Clinical experience of next generation sequencing based expanded carrier screening in high-risk couples from a tertiary healthcare center in Pakistan.

INTRODUCTION: Carrier screening for genetic conditions has long been a part of preconception and prenatal care. While the use of expanded carrier screening (ECS) is widely common in HICs (high income countries), the clinical actionability of ECS in LMICs (low middle income countries) with high consanguineous unions is not well-understood. METHOD: Retrospective chart review of couples who presented to the Prenatal Genetics Clinic at Aga Khan University Hospital, between the period of June 2018 and November 2022. All the statistical analyses were performed using the statistical software STATA version 17.0. RESULTS: Of the 202 individuals tested, 166 (82%) were identified to be carriers of at least one gene associated with a monogenic condition. Out of the 302 genes tested, individuals were found to be carriers of conditions associated with 87 genes. Clinical actionability of ECS was established in a total of 45 (45%) high risk couples undergoing screening using ECS. CONCLUSION: We report the first clinical experience of using next generation sequencing based ECS in 101 high-risk couples seeking consultation in the Genetics Clinic, at a tertiary healthcare center in Pakistan, showing that over 80% high-risk individuals are carriers of at least one condition and 45% of couples receive an actionable result to making autonomous informed reproductive decisions in future pregnancies.

Endobronchial ultrasound: A novel screening test for pulmonary hypertension prior to major pulmonary surgery.

Objectives: Pulmonary hypertension (PH) is an important physiologic variable in the assessment of patients undergoing major thoracic operations but all too often neglected because of the need for right heart catheterization (RHC) due to the inaccuracy of transthoracic echocardiography. Patients with lung cancer often require endobronchial ultrasound (EBUS) as part of the staging of the cancer. We sought to investigate whether EBUS can be used to screen these patients for PH. Methods: Patients undergoing a major thoracic operation requiring EBUS for staging were included prospectively in the study. All patients had also a RHC (gold standard). We aimed to compare the pulmonary artery pressure measurements by EBUS with the RHC values. Results: A total of 20 patients were enrolled in the study. The prevalence of abnormal pulmonary artery pressure was 65% based on RHC. All patients underwent measurement of the pulmonary vascular acceleration time (PVAT) by EBUS with no adverse events. Linear regression analysis comparing PVAT and RHC showed a correlation (r = -0.059, -0.010 to -0.018, P = .007). A receiver operator characteristic curve (area under the curve = 0.736) was used to find the optimal PVAT threshold (140 milliseconds) to predict PH; this was used to calculate a positive and negative likelihood ratio following a positive diagnosis of 2.154 and 0.538, respectively. Conclusions: EBUS interrogation of pulmonary artery hemodynamic is safe and feasible. EBUS may be used as a screening test for PH in high-risk individuals.

Childhood obesity in Tunisia: Prevalence and risk factors.

INTRODUCTION: Obesity in children is currently a major public health problem in Tunisia. AIM: To determine the prevalence of obesity among pre-schoolchildren in the city of Bardo and to identify risk factors. METHODS: We carried a cross-sectional study of 220 children between 4 and 6 years of age, recruited from kindergartens in the city of Bardo. Children with endocrinal, tumoral or genetic diseases causing secondary obesity, children on corticosteroids and children with two illiterate parents were not included. The weight status of the children was defined according to the curves of the international obesity task force. A parent is considered obese if his BMI>30 Kg/m². RESULTS: The average age was 4.65±0.77 years. A female predominance was noted (55.9% girls and 44.1% boys). The average BMI of the children was 16.93±2.46 kg/m². The prevalence of overweight among all children was 10.9% and that of obesity was 11.4%. The frequency of overweight (including obesity) was 22.3%. In multivariate analysis, factors independently related to childhood obesity were child age, child medical history and hospitalization, parental obesity, parental dyslipidemia, snack type and snacking. CONCLUSIONS: Overweight is common in pre-school children. It should be detected at an early age, especially if risk factors are present.

Integrative molecular analysis of colorectal cancer and gastric cancer: What have we learnt?

Gastrointestinal (GI) malignancies comprise a diverse group of cancers with varying aetiology, clinical course, management and prognosis. Advances over the last decade in molecular diagnostics in colorectal cancer (CRC) have helped to improve our understanding of the underlying complex mechanisms in the development and progression of this highly heterogenous disease. Large scale integrative analysis has identified molecularly distinct subgroups of CRC with differing clinical behaviour. It was hoped that these discoveries would fuel the development of novel drug targets and new treatments to shift the management of advanced CRC from an empirical strategy to a biomarker driven approach based on underlying molecular characteristics. However, biomarkers in current clinical practice remain limited in CRC. Gastric cancer (GC) has also been slow to benefit from biomarker discovery and development and the successful utilisation of targeted therapies, with the exception of trastuzumab in HER2 positive cancers. More recently, molecular analysis of GC has also identified distinct subgroups within these cancers with differing behaviour and therapeutic targets. In addition, our deeper understanding of the underlying molecular biology of GI cancers has led to the consideration of alterations above and beyond gene mutations. The clonal, stromal and immune characteristics of GI malignancies are increasingly recognised as important in therapeutic targeting. The challenge remains to apply the data generated through molecular exploration into clinical practice in order to provide personalised treatment to each individual patient.

The melanoma-specific graded prognostic assessment does not adequately discriminate prognosis in a modern population with brain metastases from malignant melanoma.

BACKGROUND: The melanoma-specific graded prognostic assessment (msGPA) assigns patients with brain metastases from malignant melanoma to 1 of 4 prognostic groups. It was largely derived using clinical data from patients treated in the era that preceded the development of newer therapies such as BRAF, MEK and immune checkpoint inhibitors. Therefore, its current relevance to patients diagnosed with brain metastases from malignant melanoma is unclear. This study is an external validation of the msGPA in two temporally distinct British populations. METHODS: Performance of the msGPA was assessed in Cohort I (1997-2008, n=231) and Cohort II (2008-2013, n=162) using Kaplan-Meier methods and Harrell's c-index of concordance. Cox regression was used to explore additional factors that may have prognostic relevance. RESULTS: The msGPA does not perform well as a prognostic score outside of the derivation cohort, with suboptimal statistical calibration and discrimination, particularly in those patients with an intermediate prognosis. Extra-cerebral metastases, leptomeningeal disease, age and potential use of novel targeted agents after brain metastases are diagnosed, should be incorporated into future prognostic models. CONCLUSIONS: An improved prognostic score is required to underpin high-quality randomised controlled trials in an area with a wide disparity in clinical care.

Phase I/II RAF kinase inhibitors in cancer therapy.

INTRODUCTION: Aberrant activation of RAF signalling is a frequent finding in human cancers. BRAF is the only RAF family member that is commonly mutated, whilst CRAF and ARAF play important roles in the signal transduction from mutant RAS. BRAF-specific inhibitors have been more effective in the treatment of BRAF-mutant melanoma than BRAF-mutant thyroid and colorectal cancers. AREAS COVERED: The review summarises the experience with RAF kinase inhibitors, including efficacy, modes of acquired resistance, and the mechanism behind the progression of pre-malignant RAS-mutant lesions observed with RAF kinase inhibitors. The authors review all the completed and ongoing Phase I or II clinical trials of RAF kinase inhibitors and discuss in detail the rationale behind the combinatorial approaches. EXPERT OPINION: The success of RAF kinase inhibitors has demonstrated the necessity of genotype-driven treatment selection for cancer patients. The spectrum of responses in different tumour types is explained by feedback events that are determined by cell lineage. Dissection of these events and the mechanisms of acquired resistance will determine the appropriate combination therapies. Ongoing characterisation of RAS-MAPK regulation in malignant cells may aid the development of novel agents that have greater potency for the inhibition of activated RAF kinase, and lesser propensity for promotion of RAS-mutant tumours.