Informing Evidence-based Practice in Nutritional Genomics: An Educational Needs Assessment of Nutrition Care Providers in Canada.

Purpose: To investigate why Canadian nutrition care providers choose, or not, to integrate nutritional genomics into practice, and to evaluate the nutritional genomics training/education experiences and needs of nutrition providers in Canada, while comparing those of dietitians to non-dietitians.Methods: A cross-sectional online survey was distributed across Canada from June 2021 to April 2022.Results: In total, 457 healthcare providers (HCPs) [n = 371 dietitians (81.2%)] met the inclusion criteria. The majority (n = 372; 82.1%) reported having no experience offering nutritional genomics to clients (n = 4 did not respond). Of the 81 respondents with experience (17.9%), the most common reason to integrate nutrigenetic testing into practice was the perception that clients would be more motivated to change their eating habits (70.4%), while the most common reason for not integrating such tests was the perception that the nutrigenetic testing process is too complicated (n = 313; 84.1%). Dietitians were more likely than non-dietitians to view existing scientific evidence as an important educational topic (p = 0.002). The most selected useful educational resource by all HCPs was clinical practice guidelines (n = 364; 85.4%).Conclusions: Both dietitians and non-dietitians express a desire for greater nutritional genomics training/education; specific educational needs differ by type of HCP. Low implementation of nutrigenetic testing may be partly attributed to other identified barriers.

[Assessment of the man in the infertile couple]. / Évaluation de l'homme du couple infertile.

BACKGROUND: Among couples consulting for infertility, there is a male component, either alone or associated with a female aetiology in around one in 2 cases. MATERIAL AND METHODS: Bibliographic search in PubMed using the keywords "male infertility", "diagnosis", "management" and "evaluation" limited to clinical articles in English and French prior to 1/01/2023. RESULTS: The AFU recommends: (1) a complete medical history including: family history, patient history affecting fertility, lifestyle habits (toxicity), treatments, symptoms, sexual dysfunctions; (2) a physical examination including: BMI, signs of hypogonadism, secondary sexual characteristics, scrotal examination (volume and consistency of testes, vas deferens, epididymal or testicular nodules, presence of varicocele); (3) two spermograms, if abnormal on the first; (4) a systematic scrotal ultrasound,± an endorectal ultrasound depending on the clinic; (5) a hormonal work-up (testosterone, FSH; if testosterone is low: LH assay to differentiate between central or peripheral hypogonadism); (6) karyotype if sperm concentration≤10 million/mL; (7) evaluation of Y chromosome microdeletions if concentration≤1 million/mL; (8) evaluation of the CFTR gene in cases of suspected bilateral or unilateral agenesis of the vas deferens and seminal vesicles. The role and usefulness of direct and indirect tests to assess the effects of oxidative stress on sperm DNA will also be explained. CONCLUSION: This review complements and updates the AFU/SALF 2021 recommendations.

Prise en charge des carcinomes ovariens de haut grade séreux et/ou endométrioïdes de stades avancés (III-IV) et testing HRD-BRCA en 2023 : actualisation selon les données publiées et/ou présentées en 2022.

Management of high grade, serous and/or endometrioid, advanced (stages III-IV) ovarian carcinomas and HRD-BRCA testing in 2023: update according to data published/presented in 2022 Molecular analysis of ovarian carcinomas must be now systematically performed to determine BRCA1 and BRCA2 status as well as genomic instability score. Several types of tests are available. From a clinical perspective, new data from phase III clinical trials presented in 2022 confirm the key role of PARP inhibitors in first-line medical treatment of high-grade serous ovarian cancers. A new algorithm that includes all new evidence is proposed for selection of first-line therapy.

Adenoid cystic carcinoma of Bartholin's gland, a case report with genomic data and literature review.

Adenoid cystic carcinoma of the Bartholin's gland (ACCBG) is a rare, slowly but aggressive malignancy. We reported the case of a 31-year-old woman who was treated by local excision and then hemi-vulvectomy, with positive margins and perineural invasion. Radiation therapy (RT) was then performed delivering 45Gy in 25 fractions in bilateral inguinal lymph nodes and 64.8Gy in 36 fractions on the vulvar area. After 30 months, there was no local relapse (LR) but the patient presented a histologically documented lung recurrence. Genomic profiling of the tumor showed a MYB-NFIB fusion transcript and a somatic mutation of PLCG1. A treatment by Lenvatinib was started. We conducted a literature review of 100 published cases. Patients were mainly treated by radical vulvectomy (30%), hemi-vulvectomy (17%), wide or local excision (21% and 24%, respectively) or other. Forty-four percent of patients received postoperative RT, more frequently in case of positive margin (71.9% versus 29.5%). RT may reduce the risk of LR regardless of margin status, with 15.4% vs. 41.9% of LR with or without RT, respectively, in patients with negative margins, and 13% vs. 33.3% of LR with or without RT, respectively, in patients with positive margins. The risk of relapse of any type was 40.9% in patients who received adjuvant RT vs. 48.2% in patients who did not. Median time to relapse was 24 months (range 6-156 months). The most frequent metastatic sites were lung (76.7%) and bone (26.7%). Optimal treatment for ACCBG is still not clearly defined but pooling the data from published case report help us better understand this rare disease and help in the therapeutic decision.

[DNA repair gene alterations testing in prostate cancer : A practical update by the prostate cancer committee of the french association of urology]. / Recherche d'altérations des gènes de réparation de l'ADN dans le cancer de la prostate : mise au point pratique du Comité de cancérologie de l'association française d'urologie.

INTRODUCTION: Current therapeutic developments in prostate cancer (PCa) tend to increasingly personalize the treatment strategy, in particular as a function of tumor genomics. Recently, poly ADP-ribose polymerase (PARPi) inhibitors have shown their efficacy at the stage of castration resistance, in case of alteration of DNA repair genes in tumor tissue. MATERIAL AND METHODS: A narrative review was carried out on recent data in the literature since 2000. A consensus among the members of the Committee was obtained in order to synthesize the current data, with a particular focus on the practical considerations regarding indications and developments of molecular testing circuits concerning DNA repair genes, for theranostics purpose. RESULTS: The establishment of an efficient molecular testing network is based on the multidisciplinary organization of the various actors and the coordination of all material resources. Its goal is the routine search for somatic mutations (in tumor tissue) of BRCA1/2 genes in patients who may benefit from PARPi. The current indications are for BRCA1 or 2 mutated castration-resistant metastatic PCa after next-generation hormone therapy failure. The demand for molecular testing must be decided in the tumor board, giving priority to archived tissue less than 10 years old. In case of unsuccess, biopsies of the primary or metastases, or even analysis of circulating tumor DNA, may be necessary. Any demand for a genetic test on tumor tissue must be accompanied by detailed information for the patient on the possible familial consequences, in case of associated germline mutation. CONCLUSION: This article aims to guide the practical implementation of molecular testing circuits for DNA repair genes alterations, in order to guide the therapeutic management of patients with advanced PCa.

Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites.

Genomic reorganization, such as rearrangements and inversions, influences how genetic information is organized within the bacterial genomes. Inversions, in particular, facilitate genome evolution through gene gain and loss, and can alter gene expression. Previous studies have investigated the impact inversions have on gene expression induced inversions targeting specific genes or examine inversions between distantly related species. This fails to encompass a genome-wide perspective of naturally occurring inversions and their post-adaptation impact on gene expression. Here, we used bioinformatic techniques and multiple RNA-seq datasets to investigate the short- and long-range impact inversions have on genomic gene expression within Escherichia coli. We observed differences in gene expression between homologous inverted and non-inverted genes even after long-term exposure to adaptive selection. In 4% of inversions representing 33 genes, differential gene expression between inverted and non-inverted homologs was detected, with greater than two-thirds (71%) of differentially expressed inverted genes having 9.4-85.6-fold higher gene expression. The identified inversions had more overlap than expected with nucleoid-associated protein binding sites, which assist in the regulation of genomic gene expression. Some inversions can drastically impact gene expression, even between different strains of E. coli, and could provide a mechanism for the diversification of genetic content through controlled expression changes.

A duplex real-time NASBA assay targeting a serotype-specific gene for rapid detection of viable Salmonella Paratyphi C in retail foods of animal origin.

Salmonella enterica serovar Paratyphi C is highly adapted to humans and can cause a typhoid-like disease with high mortality rates. In this study, three serovar-specific genes were identified by comparative genomics for Salmonella Paratyphi C, SPC_0871, SPC_0872, and SPC_0908. Based on the SPC_0908 and xcd genes for testing Salmonella spp., we developed a duplex real-time nucleic acid sequence-based amplification (real-time NASBA) with a molecular beacon approach for the simultaneous detection of viable cells of Salmonella spp. and serotype Paratyphi C. The test selectively and consistently detected 53 Salmonella spp. (representing 31 serotypes) and 18 non-Salmonella strains. Additionally, the method showed high resistance to interference from natural background flora in pork and chicken samples. The sensitivity of the established approach was determined to be 4.89 cfu/25 g in artificially contaminated pork and chicken samples after pre-enrichment. We propose this NASBA-based protocol as a potential detection method for Salmonella spp. and serotype Paratyphi C in foods of animal origin.

Identification of plasmids from Brazilian Chromobacterium violaceum strains.

Chromobacterium violaceum is an opportunistic pathogen found in tropical and subtropical regions worldwide. Chromobacterium violaceum infections are difficult to treat, and many strains are resistant to antibiotics. Recently, a novel plasmid (pChV1) was discovered in the type strain ATCC 12472, suggesting that other C. violaceum strains may harbor extra-chromosomal DNA. The aim of the present study was to detect and compare new plasmids in Brazilian strains of C. violaceum using next-generation sequencing techniques. We obtained draft genomes of six plasmids from strains isolated from the Amazon region and aligned them with pChV1. At least three plasmids, CVAC05, CVACO2, and CVT8, were similar to pChV1. Phylogenetic analysis suggested that these new extra-chromosomal DNA sequences have a common origin with pChV1 but have diverged. Many of the ORFs detected were related to plasmid segregation/maintenance, viral structural proteins, and proteins with unknown functions. These findings may enable better genetic manipulation of C. violaceum, which will enhance our ability to exploit this valuable microorganism in industrial and clinical applications.

Assessing the accuracy of imputation in the Gyr breed using different SNP panels.

The aim of this study was to evaluate the accuracy of imputation in a Gyr population using two medium-density panels (Bos taurus - Bos indicus) and to test whether the inclusion of the Nellore breed increases the imputation accuracy in the Gyr population. The database consisted of 289 Gyr females from Brazil genotyped with the GGP Bovine LDv4 chip containing 30 000 SNPs and 158 Gyr females from Colombia genotyped with the GGP indicus chip containing 35 000 SNPs. A customized chip was created that contained the information of 9109 SNPs (9K) to test the imputation accuracy in Gyr populations; 604 Nellore animals with information of LD SNPs tested in the scenarios were included in the reference population. Four scenarios were tested: LD9K_30KGIR, LD9K_35INDGIR, LD9K_30KGIR_NEL, and LD9K_35INDGIR_NEL. Principal component analysis (PCA) was computed for the genomic matrix and sample-specific imputation accuracies were calculated using Pearson's correlation (CS) and the concordance rate (CR) for imputed genotypes. The results of PCA of the Colombian and Brazilian Gyr populations demonstrated the genomic relationship between the two populations. The CS and CR ranged from 0.88 to 0.94 and from 0.93 to 0.96, respectively. Among the scenarios tested, the highest CS (0.94) was observed for the LD9K_30KGIR scenario. The present results highlight the importance of the choice of chip for imputation in the Gyr breed. However, the variation in SNPs may reduce the imputation accuracy even when the chip of the Bos indicus subspecies is used.

Genomics and bioinformatics capacity in Africa: no continent is left behind.

Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States' National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.

Genome sequence of Aspergillus flavus A7, a marine-derived fungus with antibacterial activity.

Due to the specific properties of the marine environment, marine microorganisms have exclusive physicochemical characteristics that are different from those of terrestrial microorganisms, which can produce various secondary metabolites (SMs) with considerable structural diversity and biological activity. In this study, three strains of coepiphytic Aspergillus with potential antibacterial activities, A7 (Aspergillus flavus), B27 (Aspergillus flavipes), and R12 (Aspergillus sydowii), were isolated from the South China Sea. Via the Illumina MiSeq sequencing platform, the genomes of the three strains were sequenced, and genome comparison showed the highest diversity of the biosynthetic gene clusters (BGCs) in A7. In addition, a comparison of physiological and genomic characteristics between A7 and other A. flavus strains demonstrated the superior environmental adaptability of A7, which is apparently consistent with the genetic richness of BGCs. By assigning reads to known BGCs, putative BGCs were allocated in A7 that corresponded to various SMs, including naphthopyrone, pyranonigrin E, and cyclopiazonic acids. Based on gene homology analysis, we surmise that a region is involved in the biosynthesis of ustiloxin-like RiPPs, a less thoroughly studied SM in fungi. Our results provide genetic information for the investigation of marine Aspergillus spp., which may help to elucidate their chemical diversity and adaptive strategies.

User-centric genomics infrastructure: trends and technologies.

Genomics is both a data- and compute-intensive discipline. The success of genomics depends on an adequate informatics infrastructure that can address growing data demands and enable a diverse range of resource-intensive computational activities. Designing a suitable infrastructure is a challenging task, and its success largely depends on its adoption by users. In this article, we take a user-centric view of the genomics, where users are bioinformaticians, computational biologists, and data scientists. We try to take their point of view on how traditional computational activities for genomics are expanding due to data growth, as well as the introduction of big data and cloud technologies. The changing landscape of computational activities and new user requirements will influence the design of future genomics infrastructures.

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale.

Enhancers are cis-regulatory sequences located distally to target genes. These sequences consolidate developmental and environmental cues to coordinate gene expression in a tissue-specific manner. Enhancer function and tissue specificity depend on the expressed set of transcription factors, which recognize binding sites and recruit cofactors that regulate local chromatin organization and gene transcription. Unlike other genomic elements, enhancers are challenging to identify because they function independently of orientation, are often distant from their promoters, have poorly defined boundaries, and display no reading frame. In addition, there are no defined genetic or epigenetic features that are unambiguously associated with enhancer activity. Over recent years there have been developments in both empirical assays and computational methods for enhancer prediction. We review genome-wide tools, CRISPR advancements, and high-throughput screening approaches that have improved our ability to both observe and manipulate enhancers in vitro at the level of primary genetic sequences, chromatin states, and spatial interactions. We also highlight contemporary animal models and their importance to enhancer validation. Together, these experimental systems and techniques complement one another and broaden our understanding of enhancer function in development, evolution, and disease.

[Genetic instability, a factor limiting the efficiency of targeted therapies in solid oncology]. / L'instabilité génomique, paramètre limitant l'efficacité des thérapies ciblées en oncologie.

Genomic instability is one of the main properties of tumour development, promoting first the acquisition of genetic alterations and thus carcinogenesis. Then, the chronic and anarchic proliferation of cancer cells also supports and contributes to this instability allowing a continuous evolution of the tumour. The accumulation of mutations resulting from that instability contributes to tumour heterogeneity that occurs in a specific environment. The resulting diversity of oncogenic drivers further complicates the characterization of the origin of cancer cells dysfunction and consequently therapeutic decision. However, the consideration of the molecular context in oncology has initiated the development of targeted therapies. Based on the concept of oncogene addiction and synthetic lethality, these new drugs require the characterization and identification of specific tumour biomarkers. Targeted therapies have thus considerably optimized patient management, improving efficiency and quality of life while limiting the side effects observed with conventional chemotherapies. However, despite significant clinical benefits, some major limitations to their administration remain. The study of the current issues related to these new therapeutic molecules is becoming crucial for patient management towards an improvement of personalized medicine.

First isolation and characterization of Brucella suis from yak.

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

[The role of new molecular tests in the diagnosis of melanoma in a setting of congenital nævus in an infant]. / Apport des nouveaux tests moléculaires dans le diagnostic d'un mélanome sur nævus congénital chez un nourrisson.

INTRODUCTION: Congenital and infantile melanomas are extremely rare. We report a case of a child presenting at birth with a giant congenital nevus complicated by melanoma and on long-term follow-up with exploration using new immunohistochemistry and molecular biology tools. OBSERVATION: A new-born girl presented at birth with a large congenital cervico-mandibular tumour with para-pharyngeal extension and underlying osteolysis. At 7 months, histology and immunohistochemistry of the operative specimen revealed nodules with atypical features (mitotic figures, necrosis and positive expression of KI67 and P53 in approximatively 50 % of the melanocytic nuclei). A diagnosis was made of infantile melanoma associated with congenital nevi. Repeated surgery and monitoring (clinical and imaging) were performed. At the age of 7 years, as there was no evidence of metastatic lesions, further analyses were performed on the initial operative specimen. Investigation of transcription factor expression using immunohistochemistry, comparative genomic hybridization and histology-guided mass spectrometry, although suspect, did not in itself support a diagnosis of melanoma. Finally, at the age of 7 years, hepatic and pulmonary metastases were reported. Despite combined immunotherapy with ipilimumab and nivolumab, the child died 5 months later. CONCLUSION: This case illustrates the complexity of diagnosis of infantile melanoma and the risk of metastatic involvement long after the initial diagnosis. Diagnosis may be difficult and necessitates expert advice and the application of several recent methods to reach a conclusion and initiate appropriate treatment.

Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types.

Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.

Karyotype mosaicism in early generation synthetic hexaploid wheats.

It is known that both the number and the structure of somatic chromosomes can vary in early generation hexaploid wheats. The phenomenon is generally assumed to arise as a result of the meiotic instability characteristic of freshly created allopolyploids. Here, an analysis of the somatic karyotype of a set of 33 early generation synthetic hexaploid wheats has revealed that variation, taking the form of sub-chromosomal fragments and inter-chromosomal translocations, can also arise in somatic tissue. A possible explanation for the observations was that karyotypic instability in early generation hexaploid wheat probably occurs not just during sporogenesis, but also in somatic tissue. However, other factors such as the use of nitrous oxide during the experiments could also cause the chromosome variations, and additional experimentation would be required to determine the most likely.

Impact on blood safety of the last arboviruses outbreaks in French Polynesia (2012-2018).

BACKGROUND: Several successive arbovirus outbreaks have affected French Polynesia (FP) in the recent past years due to different dengue serotypes (DENV) present for several decades, Zika (ZIKV) (2013-2014) and chikungunya (CHIKV) (2014-2015) viruses with a potential impact on blood safety and blood supply due to the geographical isolation of these islands. This study reports an assessment of the impact of these outbreaks on blood products supply and infectious safety in FP and discuss the effectiveness of implemented preventive measures. METHODS: To ensure the infectious safety of blood products during outbreaks, several measures have successively been introduced as the selection of donors suspected of infection, the nucleic acid testing (NAT) and the pathogen reduction of platelets and plasmas. RESULTS: The donor deferral rate increased by 6% between 2012 and 2014 without changes in the number of collected donations. NAT excluded five blood donations reactive for DENV RNA, 42 for ZIKV and 34 for CHIKV. As Zika screening could not been implemented before the third month of the outbreak, 36 blood products from ZIKV-infected donors were transfused to 26 recipients. However, no transfusion-transmitted arbovirus has been reported. CONCLUSION: The last past arboviruses outbreaks did not have a significant impact on blood supply in FP. The measures introduced to prevent arbovirus transmission by transfusion were able to maintain infectious safety for all blood products without impairing self-sufficiency.