Characterization of greater middle eastern genetic variation for enhanced disease gene discovery

The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia1-3, has resulted in an elevated burden of recessive disease4. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized ‘genetic purging’. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics

COVID-19: molecular and serological detection methods

Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.</jats:p

Characterization of enhancer fragments in Drosophila robo2

Receptor proteins of the Roundabout (Robo) family regulate axon guidance decisions during nervous system development. Among the three Drosophila robo family genes (robo1, robo2 and robo3), robo2 displays a dynamic expression pattern and regulates multiple axon guidance outcomes, including preventing midline crossing in some axons, promoting midline crossing in others, forming lateral longitudinal axon pathways, and regulating motor axon guidance. The identity and location of enhancer elements regulating robo2’s complex and dynamic expression pattern in different neural cell types are unknown. Here, we characterize a set of 17 transgenic lines expressing GAL4 under the control of DNA sequences derived from noncoding regions in and around robo2, to identify enhancers controlling specific aspects of robo2 expression in the embryonic ventral nerve cord. We identify individual fragments that confer expression in specific cell types where robo2 is known to function, including early pioneer neurons, midline glia and lateral longitudinal neurons. Our results indicate that robo2’s dynamic expression pattern is specified by a combination of enhancer elements that are active in different subsets of cells. We show that robo2’s expression in lateral longitudinal axons represents two genetically separable subsets of neurons, and compare their axon projections with each other and with Fasciclin II (FasII), a commonly used marker of longitudinal axon pathways. In addition, we provide a general description of each fragment’s expression in embryonic tissues outside of the nervous system, to serve as a resource for other researchers interested in robo2 expression and its functional roles outside the central nervous system

Comprehensive Analysis of Systemic Immunosuppression (SIS) Duration after Allogeneic Hematopoietic Stem Cell Transplant: Risk Score Model Provides Stratification of Patients According to Probability of SIS Discontinuation

Abstract BACKGROUND: Systemic immunosuppression (SIS) is the standard treatment for significant acute and chronic graft versus host disease (GVHD) after allogeneic hematopoietic cell transplantation (HCT). Previous studies have shown that 30-70% of patients require immunosuppressive treatment for GVHD for more than 2 years. Prolonged SIS increases the risk of infections, recurrence of malignancy and multi-organ complications including endocrine dysfunction, hypertension, myopathy and ocular complications. This study aimed to evaluate the predictive factors associated with increased likelihood of SIS discontinuation from 3 different time points: from the day of transplant in all patients, from the day of treatment of acute GVHD (aGVHD) and from the day of treatment of chronic GVHD (cGVHD). METHODS: A retrospective review was conducted in 674 consecutive patients who underwent allogeneic HCT at Princess Margaret Cancer Centre from 2004 to 2013. Analyses were done using cumulative incidence method considering competing risks for SIS discontinuation. The incidence of SIS discontinuation was calculated from 3 time points: from the day of transplant in all patients, from the day of treatment of aGVHD and from the day of treatment of cGVHD. Univariate and multivariate analyses were conducted to identify the predictive factors for SIS discontinuation and hazard ratio (HR) with 95% confidence interval (CI) was calculated using Fine-Gray model. Risk score models were generated based on the results from the multivariate analysis with respect to the 3 time points. Each predictive factor was weighted according to the HR. Risk score models are presented in the Table below: for each risk score model, the patients were divided into 3 risk groups based on the scores. The cumulative incidence of SIS discontinuation was compared according to the risk group for each risk score model as shown in the Figure below. RESULTS: With a median follow-up duration of 3.5 years, the probability of SIS cessation at 3 years was 30.7% (27.0-34.5%) in all patients (n=674), 25.4% (21.2-29.8%) in patients treated for aGVHD (n=457) and 34.6% (29.1-40.3%) in patients treated for cGVHD (n=347). Multivariate analysis confirmed the following predictive factors associated with increased likelihood of SIS discontinuation. In all patients (n=654): age &gt;50 years (vs ≤ 50 yrs; p&lt;0.001, HR 1.83), bone marrow (BM) as a source of stem cells (vs peripheral blood [PBSC]; p=0.002, HR 1.78), T-cell depletion (vs no T-cell depletion; p&lt;0.001, HR 1.98), matched related donor (vs others; p&lt;0.001, HR 1.81) and HLA match (vs partially mismatched HLA; p=0.026, HR 2.58). In patients treated for aGVHD (n=457): age&gt;50 (vs ≤ 50 yrs; p&lt;0.001, HR 1.77), BM (vs PBSC; p&lt;0.001, HR 2.38), matched related donor (vs others; p=0.025, HR 1.55) and aGVHD grade 0-2 (vs grade 3/4 aGVHD; p&lt;0.001, HR 1.77). In patients treated for cGVHD (n=347): age &gt;50 (vs ≤ 50 yrs; p=0.002, HR 1.83), BM (vs PBSC; p=0.004, HR 2.13), Grade 0-2 aGVHD (vs grade 3/4 aGVHD; p=0.003, HR 2.32), cGVHD grade (mild vs moderate vs severe; p&lt;0.001, HR 2.02) and classical subtype (vs overlap syndrome; p=0.028, HR 1.52). The risk score model stratified the patients into low, intermediate and high risk groups: for all patients, SIS discontinuation at 3 years was 52.5% (37.9-65.2%), 30.7% (26.5-35.0%) and 17% (8.6-27.7%) respectively (p&lt;0.0001); in patients treated for aGVHD, SIS discontinuation at 3 years was 70.6% (39.0-87.9%), 29.2% (24.0-34.5%) and 2.7% (0.5-8.6%) respectively (p&lt;0.001); in patients treated for cGVHD, SIS discontinuation at 3 years was 62.8% (48.4-74.3%), 36.4% (29.8-43.0%) and 5.7% (1.0-17.1%) respectively (p&lt;0.001). CONCLUSIONS: Older age, bone marrow as a source of stem cells, T-cell depletion, matched related donor and a full matched donor increase the likelihood of discontinuation of SIS after allogeneic HCT. In addition, the severity of aGVHD and cGVHD significantly affects the chance of SIS discontinuation. The proposed risk score stratifies patients into well-defined groups according to the chance of SIS discontinuation. Further studies in a larger number of patients are strongly recommended to validate this finding. Prospective validation is also warranted to confirm the utility of the risk score as a clinical tool for estimation of likelihood of SIS discontinuation in patients after allogeneic HCT. Figure. Figure. Disclosures Lipton: Pfizer: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; BMS: Consultancy, Honoraria, Research Funding. </jats:sec

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Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.A

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old