastroenteritis and are common targets in the food testing industry. While all of these organisms contain 16S DNA, not all of them wil...
Article
The Psilocybe genus is well known for the synthesis of valuable psychoactive compounds such as Psilocybin, Psilocin, Baeocystin and Aeruginascin. The ubiquity of Psilocybin synthesis in Psilocybe has been attributed to a horizontal gene transfer mechanism of a ~20Kb gene cluster. A recently published highly contiguous reference genome derived from...
Preprint
Full-text available
Codon optimization describes the process used to increase protein production by use of alternative but synonymous codon changes. In SARS-CoV-2 mRNA vaccines codon optimizations can result in differential secondary conformations that inevitably affect a protein’s function with significant consequences to the cell. Importantly, when codon optimizatio...
Article
The Psilocybe genus is well known for the synthesis of valuable psychoactive compounds such as Psilocybin, Psilocin, Baeocystin and Aeruginascin. The ubiquity of Psilocybin synthesis in Psilocybe has been attributed to a horizontal gene transfer mechanism of a ~20Kb gene cassette. A recently published highly contiguous reference genome derived from...
Article
Full-text available
Background: Cannabis products are subjected to microbial testing for human pathogenic fungi and bacteria. These testing requirements often rely on non-specific colony forming unit (CFU/g) specifications without clarity on which medium, selection or growth times are required. We performed whole genome sequencing to assess the specificity of colony f...
Article
Background: Cannabis products are subjected to microbial testing for pathogenic fungi and bacteria. These testing requirements often rely on non-specific colony forming unit (CFU/g) specifications without clarity on which medium, selection or growth times are required. We performed whole genome sequencing to assess the specificity of colony forming...
Preprint
Full-text available
The Psilocybe genus is well known for the synthesis of valuable psychoactive compounds such as Psilocybin, Psilocin, Baeocystin and Aeruginascin. The ubiquity of Psilocybin synthesis in Psilocybe has been attributed to a horizontal gene transfer mechanism of a ~20Kb gene cassette. A recently published highly contiguous reference genome derived from...
Article
The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place...
Article
Full-text available
We describe the use of high-fidelity single molecule sequencing to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig. The dataset is a...
Article
Full-text available
The performance of diagnostic tests crucially depends on the disease prevalence, test sensitivity, and test specificity. However, these quantities are often not well known when tests are performed outside defined routine lab procedures which make the rating of the test results somewhat problematic. A current example is the mass testing taking place...
Article
Full-text available
We describe the use of high-fidelity single molecule sequencing to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig. The dataset is a...
Preprint
Full-text available
We describe the use of high-fidelity single molecule sequencing (HiFi) to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig.
Preprint
Full-text available
Background:: After submitting our review report on Corman et al. (referred hereinafter as CD-report) and republishing it on a scientific preprint server (http://doi.org/10.5281/zenodo.4298004) and Researchgate.net we offered the report for public discussion at cormandrostenreview.com on 27th November 2020. The scientific community provided addition...
Preprint
Full-text available
After submitting our review report on Corman et al. (referred hereinafter as CD-report) andrepublishing it on a scientific preprint server [50] and Researchgate.net [51] we offered thereport for public discussion at cormandrostenreview.com on 27th November 2020. Thescientific community provided additional literature, references, and analyses concer...
Preprint
Full-text available
This extensive review report has been officially submitted to Eurosurveillance editorial board on 27th November 2020 via their submission-portal, enclosed to this review report is a retraction request letter, signed by all the main & co-authors. First and last listed names are the first and second main authors. All names in between are co-authors....
Preprint
Full-text available
In January of 2020, COVID-19 became a worldwide pandemic. As many industries shutdown to comply with social distancing measures, the cannabis industry was deemed an essential business in most US jurisdictions. Cannabis is manually farmed, trimmed and packaged and as a result can be a potential inhaled SARs-CoV-2 fomite. Many of the comorbidities de...
Preprint
Full-text available
Cannabis is a diverse and polymorphic species. To better understand cannabinoid synthesis inheritance and its impact on pathogen resistance, we shotgun sequenced and assembled a Cannabis trio (sibling pair and their offspring) utilizing long read single molecule sequencing. This resulted in the most contiguous Cannabis sativa assemblies to date. Th...
Article
Full-text available
Terpenes are responsible for most or all of the odor and flavor properties of Cannabis sativa, and may also impact effects users experience either directly or indirectly. We report the diversity of terpene profiles across samples bound for the Washington dispensary market. The remarkable degree of variation in terpene profiles ultimately results fr...
Preprint
Full-text available
Cannabis microbial testing presents unique challenges. Unlike food testing, cannabis testing has to consider various routes of administration beyond just oral administration. Cannabis flowers produce high concentrations of antimicrobial cannabinoids and terpenoids and thus represent a different matrix than traditional foods 1, 2. In 2018, it is est...
Preprint
Full-text available
We describe the use of a Decentralized Autonomous Organization (DAO) to crypto-fund the single molecule sequencing and publication of a Type II Cannabis plant. This resulted in the construction of the most contiguous Cannabis genome assembly to date. The combined use of the Dash cryptocurrency, DAOs, and Pacific Biosciences sequencing delivered a 1...
Article
Full-text available
Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous r...
Data
Column 1 lists the genes contained in the EpiSEEK gene panel. Column 2 lists the genes contained in the NucSEEK gene panel. (XLSX)
Data
The phenotypes associated with knockout mice are listed under each gene in column 1. Column 2 gives the general phenotype that was used to select human phenotpes and HPO terms. Column 3 indicates whether the phenotypes are neurological. Column 4 provides PMIDs for corresponding mouse knockout publications. (XLSX)
Data
Association data for CNR2, FAAH and MGLL with column headers: Gene, Phenotypes that were evaluated, Number of cases or controls in which that phenotype was present out of the total number, odds ratio (OR), 95% confidence intervals for the odds ratios, uncorrected two-tailed P-values, and P-value corrected for multiple testing. (XLSX)
Data
Column 1 provides a comprehensive listing of HPO terms derived from clinical reports for 5464 patients tested using Courtagen's NucSEEK and EpiSEEK gene panels. Column 2 provides the corresponding HPO descriptions. Columns 3–13 indicate the HPO terms corresponding to each of the general phenotypes derived from mouse knockouts according to the heade...
Data
Column 1 provides a comprehensive listing of HPO terms derived from clinical reports for 3728 patients tested using Courtagen's EpiSEEK gene panel. Column 2 provides the corresponding HPO descriptions. Columns 3–8 indicate the HPO terms corresponding to each of the general phenotypes derived from mouse knockouts according to the headers in row 3 (a...
Data
Data for rare variants discovered in this study. Headers in row 1 are self explanatory. (XLSX)
Data
This contains the same data as Table 1, with the addition of 95% confidence intervals for the odds ratios and the uncorrected two-tailed P-values. Columns identical to Table 1: Gene, Phenotypes that were evaluated, Number of cases or controls in which that phenotype was present out of the total number, odds ratio (OR), and P-value corrected for mul...
Preprint
Full-text available
Pyrethrins are a class of natural terpenoid pesticides produced by Tanacetum cinerariifolium , commonly known as chrysanthemum. Here we present evidence that cannabis may be able to produce pyrethrins endogenously. Flower from a cannabis plant grown in a closed hydroponic environment contained 2.48 parts per million pyrethrin I by weight. A compari...
Preprint
Full-text available
Rare genetic variants in the core endocannabinoid system genes CNR1 , CNR2 , DAGLA , MGLL and FAAH were identified in molecular testing data from up to 6.032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heter...
Chapter
Full-text available
Microbiological contaminants pose a potential threat to cannabis consumers. Bacteria and fungi may cause opportunistic infections in immunocompromized individuals. Even dead organisms may trigger allergies and asthma. Toxins from microbial overloads, such as Shigla toxin and aflatoxins, may pose a problem—unlikely, but possible. The Cannabis plant...
Article
Full-text available
Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quan...
Article
Full-text available
The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and...
Article
Full-text available
The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and...
Preprint
Full-text available
The Center for Disease Control estimates 128,000 people in the U.S. are hospitalized annually due to food borne illnesses. This has created a demand for food safety testing targeting the detection of pathogenic mold and bacteria on agricultural products. This risk extends to medical Cannabis and is of particular concern with inhaled, vaporized and...
Article
Full-text available
We sequenced several cannabis genomes in 2011 of June and the first and the longest contigs to emerge were the chloroplast and mitochondrial genomes. Having been a contributor to the Human Genome Project and an eye-witness to the real benefits of immediate data release, I have first hand experience with the potential mal-investment of millions of d...
Article
Functional disorders are common conditions with a substantial impact on a patients' wellbeing, and can be diagnostically elusive. There are bidirectional associations between functional disorders and mitochondrial dysfunction. In this study, provided clinical information and the exon sequence of the TRAP1 mitochondrial chaperone were retrospectivel...
Article
Mutations in the nuclear-encoded mitochondrial aminoacyl-tRNA synthetases are associated with a range of clinical phenotypes. Here we report a novel disorder in three adult patients with a phenotype including cataracts, short stature secondary to growth hormone deficiency, sensorineural hearing deficit, peripheral sensory neuropathy and skeletal dy...
Article
Full-text available
We have developed a PCR method, coined Déjà vu PCR, that utilizes six nucleotides in PCR with two methyl specific restriction enzymes that respectively digest these additional nucleotides. Use of this enzyme-and-nucleotide combination enables what we term a "DNA diode", where DNA can advance in a laboratory in only one direction and cannot feedback...
Article
Full-text available
Can methylation be the key to challenging the interpretation of existing gene patent claims? And can a novel PCR method be used to enable the sequencing of hundreds of genes?
Article
Full-text available
The HapMap project along with next-generation sequencing technologies provides unprecedented opportunities to fully characterize whole-genome polymorphism events comprising many individuals across multiple populations. Genetic variants such as single-nucleotide-polymorphisms (SNPs), small indels, large-scale indel events on the order of several kil...
Data
miRNA-MATE source code and user manual.
Data
Full-text available
Supplementary figures, figure legends and tables.
Data
A description of the proposed nomenclature for isomiRs.
Data
Full-text available
Tab-delimited text file of the raw counts of isomers detected in the libraries created in this study.
Article
Full-text available
Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological ro...
Article
Full-text available
Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem...
Article
Full-text available
The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA se...
Article
Full-text available
High-throughput sequencing technology enables population-level surveys of human genomic variation. Here, we examine the joint allele frequency distributions across continental human populations and present an approach for combining complementary aspects of whole-genome, low-coverage data and targeted high-coverage data. We apply this approach to da...
Article
Full-text available
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platfor...
Data
Comparison of different number of mismatches on detection sensitivity for methylation and incomplete bisulfite conversion. (0.05 MB DOC)
Article
Full-text available
Methylation, the addition of methyl groups to cytosine (C), plays an important role in the regulation of gene expression in both normal and dysfunctional cells. During bisulfite conversion and subsequent PCR amplification, unmethylated Cs are converted into thymine (T), while methylated Cs will not be converted. Sequencing of this bisulfite-treated...