POLD3 deficiency is associated with severe combined immunodeficiency, neurodevelopmental delay, and hearing impairment.

Combined immunodeficiency diseases (CID) represent the most severe forms of inborn errors of immunity. Defective T cell development and/or function, leading to an impairment in adaptive immunity are responsible for these diseases. The DNA polymerase δ complex is important for genome duplication and maintenance and consists of the catalytic subunit POLD1, and the accessory subunits POLD2 and POLD3 which stabilizes the complex. Mutations in POLD1 and POLD2 have been recently shown to be associated with a syndromic CID characterized by T cell lymphopenia with or without intellectual deficiency and sensorineural hearing loss. Here we report a homozygous POLD3 variant (NM_006591.3; p.Ile10Thr) in a Lebanese patient, the product of a consanguineous family, presenting with a syndromic severe combined immunodeficiency (SCID) with neurodevelopmental delay and hearing loss. The homozygous POLD3Ile10Thr variant abolishes POLD3 as well as POLD1 and POLD2 expression. Our findings implicate POLD3 deficiency as a novel cause of syndromic SCID.

Genome sequencing unveils mutational landscape of the familial Mediterranean fever: Potential implications of IL33/ST2 signalling.

Familial Mediterranean fever (FMF) is the most common auto-inflammatory disease. It is transmitted as autosomal recessive trait with mutations in MEditerranean FeVer (MEFV) gene. Despite a typical clinical expression, many patients have either a single or no mutation in MEFV. The current work is aimed to revisit the genetic landscape of FMF disease using high-coverage whole genome sequencing. In atypical patients (carrying a single or no mutation in MEFV), we revealed many rare variants in genes associated with auto-inflammatory disorders, and more interestingly, we discovered a novel variant ( a 2.1-Kb deletion) in exon 11 of IL1RL1 gene, present only in patients. To validate and screen this patient-specific variant, a tandem of allele-specific PCR and quantitative real-time PCR was performed in 184 FMF patients and 218 healthy controls and we demonstrated that the novel deletion was absent in controls and was present in more than 19% of patients. This study sheds more light on the mutational landscape of FMF. Our discovery of a disease-specific variant in IL1RL1 gene may constitute a novel genetic marker for FMF. This finding suggesting a potential role of the IL33/ST2 signalling in the disease pathogenicity highlights a new paradigm in FMF pathophysiology.

Genetic variations and population data on five supplementary STR markers in Lebanon.

Population representative short tandem repeat (STR) allele frequencies are crucial for proper probabilistic interpretation of DNA forensic evidence. STR allele frequencies also provide information about the genetic diversity of a given population. The Lebanese population is characterized by the presence of more than 18 religious communities that have high recorded rates of endogamous and consanguineous marriages, where the choice of marriages is mainly influenced by their respective geographical distributions and religious affiliation. These factors could have led to an increase in complex DNA cases, whereby high numbers of STR markers are needed to help clear the case. Allele frequencies for 23 STR loci in the Lebanese population were recently estimated and published. The present study aims at estimating the STR allele frequencies for five supplementary STRs, namely, the LPL, F13B, FESFPS, F13A01, and Penta C STR markers, which are mainly used to resolve complex kinship investigations. A DNA database representative of the Lebanese population that comprises 505 Lebanese unrelated individuals was used to amplify the five STR systems, using the CS7 kit released by Promega. The allele frequencies for these STR systems were estimated, and a significant departure from the Hardy-Weinberg equilibrium was detected after Bonferroni correction for multiple tests at locus LPL, F13A01, and Penta C. The newly added systems appeared to have variation in their discriminative power among Lebanese individuals. Penta C showed the highest power of discrimination, whereas FESFPS showed the lowest power of discrimination. The estimated frequencies and population data could provide local DNA relationship testing laboratories with additional tools that help resolve complex DNA cases.

Autosomal short tandem repeat variations and population genetic data on 23 systems in seven major subpopulations from Lebanon.

Population allele frequency is an indicator of population genetic diversity and plays significant roles in DNA profiling interpretation in human identification, kinship, and forensic testing. The Lebanese population is a mosaic of 18 religious communities with high rates of consanguinity and endogamy. Allele frequencies for 23 STR loci were estimated and analyzed in the seven major Lebanese religious subcommunities (Muslims Shiaa, Sunni, and Druze, and Christians Orthodox, Maronite, and Catholics), to assess possible significant differences among their STR allele frequencies.

Comparison of four DNA extraction methods to extract DNA from cigarette butts collected in Lebanon.

Cigarette butts collected from crime scenes represent valuable sources of DNA. However the extraction of the genetic material may deem challenging especially when different contaminants may compromise the integrity, quality, and quantity of DNA obtained. This study aims at comparing four extraction methods (Chelex-100, soaking + Chelex-100, Chelex-100 + PK, and DNA IQ™ System) with the intention of identifying the one with maximal recovery rate and profiling success. DNA was extracted using aforementioned four methods from 70 cigarette butts collected from sites across Lebanon. DNA was quantified by qPCR using TaqMan Quantifiler Kit on an Applied Biosystems 7300 SDS instrument and genotypes were obtained using the PowerPlex® 21 kit on an Applied Biosystems 3130 Genetic Analyser. The findings of this work showed that DNA extraction with Chelex-100 + PK is preferred to the other three methods when seeking both, a high yield and the generation of maximal numbers of full profiles. The Chelex-100 + PK method is simple, cost effective, and therefore suitable for routine cigarette butts case studies.

Assessing population substructure in the Lebanese population: A population study using data on 23 autosomal short tandem repeats.

BACKGROUND: Understanding the genetic substructure of a population is essential for proper forensic genetic analysis. The Lebanese population has a high rate of endogamous and consanguineous marriages and is segregated based on religious belongings. However, no genetic population studies have been performed up to date to estimate the degree of genetic substructure and inbreeding coefficients. METHODS: The present study analyzed a compendium of 23 autosomal STRs typed in 1400 individuals belonging to the seven major Lebanese religious subcommunities. Inbreeding coefficients such as F statistics were estimated. RESULTS: Results showed a Fst (theta) value of 0.002, indicating a low genetic subdivision within the Lebanese population. CONCLUSION: This study aimed at assessing the genetic substructure of the Lebanese population by analyzing 1400 Lebanese citizens' samples using 23 STR markers. F statistics were computed to evaluate the degree of genetic substructure. Results showed a Fst value of 0.002, indicating a low genetic subdivision within the Lebanese population.

A mixed DNA profile controversy revisited.

Semaan et al. (J Forensic Res, 2020, 11, 453) discuss a mock case "where eight different individuals [P1 through P8 ] could not be excluded in a mixed DNA analysis. Even though … expert DNA mixture analysis software was used." Two of these are the true donors. The LRs reported are incorrect due to the incorrect entry of propositions into LRmix Studio. This forced the software to account for most of the alleles as drop-in, resulting in LRs 60-70 orders of magnitude larger than expected. P1 , P2 , P4 , P5 , and P8 can be manually excluded using peak heights. This has relevance when using LRmix which does not use peak heights. We extend the work using the same two reference genotypes who were the true contributors as Semaan et al. (J Forensic Res, 2020, 11, 453). We simulate three two-donor mixtures with peak heights using these two genotypes and analyze using STRmix™. For the simulated 1:1 mixture, one of the non-donors' LRs supported him being a contributor when no conditioning was used. When considered in combination with any other potential donors (i.e., with conditioning), this non-donor was correctly eliminated. For the 3:1 mixture, all results correctly supported that the non-donors were not contributors. The low-template 4:1 mixture LRs with no conditioning showed support for all eight profiles as donors. However, the results from pair-wise conditioning showed that only the two ground truth donors had LRs supporting that they were contributors to the mixture. We recommend the use of peak heights and conditioning profiles, as this allows better sensitivity and specificity even when the persons share many alleles.