BRCA1 and BRCA2 5' noncoding region variants identified in breast cancer patients alter promoter activity and protein binding.

The widespread use of next generation sequencing for clinical testing is detecting an escalating number of variants in noncoding regions of the genome. The clinical significance of the majority of these variants is currently unknown, which presents a significant clinical challenge. We have screened over 6,000 early-onset and/or familial breast cancer (BC) cases collected by the ENIGMA consortium for sequence variants in the 5' noncoding regions of BC susceptibility genes BRCA1 and BRCA2, and identified 141 rare variants with global minor allele frequency < 0.01, 76 of which have not been reported previously. Bioinformatic analysis identified a set of 21 variants most likely to impact transcriptional regulation, and luciferase reporter assays detected altered promoter activity for four of these variants. Electrophoretic mobility shift assays demonstrated that three of these altered the binding of proteins to the respective BRCA1 or BRCA2 promoter regions, including NFYA binding to BRCA1:c.-287C>T and PAX5 binding to BRCA2:c.-296C>T. Clinical classification of variants affecting promoter activity, using existing prediction models, found no evidence to suggest that these variants confer a high risk of disease. Further studies are required to determine if such variation may be associated with a moderate or low risk of BC.

Expanding probe repertoire and improving reproducibility in human genomic hybridization.

Diagnostic DNA hybridization relies on probes composed of single copy (sc) genomic sequences. Sc sequences in probe design ensure high specificity and avoid cross-hybridization to other regions of the genome, which could lead to ambiguous results that are difficult to interpret. We examine how the distribution and composition of repetitive sequences in the genome affects sc probe performance. A divide and conquer algorithm was implemented to design sc probes. With this approach, sc probes can include divergent repetitive elements, which hybridize to unique genomic targets under higher stringency experimental conditions. Genome-wide custom probe sets were created for fluorescent in situ hybridization (FISH) and microarray genomic hybridization. The scFISH probes were developed for detection of copy number changes within small tumour suppressor genes and oncogenes. The microarrays demonstrated increased reproducibility by eliminating cross-hybridization to repetitive sequences adjacent to probe targets. The genome-wide microarrays exhibited lower median coefficients of variation (17.8%) for two HapMap family trios. The coefficients of variations of commercial probes within 300 nt of a repetitive element were 48.3% higher than the nearest custom probe. Furthermore, the custom microarray called a chromosome 15q11.2q13 deletion more consistently. This method for sc probe design increases probe coverage for FISH and lowers variability in genomic microarrays.

Prediction of mutant mRNA splice isoforms by information theory-based exon definition.

Mutations that affect mRNA splicing often produce multiple mRNA isoforms, resulting in complex molecular phenotypes. Definition of an exon and its inclusion in mature mRNA relies on joint recognition of both acceptor and donor splice sites. This study predicts cryptic and exon-skipping isoforms in mRNA produced by splicing mutations from the combined information contents (R(i), which measures binding-site strength, in bits) and distribution of the splice sites defining these exons. The total information content of an exon (R(i),total) is the sum of the R(i) values of its acceptor and donor splice sites, adjusted for the self-information of the distance separating these sites, that is, the gap surprisal. Differences between total information contents of an exon (ΔR(i,total)) are predictive of the relative abundance of these exons in distinct processed mRNAs. Constraints on splice site and exon selection are used to eliminate nonconforming and poorly expressed isoforms. Molecular phenotypes are computed by the Automated Splice Site and Exon Definition Analysis (http://splice.uwo.ca) server. Predictions of splicing mutations were highly concordant (85.2%; n = 61) with published expression data. In silico exon definition analysis will contribute to streamlining assessment of abnormal and normal splice isoforms resulting from mutations.

Radiation exposure determination in a secure, cloud-based online environment.

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI on dedicated computer hardware. Image processing and selection, calibration curve generation, and dose estimation of 9 test samples completed in < 2 days. ADCI Online has the capacity to alleviate analytic bottlenecks in intermediate-to-large radiation incidents. Multiple cloned software instances configured on different cloud environments accelerated dose estimation to within clinically relevant time frames.

Improved radiation expression profiling in blood by sequential application of sensitive and specific gene signatures.

PURPOSE: Combinations of expressed genes can discriminate radiation-exposed from normal control blood samples by machine learning (ML) based signatures (with 8-20% misclassification rates). These signatures can quantify therapeutically relevant as well as accidental radiation exposures. The prodromal symptoms of acute radiation syndrome (ARS) overlap those present in influenza and dengue fever infections. Surprisingly, these human radiation signatures misclassified gene expression profiles of virally infected samples as false positive exposures. The present study investigates these and other confounders, and then mitigates their impact on signature accuracy. METHODS: This study investigated recall by previous and novel radiation signatures independently derived from multiple Gene Expression Omnibus datasets on common and rare non-neoplastic blood disorders and blood-borne infections (thromboembolism, S. aureus bacteremia, malaria, sickle cell disease, polycythemia vera, and aplastic anemia). Normalized expression levels of signature genes are used as input to ML-based classifiers to predict radiation exposure in other hematological conditions. RESULTS: Except for aplastic anemia, these blood-borne disorders modify the normal baseline expression values of genes present in radiation signatures, leading to false-positive misclassification of radiation exposures in 8-54% of individuals. Shared changes, predominantly in DNA damage response and apoptosis-related gene transcripts in radiation and confounding hematological conditions, compromise the utility of these signatures for radiation assessment. These confounding conditions (sickle cell disease, thrombosis, S. aureus bacteremia, malaria) induce neutrophil extracellular traps, initiated by chromatin decondensation, DNA damage response and fragmentation followed by programmed cell death or extrusion of DNA fragments. Riboviral infections (e.g. influenza or dengue fever) have been proposed to bind and deplete host RNA binding proteins, inducing R-loops in chromatin. R-loops that collide with incoming replication forks can result in incompletely repaired DNA damage, inducing apoptosis and releasing mature virus. To mitigate the effects of confounders, we evaluated predicted radiation-positive samples with novel gene expression signatures derived from radiation-responsive transcripts encoding secreted blood plasma proteins whose expression levels are unperturbed by these conditions. CONCLUSIONS: This approach identifies and eliminates misclassified samples with underlying hematological or infectious conditions, leaving only samples with true radiation exposures. Diagnostic accuracy is significantly improved by selecting genes that maximize both sensitivity and specificity in the appropriate tissue using combinations of the best signatures for each of these classes of signatures.

Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada.

Introduction: This study aimed to produce community-level geo-spatial mapping of confirmed COVID-19 cases in Ontario Canada in near real-time to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals. Methods: COVID-19 cases and locations were curated for geostatistical analyses from March 2020 through June 2021, corresponding to the first, second, and third waves of infections. Daily cases were aggregated according to designated forward sortation area (FSA), and postal codes (PC) in municipal regions Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, and Windsor/Essex county. Hotspots were identified with area-to-area tests including Getis-Ord Gi*, Global Moran's I spatial autocorrelation, and Local Moran's I asymmetric clustering and outlier analyses. Case counts were also interpolated across geographic regions by Empirical Bayesian Kriging, which localizes high concentrations of COVID-19 positive tests, independent of FSA or PC boundaries. The Geostatistical Disease Epidemiology Toolbox, which is freely-available software, automates the identification of these regions and produces digital maps for public health professionals to assist in pandemic management of contact tracing and distribution of other resources.  Results: This study provided indicators in real-time of likely, community-level disease transmission through innovative geospatial analyses of COVID-19 incidence data. Municipal and provincial results were validated by comparisons with known outbreaks at long-term care and other high density residences and on farms. PC-level analyses revealed hotspots at higher geospatial resolution than public reports of FSAs, and often sooner. Results of different tests and kriging were compared to determine consistency among hotspot assignments. Concurrent or consecutive hotspots in close proximity suggested potential community transmission of COVID-19 from cluster and outlier analysis of neighboring PCs and by kriging. Results were also stratified by population based-categories (sex, age, and presence/absence of comorbidities). Conclusions: Earlier recognition of hotspots could reduce public health burdens of COVID-19 and expedite contact tracing.

A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections.

Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N2), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expression of viral sequences is expected to increasingly sequester RBPs - SRSF1 and RNPS1. Ordinarily, RBPs bound to nascent host transcripts prevents their annealing to complementary DNA. Their depletion induces destabilizing R-loops. Chromosomal breakage occurs when an excess of unresolved R-loops collide with incoming replication forks, overwhelming the DNA repair machinery. We estimated stoichiometry of inhibition of RBPs in host nuclear RNA by counting competing binding sites in replicating viral genomes and host RNA. Results: Host RBP binding sites are frequent and conserved among different strains of RNA viral genomes. Similar binding motifs of SRSF1 and RNPS1 explain why DNA damage resulting from SRSF1 depletion is complemented by expression of RNPS1. Clustering of strong RBP binding sites coincides with the distribution of RNA-DNA hybridization sites across the genome. SARS-CoV-2 replication is estimated to require 32.5-41.8 hours to effectively compete for binding of an equal proportion of SRSF1 binding sites in host encoded nuclear RNAs. Significant changes in expression of transcripts encoding DNA repair and apoptotic proteins were found in an analysis of influenza A and Dengue-infected cells in some individuals. Conclusions: R-loop-induced apoptosis indirectly resulting from viral replication could release significant quantities of membrane-associated virions into neighboring alveoli. These could infect adjacent pneumocytes and other tissues, rapidly compromising lung function, causing multiorgan system failure and other described symptoms.

Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing.

Splice isoform structure and abundance can be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts. When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing. Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. Splicing changes for known SNP genotypes were confirmed in HapMap lymphoblastoid cell lines with gene expression microarrays and custom designed q-RT-PCR or TaqMan assays. The majority of these SNPs (15 of 22) as well as an independent set of 24 variants were then subjected to RNAseq analysis using the ValidSpliceMut web beacon (http://validsplicemut.cytognomix.com), which is based on data from the Cancer Genome Atlas and International Cancer Genome Consortium. SNPs from different genes analyzed with gene expression microarray and q-RT-PCR exhibited significant changes in affected splice site use. Thirteen SNPs directly affected exon inclusion and 10 altered cryptic site use. Homozygous SNP genotypes resulting in stronger splice sites exhibited higher levels of processed mRNA than alleles associated with weaker sites. Four SNPs exhibited variable expression among individuals with the same genotypes, masking statistically significant expression differences between alleles. Genome-wide information theory and expression analyses (RNAseq) in tumor exomes and genomes confirmed splicing effects for 7 of the HapMap SNP and 14 SNPs identified from tumor genomes. q-RT-PCR resolved rare splice isoforms with read abundance too low for statistical significance in ValidSpliceMut. Nevertheless, the web-beacon provides evidence of unanticipated splicing outcomes, for example, intron retention due to compromised recognition of constitutive splice sites. Thus, ValidSpliceMut and q-RT-PCR represent complementary resources for identification of allele-specific, alternative splicing.

Meeting radiation dosimetry capacity requirements of population-scale exposures by geostatistical sampling.

BACKGROUND: Accurate radiation dose estimates are critical for determining eligibility for therapies by timely triaging of exposed individuals after large-scale radiation events. However, the universal assessment of a large population subjected to a nuclear spill incident or detonation is not feasible. Even with high-throughput dosimetry analysis, test volumes far exceed the capacities of first responders to measure radiation exposures directly, or to acquire and process samples for follow-on biodosimetry testing. AIM: To significantly reduce data acquisition and processing requirements for triaging of treatment-eligible exposures in population-scale radiation incidents. METHODS: Physical radiation plumes modelled nuclear detonation scenarios of simulated exposures at 22 US locations. Models assumed only location of the epicenter and historical, prevailing wind directions/speeds. The spatial boundaries of graduated radiation exposures were determined by targeted, multistep geostatistical analysis of small population samples. Initially, locations proximate to these sites were randomly sampled (generally 0.1% of population). Empirical Bayesian kriging established radiation dose contour levels circumscribing these sites. Densification of each plume identified critical locations for additional sampling. After repeated kriging and densification, overlapping grids between each pair of contours of successive plumes were compared based on their diagonal Bray-Curtis distances and root-mean-square deviations, which provided criteria (<10% difference) to discontinue sampling. RESULTS/CONCLUSIONS: We modeled 30 scenarios, including 22 urban/high-density and 2 rural/low-density scenarios under various weather conditions. Multiple (3-10) rounds of sampling and kriging were required for the dosimetry maps to converge, requiring between 58 and 347 samples for different scenarios. On average, 70±10% of locations where populations are expected to receive an exposure ≥2Gy were identified. Under sub-optimal sampling conditions, the number of iterations and samples were increased, and accuracy was reduced. Geostatistical mapping limits the number of required dose assessments, the time required, and radiation exposure to first responders. Geostatistical analysis will expedite triaging of acute radiation exposure in population-scale nuclear events.

Estimating partial-body ionizing radiation exposure by automated cytogenetic biodosimetry.

PURPOSE: Inhomogeneous exposures to ionizing radiation can be detected and quantified with the dicentric chromosome assay (DCA) of metaphase cells. Complete automation of interpretation of the DCA for whole-body irradiation has significantly improved throughput without compromising accuracy, however, low levels of residual false positive dicentric chromosomes (DCs) have confounded its application for partial-body exposure determination. MATERIALS AND METHODS: We describe a method of estimating and correcting for false positive DCs in digitally processed images of metaphase cells. Nearly all DCs detected in unirradiated calibration samples are introduced by digital image processing. DC frequencies of irradiated calibration samples and those exposed to unknown radiation levels are corrected subtracting this false positive fraction from each. In partial-body exposures, the fraction of cells exposed, and radiation dose can be quantified after applying this modification of the contaminated Poisson method. RESULTS: Dose estimates of three partially irradiated samples diverged 0.2-2.5 Gy from physical doses and irradiated cell fractions deviated by 2.3%-15.8% from the known levels. Synthetic partial-body samples comprised of unirradiated and 3 Gy samples from 4 laboratories were correctly discriminated as inhomogeneous by multiple criteria. Root mean squared errors of these dose estimates ranged from 0.52 to 1.14 Gy2 and from 8.1 to 33.3%2 for the fraction of cells irradiated. CONCLUSIONS: Automated DCA can differentiate whole- from partial-body radiation exposures and provides timely quantification of estimated whole-body equivalent dose.

RADIATION DOSE ESTIMATION BY COMPLETELY AUTOMATED INTERPRETATION OF THE DICENTRIC CHROMOSOME ASSAY.

Accuracy of the automated dicentric chromosome (DC) assay relies on metaphase image selection. This study validates a software framework to find the best image selection models that mitigate inter-sample variability. Evaluation methods to determine model quality include the Poisson goodness-of-fit of DC distributions for each sample, residuals after calibration curve fitting and leave-one-out dose estimation errors. The process iteratively searches a pool of selection model candidates by modifying statistical and filter cut-offs to rank the best candidates according to their respective evaluation scores. Evaluation scores minimize the sum of squared errors relative to the actual radiation dose of the calibration samples. For one laboratory, the minimum score for the curve fit residual method was 0.0475 Gy2, compared to 1.1975 Gy2 without image selection. Application of optimal selection models using samples of unknown exposure produced estimated doses within 0.5 Gy of physical dose. Model optimization standardizes image selection among samples and provides relief from manual DC scoring, improving accuracy and consistency of dose estimation.

Pan-cancer repository of validated natural and cryptic mRNA splicing mutations.

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. An algorithm was developed to classify variants into splicing molecular phenotypes that integrates germline heterozygosity, degree of information change and impact on expression. The classification thresholds were calibrated against the ClinVar clinical database phenotypic assignments. Variants are partitioned into allele-specific alternative splicing, likely aberrant and aberrant splicing phenotypes. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon "Validated Splicing Mutations" either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website. The website provides additional information, such as a visual representation of supporting RNAseq results, gene expression in the corresponding normal tissues, and splicing molecular phenotypes.

Validation of predicted mRNA splicing mutations using high-throughput transcriptome data.

Interpretation of variants present in complete genomes or exomes reveals numerous sequence changes, only a fraction of which are likely to be pathogenic. Mutations have been traditionally inferred from allele frequencies and inheritance patterns in such data. Variants predicted to alter mRNA splicing can be validated by manual inspection of transcriptome sequencing data, however this approach is intractable for large datasets. These abnormal mRNA splicing patterns are characterized by reads demonstrating either exon skipping, cryptic splice site use, and high levels of intron inclusion, or combinations of these properties. We present, Veridical, an in silico method for the automatic validation of DNA sequencing variants that alter mRNA splicing. Veridical performs statistically valid comparisons of the normalized read counts of abnormal RNA species in mutant versus non-mutant tissues. This leverages large numbers of control samples to corroborate the consequences of predicted splicing variants in complete genomes and exomes.

Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.

Information theory-based methods have been shown to be sensitive and specific for predicting and quantifying the effects of non-coding mutations in Mendelian diseases. We present the Shannon pipeline software for genome-scale mutation analysis and provide evidence that the software predicts variants affecting mRNA splicing. Individual information contents (in bits) of reference and variant splice sites are compared and significant differences are annotated and prioritized. The software has been implemented for CLC-Bio Genomics platform. Annotation indicates the context of novel mutations as well as common and rare SNPs with splicing effects. Potential natural and cryptic mRNA splicing variants are identified, and null mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines (U2OS, U251 and A431), which were supported by expression analyses. After filtering, tractable numbers of potentially deleterious variants are predicted by the software, suitable for further laboratory investigation. In these cell lines, novel functional variants comprised 6-17 inactivating mutations, 1-5 leaky mutations and 6-13 cryptic splicing mutations. Predicted effects were validated by RNA-seq analysis of the three aforementioned cancer cell lines, and expression microarray analysis of SNPs in HapMap cell lines.