Analysis Of Structural Variants Research Articles

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype.

The Barley and Wheat Pan-Genomes.

To unlock the genetic potential in crops, multi-genome comparisons are an essential tool. Decreasing costs and improved sequencing technologies have democratized plant genome sequencing and led to a vast increase in the amount of available reference sequences on the one hand and enabled the assembly of even the largest and most complex and repetitive crops genomes such as wheat and barley. These developments have led to the era of pan-genomics in recent years. Pan-genome projects enable the definition of the core and dispensable genome for various crop species as well as the analysis of structural and functional variation and hence offer unprecedented opportunities for exploring and utilizing the genetic basis of natural variation in crops. Comparing, analyzing, and visualizing these multiple reference genomes and their diversity requires powerful and specialized computational strategies and tools.

Exposing structural variations in SARS-CoV-2 evolution

The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.

Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing has improved the sensitivity of structural variant discovery. Here, we conduct the long-read sequencing-based structural variant analysis for 405 unrelated Chinese individuals, with 68 phenotypic and clinical measurements. We discover a landscape of 132,312 nonredundant structural variants, of which 45.2% are novel. The identified structural variants are of high-quality, with an estimated false discovery rate of 3.2%. The concatenated length of all the structural variants is approximately 13.2% of the human reference genome. We annotate 1,929 loss-of-function structural variants affecting the coding sequence of 1,681 genes. We discover rare deletions in HBA1/HBA2/HBB associated with anemia. Furthermore, we identify structural variants related to immunity which differentiate the northern and southern Chinese populations. Our study describes the landscape of structural variants in the Chinese population and their contribution to phenotypes and disease.

Multiomic Mapping of Copy Number and Structural Variation on Chromosome 1 (Chr1) Highlights Multiple Recurrent Disease Drivers

Multiomic Mapping of Copy Number and Structural Variation on Chromosome 1 (Chr1) Highlights Multiple Recurrent Disease Drivers

Pathogenic Germline Variants in Cancer Susceptibility Genes in Children and Young Adults With Rhabdomyosarcoma.

Genome sequencing of the discovery cohort (n = 273) and exome sequencing of the secondary cohort (n = 121) were conducted on germline DNA. Analyses were performed on 130 cancer susceptibility genes (CSG). Pathogenic or likely pathogenic (P/LP) variants were predicted using the American College of Medical Genetics and Genomics (ACMG) criteria. Structural variation and survival analyses were performed on the discovery cohort. We found that 6.6%-7.7% of patients with RMS harbored P/LP variants in dominant-acting CSG. An additional approximately 1% have structural variants (ATM, CDKN1C) in CSGs. CSG variants did not influence survival, although there was a significant correlation with an earlier age of tumor onset. There was a nonsignificant excess of P/LP variants in dominant inheritance genes in the patients with FOXO1 fusion-negative RMS patients versus the patients with FOXO1 fusion-positive RMS. We identified pathogenic germline variants in CSGs previously (TP53, NF1, DICER1, mismatch repair genes), rarely (BRCA2, CBL, CHEK2, SMARCA4), or never (FGFR4) reported in RMS. Numerous genes (TP53, BRCA2, mismatch repair) were on the ACMG Secondary Findings 2.0 list. In two cohorts of patients with RMS, we identified pathogenic germline variants for which gene-specific therapies and surveillance guidelines may be beneficial. In families with a proband with an RMS-risk P/LP variant, genetic counseling and cascade testing should be considered, especially for ACMG Secondary Findings genes and/or with gene-specific surveillance guidelines.

Whole genome sequencing in the diagnosis of primary ciliary dyskinesia

BackgroundIt is estimated that 1–13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD. PCD is a disorder caused by mutations in genes required for motile cilium structure or function, resulting in impaired mucociliary clearance. Symptoms appear in infancy but diagnosis is often late or missed, often due to the lack of a “gold standard” diagnostic tool and non-specific symptoms. Mutations in > 50 genes account for around 70% of cases, with additional genes, and non-coding, synonymous, missense changes or structural variants (SVs) in known genes presumed to account for the missing heritability.MethodsUK patients with no identified genetic confirmation for the cause of their PCD or bronchiectasis were eligible for whole genome sequencing (WGS) in the Genomics England Ltd 100,000 Genomes Project. 21 PCD probands and 52 non-cystic fibrosis (CF) bronchiectasis probands were recruited in Wessex Genome Medicine Centre (GMC). We carried out analysis of single nucleotide variants (SNVs) and SVs in all families recruited in Wessex GMC.Results16/21 probands in the PCD cohort received confirmed (n = 9), probable (n = 4) or possible (n = 3) diagnosis from WGS, although 13/16 of these could have been picked up by current standard of care gene panel testing. In the other cases, SVs were identified which were missed by panel testing. We identified variants in novel PCD candidate genes (IFT140 and PLK4) in 2 probands in the PCD cohort. 3/52 probands in the non-CF bronchiectasis cohort received a confirmed (n = 2) or possible (n = 1) diagnosis of PCD. We identified variants in novel PCD candidate genes (CFAP53 and CEP164) in 2 further probands in the non-CF bronchiectasis cohort.ConclusionsGenetic testing is an important component of diagnosing PCD, especially in cases of atypical disease history. WGS is effective in cases where prior gene panel testing has found no variants or only heterozygous variants. In these cases it may detect SVs and is a powerful tool for novel gene discovery.

Multiplatform discovery and regulatory function analysis of structural variations in non-small cell lung carcinoma.

Non-small cell lung carcinoma (NSCLC), the most common form of lung cancer, is the leading cause of cancer-related death worldwide. We perform whole-genome sequencing (WGS) on samples from 43 primary patients with NSCLC and matched normal samples and analyze their matched open chromatin data and transcriptome data. Our results indicate that next-generation sequencing (NGS) and the Bionano Genomics (BNG) platform should be viewed as complementary technologies in terms of structural variations detection. By creating a framework integrating these two platforms, we detect high-technical-confidence somatic structural variations (SVs) in NSCLC cases, which could aid in the efficient investigation of new candidate oncogenes, such as TRIO and SESTD1. Our findings highlight the impact of somatic SVs on NSCLC oncogenesis and lay a foundation for exploring associations among somatic SVs, gene expression, and regulatory networks in patients with NSCLC.

The boundary-spanning mechanisms of Nobel Prize winning papers.

The breakthrough potentials of research papers can be explained by their boundary-spanning qualities. Here, for the first time, we apply the structural variation analysis (SVA) model and its affiliated metrics to investigate the extent to which such qualities characterize a group of Nobel Prize winning papers. We find that these papers share remarkable boundary-spanning traits, marked by exceptional abilities to connect disparate and topically-diverse clusters of research papers. Further, their publications exert structural variations on a scale that significantly alters the betweenness centrality distributions in existing intellectual space. Overall, SVA not only provides a set of leading indicators for describing future Nobel Prize winning papers, but also broadens our understanding of similar prize-winning properties that may have been overlooked among other regular publications.

Whole genome sequencing identifies novel structural variant in a large Indian family affected with X-linked agammaglobulinemia.

X-linked agammaglobulinemia (XLA, OMIM #300755) is a primary immunodeficiency disorder caused by pathogenic variations in the BTK gene, characterized by failure of development and maturation of B lymphocytes. The estimated prevalence worldwide is 1 in 190,000 male births. Recently, genome sequencing has been widely used in difficult to diagnose and familial cases. We report a large Indian family suffering from XLA with five affected individuals. We performed complete blood count, immunoglobulin assay, and lymphocyte subset analysis for all patients and analyzed Btk expression for one patient and his mother. Whole exome sequencing (WES) for four patients, and whole genome sequencing (WGS) for two patients have been performed. Carrier screening was done for 17 family members using Multiplex Ligation-dependent Probe Amplification (MLPA) and haplotype ancestry mapping using fineSTRUCTURE was performed. All patients had hypogammaglobulinemia and low CD19+ B cells. One patient who underwent Btk estimation had low expression and his mother showed a mosaic pattern. We could not identify any single nucleotide variants or small insertion/ deletions from the WES dataset that correlates with the clinical feature of the patient. Structural variant analysis through WGS data identifies a novel large deletion of 5,296 bp at loci chrX:100,624,323-100,629,619 encompassing exons 3-5 of the BTK gene. Family screening revealed seven carriers for the deletion. Two patients had a successful HSCT. Haplotype mapping revealed a South Asian ancestry. WGS led to identification of the accurate genetic mutation which could help in early diagnosis leading to improved outcomes, prevention of permanent organ damage and improved quality of life, as well as enabling genetic counselling and prenatal diagnosis in the family.

Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis.

Analysis of structural variations (SVs) is important to understand mutations underlying genetic disorders and pathogenic conditions. However, characterizing SVs using short-read, high-throughput sequencing technology is difficult. Although long-read sequencing technologies are being increasingly employed in characterizing SVs, their low throughput and high costs discourage widespread adoption. Sequence motif-based optical mapping in nanochannels is useful in whole-genome mapping and SV detection, but it is not possible to precisely locate the breakpoints or estimate the copy numbers. We present here a universal multicolor mapping strategy in nanochannels combining conventional sequence-motif labeling system with Cas9-mediated target-specific labeling of any 20-base sequences (20mers) to create custom labels and detect new features. The sequence motifs are labeled with green fluorophores and the 20mers are labeled with red fluorophores. Using this strategy, it is possible to not only detect the SVs but also utilize custom labels to interrogate the features not accessible to motif-labeling, locate breakpoints, and precisely estimate copy numbers of genomic repeats. We validated our approach by quantifying the D4Z4 copy numbers, a known biomarker for facioscapulohumeral muscular dystrophy (FSHD) and estimating the telomere length, a clinical biomarker for assessing disease risk factors in aging-related diseases and malignant cancers. We also demonstrate the application of our methodology in discovering transposable long non-interspersed Elements 1 (LINE-1) insertions across the whole genome.

Abstract 2214: The genomic landscape of lung cancer in post-menopausal never-smoker women

Abstract Lung cancer is the deadliest form of cancer worldwide. Cigarette smoking is the primary risk factor for developing lung cancer, fueling global tobacco cessation programs. In the United States, it is projected that by 2065 there will be a 63% reduction in smoking-associated lung cancer burden. However, even with this decline, lung cancer will still account for a significant proportion of cancer-associate mortality, suggesting that factors beyond smoking contribute to lung tumorigenesis. Lung cancer in never smokers is a distinct sub-group that needs specific exploration. It is the 7th highest cause of cancer-deaths worldwide, with an increasing trend in its incidence. Thus far, the majority of tumor genome-wide sequencing efforts in lung cancer have been focused on patient cohorts with a smoking history. We know that LCNS is distinct from lung adenocarcinoma found in smokers at the genetic level, however large gaps in our understanding of this population persist. Through a unique collaboration with the Women's Health Initiative (WHI) we now have access to a large repository of tumor tissue from LCNS patients. We have performed exome-sequencing on this cohort and here we describe novel mutations, structural variants and copy number changes in this cohort. Whole-exome sequencing of 75 tumor-normal pairs was performed. Mutations were identified for the entire cohort using different computational methods. For the identification of single nucleotide variants a consensus dual-caller and filtering methodology was employed. Variants were then analyzed to identify genes with significant mutations using MutSig2CV. Structural variant analysis was performed using SvABA and copy number analysis was performed using TITAN. Finally, we perform correlative analysis of mutations with the metadata curated by the WHI and highlight key features of this cohort. Our mutational analysis reveals showed that there is an enrichment of known oncogenes including KRAS, EGFR and TP53. Additionally, we identified mutations in STK11. Here we describe novel genes and mutations previously unknown to occur in LCNS cohort and describe their potential functional implications. We also report novel structural variants and copy number alterations. Additionally we performed mutational signature analysis and identified novel signatures specific to this cohort. Mutational analysis of our LCNS cohort reveals that this cohort in general has a lower tumor mutational burden compared to their control cohort with a history of smoking. Additionally, we find that this cohort has mutations that have been previously reported in studies in LCNS patients. However, the existence of novel mutations and structural alterations may offer a unique opportunity for future target identification and therapeutic intervention. Citation Format: Sitapriya Moorthi, Amy Paguirigan, Garnet Anderson, Gavin Ha, Alice Berger. The genomic landscape of lung cancer in post-menopausal never-smoker women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2214.

Abstract 2198: Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines

Abstract Prostate cancer research has relied on a limited number of prostate cancer cell lines despite decades of effort in establishing them from human prostate cancers. These cell lines thus represent precious resources for in vitro and in vivo preclinical studies of prostate cancer and have fueled many advances in the field. While there has been tremendous effort in characterizing their molecular profiles and genomic features, comprehensive whole genome sequencing with allelic phasing of genomic alterations has not been undertaken to date. Here, we utilized powerful whole genome linked-read sequencing of high molecular weight DNA (>60Kbp) from eight common prostate cancer cell lines as well as four castrate resistant (CR) subclones derived from three of those cell lines. Long range information enabled assembly of mutations (single nucleotide variants-SNVs and small indels) and structural variants (SVs) across the genome into large phased blocks. This allowed accounting of multiple mutations within a given gene to assess whether they were present on a single allele, or on opposite alleles, to assess the “allelic status” of phased mutations. Using this phased mutational analysis, we found that in cell lines with microsatellite instability (MSI; LNCaP, LAPC4, DU145, CWR22Rv1), 10-20% of a priori defined driver genes are inactivated by at least two heterozygous mutations on opposite alleles. Overall, MSI cell lines had higher levels of mutations and fewer SVs than those that were microsatellite stable (MSS; PC3, VCaP). The phased SV analysis allowed identification of complex rearrangement chains consistent with chromothripsis (PC3, DU145) and chromoplexy (VCAP, LnCAP-C42b), including reconstruction of the complex chained TMPRSS2-ERG rearrangement in VCaP. Additionally, comparison of parental and CR subclones revealed previously known as well as several novel genomic alterations that were associated with the CR subclones, including chromosome 8 amplification (in LNCaP-Abl and LAPC4-CR), further androgen receptor amplification amongst a host of increased complex SVs (in VCAP-CR), SWI/SNF mutations and increased complex SVs (in LNCAP-C42b), CDK12 biallelic loss and numerous tandem duplications (in LAPC4-CR). This study therefore comprehensively characterizes allelically phased genomic alterations in the commonly used prostate cancer cell lines and provides a useful resource for future cancer research. Citation Format: Minh-Tam Pham, Harshath Gupta, Anuj Gupta, Ajay Vaghasia, Alyza M. Skaist, McKinzie A. Garrison, Roshan Chikamarne, Sarah J. Wheelan, William G. Nelson, Srinivasan Yegnasubramanian. Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2198.

The Genomic Landscape of Multiple Myeloma Complex Structural Variations

Multiple Myeloma (MM) represents a heterogeneous and complex hematological cancer, where karyotypic events are thought to be early drivers of disease pathogenesis. Nevertheless, aside from recurrent translocations between the immunoglobulin loci and known oncogenes, a comprehensive analysis of MM structural variations (SV) has never been performed.Here, we took advantage of whole genome sequencing (WGS) to analyse 97 samples collected at different clinical time points from a cohort of 30 MM patients (median of 2 samples per patients; range 1-4). Bam files were analysed using validated and published tools available at the Wellcome Trust Sanger Institute. For each sample, we analysed the genome-wide profile of copy-number aberrations (CNAs), cancer cell fraction (CCF) and SV using published approaches (Nik-Zainal S. et al. Cell 2012 and Nik-Zainal S. et al. Nature 2016).We defined SVs as inversions, translocations, internal tandem duplications (ITD) and deletions. We found a stunning 2419 SVs in the whole cohort, with a median of 30 unique SVs per sample (range 3-135). Of these, the only recurrent rearrangements were translocations involving MYC (14/30; 46%), CCND1 (7/30; 23%) and MMSET (3/30; 10%), suggesting MM is characterized by an incredibly complex heterogeneity of its genomic architecture. Interestingly, we observed a much higher than previously reported (7/30; 23%) number of translocations involving the light chain immunoglobulin loci (IGL), which always correlated with hyperdiploid karyotype and were mutually exclusive with those involving the heavy chain locus (IGH). Analysis of CCF confirmed that translocations involving CCND1 and MMSET were always fully clonal confirming their early driver role in MM pathogenesis. Integrating SV and CNA data, we found that a SV was responsible for 89.9% of CNAs where a breakpoint could be mapped (i.e. those not involving centromeric or telomeric regions, or whole chromosome deletions or amplifications). Even more interestingly, we found frequent (93% of patients) SVs involving multiple chromosomes and causing multiple CNAs at once, offering a pathogenic explanation to these frequent karyotypic events in MM. We found that such complex events even involved driver translocations, as 3 out of 7 t(11;14) were not simple balanced translocations but were rather associated with CNAs of the locus. MYC translocations were even more frequently associated with CNAs (13/15 cases), often resulting in focal amplifications of the 8q24 region. Focal mono or bi-allelic deletions were also observed on other important oncogenes such BIRC2/3, CDKN2A/B, CDKN2C and TRAF3, and were generally acquired during progression and/or relapse, potentially representing a mechanism of subclonal selection and treatment resistance.Overall, 20/30 (66%) of MM patients showed at least one complex event defined as an event composed by ≥ 3 independent SVs. Chromotripsis was the most frequent: 18 chromotripsis events were observed in 9/30 (30%) patients; the majority (14/18) were clonal and conserved during evolution, suggesting a potential early role in MM pathogenesis. However, chromotripsis was not the only recurrent complex event. In fact, we observed 2 chromoplexy event acquired in 2 patients at relapse. Even more interestingly, in 6 patients we describe a novel complex event characterized by multiple concatenated translocations causing small CNAs on more than 2 different chromosomes, that we named cyclo-template insertion (CTI). Interestingly, all but one CTIs resulted in a translocation involving an oncogene (4 MYC and 1 CCND1), suggesting that this is a novel relevant driver mechanism in MM pathogenesis.We finally used the Bayesian Dirichlet process (Bolli N et al. Nat Comm 2014) to reconstruct the chronological order of the main MM driver events. generating, for each sample, a phylogenetic tree incorporating mutations, CNAs and SVs. We show that during MM life history there are few, albeit often complex, genomic events with the potential to cause major selective subclonal sweeps, and these events were highly variable from patient to patient. Chromotripsis, CTI, CNAs and other SVs accounted for most of these events, confirming their critical role in MM pathogenesis. DisclosuresMoreau:Takeda: Honoraria; Janssen: Consultancy, Honoraria; Celgene, Janssen, Takeda, Novartis, Amgen, Roche: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Millennium: Consultancy, Honoraria; Amgen: Honoraria; Bristol-Myers Squibb: Honoraria; Onyx Pharmaceutical: Consultancy, Honoraria. Corradini:Roche: Honoraria; Amgen: Honoraria; Sanofi: Honoraria; Takeda: Honoraria; Celgene: Honoraria; Janssen: Honoraria; Novartis: Honoraria; Gilead: Honoraria. Anderson:Millenium Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Gilead Sciences: Membership on an entity's Board of Directors or advisory committees; Oncopep: Other: scientific founder; C4 Therapeutics: Other: scientific founder; MedImmune: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees. Avet-Loiseau:Celgene, Janssen, Amgen, Bristol-Myers Squibb, Sanofi: Honoraria, Speakers Bureau; Janssen, Sanofi, Celgene, Amgen: Consultancy; Celgene, Janssen: Research Funding.

Comprehensive Genomic Characterization of Refractory Multiple Myeloma Reveals a Complex Mutational and Structural Landscape Associated with Drug Resistance

Comprehensive Genomic Characterization of Refractory Multiple Myeloma Reveals a Complex Mutational and Structural Landscape Associated with Drug Resistance

AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis.

With the dramatic increase of pangenomic analysis, Human geneticists have generated large amount of genomic data including millions of small variants (SNV/indel) but also thousands of structural variations (SV) mainly from next-generation sequencing and array-based techniques. While the identification of the complete SV repertoire of a patient is getting possible, the interpretation of each SV remains challenging. To help identifying human pathogenic SV, we have developed a web server dedicated to their annotation and ranking (AnnotSV) as well as their visualization and interpretation (knotAnnotSV) freely available at the following address: https://www.lbgi.fr/AnnotSV/. A large amount of annotations from >20 sources is integrated in our web server including among others genes, haploinsufficiency, triplosensitivity, regulatory elements, known pathogenic or benign genomic regions, phenotypic data. An ACMG/ClinGen compliant prioritization module allows the scoring and the ranking of SV into 5 SV classes from pathogenic to benign. Finally, the visualization interface displays the annotated SV in an interactive way including popups, search fields, filtering options, advanced colouring to highlight pathogenic SV and hyperlinks to the UCSC genome browser or other public databases. This web server is designed for diagnostic and research analysis by providing important resources to the user.

How do Price medalists’ scholarly impact change before and after their awards?

How a scholar's achievement and productivity may change by the award of an academic prize is a topic of a long-term interest in research fields such as scientometrics. Numerous studies have explored the impact of receiving a Nobel Prize, a Turing Award, and other international awards on laureates' scholarly performance, but relatively less attention has been paid to the impact of Derek John de Solla Price Medal on its recipients. This paper adopts the methodology of Structural Variation Analysis (SVA) to evaluate how Price medalists' research are impacted, if any, in terms of citation, h-index, and structural variation patterns in underlying collaborative networks. Moreover, we compare the SVA metrics with other indicators such as composite scores and Highly Cited Researchers (HCR). Our results show that: a Price Medal award may not necessarily boost the medalist’s scholarly potential, actual academic impact and collaboration patterns in a degree that is statistically significant. But the SVA method is a better indicator to evaluate the Price Medalist, especially in five-year time windows.

Genome-wide analysis of structural variation.

Phased genomes from diverse human populations are assembled using multiple sequencing technologies.

Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss.

Inactivating variants as well as a missense variant in the centrosomal CEP78 gene have been identified in autosomal recessive cone-rod dystrophy with hearing loss (CRDHL), a rare syndromic inherited retinal disease distinct from Usher syndrome. Apart from this, a complex structural variant (SV) implicating CEP78 has been reported in CRDHL. Here we aimed to expand the genetic architecture of typical CRDHL by the identification of complex SVs of the CEP78 region and characterization of their underlying mechanisms. Approaches used for the identification of the SVs are shallow whole-genome sequencing (sWGS) combined with quantitative polymerase chain reaction (PCR) and long-range PCR, or ExomeDepth analysis on whole-exome sequencing (WES) data. Targeted or whole-genome nanopore long-read sequencing (LRS) was used to delineate breakpoint junctions at the nucleotide level. For all SVs cases, the effect of the SVs on CEP78 expression was assessed using quantitative PCR on patient-derived RNA. Apart from two novel canonical CEP78 splice variants and a frameshifting single-nucleotide variant (SNV), two SVs affecting CEP78 were identified in three unrelated individuals with CRDHL: a heterozygous total gene deletion of 235 kb and a partial gene deletion of 15 kb in a heterozygous and homozygous state, respectively. Assessment of the molecular consequences of the SVs on patient’s materials displayed a loss-of-function effect. Delineation and characterization of the 15-kb deletion using targeted LRS revealed the previously described complex CEP78 SV, suggestive of a recurrent genomic rearrangement. A founder haplotype was demonstrated for the latter SV in cases of Belgian and British origin, respectively. The novel 235-kb deletion was delineated using whole-genome LRS. Breakpoint analysis showed microhomology and pointed to a replication-based underlying mechanism. Moreover, data mining of bulk and single-cell human and mouse transcriptional datasets, together with CEP78 immunostaining on human retina, linked the CEP78 expression domain with its phenotypic manifestations. Overall, this study supports that the CEP78 locus is prone to distinct SVs and that SV analysis should be considered in a genetic workup of CRDHL. Finally, it demonstrated the power of sWGS and both targeted and whole-genome LRS in identifying and characterizing complex SVs in patients with ocular diseases.

Metagenomic insights into taxonomic diversity and metabolic potential of bacterial communities associated with tannery waste-contaminated soils

Long-term exposure to anthropogenic stressors can lead to perturbations in microbiomes, either selecting for novel and biotechnologically important biotypes, or reductions in the microbial diversity and disequilibrium of ecosystem services. Consequently, analysis of variations in microbial structure and function in stressful environments remains a critical issue in microbial ecology. In this study, the taxonomic structure of bacterial communities inhabiting tannery waste dumpsite soils was evaluated comparatively with those from non-contaminated soils using 16S rRNA gene sequencing. Furthermore, the metabolic potential of these communities was inferred from community level physiological profiling fingerprints. The dumpsite has been receiving tannery waste since 1982; hence, the soils are laden with heavy metals including chromium, zinc, sodium, and potassium. Consequently, the following significant differences between bacterial communities from contaminated and non-contaminated soils were observed: (1) bacterial communities from the contaminated soils were characterized by lower species diversity, albeit at comparable species evenness (Simpson index); (2) long term contamination of soil shifted the bacterial community structure to a distinct core microbiome dominated by bacterial groups such as Halomonas, Balneolaceae, Aliifodinibius, Serinicoccus, Gracilimonas, Marinobater, Penticoccus, Fordinicurvata, Dietzia, and Norcadioides. These are characteristic of saline, metal-laden environments and have potentially high organo-pollutant degradative properties; and (3) bacterial communities from the contaminated soils exhibited a robust metabolic potential utilizing both natural and anthropogenically derived polymers at a higher rate. Overall, these results highlight tannery waste dumpsite soils as microbial diversity hotspots and potential reservoirs for exploration of novel biotechnological tools for bioremediation and industrial applications.