ABSTRACT. Infantile myofibromatosis is a rare genetic disorder characterized by the development of benign tumors in the skin, muscle, bone, and viscera. The molecular pathogenesis is still incompletely known. An autosomal dominant form had been reported as causally related with mutations in the gene for platelet-derived growth factor receptor beta (PDGFRB). We report here two siblings with infantile myofibromatosis and with a PDGFRB mutation identified by exome sequence analysis. However, the unaffected mother also had the same PDGFRB mutation. We showed that both children had also inherited from their healthy father a heterozygous mutation in the gene for receptor protein tyrosine phosphatase gamma (PTPRG), an enzyme known to dephosphorylate PDGFRB. We suggest that in this family, the additional mutation in PTPRG may explain the full phenotypic penetrance in the siblings affected, in comparison with the unaffected mother.

Infantile myofibromatosis (IM) is a rare disorder characterized by the development of benign tumors in the skin, muscle, bone, and viscera. The incidence is 1/150,000 live births and the disease is the most common cause of fibrous tumors in infancy. Cases which lack visceral involvement generally have a more benign course, usually with spontaneous regression of the tumors. On the other hand, the prognosis tends to be unfavorable when there is involvement of vital organs, which can lead to significant mortality. The identification of rare variants in genes that may cause IM is the first step towards the possibility of targeted treatments; however, the molecular pathogenesis of IM is poorly understood. In the present study, we report the results of exome sequence analysis of two brothers diagnosed with visceral multicentric infantile myofibromatosis, and their healthy consanguineous parents. In the two brothers we identified novel homozygous variants in NDRG4 gene (N-myc downregulated gene family member 4) and in RLTPR gene (RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing). The healthy parents were heterozygous for both variants. Consistent with the phenotype of IM, NDRG4 is a tumor-related gene; its expression has been shown to be decreased in numerous tumor types, suggesting that it might be a tumor suppressor gene. Additionally, studies have demonstrated that NDRG4 may have a role in cell survival and tumor invasion. We thus propose that this homozygous variant in NDRG4 may be the causative variant of the autosomal recessive form of IM in the studied family and that it should be investigated in other cases of autosomal recessive infantile myofibromatosis.

Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the “1-click” method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE–Núcleo de Genética Médica in Brazil and at the Children’s University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.

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Biodiversity is currently assessed for environmental characterizations and monitoring through a laborious and time-consuming process of morphological taxonomy. We used rRNA 18S, rRNA 28S and COI, together with NGS and Bioinformatics to identify benthic invertebrate organisms from sediment samples collected in five stations in the Campos Basin in southeast Brazil, an important oil extraction area and one of the best-studied marine biota in Brazil. A total of 3.3 million sequences were clustered in Operational Taxonomic Units and more than 1.6 million sequences (about 50% of all reads) were assigned to 957 prokaryotes and 577 eukaryotes. BLAST identified 23 phyla, 60 classes, 62 orders, 70 families, 67 genus and 46 species of eukaryotes. By meta-barcoding we identified phyla that are traditionally found in samples of marine benthos, such as Annelida, Arthropoda, Mollusca and Chordata, as well as rare phyla like Entoprocta and Gastrotricha. Taxa identified with meta-barcoding were compared to morphology data from previous studies in the area (REVIZEE, Habitats Project) and geo-validated with the database Global Biodiversity Information Facility. For several taxa, this is the first evidence of occurrence in Campos the area and the number of OTU identified suggests an enormous unveiled benthic biodiversity in Campos Basin. Our study supports the application of Meta-Barcoding for environmental characterization and monitoring programs, reducing from years to few months the time currently required for species identification and biodiversity determination.