The QChip1 knowledgebase and microarray for precision medicine in Qatar

NOTCH3 p.Arg1231Cys is markedly enriched in South Asians and associated with stroke

The genetic factors of stroke in South Asians are largely unexplored. Exome-wide sequencing and association analysis (ExWAS) in 75 K Pakistanis identified NM_000435.3(NOTCH3):c.3691 C > T, encoding the missense amino acid substitution p.Arg1231Cys, enriched in South Asians (alternate allele frequency = 0.58% compared to 0.019% in Western Europeans), and associated with subcortical hemorrhagic stroke [odds ratio (OR) = 3.39, 95% confidence interval (CI) = [2.26, 5.10], p = 3.87 × 10-9), and all strokes (OR [CI] = 2.30 [1.77, 3.01], p = 7.79 × 10-10). NOTCH3 p.Arg231Cys was strongly associated with white matter hyperintensity on MRI in United Kingdom Biobank (UKB) participants (effect [95% CI] in SD units = 1.1 [0.61, 1.5], p = 3.0 × 10-6). The variant is attributable for approximately 2.0% of hemorrhagic strokes and 1.1% of all strokes in South Asians. These findings highlight the value of diversity in genetic studies and have major implications for genomic medicine and therapeutic development in South Asian populations.

Qatar's genetic counseling landscape: Current insights and future prospects

Genetic counseling is a dynamic and rapidly growing field. In Qatar, the significance of genetic counseling is underscored by the distinctive demographic characteristics of the population, including elevated rates of consanguinity and larger family sizes, contributing to the increased incidence of many genetic conditions. This emphasizes the crucial role of genetic counseling in addressing the specific needs of the community. Over the past decade, key health care institutions in Qatar, such as Hamad Medical Corporation and Sidra Medicine, have significantly expanded genetic counseling services encompassing premarital, reproductive, prenatal, pediatric, adult, and cancer care. This multifaceted approach reflects Qatar's health care system's commitment to addressing various aspects of genetic health and well-being across different life stages. A pivotal milestone in the field's development in Qatar was the establishment of a genetic counseling master's program at Qatar University in 2018, showcasing the country's dedication to fostering indigenous expertise in genetic counseling with the necessary competencies and cultural sensitivity to address the unique genetic counseling needs of the population. The recognition of genetic counseling as a profession and the licensure by the Ministry of Public Health in Qatar is another key achievement to ensure the high quality of service and protection of the profession. Contributing to global genetic knowledge, various academic and research entities in Qatar are conducting genetic/genomic/genetic counseling research toward advancing precision medicine in the country, and initiatives such as the Qatar Biobank and Qatar Genome Program have played a major role in catalyzing these efforts.

Genomic Newborn Screening for Pediatric Cancer Predisposition Syndromes: A Holistic Approach

As next-generation sequencing (NGS) has become more widely used, germline and rare genetic variations responsible for inherited illnesses, including cancer predisposition syndromes (CPSs) that account for up to 10% of childhood malignancies, have been found. The CPSs are a group of germline genetic disorders that have been identified as risk factors for pediatric cancer development. Excluding a few "classic" CPSs, there is no agreement regarding when and how to conduct germline genetic diagnostic studies in children with cancer due to the constant evolution of knowledge in NGS technologies. Various clinical screening tools have been suggested to aid in the identification of individuals who are at greater risk, using diverse strategies and with varied outcomes. We present here an overview of the primary clinical and molecular characteristics of various CPSs and summarize the existing clinical genomics data on the prevalence of CPSs in pediatric cancer patients. Additionally, we discuss several ethical issues, challenges, limitations, cost-effectiveness, and integration of genomic newborn screening for CPSs into a healthcare system. Furthermore, we assess the effectiveness of commonly utilized decision-support tools in identifying patients who may benefit from genetic counseling and/or direct genetic testing. This investigation highlights a tailored and systematic approach utilizing medical newborn screening tools such as the genome sequencing of high-risk newborns for CPSs, which could be a practical and cost-effective strategy in pediatric cancer care.

Genetic background of primary and familial HLH in Qatar: registry data and population study

Background

Familial hemophagocytic lymphohistiocytosis (FHLH) is an inherited life-threatening disease. Five types are identified, with the addition of congenital immunodeficiency syndromes in which HLH is a typical manifestation. The literature on this disease is very scarce in the Middle East, with only a few scattered reports.

Methods

We report detailed demographic, clinical, and genomic data from 28 patients diagnosed with primary and familial HLH over the last decade in Qatar. An evaluation was performed of allele frequencies of deleterious variants from 12 primary and familial HLH causative genes on the Qatar Genome Programme (QGP) cohort of 14,669 Qatari individuals.

Results

The genetic diagnosis was obtained in 15 patients, and four novel mutations in Perforin 1 (PRF1), UNC13D, LYST, and RAB27A genes were found. We identified 22,945 low/high/moderate/modifier impact variants significantly enriched in the QGP in those 12 genes. The variants rs1271079313 in PRF1 and rs753966933 in RAB27A found in our patient cohort were significantly more prevalent in the QGP compared to the Genome Aggregation Database (gnomAD) database, with a high carrier frequency in the Qatari population.

Conclusions

We established the first primary and familial HLH Registry in the Gulf Region and identified novel possibly pathogenic variants present at higher frequency in the Qatari population, which could be used for screening purposes. Raising awareness about primary and familial HLH and implementing screening activities in the Qatari highly inbred population could stem into more comprehensive premarital and prenatal evaluations and faster diagnosis.

Qatar Genome: Insights on Genomics from the Middle East

Despite recent biomedical breakthroughs and large genomic studies growing momentum, the Middle Eastern population, home to over 400 million people, is under-represented in the human genome variation databases. Here we describe insights from phase 1 of the Qatar Genome Program with whole genome sequenced 6,047 individuals from Qatar. We identified more than 88 million variants of which 24 million are novel and 23 million are singletons. Consistent with the high consanguinity and founder effects in the region, we found that several rare deleterious variants were more common in the Qatari population while others seem to provide protection against diseases and have shaped the genetic architecture of adaptive phenotypes. These results highlight the value of our data as a resource to advance genetic studies in the Arab and neighbouring Middle Eastern populations and will significantly boost the current efforts to improve our understanding of global patterns of human variations, human history and genetic contributions to health and diseases in diverse populations. This article is protected by copyright. All rights reserved.