Structural Variants Research Articles

Genomic complexity and clinical significance of the RCCX locus.

Nearly identical, repetitive elements in the genome contribute to the variability in genetic inheritance patterns, particularly in regions like the RCCX locus, where such repeats can lead to structural variations. In addition, during the formation of gametes as a result of meiosis, variants of loci with repetitive elements that do not code for the required proteins may occur. As a result, an individual with certain genetic rearrangements in this region may have an increased risk of developing a congenital disorder, particularly in cases where the non-functional allele is inherited dominantly. At the same time, there is still no routine or generally recognized diagnostic method to determine the sequence of the repetitive fragments. The functionally important RCCX locus consists of such repetitive fragments. The available knowledge about the genomic variants of the RCCX locus is fragmented, as there is no standardized method to determine its structure. It should be noted that in some structural variants of the RCCX locus, the sequence of protein-coding genes is disrupted, leading to the development of diseases such as congenital adrenal hyperplasia (CAH). Although genetic testing is generally accepted as a gold standard for CAH diagnosis, there are a myriad of strategies on which exact methods to use and in which order. The reason for this inconsistency lies in the complexity of the RCCX locus and the fact that each patient or carrier may have a highly individualized mutation or combination thereof. In this review, we have discussed all known methods that can be used to study the structure of the RCCX locus. As a result, optimal approaches are proposed for the diagnosis of the most common disease caused by lesions in the RCCX-CAH due to CYP21A2 deficiency.

Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions

Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.

Resolution of ring chromosomes, Robertsonian translocations, and complex structural variants from long-read sequencing and telomere-to-telomere assembly.

Delineation of structural variants (SVs) at sequence resolution in highly repetitive genomic regions has long been intractable. The sequence properties, origins, and functional effects of classes of genomic rearrangements such as ring chromosomes and Robertsonian translocations thus remain unknown. To resolve these complex structures, we leveraged several recent milestones in the field, including (1) the emergence of long-read sequencing, (2) the gapless telomere-to-telomere (T2T) assembly, and (3) a tool (BigClipper) to discover chromosomal rearrangements from long reads. We applied these technologies across 13 cases with ring chromosomes, Robertsonian translocations, and complex SVs that were unresolved by short reads, followed by validation using optical genome mapping (OGM). Our analyses resolved 10 of 13 cases, including a Robertsonian translocation and all ring chromosomes. Multiple breakpoints were localized to genomic regions previously recalcitrant to sequencing such as acrocentric p-arms, ribosomal DNA arrays, and telomeric repeats, and involved complex structures such as a deletion-inversion and interchromosomal dispersed duplications. We further performed methylation profiling from long-read data to discover phased differential methylation in a gene promoter proximal to a ring fusion, suggesting a long-range position effect (LRPE) with heterochromatin spreading. Breakpoint sequences suggested mechanisms of SV formation such as microhomology-mediated and non-homologous end-joining, as well as non-allelic homologous recombination. These methods provide some of the first glimpses into the sequence resolution of Robertsonian translocations and illuminate the structural diversity of ring chromosomes and complex chromosomal rearrangements with implications for genome biology, prediction of LRPEs from integrated multi-omics technologies, and molecular diagnostics in rare disease cases.

Landscape of structural variants reveals insights for local adaptations in the Asian corn borer

Capturing the genetic diversity of different wild populations is crucial for unraveling the mechanisms of adaptation and establishing links between genome evolution and local adaptation. The Asian corn borer (ACB) moth has undergone natural selection during its adaptative evolution. However, structural variants (SVs), which play significant roles in these adaptation processes, have not been previously identified. Here, we constructed a multi-assembly graph pan-genome to highlight the importance of SVs in local adaptation. Our analysis revealed that the graph pan-genome contained 176.60 Mb (∼37.33%) of unique sequences. Subsequently, we performed an analysis of expression quantitative trait loci (QTLs) to explore the impact of SVs on gene expression regulation. Notably, through QTL mapping analysis, we identified the FTZ-F1 gene as a potential candidate gene associated with the traits of larval development rate. In sum, we explored the impact of SVs on the local adaptation of pests, therefore facilitating accelerated pest management strategies.

Prenatal risk assessment of Xp21.1 duplication involving the DMD gene by optical genome mapping.

Structural variants (SVs) of unknown significance are great challenges for prenatal risk assessment, especially when involving dose-sensitive genes such as DMD The pathogenicities of 5'-terminal DMD duplications in the database remain controversial. Four prenatal cases with Xp21.1 duplications were identified by routine prenatal genomic testing, encompassing the 5'-UTR to exons 1-2 in family 1 and family 2, and to exons 1-9 in family 3. The duplication in family 4 was non-contiguous covering the 5'-UTR to exon 1 and exons 3-7. All were traced to unaffected males in the family pedigrees. A new genome-wide approach of optical genome mapping was performed in families 1, 2, and 3 to delineate the breakpoints and orientation of the duplicated fragments. The extra copies were tandemly inserted into the upstream of DMD, preserving the integrity of ORF from the second copy. The pathogenicities were thus reclassified as likely benign. Our data highlight the importance of structural delineation by optical genome mapping in prenatal risk assessment of incidentally identified SVs involving DMD and other similar large dose-sensitive genes.

An evaluation of genetic predisposition to congenital anomalies and pediatric cancer supports KAT6B as a novel neuroblastoma susceptibility gene.

PurposeWhile congenital anomalies are among the strongest risk factors for developing pediatric cancer, the genetic underpinnings remain unclear. Therefore, we evaluated germline susceptibility in children with congenital anomalies and cancer. MethodsThrough the Genetic Overlap Between Anomalies and Cancer in Kids (GOBACK) Study, we recruited 47 participants with anomalies and cancer, along with their biological families. Genome sequencing was performed, focusing on single nucleotide variants, indels, and structural variants. Pathogenic or likely pathogenic (P/LP) variants were identified by American College of Medical Genetics and Genomics (ACMG) classification. ResultsWe identified P/LP variants in 23.4% (11 of 47) of participants. These variants encompassed: 1) Four genes associated with both anomalies and cancer (WT1, USP9X, PTPN1, and LZTR1), 2) Two established cancer predisposition genes (TP53 in 2 participants and PAX5), and 3) Four genes that are associated with anomalies (MMUT, FBN1, COL3A1, and KAT6B). We further investigated the role of KAT6B on neuroblastoma in a gene-based analysis from 409 neuroblastoma cases and 952 controls. This analysis demonstrated a significant enrichment of rare, predicted deleterious variants (p = 0.017), with odds ratios ranging from 2 to 4 based on the conditions we applied. ConclusionThis study demonstrates a molecular diagnostic yield of 23.4% in participants with both anomalies and cancer. Additionally, the findings further implicate the role of KAT6B as a novel neuroblastoma predisposition gene.

Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis

The population structure of the malaria parasite Plasmodium falciparum can reveal underlying adaptive evolutionary processes. Selective pressures to maintain complex genetic backgrounds can encourage inbreeding, producing distinct parasite clusters identifiable by population structure analyses. We analysed population structure in 3783 Pfalciparum genomes from 21countries across Africa, provided by the MalariaGEN Pf7 dataset. We used Principal Coordinate Analysis to cluster parasites, identity by descent (IBD) methods to identify genomic regions shared by cluster members, and linkage analyses to establish their co-inheritance patterns. Structural variants were reconstructed by de novo assembly and verified by long-read sequencing. We identified a strongly differentiated cluster of parasites, named AF1, comprising 47 (1·2%) of 3783samples analysed, distributed over 13countries across Africa, at locations over 7000km apart. Members of this cluster share a complex genetic background, consisting of up to 23loci harbouring many highly differentiated variants, rarely observed outside the cluster. IBD analyses revealed common ancestry at these loci, irrespective of sampling location. Outside the shared loci, however, AF1 members appear to outbreed with sympatric parasites. The AF1 differentiated variants comprise structural variations, including a gene conversion involving the dblmsp and dblmsp2 genes, and numerous single nucleotide polymorphisms. Several of the genes harbouring these mutations are functionally related, often involved in interactions with red blood cells including invasion, egress, and erythrocyte antigen export. We propose that AF1 parasites have adapted to some unidentified evolutionary niche, probably involving interactions with host erythrocytes. This adaptation involves a complex compendium of interacting variants that are rarely observed in Africa, which remains mostly intact despite recombination events. The term cryptotype was used to describe a common background interspersed with genomic regions of local origin. Bill & Melinda Gates Foundation.

Carrier frequency and molecular basis of hemoglobinopathies among blood donors in eastern Morocco: Implications for blood donation and genetic diagnosis

BackgroundHemoglobinopathies represent the most commonly inherited autosomal recessive blood disorders in the world. The aim of this study was to determine the carrier frequency and molecular basis of hemoglobinopathies among blood donors in eastern Morocco. This is the first study of its kind for this country. MethodsHealthy blood donors of the BRO Biobank were included in this study. Blood samples were analyzed using an automatic blood cell analyzer for complete blood counts. Hemoglobin fractions were analyzed by capillary electrophoresis and serum ferritin was measured on a chemical and immunological analyzer. Suspected hemoglobinopathy carriers were further characterized by Sanger sequencing, Gap PCR and PCR-RFLP. ResultsThe study involved 2013 blood donors, of whom 1063 were male and 950 were female (sex ratio male-to-female of 1.1). The median age of these donors was 35 years. The overall carrier frequency of hemoglobinopathies was 1.84 %, with β-thalassemia carriers being the most prevalent (0.65 %) followed by HbAC (0.55 %), α-thalassemia carriers (0.30 %), HbAS (0.1 %), HbAG-Philadelphia (0.1 %), HbAD-Ouled Rabah (0.05 %) and HbAO-Arab (0.05 %). Additionally, novel β-thalassemia variants (C6(−G) and −83(A > G)) and a structural variant (Hb D-Ouled Rabah) were discovered for the first time in Morocco. ConclusionsThis study provided the first report on carrier frequency and molecular basis of hemoglobinopathies among healthy donors in Morocco. These findings are valuable for the implementation of carrier screening and genetic diagnosis for hemoglobinopathies. Furthermore, these results justify the need to introduce pre-donation screening for hemoglobinopathy carriers in Morocco, particularly in areas with a high prevalence of carriers to enhance the overall quality of the national blood supply.

INDELible impact: How structural variants drive virulence and resistance

Tuberculosis remains a formidable global health challenge, with Mycobacterium tuberculosis responsible formillions of cases and deaths annually. In this issue of Cell Host & Microbe, Worakitchanon etal. present a method to identify structural variants in Mtb and explore associations with bacterial phenotypes such as virulence and antibiotic resistance.

Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions.

Normal tissues adjacent to the tumor (NATs) may harbor early breast carcinogenesis events driven by field cancerization. Although previous studies have characterized copy-number (CN) and transcriptomic alterations, the evolutionary history of NATs in breast cancer (BC) remains poorly characterized. Utilizing whole-genome sequencing (WGS), methylation profiling, and RNA sequencing (RNA-seq), we analyzed paired germline, NATs, and tumor samples from 43 individuals with BC in Hong Kong (HK). We found that single-nucleotide variants (SNVs) were common in NATs, with one-third of NAT samples exhibiting SNVs in driver genes, many of which were present in paired tumor samples. The most frequently mutated genes in both tumor and NAT samples were PIK3CA, TP53, GATA3, and AKT1. In contrast, large-scale aberrations such as somatic CN alterations (SCNAs) and structural variants (SVs) were rarely detected in NAT samples. We generated phylogenetic trees to investigate the evolutionary history of paired NAT and tumor samples. They could be categorized into tumor only, shared, and multiple-tree groups, the last of which is concordant with non-genetic field cancerization. These groups exhibited distinct genomic and epigenomic characteristics in both NAT and tumor samples.Specifically, NAT samples in the shared-tree group showed higher number of mutations, while NAT samples belonging to the multiple-tree group showed a less inflammatory tumor microenvironment (TME), characterized by a higher proportion ofregulatory Tcells (Tregs) and lower presence of CD14 cell populations. In summary, our findings highlight the diverse evolutionary history in BC NAT/tumor pairs and the impact of field cancerization and TME in shaping the genomic evolutionary historyof tumors.

Genomic and transcriptomic profiling of inflammatory breast cancer reveals distinct molecular characteristics to non-inflammatory breast cancers.

Inflammatory breast cancer (IBC), a rare and highly aggressive form of breast cancer, accounts for 10% of breast cancer-related deaths. Previous omics studies of IBC have focused solely on one of genomics or transcriptomics and did not discover common differences that could distinguish IBC from non-IBC. Seventeen IBC patients and five non-IBC patients as well as additional thirty-three Asian breast cancer samples from TCGA-BRCA were included for the study. We performed whole-exon sequencing (WES) to investigate different somatic genomic alterations, copy number variants, and large structural variants between IBC and non-IBC. Bulk RNA sequencing (RNA-seq) was performed to examine the differentially expressed genes, pathway enrichment, and gene fusions. WES and RNA-seq data were further investigated in combination to discover genes that were dysregulated in both genomics and transcriptomics. Copy number variation analysis identified 10 cytobands that showed higher frequency in IBC. Structural variation analysis showed more frequent deletions in IBC. Pathway enrichment and immune infiltration analysis indicated increased immune activation in IBC samples. Gene fusions including CTSC-RAB38 were found to be more common in IBC. We demonstrated more commonly dysregulated RAS pathway in IBC according to both WES and RNA-seq. Inhibitors targeting RAS signaling and its downstream pathways were predicted to possess promising effects in IBC treatment. We discovered differences unique in Asian women that could potentially explain IBC etiology and presented RAS signaling pathway as a potential therapeutic target in IBC treatment.

Synthesis of Na3WH9 and Na3ReH8 Ternary Hydrides at High Pressures.

The Na-W-H and Na-Re-H ternary systems were studied in a diamond anvil cell through X-ray diffraction and Raman spectroscopy, supported by density functional theory and molecular dynamics calculations. Na3WH9 can be synthesized above 7.8 GPa and 1400 K, remaining stable between at least 0.1 and 42.1 GPa. The rhenium analogue Na3ReH8 can form at 10.1 GPa upon laser heating, being stable between at least 0.3 and 32.5 GPa. Na3WH9 and Na3ReH8 host [WH9]3- and [ReH8]3- anions, respectively, forming homoleptic 18-electron complexes in both cases. Both ternary hydrides show similar structural types and pressure dependent phase transitions. At the highest pressures they adopt a distorted fcc Heusler structure (Na3WH9-II' and Na3ReH8-II') while upon decompression the structure symmetrizes becoming fcc between ∼6.4 and 10 GPa for Na3WH9-II and at 17 GPa for Na3ReH8-II. On further pressure release, the fcc phases transform into variants of a (quasi-) hexagonal structure at ∼3 GPa, Na3WH9-I and Na3ReH8-I.

Cardiomyopathies in 100,000 genomes project: interval evaluation improves diagnostic yield and informs strategies for ongoing gene discovery

BackgroundCardiomyopathies are clinically important conditions, with a strong genetic component. National genomic initiatives such as 100,000 Genome Project (100KGP) provide opportunity to study these rare conditions at scale beyond conventional research studies.MethodsWe present the clinical and molecular characteristics of the 100KGP cohort, comparing paediatric and adult probands with diverse cardiomyopathies. We assessed the diagnostic yield and spectrum of genetic aetiologies across clinical presentations. We re-analysed existing genomic data using an updated analytical strategy (revised gene panels; unbiased analyses of de novo variants; and improved variant prioritisation strategies) to identify new causative variants in genetically unsolved children.ResultsWe identified 1918 individuals (1563 probands, 355 relatives) with cardiomyopathy (CM) in 100KGP. Probands, comprising 273 children and 1290 adults, were enrolled under > 55 different recruitment categories. Paediatric probands had higher rates of co-existing congenital heart disease (12%) compared to adults (0.9%). Diagnostic yield following 100KGP’s initial analysis was significantly higher for children (19%) than for adults (11%) with 11% of diagnoses overall made in genes not on the existing UK paediatric or syndromic CM panel. Our re-analysis of paediatric probands yields a potential diagnosis in 40%, identifying new probable or possible diagnoses in 49 previously unsolved paediatric cases. Structural and intronic variants accounted for 11% of all potential diagnoses in children while de novo variants were identified in 17%.Conclusions100KGP demonstrates the benefit of genome sequencing over a standalone panel in CM. Re-analysis of paediatric CM probands allowed a significant uplift in diagnostic yield, emphasising the importance of iterative re-evaluation in genomic studies. Despite these efforts, many children with CM remain without a genetic diagnosis, highlighting the need for better gene-disease relationship curation and ongoing data sharing. The 100KGP CM cohort is likely to be useful for further gene discovery, but heterogeneous ascertainment and key technical limitations must be understood and addressed.

Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing.

Rare or de novo structural variation, primarily in the form of copy number variants, is detected in 5%-10% of autism spectrum disorder (ASD) families. While complex structural variants involving duplications can generally be detected using microarray or short-read genome sequencing (GS), these methods frequently fail to characterize breakpoints at nucleotide resolution, requiring additional molecular methods for validation and fine-mapping. Here, we use Oxford Nanopore Technologies PromethION long-read GS to characterize complex genomic rearrangements (CGRs) involving large duplications that segregate with ASD in five families. In total, we investigated 13 CGR carriers and were able to resolve all breakpoint junctions at nucleotide resolution. While all breakpoints were identified, the precise genomic architecture of one rearrangement remained unresolved with three different potential structures. The findings in two families include potential fusion genes formed through duplication rearrangements, involving IL1RAPL1-DMD and SUPT16H-CHD8 In two of the families originating from the same geographical region, an identical rearrangement involving ANK2 was identified, which likely represents a founder variant. In addition, we analyze methylation status directly from the long-read data, allowing us to assess the activity of rearranged genes and regulatory regions. Investigation of methylation across the CGRs reveals aberrant methylation status in carriers across a rearrangement affecting the CREBBP locus. In aggregate, our results demonstrate the utility of nanopore sequencing to pinpoint CGRs associated with ASD in five unrelated families, and highlight the importance of a gene-centric description of disease-associated complex chromosomal rearrangements.

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data

Copy number variants (CNVs) are structural variants within the eukaryotic genome that vary among individuals of a species. These variants have been associated with different phenotypic traits, making them a valuable consideration as markers for designing breeding programmes. In this study, whole genome sequence data of 60 dromedary camel samples originating from the Arabian Peninsula were analyzed to construct a comprehensive dromedary CNV map. Utilizing four CNV callers employing read-depth, split-read and paired-end mapping approaches, a total of 37,519 CNV events (17,847 deletions and 19,672 duplications) were called on the dromedary autosomes. These CNV events were merged into 2,557 regions, categorized as 1,322 losses, 122 gains, and 1,113 “mixed regions” comprising both types. The cumulative size of the CNV regions amounted to 22.5 Mb, covering roughly 1.16% of the dromedary autosomes. Approximately 32% of the defined CNV regions (comprising 60% losses, 18% gains, and 0.27% mixed regions) were found in ≥ 90% of the dromedary samples, classifying them as prevalent regions. Genes with biological functions related to the different adaptive physiologies of dromedary camels, such as fertility, heat stress, musculoskeletal development, and fat metabolism, were overlapping with or in close proximity to ~ 68% of the defined CNV regions, demonstrating their potential role in dromedaries’ physiology. This study presents the first comprehensive CNV map of dromedary camels and builds on the present knowledge in understanding the genetic structure of this species.

K-mer analysis of long-read alignment pileups for structural variant genotyping.

Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. We benchmark kanpig against the latest SV benchmarks and show single-sample genotyping concordance of 82.1%, which is higher than existing genotypers averaging 66.3%. We explore kanpig's applicability to multi-sample projects by benchmarking project-level VCFs containing 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), achieving much higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single sample's 20x long-reads and can be run on PacBio or ONT long-reads.

Toxigenic Cyanobacteria and Microcystins in a Large Northern Oligotrophic Lake Onego, Russia

Toxigenic cyanobacteria and microcystins in the oligotrophic pelagic zone and mesotrophic bay of Lake Onego—the second largest lake in Europe—were found for the first time. Microscopic analysis revealed that Dolichospermum lemmermannii, D. circinale and D. spiroides dominated in bloom spots in the oligotrophic zone of the lake and D. flos-aquae and Microcystis aeruginosa OKin the eutrophic bay. The abundance of cyanobacteria in bloom spots is potentially hazardous for humans and animals. PCR-analysis showed that mcyA gene involved in microcystin biosynthesis was found in cyanobacteria of the genera Dolichospermum and Microcystis. Five structural variants of intracellular microcystins were detected in a trace amount using high-performance liquid chromatography–mass-spectrometry of high resolution. The most hazardous hepatotoxin, MC-LR, was found only in the eutrophic bay. In the present study, the reasons for the low cyanotoxin content in the phytoplankton dominated by Dolichospermum are discussed. The findings of our study make a significant contribution to the accumulation of facts which state that toxigenic cyanobacterial blooms can occur in large oligotrophic lakes.

Identification of novel 3D-genome altering and complex structural variants underlying retinitis pigmentosa type 17 through a multistep and high-throughput approach.

Autosomal dominant retinitis pigmentosa type 17 (adRP, type RP17) is caused by complex structural variants (SVs) affecting a locus on chromosome 17 (chr17q22). The SVs disrupt the 3D regulatory landscape by altering the topologically associating domain (TAD) structure of the locus, creating novel TAD structures (neo-TADs) and ectopic enhancer-gene contacts. Currently, screening for RP17-associated SVs is not included in routine diagnostics given the complexity of the variants and a lack of cost-effective detection methods. The aim of this study was to accurately detect novel RP17-SVs by establishing a systematic and efficient workflow. Genetically unexplained probands diagnosed with adRP (n = 509) from an international cohort were screened using a smMIPs or genomic qPCR-based approach tailored for the RP17 locus. Suspected copy number changes were validated using high-density SNP-array genotyping, and SV breakpoint characterization was performed by mutation-specific breakpoint PCR, genome sequencing and, if required, optical genome mapping. In silico modeling of novel SVs was performed to predict the formation of neo-TADs and whether ectopic contacts between the retinal enhancers and the GDPD1-promoter could be formed. Using this workflow, potential RP17-SVs were detected in eight probands of which seven were confirmed. Two novel SVs were identified that are predicted to cause TAD rearrangement and retinal enhancer-GDPD1 contact, one from Germany (DE-SV9) and three with the same SV from the United States (US-SV10). Previously reported RP17-SVs were also identified in three Australian probands, one with UK-SV2 and two with SA-SV3. In summary, we describe a validated multi-step pipeline for reliable and efficient RP17-SV discovery and expand the range of disease-associated SVs. Based on these data, RP17-SVs can be considered a frequent cause of adRP which warrants the inclusion of RP17-screening as a standard diagnostic test for this disease.

Towards the genomic sequence code of DNA fragility for machine learning.

Genomic DNA breakages and the subsequent insertion and deletion mutations are important contributors to genome instability and linked diseases. Unlike the research in point mutations, the relationship between DNA sequence context and the propensity for strand breaks remains elusive. Here, by analyzing the differences and commonalities across myriads of genomic breakage datasets, we extract the sequence-linked rules and patterns behind DNA fragility. We show the overall deconvolution of the sequence influence into short-, mid- and long-range effects, and the stressor-dependent differences in defining the range and compositional effects on DNA fragility. We summarize and release our feature compendium as a library that can be seamlessly incorporated into genomic machine learning procedures, where DNA fragility is of concern, and train a generalized DNA fragility model on cancer-associated breakages. Structural variants (SVs) tend to stabilize regions in which they emerge, with the effect most pronounced for pathogenic SVs. In contrast, the effects of chromothripsis are seen across regions less prone to breakages. We find that viral integration may bring genome fragility, particularly for cancer-associated viruses. Overall, this work offers novel insights into the genomic sequence basis of DNA fragility and presents a powerful machine learning resource to further enhance our understanding of genome (in)stability and evolution.

Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres.

The human fungal pathogen Candida albicans poses a significant burden on global health, causing high rates of mortality and antifungal drug resistance. C. albicans is a heterozygous diploid organism that reproduces asexually. Structural variants (SVs) are an important source of genomic rearrangement, particularly in species that lack sexual recombination. To comprehensively investigate SVs across clinical isolates of C. albicans, we conducted long read sequencing and genome-wide SV analysis in three distantly related clinical isolates. Our work included a new, comprehensive analysis of transposable element (TE) composition, location and diversity. SVs and TEs are frequently close to coding sequences and many SVs are heterozygous, suggesting that SVs might impact gene and allele-specific expression. Most SVs are uniquely present in only one clinical isolate, indicating that SVs represent a significant source of intra-species genetic variation. We identified multiple, distinct SVs at the centromeres of Chromosome 4 and Chromosome 5, including inversions and transposon polymorphisms. These two chromosomes are often aneuploid in drug resistant clinical isolates, and can form isochromosome structures with breakpoints near the centromere. Further screening of 100 clinical isolates confirmed the widespread presence of centromeric SVs in C. albicans, often appearing in a heterozygous state, indicating that SVs are contributing to centromere evolution in C. albicans Together, these findings highlight that SVs and TEs are common across diverse clinical isolates of C. albicans and that the centromeres of this organism are important sites of genome rearrangement.