Homologous recombination deficiency in ovarian cancer: Global expert consensus on testing and a comparison of companion diagnostics.

Background: Poly (ADP ribose) polymerase inhibitors (PARPis) are a treatment option for patients with advanced high-grade serous or endometrioid ovarian carcinoma (OC). Recent guidelines have clarified how homologous recombination deficiency (HRD) may influence treatment decision-making in this setting. As a result, numerous companion diagnostic assays (CDx) have been developed to identify HRD.

Incorporating familial risk, lifestyle factors, and pharmacogenomic insights into personalized noncommunicable disease (NCD) reports for healthcare funder beneficiaries participating in the Open Genome Project.

Introduction: An ethics-guided decision-making framework was developed for applying pathology-supported genetic testing, a multifaceted pharmacodiagnostic approach that translates population risk stratification into clinical utility. We introduce this service, supported by the Open Genome Project, which aligns with the beneficence principle in personalized medicine.

Methods: Genetic testing of six noncommunicable disease pathways was conducted as part of a pilot program, benchmarked against a readiness checklist for implementation of genomic medicine in Africa.

IMA Genome - F19 : A genome assembly and annotation guide to empower mycologists, including annotated draft genome sequences of Ceratocystis pirilliformis, Diaporthe australafricana, Fusarium ophioides, Paecilomyces lecythidis, and Sporothrix stenoceras.

The pace at which Next Generation Sequence data is being produced continues to accelerate as technology improves. As a result, such data are increasingly becoming accessible to biologists outside of the field of bioinformatics. In contrast, access to training in the methods of genome assembly and annotation are not growing at a similar rate.

Clinical relevance of double heterozygosity revealed by next-generation sequencing of homologous recombination repair pathway genes in South African breast cancer patients.

Purpose: Genetically predisposed breast cancer (BC) patients represent a minor but clinically meaningful subgroup of the disease, with 25% of all cases associated with actionable variants in BRCA1/2. Diagnostic implementation of next-generation sequencing (NGS) resulted in the rare identification of BC patients with double heterozygosity for deleterious variants in genes partaking in homologous recombination repair of DNA. As clinical heterogeneity poses challenges for genetic counseling, this study focused on the occurrence and clinical relevance of double heterozygous BC in South Africa.

Navigating the genetic landscape of breast cancer in South Africa amidst a developing healthcare system.

Breast cancer is a significant global health issue as it represents the leading cause of death in women worldwide. In 2021, the World Health Organization established the Global Breast Cancer Initiative framework with the aim to reduce the breast cancer mortality rate by the year 2040. In countries with developing healthcare systems, such as South Africa, the implementation of first-world technologies has been slow.

Strengthening self-regulation and reducing poverty to prevent adolescent depression and anxiety: Rationale, approach and methods of the ALIVE interdisciplinary research collaboration in Colombia, Nepal and South Africa.

Aims: Depression and anxiety are the leading contributors to the global burden of disease among young people, accounting for over a third (34.8%) of years lived with disability. Yet there is limited evidence for interventions that prevent adolescent depression and anxiety in low- and middle-income countries (LMICs), where 90% of adolescents live.

The Unique Homothallic Mating-Type Loci of the Fungal Tree Pathogens and from Africa.

and are ascomycete tree pathogens first described from Zambia, causing stem canker on and , respectively. The taxonomic descriptions of these two species were based on their anamorphic states, as no sexual states are known. The main purpose of this work was to use whole genome sequences to identify and define the mating-type () loci of these two species.

Pathology-supported genetic testing for the application of breast cancer pharmacodiagnostics: family counselling, lifestyle adjustments and change of medication.

Background: Pathology-supported genetic testing (PSGT) enables transitioning of risk stratification from the study population to the individual.

Research Design And Methods: We provide an overview of the translational research performed in postmenopausal breast cancer patients at increased risk of osteoporosis due to aromatase inhibitor therapy, as the indication for referral. Both tumor histopathology and blood biochemistry levels were assessed to identify actionable disease pathways using whole exome sequencing (WES).

Implementation of multigene panel testing for breast and ovarian cancer in South Africa: A step towards excellence in oncology for the public sector.

Translation of genomic knowledge into public health benefits requires the implementation of evidence-based recommendations in clinical practice. In this study, we moved beyond susceptibility testing in breast and ovarian cancer patients to explore the application of pharmacogenetics across multiple genes participating in homologous recombination DNA damage repair. This involved the utilisation of next-generation sequencing (NGS) at the intersection of research and service delivery for development of a comprehensive genetic testing platform in South Africa.

Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings.

The use of whole exome sequencing (WES) in medical research is increasing in South Africa (SA), raising important questions about whether and which individual genetic research results, particularly incidental findings, should be returned to patients. Whilst some commentaries and opinions related to the topic have been published in SA, there is no qualitative data on the views of professional stakeholders on this topic. Seventeen participants including clinicians, genomics researchers, and genetic counsellors (GCs) were recruited from the Western Cape in SA.

The Identification and Characterization of Endopolygalacturonases in a South African Isolate of .

is an economically important plant pathogen that has caused devastating losses to the avocado industry worldwide. To facilitate penetration and successful colonization of the host plant, pathogens have been reported to secrete polygalacturonases (PGs). Although a large PG gene family has been reported in , in-depth bioinformatics analyses and characterization of these genes is still lacking.

A South African Indian population group dataset for breast cancer and variants.

No datasets are available on the basis of confirmed familial breast cancer patients and their respective mutation status for the South African Indian population. This dataset contains information collected in South Africa specifically for the South African Indian population (n = 223). The data involved a combined collection of laboratory confirmed genetic testing results, accompanied by immunohistochemical and anatomical pathology results.

Prevalence of Clinically Relevant Germline Variants in a Large Unselected South African Breast and Ovarian Cancer Cohort: A Public Sector Experience.

Breast cancer is a multifaceted disease that currently represents a leading cause of death in women worldwide. Over the past two decades (1998-2020), the National Health Laboratory Service's Human Genetics Laboratory in central South Africa screened more than 2,974 breast and/or ovarian cancer patients for abnormalities characteristic of the widely known familial breast cancer genes, Breast Cancer gene 1 () and Breast Cancer gene 2 () Patients were stratified according to the presence of family history, age at onset, stage of the disease, ethnicity and mutation status relative to . Collectively, 481 actionable (likely-to pathogenic) variants were detected in this cohort among the different ethnic/racial groups.

RNA-based therapy in the management of lipid disorders: a review.

This review focuses on antisense oligonucleotides and small interfering ribonucleic acid therapies approved or under development for the management of lipid disorders. Recent advances in RNA-based therapeutics allow tissue-specific targeting improving safety. Multiple potential target proteins have been identified and RNA-based therapeutics have the potential to significantly improve outcomes for patients with or at risk for atherosclerotic cardiovascular disease.

Behavioral and Biological Indicators of Risk and Well-Being in a Sample of South African Youth.

Unlabelled: Self report measures have been widely used in research to illustrate high rates of exposure to violence among youth in trauma-saturated regions, such as Cape Town, South Africa. To better understand the risk and resilience factors of youth who have been exposed to, witnessed, or directly experienced violence, the current study used a multi-method assessment in a naturalistic setting that included heart rate variability (an index of regulatory flexibility and cardiovascular health), a computerized risk-taking task, and self report measures. Youth (N = 83) from Cape Town, South Africa, participated in a psychobiological assessment.

Pioneering Point-Of-Care Testing for Integration of Germline and Tumor Genetics in Breast Cancer Risk Management: A Vision for the Future of Translational Pharmacogenomics.

Research performed in South African (SA) breast, ovarian and prostate cancer patients resulted in the development of a rapid BRCA point-of-care (POC) assay designed as a time- and cost-effective alternative to laboratory-based technologies currently used for first-tier germline DNA testing. In this study the performance of the new assay was evaluated for use on a portable screening device (ParaDNA), with the long-term goal to enable rollout at POC as an inventive step to meet the World Health Organization's sustainable development goals for Africa. DNA samples for germline testing were obtained retrospectively from 50 patients with early-stage hormone receptor-positive breast cancer referred for genomic tumor profiling (MammaPrint).

: more than a node or a foot-shaped basal cell.

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family . Thus, an alternate hypothesis, namely a very broad concept of the genus was proposed. In doing so, however, a significant body of data that supports distinct genera in based on morphology, biology, and phylogeny is disregarded.

Mutations in BRCA-related breast and ovarian cancer in the South African Indian population: A descriptive study.

Knowledge of the genetic landscape of a specific population group is vital for population-specific diagnosis and treatment of familial breast cancer. Although BRCA-related diagnostic testing has long been implemented in South Africa, the genotyping approach previously failed for the SA Indian population as it was based on other SA population groups. Because this population is uniquely admixed, the lack of population-specific data resulted in the implementation of comprehensive mutation screens for BRCA1/2.

Globally Rare Variants With Founder Haplotypes in the South African Population: Implications for Point-of-Care Testing Based on a Single-Institution Next-Generation Sequencing Study.

Breast cancer patients historically benefitted from population-based genetic research performed in South Africa, which led to the development of founder-based diagnostic tests. With the advent of next-generation sequencing (NGS) technologies, the clinical utility of limited, targeted genetic assays were questioned. The study focused on mining NGS data obtained from an extensive single-institution NGS series (n=763).

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota.

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach.

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed.

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds.

Cryphonectriaceae associated with rust-infected in Hawaii.

(Myrtales, Myrtaceae) trees in Hawaii are severely affected by a rust disease caused by (Pucciniales, Sphaerophragmiaceae), but they are commonly co-infected with species of Cryphonectriaceae (Diaporthales). In this study, and other trees in the Myrtales were examined on three Hawaiian Islands for the presence of Cryphonectriaceae. Bark samples with fruiting bodies were collected from infected trees and fungi were isolated directly from these structures.

Optimizing G6PD testing for case management and beyond: why sex, counseling, and community engagement matter.

Safe access to the most effective treatment options for   malaria are limited by the absence of accurate point-of-care testing to detect glucose-6-phosphate dehydrogenase (G6PD) deficiency, the most common human genetic disorder. G6PD-deficient patients are at risk of life-threatening hemolysis when exposed to 8-aminoquinolines, the only class of drugs efficacious against  hypnozoites. Until recently, only qualitative tests were available in most settings.

Family history identifies sporadic schizoaffective disorder as a subtype for genetic studies.

Background: Schizophrenia is a heterogeneous disorder with strong genetic vulnerability. Family history of schizophrenia has been considered in genetic studies under several models. genetic events seem to play a larger role in sporadic cases.

The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer.

Background: Pathogenic variants that occur in the familial breast cancer genes (BRCA1/2) lead to truncated ineffective proteins in the majority of cases. These variants are mostly represented by small deletions/insertions, nonsense- and splice-site variants, although some larger pathogenic rearrangements occur. Currently, their contribution to familial breast cancer (BC) and ovarian cancer (OVC) in South Africa (SA) is unknown.