Resolving complex structures at oncovirus integration loci with conjugate graph

ABSTRACTOncovirus integrations cause complex structural variations (SVs) on host genomes. We propose a conjugate graph model to reconstruct the rearranged local genomic map (LGM) at integrated loci. Simulation tests prove the reliability and credibility of the algorithm. Applications of the algorithm to whole-genome sequencing data of Human papillomavirus (HPV) and hepatitis B virus (HBV)-infected cancer samples gained biological insights on oncovirus integrations. We observed five affection patterns of oncovirus integrations from the HPV and HBV-integrated cancer samples, including the exon loss, promoter gain, hyper-amplification of tumor gene, the viral cis-regulation inserted at the single intron and at the intergenic region. We found that the focal duplicates and host SVs are frequent in the HPV-integrated LGMs, while the focal deletions and complex virus SVs are prevalent in HBV-integrated LGMs. Furthermore, with the results yields from our method, we found the enhanced microhomology-mediated end joining (MMEJ) might lead to both HPV and HBV integrations, and conjectured that the HPV integrations might mainly occur during the DNA replication process.

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Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin–Siris Syndrome

Frontiers in Genetics ◽

10.3389/fgene.2021.708348 ◽

2021 ◽

Vol 12 ◽

Author(s):

Christopher M. Grochowski ◽

Ana C. V. Krepischi ◽

Jesper Eisfeldt ◽

Haowei Du ◽

Debora R. Bertola ◽

...

Keyword(s):

De Novo ◽

Chromosomal Rearrangements ◽

Whole Genome Sequencing Data ◽

Mendelian Disease ◽

Derivative Chromosome ◽

Sequencing Data ◽

End Joining ◽

Single Chromosome ◽

Complex Structural ◽

Non Homologous End Joining

Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein, we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin–Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90-Mb pericentric and a 47-Mb paracentric inversion on a single chromosome. Subsequent analysis of short-read whole-genome sequencing data and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting ARID1B for which haploinsufficiency leads to the CSS1 disease trait (MIM:135900). The aggregate structural variant data show that the resolved, the resolved derivative chromosome architecture presents four de novo inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene ARID1B is shown to occur between the fourth and fifth exon of the canonical transcript with subsequent qPCR studies confirming a decrease in ARID1B expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient’s clinical phenotype or resolving unsolved Mendelian disease cases.

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Complex structural variations in non-human primate hepatitis B virus

Virology Journal ◽

10.1186/s12985-021-01667-0 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Yoshihito Nagura ◽

Kei Fujiwara ◽

Kentaro Matsuura ◽

Etsuko Iio ◽

Yasuhito Tanaka ◽

...

Keyword(s):

Hepatitis B ◽

Core Region ◽

Structural Variations ◽

Hbv Genotype ◽

The Core ◽

B Virus ◽

Genetic Sequences ◽

Complex Structural ◽

Genotype A ◽

Human Primate

Abstract Background Recent genome sequence technology has revealed a novel type of genetic rearrangement referred to as complex structural variations (SVs). Previous studies have elucidated the complex SVs in human hepatitis B viruses (HBVs). In this study, we investigated the existence of complex SVs in HBVs from non-human primates (NHPs). Methods Searches for nucleotide sequences of NHP HBV were conducted using the PubMed, and genetic sequences were retrieved from databases. The candidate genetic sequences harboring complex SVs were analyzed using the CLUSTALW program and MAFFT. Additional bioinformatical analyses were performed to determine strains with complex SVs and to elucidate characteristics of NHP HBV strains. Results One hundred and fifty-four HBV strains from NHPs were identified from databases. SVs and complex SVs were observed in 11 (7.1%) strains. Three gibbon HBV (GiHBV) strains showed complex SVs consisting of an insertion and a deletion in the pre-S1 region. One GiHBV strain possessed a 6-nt insertion, which are normally specific to human HBV genotype A (HBV/A) in the Core region, and further analyses clarified that the 6-nt insertion was not caused by recombination, but rather by simple insertion. Another chimpanzee HBV strain showed complex SVs in the pre-S1 region, which were composed of human HBV/E, G-specific polymorphic SV, and an additional 6-nt insertion. Conclusions In this study, complex SVs were observed in HBV strains from NHPs, in addition to human HBV strains, as shown in previous studies. These data suggest that complex SVs could also be found in other members of hepadnaviruses, and may play a role in their genetic diversity.

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Characterization of Hepatitis B Virus with Complex Structural Variations

Human Viruses: Diseases, Treatments and Vaccines ◽

10.1007/978-3-030-71165-8_15 ◽

2021 ◽

pp. 313-325

Author(s):

Kei Fujiwara

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Structural Variations ◽

B Virus ◽

Complex Structural

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Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Genes ◽

10.3390/genes11121444 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1444

Author(s):

Nazeefa Fatima ◽

Anna Petri ◽

Ulf Gyllensten ◽

Lars Feuk ◽

Adam Ameur

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Single Molecule ◽

Large Scale ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Structural Variations ◽

Single Molecule Sequencing ◽

Human Samples

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

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Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

10.1101/333617 ◽

2018 ◽

Cited By ~ 11

Author(s):

Isidro Cortés-Ciriano ◽

June-Koo Lee ◽

Ruibin Xi ◽

Dhawal Jain ◽

Youngsook L. Jung ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Copy Number ◽

Human Cancer ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

End Joining ◽

Cancer Types ◽

Non Homologous End Joining

SummaryChromothripsis is a newly discovered mutational phenomenon involving massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in cancer suggest that chromothripsis may be far more common than initially inferred from low resolution DNA copy number data. Here, we analyze the patterns of chromothripsis across 2,658 tumors spanning 39 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of >50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy number states, a considerable fraction of the events involves multiple chromosomes as well as additional structural alterations. In addition to non-homologous end-joining, we detect signatures of replicative processes and templated insertions. Chromothripsis contributes to oncogene amplification as well as to inactivation of genes such as mismatch-repair related genes. These findings show that chromothripsis is a major process driving genome evolution in human cancer.

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SearcHPV: a novel approach to identify and assemble human papillomavirus-host genomic integration events in cancer

10.1101/2021.02.11.430847 ◽

2021 ◽

Author(s):

Lisa M. Pinatti ◽

Wenjin Gu ◽

Yifan Wang ◽

Ahmed El Hossiny ◽

Apurva D. Bhangale ◽

...

Keyword(s):

Human Papillomavirus ◽

Integrated Analysis ◽

Sequencing Data ◽

End Joining ◽

Structural Variations ◽

Contig Assembly ◽

Novel Approach ◽

Integration Sites ◽

Targeted Capture ◽

The Impact

ABSTRACTBackgroundHuman papillomavirus (HPV) is a well-established driver of malignant transformation in a number of sites including head and neck, cervical, vulvar, anorectal and penile squamous cell carcinomas; however, the impact of HPV integration into the host human genome on this process remains largely unresolved. This is due to the technical challenge of identifying HPV integration sites, which includes limitations of existing informatics approaches to discover viral-host breakpoints from low read coverage sequencing data.MethodsTo overcome this limitation, we developed a new HPV detection pipeline called SearcHPV based on targeted capture technology and applied the algorithm to targeted capture data. We performed an integrated analysis of SearcHPV-defined breakpoints with genome-wide linked read sequencing to identify potential HPV-related structural variations.ResultsThrough analysis of HPV+ models, we show that SearcHPV detects HPV-host integration sites with a higher sensitivity and specificity than two other commonly used HPV detection callers. SearcHPV uncovered HPV integration sites adjacent to known cancer-related genes including TP63 and MYC, as well as near regions of large structural variation. We further validated the junction contig assembly feature of SearcHPV, which helped to accurately identify viral-host junction breakpoint sequences. We found that viral integration occurred through a variety of DNA repair mechanisms including non-homologous end joining, alternative end joining and microhomology mediated repair.ConclusionsIn summary, we show that SearcHPV is a new optimized tool for the accurate detection of HPV-human integration sites from targeted capture DNA sequencing data.

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TumorFusions: an integrative resource for reporting cancer-associated transcript fusions in 33 tumor types

10.1101/162180 ◽

2017 ◽

Author(s):

Xin Hu ◽

Qianghu Wang ◽

Floris Barthel ◽

Ming Tang ◽

Samirkumar Amin ◽

...

Keyword(s):

The Cancer Genome Atlas ◽

Whole Genome Sequencing Data ◽

Fusion Genes ◽

Sequencing Data ◽

Structural Variations ◽

Cancer Genome Atlas ◽

Cancer Types ◽

Tumor Types ◽

Fusion Detection ◽

Genome Atlas

Fusion genes, particularly those involving kinases, have been demonstrated as drivers and are frequent therapeutic targets in cancer1. Here, we describe our results on detecting transcript fusions across 33 cancer types from The Cancer Genome Atlas (TCGA), totaling 9,966 cancer samples and 648 normal samples2. Preprocessing, including read alignment to both genome and transcriptome, and fusion detection were carried out using a uniform pipeline3. To validate the resultant fusions, we also called somatic structural variations for 561 cancers from whole genome sequencing data. A summary of the data used in this study is provided in Table S1. Our results can be accessed per our portal at http://www.tumorfusions.org.

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Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

10.1101/179176 ◽

2017 ◽

Cited By ~ 4

Author(s):

Kadir C. Akdemir ◽

Yilong Li ◽

Roel G. Verhaak ◽

Rameen Beroukhim ◽

Peter Cambell ◽

...

Keyword(s):

Genome Organization ◽

De Novo ◽

Human Cancer ◽

Hierarchical Level ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Structural Variations ◽

High Coverage ◽

Chromosome Conformation ◽

Human Cancers

Genomic material within the nucleus is folded into successive layers in order to package and organize the long string of linear DNA. This hierarchical level of folding is closely associated with transcriptional regulation and DNA replication. Microscopic studies concluded that genome organization inside the nucleus is not random and chromosomes within the nucleus create territories1. More recent chromosome conformation studies have revealed that mammalian chromosomes are structured into tissue-invariant topologically associating domains (TADs) where the DNA within a given domain interacts more frequently together than with regions in other domains2,3. Genes within the same TADs represent similar expression and histone-modification profiles4. In addition, enhancer-promoter pairs within the same TAD respond similarly to hormone induction5 or differentiation cues6. Therefore, regions separating different TADs (boundaries) have important roles in reinforcing the stability of these domain-wide features. Indeed, TAD boundary disruptions in human genetic disorders7,8 or human cancers lead to misregulation of certain genes9,10, due to de novo enhancer exposure to promoters. Here, to understand effects and distributions of somatic structural variations across TADs, we utilized single nucleotide variations, deletions, inversions, tandem-duplications and complex rearrangements from 2658 high-coverage whole genome sequencing data across various cancer types with paired normal samples. We comprehensively profiled structural variations with respect to their effect on TAD boundaries, on the regulation of genes in human cancers.

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