CTSA has been associated with an autosomal recessive form of Galactosialidosis (OMIM: 613111), for which intellectual disability is a common symptom. We only had two multiplex families in the setting of parental consanguinity in our cohort (each with three affected siblings). While we expected ...
Their research revealed that CoTS from various regions, including the Great Barrier Reef (GBR), Vietnam, the Philippines, Japan, and Micronesia, form a Pan-Pacific clade (PP-C) capable of spawning repeated outbreaks. Iguchi et al. [23] examined CoTS populations in the Ryukyu Archipelago and ...
The questionnaire consisted of open-ended questions in both Arabic and French languages. The questionnaires, as well as the collected samples, were anonymous and systematically stored in a coded clinical record form in order to guarantee participants’ personal data protection. Phenotypic data collection...
The grapevine (Vitis vinifera) is an economically important crop of global significance, cultivated across the world to produce grape-based commodities such as wine, raisins, and grape juice. Historically, its productivity has been endangered by its high susceptibility to biotic and abiotic stresses, ...
In this work, we extend vcfdist to be the first variant call benchmarking tool to jointly evaluate phased single-nucleotide polymorphisms (SNPs), small insertions/deletions (INDELs), and structural variants (SVs) for the whole genome. First, we find that a joint evaluation of small and structu...
GATK software v.4.0.10.1 [90] was used for marking the duplicate reads, followed by calling the SNPs and finally generating a variant call format (VCF) file. The following raw SNPs were extracted and hard-filtered for quality and depth using GATK [90]: QD < 2.0; FS > 60; ...
Hypomethylation levels of Alu are associated with high fasting blood sugar, HbA1c and blood pressure in leukocytes of T2D patients [45]. In addition, CBX7 is a component of Polycomb group (PcG) of proteins, which form Polycomb Repressive complexes (PRCs) to regulate gene expression through hist...
Quality control of the DNA was performed. Their DNA sequences were compared and analyzed with the published gene sequence. The Genome Analysis Toolkit (Broad Institute, Cambridge, MA, USA) was used to detect variants in the BAM file that passed quality control and a VCF format file was ...
by the mpileup function of SAMtools. Each was used to call variants in tumor-only mode, meaning mutations were called relative to the hg19 genome. Each program outputs some form of variant call file (VCF), from which we extracted SNV calls along with associated information provided by the ...
Graphical representation of the HerpesDRG annotation of FASTA sequence input or VCF inputs (dashed lines). Q Query sequence, R NCBI Reference sequence Full size image A concise clinical output can then be generated from this table using the “make_clin_table” function (Fig. 2). Here for ea...