Clinicopathological pattern of oestrogen receptor, progesterone receptor and human epidermal growth factor receptor-2 over-expression of epithelial ovarian carcinomas in Nigeria.

Background: Ovarian cancer is the leading cause of death from all gynaecological malignancies. Only few biomarkers of epithelial ovarian cancer (EOC) prognosis have been studied so far among Nigerian patients.

Objective: To determine the pattern of oestrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER-2) expression in patients with EOC seen in Nigeria.

Prognostic Values of Gene Copy Number Alterations in Prostate Cancer.

Whilst risk prediction for individual prostate cancer (PCa) cases is of a high priority, the current risk stratification indices for PCa management have severe limitations. This study aimed to identify gene copy number alterations (CNAs) with prognostic values and to determine if any combination of gene CNAs could have risk stratification potentials. Clinical and genomic data of 500 PCa cases from the Cancer Genome Atlas stable were retrieved from the Genomic Data Commons and cBioPortal databases.

Chromosome-specific segment size alterations are determinants of prognosis in prostate cancer.

Currently, risk stratification is the most difficult problem in prostate cancer (PCa) management. Gleason grading cannot adequately predict cancer progression. This study aimed to identify chromosome-specific segment size alterations that could aid risk stratification and predict metastasis using a retrospective cohort-study strategy.

Prevalence and predictors of squamous intraepithelial lesions in human immunodeficiency virus positive women in Sagamu, southwest Nigeria.

Background: Cervical cancer is still a public health problem in many developing countries, like Nigeria. HIV infection makes HPV infections last longer, progress to squamous intraepithelial lesion of the cervix, and eventually lead to invasive cervical cancer.

Objective: Find out how often squamous intraepithelial lesions (SIL) happen and what causes them in HIV-positive women in Sagamu, southwest Nigeria.

Semantic annotation for computational pathology: multidisciplinary experience and best practice recommendations.

Recent advances in whole-slide imaging (WSI) technology have led to the development of a myriad of computer vision and artificial intelligence-based diagnostic, prognostic, and predictive algorithms. Computational Pathology (CPath) offers an integrated solution to utilise information embedded in pathology WSIs beyond what can be obtained through visual assessment. For automated analysis of WSIs and validation of machine learning (ML) models, annotations at the slide, tissue, and cellular levels are required.

MSI-WES: a simple approach for microsatellite instability testing using whole exome sequencing.

To demonstrate that MSI-WES is an accurate testing method for microsatellite instability (MSI). Microsatellite-based indels were counted in the variant call-formatted whole exome sequencing (WES) data of 441 gastric cancer cases using Unix-based algorithms, and the counts expressed as a fraction of the genome sequenced to obtain next-generation sequencing-based MSI indices. The next-generation sequencing-based MSI indices showed a near-perfect concordance with PCR-based MSI status, and moderate to good correlations with the molecular targets of MSI index, expression and methylation status, at a level comparable to the strengths of correlation between PCR-based MSI status and molecular targets of MSI index/ expression and methylation.

Targeted next generation sequencing reveals a common genetic pathway for colorectal cancers with chromosomal instability and those with microsatellite and chromosome stability.

Introduction: Microsatellite stable sporadic colorectal cancers (CRCs) can be classified as either tumours with chromosomal instability (CIN+) or tumours that are 'Microsatellite and Chromosomal Stable' (MACS). The CIN + tumours are aneuploid whilst MACS are near-diploid; little else is known about their differences. We compared the mutation profiles of CIN + and MACS CRCs.

Targeted Next-Generation Sequencing Validates the Use of Diagnostic Biopsies as a Suitable Alternative to Resection Material for Mutation Screening in Colorectal Cancer.

Background: Mutation testing in the context of neoadjuvant therapy must be performed on biopsy samples. Given the issue of tumour heterogeneity, this raises the question of whether the biopsies are representative of the whole tumour. Here we have compared the mutation profiles of colorectal biopsies with their matched resection specimens.

Prevalence, Predictive Factors, and Characteristics of Osteoporosis in Hyperthyroid Patients.

Objective: The osteoporosis in thyroid disorder has the lowest report especially in sub-Saharan Africa. This study aims to determine the prevalence, predictive factors, and characteristics of osteoporosis in hyperthyroid patients.

Method: Forty (40) hyperthyroid patients and healthy controls ages 21-50 years were recruited in this study.

N_LyST: a simple and rapid screening test for Lynch syndrome.

Aims: We sought to use PCR followed by high-resolution melting analysis to develop a single closed-tube screening panel to screen for Lynch syndrome. This comprises tests for microsatellite instability (MSI), MLH1 methylation promoter and mutation.

Methods: For MSI testing, five mononucleotide markers (BAT25, BAT26, BCAT25, , ) were developed.

Checkpoint Kinase 1 Expression Predicts Poor Prognosis in Nigerian Breast Cancer Patients.

Background: Checkpoint kinase 1 (CHEK1), a DNA damage sensor and cell death pathway stimulator, is regarded as an oncogene in tumours, where its activities are considered essential for tumourigenesis and the survival of cancer cells treated with chemotherapy and radiotherapy. In breast cancer, CHEK1 expression has been associated with an aggressive tumour phenotype, the triple-negative breast cancer subtype, an aberrant response to tamoxifen, and poor prognosis. However, the relevance of CHEK1 expression has, hitherto, not been investigated in an indigenous African population.

A refined method to study gene dosage changes in vitro using CRISPR/Cas9.

Aims: Gene dosage can have a major impact on cell biology, although, hitherto, it has been difficult to study using in vitro models. We sought to refine and accelerate the development of 'gene dosage' models through using CRISPR/Cas9 (a gene editing technology) for sequential knockout of gene alleles.

Methods: Our method involved (1) using Cas9 nuclease mRNA rather than expression plasmids, (2) using a fluorescently labelled FAM-6 tracr complexed with guide RNA and (3) using high-resolution melting (HRM) analysis to screen for mutations.

"Squirrel" Primer-Based PCR Assay for Direct and Targeted Sanger Sequencing of Short Genomic Segments.

Currently, short DNA segments of sub-100 bp can be sequenced either directly by next-generation sequencing and pyrosequencing, which are expensive, or indirectly, Sanger sequencing combined with the cumbersome and failure-prone plasmid cloning. To circumvent these issues, we have generated a novel sequencing-purposed PCR assay using long-tailed primers (squirrel primers) to Sanger sequence directly sub-100 bp genomic amplicons. Squirrel primers, 40-65 nt in length, were used to amplify 51-93 bp long genomic sequences of exons 2 and 3, exon 15, exon 20, and exon 3 from colorectal cancer (CRC) cell lines and preamplified clinical CRC samples with known mutation status by PCR.

QMC-PCRx: a novel method for rapid mutation detection.

Aims: We previously described the quick multiplex consensus PCR (QMC-PCR) as a method for rapid mutation screening in low-quality template. QMC-PCR has two-stages: a prediagnostic multiplex (PDM) reaction followed by a single specific diagnostic reaction with high-resolution melting (HRM) analysis. We aimed to develop QMC-PCRx in which second stage was multiplexed to allow testing of multiple targets.

Clinicopathological and molecular characteristics of Ku 70/80 expression in Nigerian breast cancer and its potential therapeutic implications.

Ku 70/80 is a regulator of the Non-Homologous End Joining (NHEJ) roles in clinicopathological features, and has prognostic significance in breast cancer (BC) in Caucasian populations. However, its significance in the Nigerian BC population, which is characterized by a higher rate of the triple-negative and basal phenotype, p53 mutation rate and BRCA1 deficiency, still needs to be investigated. We hypothesize that Ku70/80 expression shows adverse expression in Nigerian BC and, furthermore, that it is likely to have a therapeutic implication for Black BC management.

Spectrum and prevalence of thyroid diseases seen at a tertiary health facility in Sagamu, South-West Nigeria.

Background: The prevalence of goitrous swelling has reduced in Nigeria since the introduction of salt iodisation programme. Thyroid disorders are the second most common endocrine disorder after diabetes mellitus worldwide. They present to general outpatient, medical and surgical clinics accompanied by great anxiety and poor health-related quality of life.

Tumour cell membrane laminin expression is associated with basal-like phenotype and poor survival in Nigerian breast cancer.

Introduction: Laminin is a glycoprotein with diverse functions in carcinogenesis including cell proliferation, invasion, metastases and epithelial-mesenchymal transition (EMT). In breast cancer (BC) laminin expression is speculated to be associated with unfavourable clinicopathological and molecular characteristics. We hypothesize that laminin expression would contributed to the aggressive nature of basal like and triple negative BC phenotype observed in Black women.

Cancer mutation screening: Comparison of high-resolution melt analysis between two platforms.

High-resolution melt analysis (HRMA) is a cheap and reliable post-polymerase chain reaction (PCR) cancer mutation screening technique, which is fast gaining clinical relevance. The HRMA capabilities of the LightScanner (Idaho Technology) have been severally studied. However, the ABI 7500 HRM has not been tested against the purpose-built HRM instrument such as the LightScanner.

Clinicopathological features of gastric carcinoma in Ibadan, Nigeria, 2000-2011.

Aim: The most recent study on the clinicopathological features of gastric carcinoma from the University College Hospital (UCH), Ibadan, was done in 2000. The aim of this study is to update the knowledge on the clinicopathological features of gastric carcinoma diagnosed in the Pathology Department of the UCH Ibadan between 2000 and 2011.

Materials And Methods: This was a 12-year retrospective review of clinical and demographic data and the histopathological features of gastric cancers diagnosed at the Pathology Department of the UCH.

High resolution melt analysis, DNA template quantity disparities and result reliability.

Background: Disparities in DNA template quantity across sample wells is a common occurrence in PCR experiments and a frequent cause of bogus results in research and diagnostics. High Resolution Melt (HRM) analysis, a robust genotyping technique, was shown to be highly reproducible irrespective of the reaction volume and DNA template concentration used for PCR. The aim of this study is to determine if HRM can maintain its reproducibility/reliability when varying amounts of starting DNA templates are utilized for the upstream PCR.

Autopsy findings and pattern of mortality in Nigerian sickle cell disease patients.

Introduction: Sickle Cell Disease (SCD) has a high mortality rate in the environment where we practice. There is lack of contemporal autopsy studies describing causes of death among SCD patients at our centre.

Methods: This is a retrospective study of SCD patients who died between January 1991 and December 2008 and that had autopsy examination to confirm the cause of death in a Nigerian teaching hospital.

Correlation of cag-A serological status with histological parameters of chronic gastritis among dyspeptic patients in south western Nigeria.

Background: The aim of this study was to determine the sero-prevalence of Cag-A strains of Helicobacter pylori in both dyspeptic and non-dyspeptic individuals and also correlate the serological status of Gag-A strain of H. pylori with the various graded histological variables of chronic gastritis in the dyspeptic patients.

Methods: Using helicobacter p120 Cag-A enzyme linked immunosorbent assay, Cag-A serology test was carried out on 65 dyspeptic patients and 65 age and sex matched non-dyspeptic controls.

Correlation of serum anti-helicobacter pylori immunoglobulin a (IgA) with histological parameters of chronic gastritis in ibadan, Nigeria.

Background: The seroprevalence of anti-H. pylori IgA antibodies has been reported to vary among populations and in relation to strains of Helicobacter pylori bacterium. However, there has been conflicting reports on the association between IgA serological status and the histological variables of chronic gastritis.