Papers by Francesco Musacchia
Additional file 7 of Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Figshare, 2022
Additional file 3 of Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Figshare, 2022
Additional file 5 of Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Figshare, 2022
Additional file 2 of Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Figshare, 2022
Additional file 10 of Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain
Figshare, 2022
Additional file 10: Table S8. of De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum
Selected PERNI transcripts for qPCR validation of the in silico expression levels. (XLS 26Â kb)
Additional file 6: Table S4. of De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum
Summary of the RepeatMasker search for TEs in the sand flies transcriptomes. (XLS 42Â kb)
Additional file 1: Table S1. of De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum
Ortholog hit ratio calculation of the transcriptome of P. perniciosus respect to D. melanogaster ... more Ortholog hit ratio calculation of the transcriptome of P. perniciosus respect to D. melanogaster and P. papatasi. (XLS 876Â kb)
FILE2
<p>file2</p
Cantù syndrome: Report of a patient with a novel variant in <scp> <i>KCNJ8</i> </scp> and revision of literature
American Journal of Medical Genetics, Mar 3, 2022
Cantù syndrome (CS) is a rare multisystemic disorder, characterized by congenital hypertrichosis,... more Cantù syndrome (CS) is a rare multisystemic disorder, characterized by congenital hypertrichosis, macrocephaly, facial dysmorphisms, cardiomegaly, vascular, and skeletal anomalies. From the cognitive point of view, most of the patients show a mild speech delay and a few of them present intellectual disability and learning difficulties. To date, most CS-reported cases are caused by heterozygous ABCC9 gene mutations. Only three patients with CS and heterozygous KCNJ8 gene variants have been reported. The authors here present the fourth case of CS with a variant in KCNJ8 in a 6-month-old baby. Diagnosis was reached through Trio-Whole Exome analysis that revealed a de novo missense variant in KCNJ8.
BMC genomics, 2015
The phlebotomine sand fly Phlebotomus perniciosus (Diptera: Psychodidae, Phlebotominae) is a majo... more The phlebotomine sand fly Phlebotomus perniciosus (Diptera: Psychodidae, Phlebotominae) is a major Old World vector of the protozoan Leishmania infantum, the etiological agent of visceral and cutaneous leishmaniases in humans and dogs, a worldwide re-emerging diseases of great public health concern, affecting 101 countries. Despite the growing interest in the study of this sand fly species in the last years, the development of genomic resources has been limited so far. To increase the available sequence data for P. perniciosus and to start studying the molecular basis of the sexual differentiation in sand flies, we performed whole transcriptome Illumina RNA sequencing (RNA-seq) of adult males and females and de novo transcriptome assembly. We assembled 55,393 high quality transcripts, of which 29,292 were unique, starting from adult whole body male and female pools. 11,736 transcripts had at least one functional annotation, including full-length low abundance salivary transcripts, 9...
Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses
We report the diagnostic results of a comprehensive copy number variant (CNV) reanalysis of 9,171... more We report the diagnostic results of a comprehensive copy number variant (CNV) reanalysis of 9,171 exome sequencing (ES) datasets from 5,757 families, including 6,143 individuals affected by a rare disease (RD). The data analysed was extremely heterogeneous, having been generated using 28 different exome enrichment kits, and sequenced on multiple short-read sequencing platforms, by 42 different research groups across Europe partnering in the Solve-RD project. Each of these research groups had previously undertaken their own analysis of the ES data but had failed to identify disease-causing variants.We applied three CNV calling algorithms to maximise sensitivity: ClinCNV, Conifer, and ExomeDepth. Rare CNVs overlapping genes of interest in custom lists provided by one of four partner European Reference Networks (ERN) were identified and taken forward for interpretation by clinical experts in RD. To facilitate interpretation, Integrative Genomics Viewer (IGV) screenshots incorporating a...
European Journal of Human Genetics, 2021
Human Genomics
Background Exome and genome sequencing are the predominant techniques in the diagnosis and resear... more Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivi...
Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14
Human Genetics and Genomics Advances
CHAMP1-related disorders: pathomechanisms triggered by different genomic alterations define distinct nosological categories
European Journal of Human Genetics, Feb 16, 2023
Nature Communications
Challenges to the widespread application of gene therapy with adeno-associated viral (AAV) vector... more Challenges to the widespread application of gene therapy with adeno-associated viral (AAV) vectors include dominant conditions due to gain-of-function mutations which require allele-specific knockout, as well as long-term transgene expression from proliferating tissues, which is hampered by AAV DNA episomal status. To overcome these challenges, we used CRISPR/Cas9-mediated homology-independent targeted integration (HITI) in retina and liver as paradigmatic target tissues. We show that AAV-HITI targets photoreceptors of both mouse and pig retina, and this results in significant improvements to retinal morphology and function in mice with autosomal dominant retinitis pigmentosa. In addition, we show that neonatal systemic AAV-HITI delivery achieves stable liver transgene expression and phenotypic improvement in a mouse model of a severe lysosomal storage disease. We also show that HITI applications predominantly result in on-target editing. These results lay the groundwork for the app...
Next generation sequencing technologies, specifically RNA-seq, promise to give a comprehensive po... more Next generation sequencing technologies, specifically RNA-seq, promise to give a comprehensive portrait of the whole transcriptome in a given organism, even in the absence of a reference genome (Grabherr et al. 2011), thus optimized tools for the annotation are required. Furthermore, unambiguously identification of long non-coding RNAs (lncRNAs) is challenging since they are being discovered in almost all organisms (e.g. mammals (Cabili et al. 2011), fishes (Pauli et al. 2012), insects (Young et al. 2012), etc.). Current software to annotate transcriptomes, search for homologies with known proteins and domains, but they do not have the ability to identify putative lncRNAs (Conesa and Götz 2008; Schmid and Blaxter 2008, 8; Philipp et al. 2012; Koski et al. 2005). We developed Annocript: an automated pipeline to annotate large transcripome datasets and predict putative lncRNAs. The pipeline is developed using PERL, R and MySQL and organized in modules. The first module generates a MyS...
Uploads
Papers by Francesco Musacchia