Severe Transfusion-Dependent Thalassemia in Compound Heterozygote Palestinian Siblings with Two α-Globin Gene Defects, Hb Taybe D HBA1: C.119_121delCCA Mutation and HBA2: C.*94A > G Mutation.

Alpha and Beta Thalassemia are autosomal recessive anemias that cause significant morbidity and mortality worldwide, especially in the Middle East and North Africa (MENA) region where carrier rates reach up to 50%. We report the case of two siblings of Palestinian origin born who presented to our tertiary healthcare center for the management of severe transfusion dependent hemolytic anemia. Before presentation to our center, the siblings were screened for a-thalassemia using the Alpha-globin StripAssay. They were found to carry the α2 polyA-1 [AATAAA > AATAAG] mutation in the heterozygous form, which was insufficient to make a diagnosis. No pathogenic variants were detected on Sanger sequencing of the HBB gene. Full sequencing of the a-gene revealed compound heterozygous variants (HBA1:c.119_121delCCA and the previously detected HBA2:c.*+94A > G Poly A [A->G]) with trans inheritance. This report highlights the impact of non-deletional mutations on α-globin chain stability. The compound heterozygosity of a rare α-globin chain pathogenic variant with a polyadenylation mutation in the probands leads to clinically severe a-thalassemia. Due to the high carrier status, the identification of rare mutations through routine screening techniques in our populations may be insufficient. Ongoing collaboration among hematologists, medical geneticists, and counselors is crucial for phenotypic-genotypic correlation and assessment of adequate genetic testing schemes.

Comparison between the accuracy of chest computerized tomography vs. reverse transcriptase polymerase chain reaction in a tertiary care center in Lebanon; along with their correlation to mortality, morbidity and symptoms in COVID-19 patients.

Objectives: Chest Computerized Tomography has been widely used in COVID patients' assessment. Hence the question arises as to whether there is any correlation between the Ct value and findings on Chest CT scan or clinical presentation of the patient. We wanted to test the hypothesis of whether low Ct values (≤30) in RT-PCR were associated with a high mortality rate, CT scan findings, or with comorbidities such as immunosuppression and lung disease. Methods: The radiographic records and RT-PCR Ct values of 371 COVID patents diagnosed at the American University of Beirut Medical Center were reviewed. Results: We found out that the sensitivity of chest CT scan compared to RT-PCR, the gold standard, turned out to be 74% (95% CI 69-79%). Specificity, on the other hand was 33% (95% CI 16-55%). The positive predictive value of CT was 94% (95% CI 91-97%) and the negative predictive value was 8% (95% CI 4-16%). low Ct values in RT-PCR were not associated with a higher mortality rate (p-value = 0.416). There was no significant positive association between low Ct value and suspicious CT scan findings (typical and indeterminate for COVID-19), with a p-value of 0.078. There was also no significant association between low Ct value and immunosuppression (p-value = 0.511), or lung disease (p-value =0.06). CT scan findings whether suspicious or not for COVID-19 infection, were not shown to be significantly associated with respiratory symptoms of any kind.No association was found between a history of lung disease, immunosuppression and suspicious CT scan findings for COVID-19. Conclusion: As long as this pandemic exists, nucleic acid testing was and remains the gold standard of COVID-19 diagnosis worldwide and in our community as it has a superior diagnostic accuracy to CT scan and higher sensitivity (94% vs 74%).

Insight into the 8p23.1 duplication syndrome: Case report of a young women with infertility.

Objective: To report the case of a young woman with repeated conception failure, whose karyotype showed an unbalanced complex chromosomal rearrangement involving a large duplication harboring >115 genes and overlapping the 8p23.1 duplication syndrome region. The 8p23.1 duplication syndrome results from a tandem duplication on the short arm of chromosome 8 containing the 4 genes (GATA4, TNKS, SOX7, XKR6) responsible for the most common phenotypic features: developmental delay/learning disabilities, congenital heart disease and dysmorphism. Design: Case report and review of the literature. Setting: American University of Beirut Medical Center, department of Pathology and Laboratory medicine.Patient(s): Young woman referred to the genetic clinics for the workup of secondary idiopathic infertility with multiple unsuccessful inseminations and in vitro fertilizations. Interventions: Peripheral blood karyotype analysis from the patient and her parents. Elucidation of the CCR required whole chromosome painting Fluorescent in Situ Hybridization and Chromosomal Microarray. Main outcome measures: The few published reports on 8p23.1 duplication syndrome (<50 cases) describing carriers reveal a wide range of phenotypic consequences with heterogeneous severity. The main outcome is to further understand this syndrome. Results: Chromosomal microarray analysis detected a large (12Mb) pathogenic Copy Number Variant (CNV) at 8p23.3p23.1, overlapping the 8p23.1 duplication syndrome region. This CNV, classified as pathogenic, was shown to carry little significance in our patient. Conclusions: 8p23.1 duplication syndrome display a variable expressivity, ranging from overt syndromic features to minimal effect on the phenotype as shown in this case. Interpretation of prenatal detection of 8p23.1 duplication especially in preimplantation diagnosis is thus challenging. Nevertheless, this case emphasizes the importance of genetic testing in infertile patients displaying a normal phenotype.

Using the SLIPTA checklist to assess laboratory readiness for Joint Commission International accreditation.

Background: The Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA) helps prepare laboratories in low- and middle-income countries to achieve international accreditation aligned with the ISO 15189:2012 standards. Accreditation by the Joint Commission International (JCI) is among the highest sought by hospitals worldwide. While the readiness of laboratories with a five-star SLIPTA score to undergo ISO 15189:2012 accreditation was recently assessed, the compliance of the SLIPTA checklist with JCI is still unknown. Objective: The study evaluated the SLIPTA checklist's utility in assessing laboratories to meet the JCI standards. Methods: We conducted a detailed gap analysis between SLIPTA and JCI laboratory standards from January 2021 to January 2022. We cross-matched the JCI standard requirements to SLIPTA clauses and categorised each standard into 'met', 'partially met', and 'not met'. We highlighted similarities, discrepancies, and improvement areas. Results: A total of 109 JCI standards were included. The SLIPTA checklist completely met 61 standards, partially met four, but did not meet 44. The unmet JCI standards focused on the quality planning, control, and improvement sections. Healthcare organisation management and quality control processes, including selecting an accredited reference laboratory, collecting quality management data, creating of post-analytical policies and procedures, and validating monitoring systems, constitute the basis of this preparation. Conclusion: The SLIPTA checklist covers major quality management system elements of the JCI standards for laboratories. However, some components should be addressed to assure readiness for JCI accreditation. What this study adds: This study identified additional areas not covered by the SLIPTA checklist that are required for JCI accreditation.

AML with inv(16)/t(16;16) and high-risk cytogenetic abnormalities: atypical features and unfavorable outcome.

OBJECTIVES: Acute myeloid leukemia (AML) with inv(16)/t(16;16) is among the most frequent AML subtypes. It is recognized by the detection of the CBFB-MYH11 fusion which confers a favorable prognosis, irrespective of the presence of secondary cytogenetic abnormalities. However, the effect of additional genetic anomalies on the behavior of inv(16) AML is debatable. Recent case reports describe an unfavorable prognosis for those patients, characterized by early relapse and death. In this study, we present a series of patients with CBFB-MYH11 fusion and high-risk rearrangements to increase knowledge about this potentially distinct subgroup. METHODS: All cases with inv(16)/ t(16;16) and one or more high risk abnormalities were reviewed at two tertiary healthcare centers between years 2006 and 2020 in terms of demographics, biological and clinical data. RESULTS: Among the total 1447 and 1283 AML cases, the frequency was found to be 0,2% and 0.3%. Clinical data could be retrieved for 5 patients. Detected high-risk abnormalities included TP53 and 5q deletion, complex and monosomal karyotype. The median age was 67 years, with a majority of females (M:F = 1:1.5). Two out of 5 patients presented with therapy related AML, with short latency periods. All patients presented with thrombocytopenia and/or leukocytopenia. Bone marrow aspirates revealed atypical morphology and the detection of rare CBFB-MYH11 fusion transcripts. All 5 patients died, with a short mean overall survival of 5.8 months. DISCUSSION AND CONCLUSION: Our series suggests that the presence of high risk abnormalities confers distinct biological features and poor prognosis to inv(16) AML.

KMT2A-ARHGEF12, a therapy related fusion with poor prognosis.

BACKGROUND: The detection of KMT2A gene rearrangements have an important impact on the prognosis and management of acute leukemias. These alterations most commonly involve reciprocal translocations at specific breakpoint regions within KMT2A. To date, more than 100 translocation partner genes of KMT2A have been identified, with different effects on risk stratification. METHODS AND RESULTS: We report the case of a mature plasmacytoid dendritic cells proliferation associated with B lymphoblasts harboring a KMT2A-ARHGEF12 fusion. This rare rearrangement, resulting from a cryptic deletion on the long arm of chromosome 11, is located outside the known major and minor breakpoint regions of KMT2A, not reported to date. The review of the few cases of KMT2A-ARHGEF12 reveals the tendency of this deletion to occur in therapy related hematologic neoplasm and confer unfavorable prognosis. CONCLUSION: This review sheds light into the rare KMT2A-ARHGEF12 fusion in leukemia. Reporting rare chimeras is essential to improve knowledge about the biological mechanism and associated clinical consequences.

Diagnosing Lymphoproliferative Disorders Using Core Needle Biopsy Versus Surgical Excisional Biopsy: Three-Year Experience of a Reference Center in Lebanon.

BACKGROUND: Despite current guidelines, a significant increase in the use of core needle biopsy (CNB) has been noted. Our aims were to determine the profile of patients referred for image-guided biopsies, to assess the diagnostic yield of these biopsies, and to learn whether CNB is an effective alternative to surgical excisional biopsy (SEB). PATIENTS AND METHODS: All lymph node biopsy samples evaluated in the Department of Pathology and Laboratory Medicine from 2014 to 2017 were included. Patients' demographics, biopsy type, and final diagnosis were recorded and classified as diagnostic or nondiagnostic. The reasons for the latter were evaluated and follow-up was obtained, where available. RESULTS: A total of 373 cases, 210 CNB and 163 SEB, were collected. The diagnostic yield was 79% for CNB compared to 97% for SEB. The choice of CNB versus SEB was not dependent on patient's age, gender, or clinical suspicion of malignancy. Failure to reach a diagnosis was due to insufficient or suboptimal tissue in most nondiagnostic CNBs. Lymphoma was equally diagnosed among CNB and SEB. CNB was at an advantage in diagnosing large B-cell lymphomas. CONCLUSION: When performed adequately, CNB is a good substitute for SEB. Strict and specific guidelines need to be updated and adopted to indicate how and when it can be used, including the recommendation of concomitant complementary diagnostic laboratory testing such as flow cytometry. The latter should be readily available in order to not compromise the quality and accuracy of the diagnoses.

Plasma cells and lymphoid aggregates in sleeve gastrectomy specimens: Normal or gastritis?

Lymphoid follicles/aggregates in gastric biopsies have been traditionally linked to Helicobacter pylori gastritis, and less commonly to other inflammatory and neoplastic conditions. The frequency of such aggregates in normal stomachs has yet to be adequately evaluated. This is especially relevant when it comes to diagnosing non-specific chronic gastritis in biopsy specimens with chronic inflammation but no evidence of H pylori infection. Sleeve gastrectomies represent an opportunity to study adequately preserved gastric mucosa in patients who are otherwise asymptomatic and lack a history of gastric disease.To study sleeve gastrectomy specimens to quantify the amount of lymphoid follicles/aggregates and lymphocytic infiltration in normal stomachs.Sixty-eight bariatric sleeve gastrectomies and 13 control specimens from Whipple resections were examined for multiple histologic features including type, quantity, and distribution of chronic inflammation and lymphoid follicles/aggregates. Presence of H pylori was documented by both Hematoxylin and eosin-stained (H&E) and immunohistochemistry (IHC). Clinical information including age, sex, medication intake, prior endoscopy, and/or H pylori infection was recorded. The patient population was divided in 2 groups, H pylori negative versus H pylori positive, and statistical analysis was performed by a biostatistician.Two hundred sixty three fundic sections from 68 bariatric patients were examined. Fifty three patients were found to be H pylori-negative, compared with 15 who were positive for H pylori. Among the H pylori-negative group, the average number of lymphoid aggregates was 3.33, compared with an average of 6.26 in the H pylori positive group (the difference was statistically significant with a P-value of .008). The average number of plasma cells per high power field was 2.15 in the H pylori negative group, compared and average of 5.07 in the H pylori positive group (the difference was also statistically significant with a P-value <.001). Clinically, 10 of the 53 H pylori-negative patients had esophagogastroduodenoscopy (EGD) that showed endoscopic mild non-erosive gastric erythema. The remaining had no documentation of symptoms or medication intake, including Non-steroidal anti-inflammatory drugs (NSAIDs) and Proton Pump Inhibitors (PPI).Our results suggest that the presence of lymphoid aggregates and plasma cells infiltration can be a normal finding in otherwise normal gastric mucosa, though more pronounced in H pylori infected patients.

Prevalence of T790M mutation among TKI-therapy resistant Lebanese lung cancer patients based on liquid biopsy analysis: a first report from a major tertiary care center.

Lung adenocarcinoma patients have variable prognosis due to many factors. Detection of epidermal growth factor receptor (EGFR) activating mutations is one of the factors that implies the need for initiating a first-line EGFR tyrosine kinase inhibitor (TKI) treatment. However, T790M resistance mutation emergence during treatment accounts for most EGFR-TKI drug resistance. The traditional sample taken for T790M mutation analysis is tissue biopsy, but its numerous disadvantages have introduced liquid biopsy as a preferred method for testing. We studied the prevalence of T790M mutation among pulmonary adenocarcinoma patients in Lebanese patients based on liquid biopsy testing the circulating tumor DNA (ctDNA). We have reviewed the laboratory charts of 52 patients who developed resistance on treatment and referred to AUBMC for EGFR T790M Liquid Biopsy to analyze the mutational analysis results for EGFR T790M. In total, 82.6% of the tested lung cancer patients were positive for a specific EGFR mutation. Among these patients, a total 26.9% were positive for T790M, which is comparable to the international prevalence of this mutation. However, for those cases who developed resistance with circulating DNA showing an EGFR mutation, 50% were positive for T790M that is also comparable to the international literature. This is the first report from Lebanon to discuss the prevalence of T790M mutation using liquid biopsy among Lebanese population. An important landmark molecular epidemiology study that will be a reference to all oncologists in Lebanon and the region in assessing the potential for targeted therapy options in the country. In addition, the data will be of an asset to the building international literature related to this disease.

Molecular profiling of adult acute myeloid and lymphoid leukemia in a major referral center in Lebanon: a 10-year experience report and review of the literature.

Recurrent genetic abnormalities confer distinct morphologic features and play a role in determining the clinical behavior, prognosis and adequate treatment of acute leukemia. In the MENA region, only one study targets the frequency of genetic modifications in AML, reporting a higher occurrence of acute promyelocytic leukemia in Lebanon. Determining the frequency of translocations and gene mutations in acute myeloid and lymphoid leukemia cases in an adult patients' population in Lebanon and comparing the resultant genetic profile with the published international molecular profile of adult acute leukemia. Laboratory results of adult patients diagnosed with AML or ALL presenting to AUBMC for genetic profiling between years 2006 until June 2016 were reviewed. Genetic profiling of AML cases in our CAP accredited molecular diagnostics laboratory consists of a validated lab developed RT-PCR for the detection of RUNX1/RUNX1T1, CBFB/MYH11, KMT2A/MLLT3, PML-RARA, and BCR-ABL and mutations in the FLT3 receptor, NPM1, c-kit and CEPBA genes. The ALL panel tests for the presence of BCR-ABL1, ETV6/RUNX1; KMT2A/AFF1, and TCF3-PBX1. We reviewed 580 AML and 175 ALL cases. In the AML cohort, the M:F ratio was 1.3:1 with a mean age of 50 years. t(15;17) was present in 7.6%, t(8;21) in 4.2%, inv(16) in 3.7%, t(9;22) in 2.2% and t(9;11) in 1.7% of cases. FLT3 mutation (ITD or TKD) was present in 25.2% of all cases and 30.1% of Cytogenetics-normal (CN) patients. Mutations of the NPM1 gene was present in 31.4% of AML cases and in 43.8% of CN patients. Double positive (NPM1+/FLT3+) cases accounted for 20% of NK patients. CEBPA and c-kit mutations were detected in 7.3% and 2.4% respectively. In the ALL cohort, the mean age was 37 years. B- and T-lymphoblastic leukemia constituted 84.6% and 15.4% of ALL cases and the M:F ratio was 1.2:1 and 2.86:1 respectively. B-ALL patients were positive for t(9;22) in 14.2%, t(4;11) in 5.4%, t(1;19) in 2.7% and t(12;21) in 1.4%. T-ALL patients were negative for translocations found in our ALL panel. A lower mean age was found in our adult leukemic Lebanese population as compared to the Western cases. Other interesting findings were the lower percentage of inv(16), lower incidence of TCF3-PBX1, and the mild increase in Philadelphia positivity in our AML cohort. In our ALL cohort, t(9;22) positivity was less than expected for adult lymphoblastic leukemia. Full molecular profiling by next generation sequencing is required for further classification of cases into prognostic categories. This study will be a baseline reference for future research and epidemiological data useful for transplant centers and oncologists both in Lebanon and the region.

Genetics of multifactorial disorders: proceedings of the 6th Pan Arab Human Genetics Conference.

The 6th Pan Arab Human Genetics Conference (PAHGC), "Genetics of Multifactorial Disorders" was organized by the Center for Arab Genomic Studies (http://www.cags.org.ae) in Dubai, United Arab Emirates from 21 to 23 January, 2016. The PAHGCs are held biennially to provide a common platform to bring together regional and international geneticists to share their knowledge and to discuss common issues. Over 800 delegates attended the first 2 days of the conference and these came from various medical and scientific backgrounds. They consisted of geneticists, molecular biologists, medical practitioners, postdoctoral researchers, technical staff (e.g., nurses and lab technicians) and medical students from 35 countries around the world. On the 3rd day, a one-day workshop on "Genetic Counseling" was delivered to 26 participants. The conference focused on four major topics, namely, diabetes, genetics of neurodevelopmental disorders, congenital anomalies and cancer genetics. Personalized medicine was a recurrent theme in most of the research presented at the conference, as was the application of novel molecular findings in clinical settings. This report discusses a summary of the presentations from the meeting.