Performance and Diagnostic Value of Genome-Wide Noninvasive Prenatal Testing in Multiple Gestations.

OBJECTIVE: To evaluate the accuracy and diagnostic value of genome-wide noninvasive prenatal testing (NIPT) for the detection of fetal aneuploidies in multiple gestations, with a focus on dichorionic-diamniotic twin pregnancies. METHODS: We performed a retrospective cohort study including data from pregnant women with a twin or higher-order gestation who underwent genome-wide NIPT at one of the eight Belgian genetic centers between November 1, 2013, and March 1, 2020. Chorionicity and amnionicity were determined by ultrasonography. Follow-up invasive testing was carried out in the event of positive NIPT results. Sensitivity and specificity were calculated for the detection of trisomy 21, 18, and 13 in the dichorionic-diamniotic twin cohort. RESULTS: Unique NIPT analyses were performed for 4,150 pregnant women with a multiple gestation and an additional 767 with vanishing gestations. The failure rate in multiple gestations excluding vanishing gestations ranged from 0% to 11.7% among the different genetic centers. Overall, the failure rate was 4.8%, which could be reduced to 1.2% after single resampling. There were no common fetal trisomies detected among the 86 monochorionic-monoamniotic and 25 triplet cases. Two monochorionic-diamniotic twins had an NIPT result indicative of a trisomy 21, which was confirmed in both fetuses. Among 2,716 dichorionic-diamniotic twin gestations, a sensitivity of 100% (95% CI 74.12-100%) and a specificity of 100% (95% CI 99.86-100%) was reached for trisomy 21 (n=12). For trisomy 18 (n=3), the respective values were 75% (95% CI 30.06-95.44%) sensitivity and 100% (95% CI 99.86-100%) specificity, and for trisomy 13 (n=2), 100% (95% CI 20.65-100%) sensitivity and 99.96% (95% CI 99.79-99.99%) specificity. In the vanishing gestation group, 28 NIPT results were positive for trisomy 21, 18, or 13, with only five confirmed trisomies. CONCLUSION: Genome-wide NIPT performed accurately for detection of aneuploidy in dichorionic-diamniotic twin gestations

Hematopoietic Malignancies with Germline Predisposition Diagnosis with Filtered Whole Exome Sequencing and in silico Panel Analysis.

In the frame of the development of new analytical methods for the diagnostic of patients suffering of suspected inherited malignancies with poor access to rapid diagnosis due to a restricted number of analytical sites or the current use of non-comprehensive targeted panels, we developed a new NGS panel for the analysis of several haematological diseases based on a filtered whole exome sequencing approach. We aim to provide physicians with a comprehensive diagnostic panel for the diagnostic work-up of patients affected (or suspected to be affected) by inherited haematological malignancies and related diseases enhancing the patient’s chances to benefit from a personalized medicine approach; together with a view to increase the knowledge about those (rare) conditions

Détection globale de la déficience en recombinaison homologue par séquençage Nanopore

Comprehensive detection of homologous recombination deficiency by Nanopore sequencin

Classification of dermatophytes by a multilocus phylogenetic approach based on Tef-1α, beta tubulin and ITS genes

peer reviewedObjectives: Identification of dermatophytes to the species level is epidemiologically, ecologically and therapeutically significant. The use of phylogenetic species concepts based on rDNA internal transcribed spacer (ITS) regions have improved the taxonomy of dermatophytes. However, it has been shown that for some species, confirmation and refinement using other genes are needed. Indeed, there are problems with accurate definition and characterization of dermatophytes especially among the Trichophyton mentagrophytes series. Intra- and interspecies variations of the translation elongation factor 1-α (Tef-1α) gene were evaluated as a new identification marker in a wide range of dermatophytes. The aim of this study was to evaluate the discriminatory power of a phylogenetic tool based on concatenated sequences of three genomic regions including Tef-1α, ITS (ITS1 to ITS2) and beta-tubulin to differentiate: 1/ the anthropophilic Trichophyton interdigitale species from the zoophilic Trichophyton mentagrophytes 2/ the two closely related African anthropophilic species Trichophyton violaceum from Trichophyton soudanense. Methods: 26 well characterized strains of T. interdigitale/mentagrophytes have been selected including 3 IHEM reference strains; 30 well characterized strains of T. soudanense/T.violaceum including 2 IHEM reference strains were also included. All strains were submitted to ITS, beta-tubulin and Tef-1α PCR/sequencing. Moreover, identification was completed by real time PCR DermaGenius® (PathoNostics). Alignments were performed using MUSCLE in Seaview. The alignments for each of the three genes were then concatenated together based on the name of the sample and gaps were added between genes. Phylogenies were then inferred on the concatenated alignment using PhyML. Results: After generation of the phylogenetic tree by concatenation of the three sequence genes, the differentiation between T. interdigitale and T. mentagrophytes was clear. The 16 strains of T. interdigitale were well classified into one distinct group on the dendrogram. The 10 strains of zoophilic T. mentagrophytes were well distinct of the anthropophilic group and defined by another clade on the dendrogram. Reference strains were correctly classified into the two previously defined groups. Regarding the differentiation between T. soudanense and T. violaceum, the concatenation permitted to define two well distinct clades on the dendrogram. One clade containing 10 T. violaceum tested and the other containing 20 T. soudanense included in the study and one strain previously identified as T. violaceum . Reference strains were correctly classified into each corresponding clade. Conclusion: The concatenation of ITS, beta-tubulin and Tef-1α genes sequences allows the generation of a discriminating dendrogram between the zoophilic T. mentagrophytes and the anthropophilic T. interdigitale. This is less powerfull between the two closely related African anthropophilic species T. violaceum and T. soudanense. Anyway This multilocus phylogenetic approach allows to better define the species boundaries between these dermatophytes and facilitates the molecular characterization of these species in routine diagnostic

Case Report Series: Aggressive HR Deficient Colorectal Cancers Related to BRCA1 Pathogenic Germline Variants.

[en] Objective: The link between BRCA1 and homologous recombination deficiency (HRD) in cancer has gained importance with the emergence of new targeted cancer treatments, while the available data on the role of the gene in colorectal cancer (CRC) remain contradictory. The aim of this case series was to elucidate the role of known pathogenic BRCA1 variants in the development of early-onset CRC. Design: Patients were evaluated using targeted next generation sequencing, exome sequencing and chromosomal microarray analysis of the paired germline and tumor samples. These results were used to calculate the HRD score and the frequency of mutational signatures in the tumors. Results: Three patients with metastatic CRC were heterozygous for a previously known BRCA1 nonsense variant. All tumors showed remarkably high HRD scores, and the HRD-related signature 3 had the second highest contribution to the somatic pattern of variant accumulation in the samples (23% in 1 and 2, and 13% in sample 3). Conclusions: A BRCA1 germline pathogenic variant can be involved in CRC development through HRD. Thus, BRCA1 testing should be considered in young patients with a personal history of microsatellite stable CRC as this could further allow a personalized treatment approach