BRCA1-specific machine learning model predicts variant pathogenicity with high accuracy.

Identification of novel BRCA1 variants outpaces their clinical annotation which highlights the importance of developing accurate computational methods for risk assessment. Therefore our aim was to develop a BRCA1-specific machine learning model to predict the pathogenicity of all types of BRCA1 variants and to apply this model and our previous BRCA2-specific model to assess BRCA variants of uncertain significance (VUS) among Qatari patients with breast cancer. We developed an XGBoost model that utilizes variant information such as position frequency and consequence as well as prediction scores from numerous in silico tools. We trained and tested the model with BRCA1 variants that were reviewed and classified by the Evidence-Based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium. In addition we tested the model's performance on an independent set of missense variants of uncertain significance with experimentally determined functional scores. The model performed excellently in predicting the pathogenicity of ENIGMA-classified variants (accuracy: 99.9%) and in predicting the functional consequence of the independent set of missense variants (accuracy: 93.4%). Moreover it predicted 2 115 potentially pathogenic variants among the 31 058 unreviewed BRCA1 variants in the BRCA exchange database. Using two BRCA-specific models we did not identify any pathogenic BRCA1 variants among those found in patients in Qatar but predicted four potentially pathogenic BRCA2 variants, which could be prioritized for functional validation.

Congenital Methemoglobinemia: First Confirmed Case in the Arab Population with a Novel Variant in the CYB5R Gene in the State of Qatar: A Case Report.

Methemoglobinemia (MetHb) is a rare hematological condition characterized by high methemoglobin levels in the blood. It happens when hemoglobin is oxidized, resulting in hypoxia and cyanosis, which may occur in inherited or acquired forms. Inherited or congenital methemoglobinemia is a rare autosomal recessive condition and has never been reported in the Arab population. Here we report a case of a 22-year-old Arab man with a positive family history who presented with bluish discoloration of the fingers and lips and was found to have methemoglobinemia. Genetic study on the patient and his family revealed compound heterozygous variants in the CYB5R3 Exon 5 c.431G>A p.Gly144Asp likely pathogenic variant and CYB5R3 Exon 9 c.871G>A p.Val291Met variant of unknown significance. We suggest that the novel c.871G>A p.Val291Met variant could be causative for methemoglobinemia.

Prevalence and Genotype-Phenotype Correlation of Lynch Syndrome in a Selected High-Risk Cohort from Qatar's Population.

Lynch syndrome (LS) is the most common cause of hereditary colorectal cancers (CRC) and is associated with an increased risk for ovarian and endometrial cancers. There is lack of knowledge on the epidemiology of LS in the non-Caucasian populations especially in Qatar. The aim of this retrospective study is to explore the prevalence of LS in a selected high-risk cohort in the State of Qatar in addition to investigating the frequency and genotype-phenotype correlation associated with mismatch repair genes pathogenic variants. Retrospective review of medical records of 31 individuals with LS, 20 affected with colorectal cancer and 11 unaffected with family history of cancers, referred from January 2017 until August 2020. The prevalence of LS among affected and unaffected patients is 22% (20/92) and 2.2% respectively. Among affected individuals, MLH1 and MSH2 genes were highly frequent while for unaffected individuals, a recurrent PMS2 pathogenic variant was reported in several related individuals suggesting a tribal effect. This study highlights the epidemiology of LS in high-risk cohort in Qatar which helps to provide recommendations on genetic testing, and personalize surveillance and management programs.

Expanding on the phenotypic spectrum of Woodhouse-Sakati syndrome due to founder pathogenic variant in DCAF17: Report of 58 additional patients from Qatar and literature review.

Woodhouse-Sakati syndrome (WSS) is a rare autosomal recessive neuroendocrine and ectodermal disorder caused by variants in the DCAF17 gene. In Qatar, the c.436delC variant has been reported as a possible founder pathogenic variant with striking phenotypic heterogeneity. In this retrospective study, we report on the clinical and molecular characteristics of additional 58 additional Qatari patients with WSS and compare them to international counterparts' findings. A total of 58 patients with WSS from 32 consanguineous families were identified. Ectodermal and endocrine (primary hypogonadism) manifestations were the most common presentations (100%), followed by diabetes mellitus (46%) and hypothyroidism (36%). Neurological manifestations were overlapping among patients with intellectual disability (ID) being the most common (75%), followed by sensorineural hearing loss (43%) and both ID and aggressive behavior (10%). Distinctive facial features were noted in all patients and extrapyramidal manifestations were uncommon (8.6%). This study is the largest to date on Qatari patients with WSS and highlights the high incidence and clinical heterogeneity of WSS in Qatar due to a founder variant c.436delC in the DCAF17 gene. Early suspicion of WSS among Qatari patients with hypogonadism and ID, even in the absence of other manifestations, would shorten the diagnostic odyssey, guide early and appropriate management, and avoid potential complications.

A founder RAB27A variant causes Griscelli syndrome type 2 with phenotypic heterogeneity in Qatari families.

Griscelli syndrome type 2 (GS2) is a rare autosomal recessive disorder caused by pathogenic variants in the RAB27A gene and characterized by partial albinism, immunodeficiency, and occasional hematological and neurological involvement. We reviewed and analyzed the medical records of 12 individuals with GS2 from six families belonging to a highly consanguineous Qatari tribe and with a recurrent pathogenic variant in the RAB27A gene (NM_004580.4: c.244C > T, p.Arg82Cys). Detailed demographic, clinical, and molecular data were collected. Cutaneous manifestations were the most common presentation (42%), followed by neurological abnormalities (33%) and immunodeficiency (25%). The most severe manifestation was HLH (33%). Among the 12 patients, three patients (25%) underwent HSCT, and four (33%) died. The cause of death in all four patients was deemed HLH, providing evidence for this complication's fatal nature. Interestingly, two affected patients (16%) were asymptomatic. This report highlights the broad spectrum of clinical presentations of GS2 associated with a founder variant in the RAB27A gene (c.244C > T, p.Arg82Cys). Early suspicion of GS2 among Qatari patients with cutaneous manifestations, neurological findings, immunodeficiency, and HLH would shorten the diagnostic odyssey, guide early and appropriate treatment, and prevent fatal outcomes.

Pancytopenia And Limbic Encephalopathy Complicating Immunotherapy For Clear Cell Endometrial Cancer With Microsatellite Instability-High (MSI-H).

BACKGROUND: Clear cell carcinoma of the endometrium (CCE) has a tendency to occur in a mismatch repair protein deficient molecular background. Treatment with immunotherapy can predict a favorable response. CASE PRESENTATION: We are presenting a 53-year-old female, diagnosed with CCE 17 years ago, who was treated initially with hysterectomy and left salpingo-oophorectomy, who relapsed a few months later, and was then treated with left pelvic mass excision and sigmoidectomy. Recently, the disease recurred as a retroperitoneal lymphadenopathy, which was resected but then relapsed locally, spread to the lungs, and progressed further after three lines of chemotherapy. On pathological review of the tumor, it was found to harbor loss of nuclear expression of MLH-1 and PMS-2. Based on a strong predictor of response to immunotherapy, pembrolizumab was tried. However, within a few days of the single dose of pembrolizumab, immune thrombocytopenia followed by pancytopenia, recurrent seizures, visual hallucination, and cerebellar signs consistent with limbic encephalitis developed, which were not responding to steroid and intravenous immunoglobulin. CONCLUSION: We are presenting a case of a CCE with deficient mismatch repair that developed two autoimmune side effects, pancytopenia and limbic encephalitis, within a few days of a single injection of pembrolizumab.

Clinical exome sequencing in 509 Middle Eastern families with suspected Mendelian diseases: The Qatari experience.

BACKGROUND: Clinical exome sequencing (CES) is rapidly becoming the diagnostic test of choice in patients with suspected Mendelian diseases especially those that are heterogeneous in etiology and clinical presentation. Reporting large CES series can inform guidelines on best practices for test utilization, and improves accuracy of variant interpretation through clinically-oriented data sharing. METHODS: This is a retrospective series of 509 probands from Qatar who underwent singleton or trio CES either as a reflex or naïve (first-tier) test from April 2014 to December 2016 for various clinical indications. RESULTS: The CES diagnostic yield for the overall cohort was 48.3% (n = 246). Dual molecular diagnoses were observed in 2.1% of cases; nearly all of whom (91%) were consanguineous. We report compelling variants in 11 genes with no established Mendelian phenotypes. Unlike reflex-WES, naïve WES was associated with a significantly shorter diagnostic time (3 months vs. 18 months, p < 0.0001). CONCLUSION: Middle Eastern patients tend to have a higher yield from CES than outbred populations, which has important implications in test choice especially early in the diagnostic process. The relatively high diagnostic rate is likely related to the predominance of recessive diagnoses (60%) since consanguinity and positive family history were strong predictors of a positive CES.

Exploring the effectiveness of crisis counseling and psychoeducation in relation to improving mental well-being, quality of life and treatment compliance of breast cancer patients in Qatar.

BACKGROUND: An insufficient number of studies have been carried out in the Middle East to evaluate the role of structured psychotherapeutic interventions in enhancing breast cancer patients' psychological well-being, quality of life and treatment compliance. This study has been designed to address this limitation by exploring the benefit of two structured psychotherapeutic interventions, crisis counseling and psychoeducation, in enhancing breast cancer patients' psychological well-being, quality of life and treatment compliance in Qatar. METHODS: A total of 201 women with early-stage breast cancer from the state of Qatar were recruited and randomized into either the control group or one of the treatment groups (crisis counseling or psychoeducation). Each of the two treatment interventions consisted of a total of six 60- to 90-minute sessions, which were provided over a period of 12 weeks. The short- and long-term benefits of the crisis counseling and psychoeducation interventions were evaluated in terms of improving patients' psychological well-being, quality of life and treatment compliance by asking all the patients to complete the Depression, Anxiety and Stress Scale, 21 item version (DASS-21) and European Organization for Research and Treatment of Cancer Quality of Life scale (QLQ-C30) instruments at different points in time and by monitoring their compliance to chemotherapy and radiotherapy treatment. RESULTS: This study revealed that both of the study interventions, crisis counseling and psychoeducation, were effective in improving women's psychological well-being and quality of life over time in comparison to the control group, but had no significant impact on patients' compliance with treatment. In addition, the study showed that psychoeducation conferred a greater advantage than did the crisis counseling model, especially in improving women's psychological well-being over time. CONCLUSION: This study is considered the first of its kind in Qatar to provide evidence on the benefit of crisis counseling and psychoeducation interventions in improving the psychological well-being and quality of life of women with early-stage breast cancer in Qatar. In addition, this study has provided innovative research that can be used as evidence to propose changes to the psychotherapy services for breast cancer patients in Qatar. This research study aims to provide a first step toward further research in the future, which will hopefully lead to a better health care system for cancer patients in Qatar.