Jonathan LoTempio
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View article: GREGoR: accelerating genomics for rare diseases
GREGoR: accelerating genomics for rare diseases Open
View article: Genome sequencing reveals the impact of pseudoexons in rare genetic disease
Genome sequencing reveals the impact of pseudoexons in rare genetic disease Open
Genome sequencing can overcome limitations of clinical genetic testing, such as the inability to call intronic variants. Our findings highlight pseudoexons as a common mechanism via which deep intronic variants cause Mendelian disease.
View article: Ethics choices during the Human Genome Project reflected their policy world, not ours
Ethics choices during the Human Genome Project reflected their policy world, not ours Open
Since human genomic data produced in the 1990s are still a significant part of the reference genome, decades-old decisions pertinent to the creation of these data persist. Here, we discuss how historical documents illustrate the 1990s poli…
View article: Genome-wide profiling of highly similar paralogous genes using HiFi sequencing
Genome-wide profiling of highly similar paralogous genes using HiFi sequencing Open
Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Parap…
View article: Identification of <i>de novo</i> variants from parent-proband duos via long-read sequencing
Identification of <i>de novo</i> variants from parent-proband duos via long-read sequencing Open
While de novo variants cause many Mendelian disorders, their detection currently requires sequencing of the proband and both biological parents. This is not feasible when only one parent is available, a limitation for millions of families.…
View article: Limited Objection of Intellectual Property, Health Law and Bioethics Scholars to Debtors' Proposed Asset Sale in the Bankruptcy of 23andMe Holding Co.
Limited Objection of Intellectual Property, Health Law and Bioethics Scholars to Debtors' Proposed Asset Sale in the Bankruptcy of 23andMe Holding Co. Open
View article: O28: GREGoR: Accelerating genomics for rare diseases
O28: GREGoR: Accelerating genomics for rare diseases Open
View article: P539: Chatbot-assisted informed consent in genomics research*
P539: Chatbot-assisted informed consent in genomics research* Open
View article: Genome sequencing reveals the impact of pseudoexons in rare genetic disease
Genome sequencing reveals the impact of pseudoexons in rare genetic disease Open
Purpose Advancements in sequencing technologies have significantly improved clinical genetic testing, yet the diagnostic yield remains around 30-40%. Emerging sequencing technologies are now being deployed in the clinical setting to addres…
View article: P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia*
P821: Long-read sequencing resolves CYP21A2 alleles in congenital adrenal hyperplasia* Open
We sought to evaluate clinical utility of long-read sequencing (LRS) de novo assemblies and optical genome mapping (OGM) in a research clinical setting for rare disease diagnosis. We focused on regions of the genome of critical importance …
View article: Benchmarking long-read genome sequence alignment tools for human genomics applications
Benchmarking long-read genome sequence alignment tools for human genomics applications Open
Background The utility of long-read genome sequencing platforms has been shown in many fields including whole genome assembly, metagenomics, and amplicon sequencing. Less clear is the applicability of long reads to reference-guided human g…
View article: Using a chat-based informed consent tool in large-scale genomic research
Using a chat-based informed consent tool in large-scale genomic research Open
Objective We implemented a chatbot consent tool to shift the time burden from study staff in support of a national genomics research study. Materials and Methods We created an Institutional Review Board-approved script for automated chat-b…
View article: Increased diagnostic yield from negative whole genome‐slice panels using automated reanalysis
Increased diagnostic yield from negative whole genome‐slice panels using automated reanalysis Open
We evaluated the diagnostic yield using genome‐slice panel reanalysis in the clinical setting using an automated phenotype/gene ranking system. We analyzed whole genome sequencing (WGS) data produced from clinically ordered panels built as…
View article: “Development and Implementation of Novel Chatbot-based Genomic Research Consent”
“Development and Implementation of Novel Chatbot-based Genomic Research Consent” Open
Objective To conduct a retrospective analysis comparing traditional human-based consenting to an automated chat-based consenting process. Materials and Methods We developed a new chat-based consent using our IRB-approved consent forms. We …
View article: Benchmarking long-read genome sequence alignment tools for human genomics applications
Benchmarking long-read genome sequence alignment tools for human genomics applications Open
Background The utility of long-read genome sequencing platforms has been shown in many fields including whole genome assembly, metagenomics, and amplicon sequencing. Less clear is the applicability of long reads to reference-guided human g…
View article: Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States
Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States Open
The evolution of SARS-CoV2 virus has led to the emergence of variants of concern (VOC). Children, particularly <12 years old not yet eligible for vaccines, continue to be important reservoirs of SARS-CoV-2 yet VOC prevalence data in this p…
View article: Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreak
Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreak Open
The SARS-CoV-2 virus has emerged as a global pandemic, severely impacting everyday life. Significant resources have been dedicated towards profiling the viral genome in the adult population. We present an analysis of viral genomes acquired…
View article: Mitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane
Mitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane Open
Mitochondrial enzymes involved in energy transformation are organized into multiprotein complexes that channel the reaction intermediates for efficient ATP production. Three of the mammalian urea cycle enzymes: N-acetylglutamate synthase (…
View article: Paucity and Disparity of Publicly Available Sex-Disaggregated Data for the COVID-19 Epidemic Hamper Evidence-Based Decision-Making
Paucity and Disparity of Publicly Available Sex-Disaggregated Data for the COVID-19 Epidemic Hamper Evidence-Based Decision-Making Open
View article: Mitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane
Mitochondrial Enzymes of the Urea Cycle Cluster at the Inner Mitochondrial Membrane Open
Mitochondrial enzymes involved in energy transformation are organized into multiprotein complexes that channel the reaction intermediates for efficient ATP production. Three of the mammalian urea cycle enzymes: N-acetylglutamate synthase (…
View article: Paucity and disparity of publicly available sex-disaggregated data for the COVID-19 epidemic hamper evidence-based decision-making
Paucity and disparity of publicly available sex-disaggregated data for the COVID-19 epidemic hamper evidence-based decision-making Open
COVID-19 has joined the long list of human disorders with sexually dimorphic expression. Increased lethality in men was evident in the first large reports from ChinaCDC and WHO-China, and the gender gap appeared even wider in the early Ita…
View article: Baseline human gut microbiota profile in healthy people and standard reporting template
Baseline human gut microbiota profile in healthy people and standard reporting template Open
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or …
View article: Peer Review #1 of "Robust and automatic definition of microbiome states (v0.1)"
Peer Review #1 of "Robust and automatic definition of microbiome states (v0.1)" Open
Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of ri…
View article: Peer Review #1 of "Robust and automatic definition of microbiome states (v0.2)"
Peer Review #1 of "Robust and automatic definition of microbiome states (v0.2)" Open
Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of ri…
View article: Baseline human gut microbiota profile in healthy people and standard reporting template
Baseline human gut microbiota profile in healthy people and standard reporting template Open
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or …