IMPORTANCESevere coronavirus disease 2019 (COVID-19) can occur in younger, predominantly male, patients without preexisting medical conditions. Some individuals may have primary immunodeficiencies that predispose to severe infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).OBJECTIVE To explore the presence of genetic variants associated with primary immunodeficiencies among young patients with COVID-19. DESIGN, SETTING, AND PARTICIPANTSCase series of pairs of brothers without medical history meeting the selection criteria of young (age <35 years) brother pairs admitted to the intensive care unit (ICU) due to severe COVID-19. Four men from 2 unrelated families were admitted to the ICUs of 4 hospitals in the Netherlands between March 23 and April 12, 2020. The final date of follow-up was May 16, 2020. Available family members were included for genetic variant segregation analysis and as controls for functional experiments.EXPOSURE Severe COVID-19. MAIN OUTCOME AND MEASURESResults of rapid clinical whole-exome sequencing, performed to identify a potential monogenic cause. Subsequently, basic genetic and immunological tests were performed in primary immune cells isolated from the patients and family members to characterize any immune defects. RESULTSThe 4 male patients had a mean age of 26 years (range, 21-32), with no history of major chronic disease. They were previously well before developing respiratory insufficiency due to severe COVID-19, requiring mechanical ventilation in the ICU. The mean duration of ventilatory support was 10 days (range, 9-11); the mean duration of ICU stay was 13 days (range, 10-16). One patient died. Rapid clinical whole-exome sequencing of the patients and segregation in available family members identified loss-of-function variants of the X-chromosomal TLR7. In members of family 1, a maternally inherited 4-nucleotide deletion was identified (c.2129_2132del; p.[Gln710Argfs*18]); the affected members of family 2 carried a missense variant (c. 2383G>T; p.[Val795Phe]). In primary peripheral blood mononuclear cells from the patients, downstream type I interferon (IFN) signaling was transcriptionally downregulated, as measured by significantly decreased mRNA expression of IRF7, IFNB1, and ISG15 on stimulation with the TLR7 agonist imiquimod as compared with family members and controls. The production of IFN-γ, a type II IFN, was decreased in patients in response to stimulation with imiquimod. CONCLUSIONS AND RELEVANCEIn this case series of 4 young male patients with severe COVID-19, rare putative loss-of-function variants of X-chromosomal TLR7 were identified that were associated with impaired type I and II IFN responses. These preliminary findings provide insights into the pathogenesis of COVID-19.

The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing repetitive regions, phasing of alleles and distinguishing highly homologous genomic regions. These limitations may significantly contribute to the diagnostic gap in patients with genetic disorders who have undergone standard NGS, like whole exome or even genome sequencing. Now, the emerging long-read sequencing (LRS) technologies may offer improvements in the characterization of genetic variation and regions that are difficult to assess with the prevailing NGS approaches. LRS has so far mainly been used to investigate genetic disorders with previously known or strongly suspected disease loci. While these targeted approaches already show the potential of LRS, it remains to be seen whether LRS technologies can soon enable true whole genome sequencing routinely. Ultimately, this could allow the de novo assembly of individual whole genomes used as a generic test for genetic disorders. In this article, we summarize the current LRS-based research on human genetic disorders and discuss the potential of these technologies to facilitate the next major advancements in medical genetics.

Comparative LDH secretion, Ext_data_figure2.ep a, Assessment of Candida induced cell death of PBMCs after 24 hours Extended Data Fig. 2.Extended Data Fig. 3 Relative C. auris induced ROS production and heatsensitivity of the cell wall components responsible for the C. auris induced cytokine production. Ext_data_figure3.ep sa, Neutrophil ROS release after 1-hour stimulation without (RPMI; negative control) or with heat-killed C. albicans, C. auris strains or zymosan (positive control), depicted in relative light units (RLU) either as time-course (left) or as area under the curve (AUC, right), n=9. b, PBMC ROS release after 1-hour stimulation without (RPMI; negative control) or with heat-killed C. albicans, C. auris strains or zymosan (positive control), depicted in RLU either as time-course (left) or as AUC (right), n=6. c, TNF-α, IL-6, IL-1β, and IL-1Ra levels in the supernatant of PBMCs after stimulation without (RPMI; negative control) or with heat-killed C. albicans and C. auris from all five geographical clades for 24 hours, n=8. d, PBMC production of cytokines IFN-γ (n=10; n=7 for C. auris 10051895), IL-10 (n=6), IL-17 (n=6), and IL-22 (n=14; n=6 for C. auris 10051893; n=11 for C. auris 10051895) after stimulation without (RPMI; negative control) or with heat-killed C. albicans and C. auris for 7 days. Graphs represent mean ± SEM, data are pooled from at least two independent experiments. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p = 0.001, a-b Time curves (left panels) were assessed for statistical differences between C. auris strains and C. albicans by a two-way ANOVA, Area Under curve (AUC) means (right panels) were compared using the two-sided Wilcoxon signed rank test, c-d twosided Wilcoxon matched pairs signed-rank test comparing respective C. auris strains with C. albicans as control or reference species. Data used to make this figure can be found in Source Data Extended Data Fig. 3.Extended Data Fig. 4 Transcriptional changes induced by purified cell wall components and their respective exposure on C. albicans and C. auris Ext_data_figure4.ep s . a, Heatmap displaying the Log 2 Fold change (color scale) of the top 50 DEG of C. albicans live, for both Candida species and their cell wall components, β-glucan and mannan, at 4 hour (left panel) and 24 hours (right panel). b, Flow cytometry plot based on forward scatter component (FSC) and side scatter component (SSC), demonstrating C. surface. auris strains are slightly smaller and of higher complexity than C. albicans. c, Flow cytometry-based comparison of cell wall components of C. albicans and C. auris strains. Mean fluorescent intensity (MFI) of thimerosal-fixed Candida cells stained for Fc-Dectin-1, a marker for β-glucan (left), and ConA, a marker for mannans (right). Graphs represent mean ± SEM of the 3 means, each performed with three replicates in three independent measurements, * p < 0.05, Kruskall Wallis test with two-sided Dunn's multiple comparison test was performed comparing the respective C. auris strains with the two C. albicans refere...

Functional genomics approaches can overcome limitations-such as the lack of identification of robust targets and poor clinical efficacy-that hamper cancer drug development. Here we performed genome-scale CRISPR-Cas9 screens in 324 human cancer cell lines from 30 cancer types and developed a data-driven framework to prioritize candidates for cancer therapeutics. We integrated cell fitness effects with genomic biomarkers and target tractability for drug development to systematically prioritize new targets in defined tissues and genotypes. We verified one of our most promising dependencies, the Werner syndrome ATP-dependent helicase, as a synthetic lethal target in tumours from multiple cancer types with microsatellite instability. Our analysis provides a resource of cancer dependencies, generates a framework to prioritize cancer drug targets and suggests specific new targets. The principles described in this study can inform the initial stages of drug development by contributing to a new, diverse and more effective portfolio of cancer drug targets.