Emmanuèle C. Délot
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View article: GREGoR: accelerating genomics for rare diseases
GREGoR: accelerating genomics for rare diseases Open
View article: Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe Open
View article: Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe Open
1 Abstract We previously introduced Giraffe, a short-read-to-pangenome graph mapper available in the vg pangenomics toolkit. Giraffe was fast and accurate for mapping short reads to human-scale pangenomes, but struggled with long reads. Lo…
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: 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: Long-read sequencing resolves the clinically relevant<i>CYP21A2</i>locus, supporting a new clinical test for Congenital Adrenal Hyperplasia
Long-read sequencing resolves the clinically relevant<i>CYP21A2</i>locus, supporting a new clinical test for Congenital Adrenal Hyperplasia Open
Congenital Adrenal Hyperplasia (CAH), one of the most common inherited disorders, is caused by defects in adrenal steroidogenesis. It is potentially lethal if untreated and is associated with multiple comorbidities, including fertility iss…
View article: Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection 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: Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis
Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis Open
To assess the impact of postnatal processing on placental DNA methylation, array data from flash-frozen placental tissue was compared to perfluorocarbon-immersed and formalin-fixed paraffin-embedded placental tissue. We observed that tissu…
View article: Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection Open
More than 50% of families with suspected rare monogenic diseases remain unsolved after whole genome analysis by short read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnostic gap by capturing variants inaccessibl…
View article: De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome
De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome Open
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 a gene family. We applied Paraphase to 160 …
View article: <i>De novo</i>variants in the non-coding spliceosomal snRNA gene<i>RNU4-2</i>are a frequent cause of syndromic neurodevelopmental disorders
<i>De novo</i>variants in the non-coding spliceosomal snRNA gene<i>RNU4-2</i>are a frequent cause of syndromic neurodevelopmental disorders Open
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes 1 . Increasingly, large genome-sequenced cohorts are improving our ability to disco…
View article: Reprograming skin fibroblasts into Sertoli cells: a patient-specific tool to understand effects of genetic variants on gonadal development
Reprograming skin fibroblasts into Sertoli cells: a patient-specific tool to understand effects of genetic variants on gonadal development Open
Background Disorders/differences of sex development (DSD) are congenital conditions in which the development of chromosomal, gonadal, or anatomical sex is atypical. With overlapping phenotypes and multiple genes involved, poor diagnostic y…
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: Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic
Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic Open
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: Beyond the exome: What’s next in diagnostic testing for Mendelian conditions
Beyond the exome: What’s next in diagnostic testing for Mendelian conditions Open
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: Beyond the exome: what's next in diagnostic testing for Mendelian conditions
Beyond the exome: what's next in diagnostic testing for Mendelian conditions Open
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly un…
View article: P148: Novel molecular diagnoses in individuals with holoprosencephaly and prior negative sequencing*
P148: Novel molecular diagnoses in individuals with holoprosencephaly and prior negative sequencing* Open
View article: P227: De novo GATA4 deletion in a 46,XX boy with hypospadias and pulmonic valve stenosis
P227: De novo GATA4 deletion in a 46,XX boy with hypospadias and pulmonic valve stenosis Open
View article: Reprograming human fibroblasts into Sertoli cells: a tool for personalized medicine
Reprograming human fibroblasts into Sertoli cells: a tool for personalized medicine Open
Disorders/Differences of Sex Development (DSD) are congenital conditions in which the development of chromosomal, gonadal, or anatomical sex is atypical. With overlapping phenotypes and multiple genes involved, poor diagnostic yields are a…
View article: Precocious Puberty in a Boy With Bilateral Leydig Cell Tumors due to a Somatic Gain-of-Function <i>LHCGR</i> Variant
Precocious Puberty in a Boy With Bilateral Leydig Cell Tumors due to a Somatic Gain-of-Function <i>LHCGR</i> Variant Open
Context Autosomal dominant and rarely de novo gain-of-function variants in the LHCGR gene are associated with precocious male puberty, while somatic LHCGR variants have been found in isolated Leydig cell adenomas and Leydig cell hyperplasi…
View article: eP192: Differences of Sex Development (DSD) in Central Africa: Genetics, psychosocial adaptation and perceptions
eP192: Differences of Sex Development (DSD) in Central Africa: Genetics, psychosocial adaptation and perceptions Open