Relevant Variants Research Articles

Molecular and genetic characteristic of some Omicron variants of the SARS-CoV-2 virus and prospects for vaccine prevention of COVID-19

Over a period of 5 years, the emergent SARS-CoV-2 virus underwent a process of adaptation to the human body as a species host and acquired evolutionary changes that bring it closer to routine respiratory viruses in terms of epidemic and clinical characteristics. The work presents systematized information on the molecular genetics and antigenic characteristics of variants of the SARS-CoV-2 virus, categories of their potential danger with a detailed description of spike mutations of current sub-variants of the Omicron virus (Variants of Interest (VOI) - BA.2.86, JN.1; Variants under Monitoring (VUM) - JN.1.7, JN.1.18, KP.2, KP.3, KP.3.1.1, LB.1 and XEC) and its de-escalated subvariants. The effect of some mutations or their combinations on the properties of the virus is characterized. The current trends in the prevalence of the priority Omicron VOI and VUM variants of the SARS-CoV-2 virus in the world are estimated and the trend of a rapid increase in the intensity of circulation of the KP.3.1.1 and XEC variants against the background of a decrease in the circulation of other variants in the fall of 2024 is shown. The issue of immune imprinting for COVID-19 associated with both natural infection and vaccination depending on vaccine strain variants is considered. The characterization of the FDA-recommended COVID-19 vaccines for the 2024/2025 season is provided, taking into account the manufacturing technology, vaccine strains, and purpose. Based on the analysis of the current data on the effectiveness of vaccines in relation to the risks of infection, the severity of the course of the disease and mortality, the need to vaccinate individuals only from risk groups, that is, according to medical and age indications, is emphasized in order to reduce the severity of the clinical course of the disease and mortality. However, the composition of these vaccines must correspond to the epidemically relevant variants of the SARS-CoV-2 virus.

The role of genetic sequencing in the diagnostic work-up for chronic immune thrombocytopenia.

Immune Thrombocytopenia (ITP) is a heterogenous autoimmune disorder diagnosed by excluding other conditions. Misdiagnosis of primary ITP occurs in patients with inherited thrombocytopenia and primary immunodeficiency syndromes. This study investigates whether genetic testing for inherited thrombocytopenia or primary immunodeficiency can enhance diagnostic accuracy in ITP, and guide treatment strategies. We performed whole genome sequencing or targeted panel sequencing on peripheral blood samples in a cohort of 80 participants with chronic ITP, utilising the ThromboGenomics (TG) Panel (n=72) and the Genomics of Rare Immune Disorders (GRID) panel (n=50) consisting of genes known to cause bleeding and platelet disorders (BPDG) or primary immunodeficiency syndromes (PIDG) respectively. A replication cohort of 73 patients underwent clinical genomics testing with either the R90 (BPDG, n=35) or R15 (PIDG, n=50) NHS Genomics panels. Known pathogenic or likely pathogenic, disease-causing, variants were identified in 9 patients in the first cohort (11% CI:5-20); 7 patients (10% CI:4-19) in BPDG and 2 patients (4% CI:1-14) in PIDG. Additionally, 26 patients (32.5%) carried variants of uncertain significance (VUS). In the replication cohort, 8% (CI:2-20) and 9% (CI:2- 23) of patients had a pathogenic variant identified on the R15 (PIDG) or R90 panel (BPDG) respectively. The findings impacted clinical management such as avoidance of immunosuppression (ANKRD26, GP1BB, ETV6, TUBB1, ITGB3) and eligibility for allogeneic stem cell transplantation (UNC13D). Our findings demonstrate that genomic sequencing identifies diagnostically relevant variants in patients with chronic ITP. Identification of these variants can guide treatment decisions and improve patient outcome.

MRNA vaccines with RBD mutations have broad-spectrum activity against SARS-CoV-2 variants in mice

The emergence of SARS-CoV-2 variants with defined mutations that enhance pathogenicity or facilitate immune evasion has resulted in a continual decline in the protective efficacy of existing vaccines. Therefore, there is a pressing need for a vaccine capable of combating future variants. In this study, we designed new mRNA vaccines, BSCoV05 and BSCoV06, and generated point mutations in the receptor-binding domain (RBD) of the original Wuhan strain to increase their broad-spectrum antiviral activity. Additionally, we used the BA.1 RBD as a control. Both vaccines elicited a robust immune response in BALB/c and K18-hACE2 mice, generating high levels of specific binding antibodies against the BA.2 RBD. Moreover, all three vaccines induced neutralizing antibodies against the prototype viral strain and relevant variants, including the Alpha and Beta strains and the Omicron variants BA.1, BA.2, BA.5, XBB.1.5, XBB.1.16, EG.5.1, and EG.5.1.1, with BSCoV06 demonstrating broader neutralizing antibody activity. Both BSCoV05 and BSCoV06 also elicited a cellular immune response. After the challenge, both BSCoV05 and BSCOV06 provided protection against the EG.5.1 strain in both mouse strains. Therefore, these two vaccines merit further evaluation in nonhuman primates, and this vaccine design strategy should be explored for its potential application in combating future SARS-CoV-2 variants, offering valuable insights into broad-spectrum vaccine development.

The experience of "at-risk" status for familial frontotemporal dementia (fFTD) and its impact on reproductive decision-making: A qualitative study.

Familial frontotemporal dementia (fFTD) is an autosomal dominant heritable form of FTD, onsetting in mid-life, characterized by behavioral and personality changes. Children of an affected parent are at 50% risk of inheriting the relevant fFTD gene variant and developing FTD. Genetic testing means a growing group of people are aware of or considering learning their risk status. This knowledge, combined with witnessing parents' symptoms, has implications for reproduction. This study explores attitudes and approaches to reproductive decision-making among those at risk for fFTD. Thirteen qualitative interviews were conducted with at-risk individuals, including parents and non-parents, and analyzed using Thematic Analysis to explore experiences of at-risk relatives of people with symptomatic FTD, attitudes toward reproductive decision-making, and, among parents, influences of genetic risk status on parenting. The themes identified were: (1) Fear of repetition of own experience with symptomatic relatives; (2) Approaches to mitigating repetition; (3) Responses to genetic risk in reproductive decision-making; (4) Accounting for timing in reproductive decision-making; (5) Challenges of disclosing genetic risk to children; (6) Other mitigating factors in reproductive decision-making. Findings highlight the key role of previous experiences with symptomatic relatives in shaping attitudes toward genetic risk status and approaches to managing it in reproductive decision-making. Findings highlight a need for responsive genetic counseling focused on exploring options alongside providing information and signposting to practical legal and financial support. Future research should specifically compare experiences in fFTD with experiences in other heritable neurodegenerative disorders and explore reproductive decision-making for couples where one partner is at risk of fFTD.

CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs).

The Genetics of Neurodevelopmental Disorders Lab in Padua provided a new intellectual disability (ID) Panel challenge for computational methods to predict patient phenotypes and their causal variants in the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6). Eight research teams submitted a total of 30 models to predict phenotypes based on the sequences of 74 genes (VCF format) in 415 pediatric patients affected by Neurodevelopmental Disorders (NDDs). NDDs are clinically and genetically heterogeneous conditions, with onset in infant age. Here, we assess the ability and accuracy of computational methods to predict comorbid phenotypes based on clinical features described in each patient and their causal variants. We also evaluated predictions for possible genetic causes in patients without a clear genetic diagnosis. Like the previous ID Panel challenge in CAGI5, seven clinical features (ID, ASD, ataxia, epilepsy, microcephaly, macrocephaly, hypotonia), and variants (Pathogenic/Likely Pathogenic, Variants of Uncertain Significance and Risk Factors) were provided. The phenotypic traits and variant data of 150 patients from the CAGI5 ID Panel Challenge were provided as training set for predictors. The CAGI6 challenge confirms CAGI5 results that predicting phenotypes from gene panel data is highly challenging, with AUC values close to random, and no method able to predict relevant variants with both high accuracy and precision. However, a significant improvement is noted for the best method, with recall increasing from 66% to 82%. Several groups also successfully predicted difficult-to-detect variants, emphasizing the importance of variants initially excluded by the Padua NDD Lab.

Quantitative Analysis of Pseudogene-Associated Errors During Germline Variant Calling.

A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent a significant challenge in genome analysis due to their high sequence similarity to the parent genes and their frequent absence in the reference genome. This homology can lead to errors in variant identification, as sequences derived from processed pseudogenes can be incorrectly assigned to parental genes, complicating correct variant calling. In this study, we quantified the occurrence of variant calling errors associated with pseudogenes, generated by the most popular germline variant callers, namely GATK-HC, DRAGEN, and DeepVariant, when analysing 30x human whole-genome sequencing data (n = 13,307). The results show that the presence of pseudogenes can interfere with variant calling, leading to false positive identifications of potentially clinically relevant variants. Compared to other approaches, DeepVariant was the most effective in correcting these errors.

HiFi long-read genomes for difficult-to-detect, clinically relevant variants.

Clinical short-read exome and genome sequencing approaches have positively impacted diagnostic testing for rare diseases. Yet, technical limitations associated with short reads challenge their use for the detection of disease-associated variation in complex regions of the genome. Long-read sequencing (LRS) technologies may overcome these challenges, potentially qualifying as a first-tier test for all rare diseases. To test this hypothesis, we performed LRS (30× high-fidelity [HiFi] genomes) for 100 samples with 145 known clinically relevant germline variants that are challenging to detect using short-read sequencing and necessitate a broad range of complementary test modalities in diagnostic laboratories. We show that relevant variant callers readily re-identified the majority of variants (120/145, 83%), including ∼90% of structural variants, SNVs/insertions or deletions (indels) in homologous sequences, and expansions of short tandem repeats. Another 10% (n= 14) was visually apparent in the data but not automatically detected. Our analyses also identified systematic challenges for the remaining 7% (n= 11) of variants, such as the detection of AG-rich repeat expansions. Titration analysis showed that 90% of all automatically called variants could also be identified using 15-fold coverage. Long-read genomes thus identified 93% of challenging pathogenic variants from our dataset. Even with reduced coverage, the vast majority of variants remained detectable, possibly enhancing cost-effective diagnostic implementation. Most importantly, we show the potential to use a single technology to accurately identify all types of clinically relevant variants.

Deep learning–based assessment of missense variants in the COG4 gene presented with bilateral congenital cataract

ObjectiveWe compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and ThermoMPNN for the first time.Methods and analysisThe sequences...

Analytical Validation of the Labcorp Plasma Complete Test, a Cell-Free DNA Comprehensive Genomic Profiling Tool for Precision Oncology.

To help guide treatment decisions and clinical trial matching, tumor genomic profiling is an essential precision oncology tool. Liquid biopsy, a complementary approach to tissue testing, can assess tumor-specific DNA alterations circulating in the blood. Labcorp Plasma Complete is a next-generation sequencing, cell-free DNA comprehensive genomic profiling test that identifies clinically relevant somatic variants across 521 genes in advanced and metastatic solid cancers. Over 800 unique sequencing libraries across 27 cancer types were evaluated to establish analytical sensitivity, specificity, accuracy, and precision, reproducibility, and repeatability. Sensitivity was verified for each variant type, with a median variant allele frequency (VAF) of 1.25% and 1.27% for panel-wide single-nucleotide variants and insertions/deletions (sequence variants), respectively, with <1% VAF sensitivity observed for clinically actionable variants, 1.72-fold for copy number amplifications, 0.48% fusion read fraction for translocations, and 0.47% sequence mutation VAF for microsatellite instability-high. Analytical specificity was 99.9999% for single-nucleotide variants and 100% for all other variant types. Precision, reproducibility, and repeatability resulted in 94.9% average positive agreement and 99.9% average negative agreement for sequence variants and 100% average positive agreement and average negative agreement for copy number amplifications, translocations, and microsatellite instability. Orthogonal assays were used to assess accuracy, demonstrating an aggregate analytical concordance of 97.4% positive percentage agreement and >99.99997% negative percentage agreement for all variants. Overall, the test demonstrates high sensitivity, specificity, accuracy, and robustness to enable informed clinical decision-making.

Detection of clinically relevant variants in the TP53 gene below 10% allelic frequency: A multicenter study by ERIC, the European Research Initiative on CLL.

In chronic lymphocytic leukemia, the reliability of next-generation sequencing (NGS) to detect TP53 variants ≤10% allelic frequency (low-VAF) is debated. We tested the ability to detect 23 such variants in 41 different laboratories using their NGS method of choice. The sensitivity was 85.6%, 94.5%, and 94.8% at 1%, 2%, and 3% VAF cut-off, respectively. While only one false positive (FP) result was reported at >2% VAF, it was more challenging to distinguish true variants <2% VAF from background noise (37 FPs reported by 9 laboratories). The impact of low-VAF variants on time-to-second-treatment (TTST) and overall survival (OS) was investigated in a series of 1092 patients. Among patients not treated with targeted agents, patients with low-VAF TP53 variants had shorter TTST and OS versus wt-TP53 patients, and the relative risk of second-line treatment or death increased continuously with increasing VAF. Targeted therapy in ≥2 line diminished the difference in OS between patients with low-VAF TP53 variants and wt-TP53 patients, while patients with high-VAF TP53 variants had inferior OS compared to wild type-TP53 cases. Altogether, NGS-based approaches are technically capable of detecting low-VAF variants. No strict threshold can be suggested from a technical standpoint, laboratories reporting TP53 mutations should participate in a standardized validation set-up. Finally, whereas low-VAF variants affected outcomes in patients receiving chemoimmunotherapy, their impact on those treated with novel therapies remains undetermined. Our results pave the way for the harmonized and accurate TP53 assessment, which is indispensable for elucidating the role of TP53 mutations in targeted treatment.

A TAF11 variant contributes to non-syndromic cleft lip only through modulating neural crest cell migration.

The NC_000006.12: g.34887814C>G variant in TAF11 was identified as a potential functional variant in a Chinese pedigree including two non-syndromic cleft lip only (NSCLO) cases. Applying Chromatin Immunoprecipitation (ChIP), Electrophoretic mobility shift and super-shift assays, we found that the mutant G allele recruited more STAT1 and STAT3, and increased the expression of TAF11. RNA sequencing, GO and KEGG pathway enrichment, ChIP and dual-luciferase reporter assays revealed that TAF11 downregulated CDH1 and CTNND1 in the cell adhesion pathway by binding to their promoter regions and inhibiting transcriptional activities. Alcian blue staining, time-lapse photography, whole-mount in situ hybridization, phospho-Histone H3 immunofluorescence and TUNEL assays indicated that TAF11 and taf11 overexpression (TAF11OE and taf11OE, respectively) contributed to disturbed migration of cranial neural crest cells and abnormal craniofacial development, as well as increased death and deformity rates in zebrafish. In conclusion, a functionally relevant TAF11 variant, affecting cell migration via modulating CDH1 and CTNND1, was associated with etiology of NSCLO.

Catalogue of inherited autosomal recessive disorders found amongst the Roma population of Europe.

The Roma population are an endogamous, genetically isolated, minority population who migrated from North-Western India to Europe from the 10th Century throughout the Byzantine period and continues to the present day. Approximately 10-12 million Romani people reside in segregated settlements in Europe, and smaller populations live in North America and China. In addition to the endogamy, they also practice consanguinity. This has resulted in a higher frequency of rare autosomal recessive disorders some of which are unique to the Roma population. Some disorders result from founder variants whilst others are private variants, occurring within one nuclear family. Most are found as homozygous variants but compound heterozygosity is seen in a number of conditions. Clinicians and scientists with experience in managing and diagnosing rare diseases in this population in Ireland, Romania and Greece have developed a comprehensive catalogue of autosomal recessive inherited disorders found in the Roma population. Our aim is that this catalogue will aid rapid diagnosis and highlight the differential diagnoses to consider in challenging cases. We performed a detailed literature search to identify relevant publications and disease variants described in patients whose ethnicity was described as Roma. In addition, we interrogated data from local clinicians and colleagues in Ireland and Romania to collect additional unpublished variants which have yet to be reported in the medical literature. Where possible, we have mapped these disorders back to their European country of origin. Furthermore, we searched the variants allele frequencies on ClinVar. We analysed exome data from New Delhi, India to trace any of these founder variants back their origins. We identified 90 distinct autosomal recessive disorders, manifesting as 91 distinct phenotypes and 111 pathogenic disease variants. These include both published (n=91) and unpublished (n=20) findings identified in the Roma population in Europe. The Indian exome data revealed that only 12/111 variants were identified. We have assembled a catalogue of inherited autosomal recessive disorders and 111 pathogenic variants found in the Roma population. We hope that this will assist the medical and scientific community to make prompt diagnoses and consider adaptation of a targeted genetic approach to facilitate timely and cost-effective diagnoses in this population.

IDENTIFICATION OF CLINICALLY RELEVANT GENE VARIANTS IN COLON ADENOCARCINOMA SAMPLES OF UKRAINIAN PATIENTS USING A COMPREHENSIVE CANCER PANEL: A PILOT STUDY.

We have studied 20 samples of Ukrainian patients with colorectal adenocarcinomas of various differentiation grades. To identify the clinically relevant gene variants, the CCP data were filtered using the Franklin by Genoox database. A total of 79 clinically relevant gene variant alterations (SNVs, INDELs) were found in 28 of 409 genes. The largest number of mutations was found in 3 genes, APC, TP53, and KRAS (16, 14, and 8, accordingly). We revealed 4 variants in PTEN and SMAD4, 3 variants in CHEK2, ERBB2, and PIK3CA genes, and 2 variants in AKT1, ATM, DST, IDH1, and TCF12. Mutations for 7 genes, KRAS, TP53, CHEK2, PTEN, AKT1, APC, and SMAD4, were found in more than 1 tumor tissue sample. Tier 1-2 gene variants rate was about 50% of all genetic variants. The therapeutic significance was found in more than 55% of mutations. Additionally, 11 novel genetic mutations in 9 genes have been identified, including G6PD, APC, DST, SINE1, SMAD2, and FLCN. These data suggest a high level of clinical relevance of the NGS CCP approach. Further confirmation on a larger number of samples and using a deeper analysis by other approaches is required.

Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.

Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of the SVs present in any one individual. Long-read sequencing (LRS) enhances our ability to detect disease-associated and functionally relevant structural variants (SVs); however, its application in large-scale genomic studies has been limited by challenges in sample preparation and high costs. Here, we leverage a new scalable wet-lab protocol and computational pipeline for whole-genome Oxford Nanopore Technologies sequencing and apply it to neurologically normal control samples from the North American Brain Expression Consortium (NABEC) (European ancestry) and Human Brain Collection Core (HBCC) (African or African admixed ancestry) cohorts. Through this work, we present a publicly available long-read resource from 351 human brain samples (median N50: 27 Kbp and at an average depth of ∼40x genome coverage). We discover approximately 234,905 SVs and produce locally phased assemblies that cover 95% of all protein-coding genes in GRCh38. Utilizing matched expression datasets for these samples, we apply quantitative trait locus (QTL) analyses and identify SVs that impact gene expression in post-mortem frontal cortex brain tissue. Further, we determine haplotype- specific methylation signatures at millions of CpGs and, with this data, identify cis-acting SVs. In summary, these results highlight that large-scale LRS can identify complex regulatory mechanisms in the brain that were inaccessible using previous approaches. We believe this new resource provides a critical step toward understanding the biological effects of genetic variation in the human brain.

Analyses of Human Genetic Data to Identify Clinically Relevant Domains of Neuroligins.

Background/Objectives: Neuroligins (NLGNs) are postsynaptic adhesion molecules critical for neuronal development that are highly associated with autism spectrum disorder (ASD). Here, we provide an overview of the literature on NLGN rare variants. In addition, we introduce a new approach to analyze human variation within NLGN genes to identify sensitive regions that have an increased frequency of ASD-associated variants to better understand NLGN function. Methods: To identify critical protein subdomains within the NLGN gene family, we developed an algorithm that assesses tolerance to missense mutations in human genetic variation by comparing clinical variants from ClinVar to reference variants from gnomAD. This approach provides tolerance values to subdomains within the protein. Results: Our algorithm identified several critical regions that were conserved across multiple NLGN isoforms. Importantly, this approach also identified a previously reported cluster of pathogenic variants in NLGN4X (also conserved in NLGN1 and NLGN3) as well as a region around the highly characterized NLGN3 R451C ASD-associated mutation. Additionally, we highlighted other, as of yet, uncharacterized regions enriched with mutations. Conclusions: The systematic analysis of NLGN ASD-associated variants compared to variants identified in the unaffected population (gnomAD) reveals conserved domains in NLGN isoforms that are tolerant to variation or are enriched in clinically relevant variants. Examination of databases also allows for predictions of the presumed tolerance to loss of an allele. The use of the algorithm we developed effectively allowed the evaluation of subdomains of NLGNs and can be used to examine other ASD-associated genes.

Microdissection of Distinct Morphological Regions Within Uveal Melanomas Identifies Novel Drug Targets.

Background/Objectives: Uveal melanomas (UMs) are rare but often deadly malignancies that urgently require viable treatment options. UMs often exhibit tumour heterogeneity, with macroscopic and microscopic differences in morphology between different regions of the same tumour. However, to date, the clinical significance of this and how it may help guide personalised therapy have not been realised. Methods: Using targeted DNA and RNA sequencing of a small case series of large, high-risk primary UMs, we explored whether morphologically distinct regions of the same tumour were associated with distinct molecular profiles. Results: In four of the seven tumours analysed, we detected different sets of genetic variants following the separate analysis of microdissected melanotic and amelanotic regions of the same tumour. These included a MET exon 14 skipping RNA transcript that predicts sensitivity to crizotinib and variants in other genes that are important in active clinical trials for patients with UM and advanced solid tumours. The integration of TCGA data also identified recurrent mutational events in genes that were not previously implicated in UM development (FANCA, SLX4, BRCA2, and ATRX). Conclusions: Our findings show that the molecular analysis of spatially separated and morphologically distinct regions of the same tumour may yield additional, therapeutically relevant genetic variants in uveal melanomas and have implications for the future molecular testing of UMs to identify targeted therapies.

Analysis of a Chinese pedigree with female infertility due to WEE2 gene c.495del homozygous frameshifting variant induced fertilization disorder

To explore the genetic basis for a patient with repeated fertilization failure during assisted reproductive therapy, and to identify the source and mode of mutation. A couple treated at the Center for Reproductive Medicine, Gansu Provincial Maternal and Child Health Care Hospital in January 2024 for infertility with incomplete left tube obstruction was selected as the study subject. Relevant clinical data was collected. The couple was subjected to whole exome sequencing (WES), and the candidate variant was verified by Sanger sequencing of their family members and bioinformatic analysis. WES has identified a homozygous c.495del frameshifting mutation of the WEE2 gene in the female partner, whilst no relevant variant was suspected in the male partner. The elder brother of the female partner was homozygous for the above variant, while her parents, maternal and paternal aunts, uncle, grandmother, and grandmother were heterozygous for it. Based on the guidelines from the American College of Medical Genetics and Genomics, above variant was rated to be pathogenic. The homozygous c.495del frameshifting mutation of the WEE2 gene probably underlay the oocyte fertilization disorder in this couple, which has conformed to an autosomal recessive inheritance.

MIP4IBD: An Easy and Rapid Genotyping-by-Sequencing Assay for the Inflammatory Bowel Diseases Risk Loci.

Inflammatory bowel diseases (IBD) are polygenic, with many genetic variants contributing to disease risk. Knowing the genotype of specific variants or calculating a combined genetic risk score benefits translational and functional research. To address this, we developed MIP4IBD, a flexible and cost-effective genotyping-by-sequencing assay using molecular inversion probes (MIPs). The assay targets 463 IBD risk variants, and 77 additional relevant variants. Molecular inversion probes capture and library preparation were optimized using 15 IBD DNA samples, comparing genotypes with immunochip. A custom GitHub pipeline was created for data processing, performance testing, and genotype calling. The final design was validated on a larger scale (149 IBD patients, 104 non-IBD controls, and 3 external cell lines), incorporating post hoc quality control criteria. The assay achieved a 3.5-day turnaround time at €15 per sample with optimal sample throughput, demonstrating a 92.6% success rate in variant capture and genotype concordance rates of 99.3% and 99.6% with Infinium Global Screening Array24 BeadChip and WGS, respectively. A downstream application involved the calculation of a weighted IBD polygenic risk score (PRS), which was significantly higher in IBD patients than controls (mean 0.42 vs -0.49, P = 1.95E-11). Individuals in the highest PRS quartile had a 15.7-fold (95% CI: 6.5-38.3) risk of developing IBD and an earlier age of onset (26 vs 37 years, P = 0.02), compared to the lowest quartile. MIP4IBD is a validated, scalable genotyping assay targeting IBD risk loci, with an integrated bioinformatics pipeline from sequencing data to genotypes and PRS calculation. Its cost-effectiveness and flexibility for additional variants make it particularly appealing for translational and clinical applications.

Expression quantitative trait loci influence DNA damage-induced apoptosis in cancer

BackgroundGenomic instability and evading apoptosis are two fundamental hallmarks of cancer and closely linked to DNA damage response (DDR). By analyzing expression quantitative trait loci (eQTL) upon cell stimulation (called exposure eQTL (e2QTL)) it is possible to identify context specific gene regulatory variants and connect them to oncological diseases based on genome-wide association studies (GWAS).ResultsWe isolate CD8+ T cells from 461 healthy donors and stimulate them with high doses of 5 different carcinogens to identify regulatory mechanisms of DNA damage-induced apoptosis. Across all stimuli, we find 5,373 genes to be differentially expressed, with 85% to 99% of these genes being suppressed. While upregulated genes are specific to distinct stimuli, downregulated genes are shared across conditions but exhibit enrichment in biological processes depending on the DNA damage type. Analysis of eQTL reveals 654 regulated genes across conditions. Among them, 47 genes are significant e2QTL, representing a fraction of 4% to 5% per stimulus. To unveil disease relevant genetic variants, we compare eQTL and e2QTL with GWAS risk variants. We identify gene regulatory variants for KLF2, PIP4K2A, GPR160, RPS18, ARL17B and XBP1 that represent risk variants for oncological diseases.ConclusionOur study highlights the relevance of gene regulatory variants influencing DNA damage-induced apoptosis in cancer. The results provide new insights in cellular mechanisms and corresponding genes contributing to inter-individual effects in cancer development.

Genomic correlates of response and resistance to the irreversible FGFR1-4 inhibitor futibatinib based on biopsy and circulating tumor DNA profiling.

Futibatinib is the only covalent inhibitor of FGFR1-4 to gain regulatory approval in oncology. Here, we present genomic analyses of tissue biopsies and circulating tumor DNA (ctDNA) from patients with one of nearly 20 tumor types treated with futibatinib in the phase I/II FOENIX study. Eligible patients included those with ctDNA samples collected per protocol at baseline and/or progression on futibatinib in the phase Ib portion of the study for FGF/FGFR-altered advanced solid tumors or the phase II portion of the study for FGFR2 fusion/rearrangement-positive cholangiocarcinoma. Assessments included analytical concordance between tumor and ctDNA analyses for detection of FGFR alterations, association of ctDNA-detected co-occurring genomic alterations with response to futibatinib, and determination of patterns of acquired resistance following progression on futibatinib. Among 300 patients treated with futibatinib, 226 were eligible for this analysis, including 139 (62%) with cholangiocarcinoma. Among patients with known FGFR2 fusions/rearrangements, FGFR1 fusions, FGFR3 fusions, or FGFR2 amplifications per tissue analysis, detection rates in ctDNA for these aberrations were 84%, 0%, 11%, and 59%, respectively. Objective response rates on futibatinib were not significantly different between patients with TP53 altered versus unaltered solid tumors; progression-free survival was reduced in patients with CDKN2B altered versus unaltered cholangiocarcinoma (median, 4.8 versus 11.0 months; P=0.03). Acquired resistance to futibatinib was frequently polyclonal and driven by an array of mutations within the relevant FGFR kinase domain, predominantly V565L, V565F, and N550K variants. In this largest and most systematic analysis of acquired resistance to an FGFR inhibitor from prospective clinical trials, emergence of secondary FGFR2 kinase domain mutations was observed in most patients receiving clinical benefit to futibatinib. ctDNA analysis shows clinically relevant potential as a noninvasive method for assessing genomic profiles, identifying patients who may benefit from FGFR inhibitor treatment, and exploring acquired resistance mechanisms.