Breast cancer in East Africa: Prevalence and spectrum of germline SNV/indel and CNVs in BRCA1 and BRCA2 genes among breast cancer patients in Tanzania

Pathogenicity classification of missense mutations based on deep generative model

Missense mutations affect the function of human proteins and are closely associated with multiple acute and chronic diseases. The identification of disease-associated missense mutations and their classification for pathogenicity can provide insights into the genetic basis of disease and protein function. This paper proposes MLAE (Method based on LSTM-Ladder AutoEncoder), a deep learning classification model for identifying disease-associated missense mutations and classifying their pathogenicity based on the Variational AutoEncoder (VAE) framework. MLAE overcomes the limitations of the VAE framework by introducing the Ladder structure, combined with LSTM networks. This reduces the loss of original information during the transmission process, thereby making the model more effective in learning. In the experiment, MLAE classified all 27572 possible missense variants of the three input proteins with an average classification AUC of 0.941. This result provides evidence that MLAE is effective in predicting pathogenicity. Additionally, MLAE provides results for multi-label classification, with an average Hamming loss of 0.196, supporting the classification of complex variants. The proposed MLAE method provides an insightful approach to effectively capture amino acid sequence information and accurately predict the pathogenicity of mutations, thereby providing an analytical basis for the study and prevention of related diseases.

The role of clinical breast examination and fine needle aspiration cytology in early detection of breast cancer: A cross-sectional study nested in a cohort in a low-resource setting

BACKGROUND

Breast cancer is prevalent worldwide, with disparities in screening, diagnosis, treatment outcomes, and survival. In Africa, the majority of women are diagnosed at advanced stages, affecting treatment outcomes. Screening is one of the best strategies to reduce mortality rates caused by this cancer. Yet in a resource-constrained setting, there is limited access to screening and early detection services, which are available only at a few referral hospitals.

OBJECTIVES

We aimed to evaluate the prevalence and screening results of breast cancer using clinical breast examination coupled with fine needle aspiration cytology in a resource-constraint setting.

DESIGN

A combined cross-sectional and cohort study.

METHODS

Women at risk of developing breast cancer in the Kilimanjaro region of Tanzania were invited, through public announcements, to their primary healthcare facilities. A questionnaire was used to assess the participants' characteristics. The women received a clinical breast examination, and detectable lesions were subjected to a confirmatory fine needle aspiration cytology or an excisional biopsy. Preliminary data from this ongoing breast cancer control program were extracted and analyzed for this study.

RESULTS

A total of 3577 women were screened for breast cancer; their mean age was 47 ± 7.53 years. About a third of them (1145, 32%) were practicing self-breast examination at least once a month. Of 200 (5.6%) with abnormal clinical breast examination, 18 (9%) were confirmed to be breast cancer, making the prevalence to be 0.5%. The vast majority of participants with breast cancer (13, 72.2%) had early disease stages, and infiltrating ductal carcinoma, no special type, was the most common (15, 83.3%) histopathology subtype. Hormonal receptor status determination results indicated that 11 (61.1%), 7 (38.9%), and 5 (27.8%) of the tumors overexpressed estrogen receptor, progesterone receptor, and human epidermal receptor-2, respectively.

CONCLUSION

Our study demonstrates 5.6% of Tanzanian women have abnormal clinical breast examination findings, with 9% having breast cancer. Nearly three-quarters (72.2%) of breast cancer screened for early disease were detected in the early disease stages. This finding suggests that organized screening with clinical breast examination coupled with fine needle aspiration cytology, which is a simple and cost-effective screening method, has the potential to improve early detection and outcomes for breast cancer patients in a resource-constraint setting.

Cancer genetic mutation prevalence in sub-Saharan Africa: A review of existing data

BACKGROUND

Cancer represents a leading cause of death worldwide. Germline mutations in several genes increase the risk of developing several cancers, including cancers of the breast, ovary, pancreas, colorectum, and melanoma. An understanding of the population prevalence of pathogenic germline variants can be helpful in the design of public health interventions, such as genetic testing, which has downstream implications for cancer screening, prevention, and treatment. While population-based studies of pathogenic germline variants exist, most such studies have been conducted in White populations. Limited data exist regarding the prevalence of germline mutations within sub-Saharan African populations.

MATERIALS AND METHODS

We identified countries defined as sub-Saharan Africa by the World Bank and conducted a scoping literature review using PubMed. For each country, we identified and summarized studies that focused on the prevalence of germline genetic mutations with sample sizes >10 and in a population directly from sub-Saharan Africa, either with or without diseases associated with the relevant genetic mutations. Studies that evaluated the prevalence of somatic or likely benign variants were excluded.

RESULTS

Within the 48 countries in sub-Saharan Africa, we identified 34 studies which meet the inclusion criteria. Twenty studies were conducted in South Africa, Nigeria, or Burkina Faso; four countries had more than two published papers. We found that 33 of 48 countries in sub-Saharan Africa lacked any genetic studies. Notably, there has been an increase in relevant studies starting in 2020. Importantly, of the 34 studies identified, 29 included data on BRCA1 or BRCA2. Data on the prevalence of mutations contributing to familial cancer syndromes other than BRCA1 and BRCA2 was limited.

CONCLUSIONS

While some progress has been made towards understanding the prevalence of germline mutations in cancer susceptibility genes, the characterization of genetic mutations among sub-Saharan African populations remains strikingly incomplete. Given the genetic diversity in the region, there remains a great need for large-scale, population-based studies to understand the prevalence of germline pathogenic variants and adequately capture all the subpopulations in this part of the world.