John E. Gorzynski
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View article: Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing
Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing Open
Long-read DNA sequencing detects genetic variants and epigenetic modifications simultaneously, but optimal preservation of molecular length and base modifications typically requires cold-chain infrastructure. This infrastructure dependence…
View article: Long-read genome sequencing and multi-omics in aging and neurodegeneration
Long-read genome sequencing and multi-omics in aging and neurodegeneration Open
Structural variants (SVs) are a major source of genetic variation yet remain underexplored in healthy aging and neurodegenerative diseases. We performed nanopore long-read genome sequencing (lrGS) on 551 deeply-phenotyped individuals from …
View article: Scaled multidimensional assays of variant effect identify sequence-function relationships in hypertrophic cardiomyopathy
Scaled multidimensional assays of variant effect identify sequence-function relationships in hypertrophic cardiomyopathy Open
Background An estimated 1 in 500 people live with hypertrophic cardiomyopathy (HCM), a disease for which genetic diagnosis can identify family members at risk, and increasingly guide therapy. Mutations in the myosin binding protein C3 ( MY…
View article: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease Open
Rare structural variants (SVs)—insertions, deletions, and complex rearrangements—can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore Technologies long-read ge…
View article: Genetic Analysis of an Amyloid PET‐Negative Autopsy‐Confirmed Alzheimer's Pedigree
Genetic Analysis of an Amyloid PET‐Negative Autopsy‐Confirmed Alzheimer's Pedigree Open
Background Alzheimer's disease (AD) is the most common form of dementia. Neuropathologically, AD stands out as a mixed proteinopathy. Beta‐amyloid and tau biomarkers can now add in‐vivo support to the AD diagnosis. Rarely, a patient with A…
View article: Genetic Analysis of an Amyloid PET‐Negative Autopsy‐Confirmed Alzheimer’s Pedigree
Genetic Analysis of an Amyloid PET‐Negative Autopsy‐Confirmed Alzheimer’s Pedigree Open
Background Alzheimer’s disease (AD) is the most common form of dementia. Neuropathologically, AD stands out as a mixed proteinopathy. Beta‐amyloid and tau biomarkers can now add in‐vivo support to the AD diagnosis. Rarely, a patient with A…
View article: Clinical application of Complete Long Read genome sequencing identifies a 16kb intragenic duplication in EHMT1 in a patient with suspected Kleefstra syndrome
Clinical application of Complete Long Read genome sequencing identifies a 16kb intragenic duplication in EHMT1 in a patient with suspected Kleefstra syndrome Open
Long read sequencing offers benefits for the detection of structural variation in Mendelian disease. Here, we applied a new technology that generates contiguous long reads via tagmentation and sequencing by synthesis to a small cohort of p…
View article: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease Open
Rare structural variants (SVs) – insertions, deletions, and complex rearrangements – can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of …
View article: A 3′UTR Insertion Is a Candidate Causal Variant at the <i>TMEM106B</i> Locus Associated With Increased Risk for FTLD-TDP
A 3′UTR Insertion Is a Candidate Causal Variant at the <i>TMEM106B</i> Locus Associated With Increased Risk for FTLD-TDP Open
We identified a novel Alu element insertion in the 3'UTR of TMEM106B in tight linkage with the lead FTLD-TDP risk variant. The lead variant is associated with TMEM106B protein levels, but not expression. The 3'UTR insertion is a lead candi…
View article: Novel characterization of Alzheimer’s disease genetic loci using long‐read sequencing
Novel characterization of Alzheimer’s disease genetic loci using long‐read sequencing Open
Background Alzheimer’s disease (AD) is up to 60‐80% heritable, but less than ∼20% is explained by studies analyzing single nucleotide variants (SNVs). One limitation of short‐read whole‐genome sequencing (SRS) is the standard read length o…
Leveraging whole genome sequencing to promote genetic diversity and population health in zoo-housed western lowland gorillas Open
The sustainability of zoo populations is dependent on maintaining genetic diversity and controlling heritable disease. Here, we explore the integration of whole genome sequencing data in the management of the international zoological popul…
View article: Local read haplotagging enables accurate long-read small variant calling
Local read haplotagging enables accurate long-read small variant calling Open
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Bioscienc…
View article: <i>APOE</i> loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer’s Disease pathology
<i>APOE</i> loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer’s Disease pathology Open
Summary The ε4 allele of apolipoprotein E ( APOE ) is the strongest genetic risk factor for sporadic Alzheimer’s Disease (AD). Knockdown of this allele may provide a therapeutic strategy for AD, but the effect of APOE loss-of-function (LoF…
View article: A 3’UTR Insertion Is a Candidate Causal Variant at the <i>TMEM106B</i> Locus Associated with Increased Risk for FTLD-TDP
A 3’UTR Insertion Is a Candidate Causal Variant at the <i>TMEM106B</i> Locus Associated with Increased Risk for FTLD-TDP Open
Background and Objectives Single nucleotide variants near TMEM106B associate with risk of frontotemporal lobar dementia with TDP-43 inclusions (FTLD-TDP) and Alzheimer’s disease (AD) in genome-wide association studies (GWAS), but the causa…
View article: Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy
Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy Open
The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we…
View article: Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting
Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting Open
International audience
View article: Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy
Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy Open
The SARS-CoV-2 pandemic has differentially impacted populations of varied race, ethnicity and socioeconomic status. Admixture mapping and local ancestry inference represent powerful tools to examine genetic risk within multi-ancestry genom…
Rapid Sequencing Wet Lab v1 Open
Aim: To prepare an ONT non-barcoded library using LSK109, to be distributed over 48 flow cells from 2ml of whole blood.
High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs Open
During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We h…