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ClinCNV: novel method for allele-specific somatic copy-number alterations detection
[article]
<span title="2019-11-11">2019</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
</i>
<span class="release-stage" >pre-print</span>
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Large somatic copy number alterations (CNA), short indels and single nucleotide variants (SNVs) are playing important role in cancer development and can serve as a predictor for targeted therapy selection as well as prognostic factor. Genomic microarrays, FISH, MLPA and many other technologies are widely used for detection of CNAs. Whole-genome sequencing (WGS), whole-exome sequencing (WES) and targeted panel sequencing (TPS) are well established, highly accurate tools for detection of SNVs and
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... small indels, but detection of larger structural variants using WGS, WES and TPS data remains challenging. We developed a tool for high-resolution allele-specific detection of somatic CNAs in NGS data using statistical approach. We have developed a new method for read-depth and B-allele frequency (BAF) based multi-sample detection of copy-number changes in paired normal-tumor NGS data and showed its performance using large cohorts of WES and TPS sequenced samples.
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Optimal spliced alignments of short sequence reads
<span title="">2008</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a>
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Genome-wide active enhancer identification using cell type-specific signatures of epigenomic activity
[article]
<span title="2018-09-20">2018</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
</i>
<span class="release-stage" >pre-print</span>
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AbstractRecently enhancers have emerged as key players regulating crucial mechanisms such as cell fate determination and establishment of spatiotemporal patterns of gene expression during development. Due to their functional and structural complexity, an accurate in silico identification of active enhancers under specific conditions remain challenging. We present a novel machine learning based method that derives epigenomic patterns exclusively from experimentally characterized active enhancers
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... contrasted with a weighted set of non-enhancer genomic regions. We demonstrate better predictive performance over previous methods, as well as wide generalizability by identifying and annotating active enhancers genome-wide across different tissues/cell types in human and mouse.
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Bayesian Inference Of Cancer Driver Genes Using Signatures Of Positive Selection
[article]
<span title="2017-04-13">2017</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
</i>
<span class="release-stage" >pre-print</span>
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Tumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cellular prevalence, population recurrence, and functional impact of somatic mutations as signatures of positive selection into a Bayesian model for driver prediction. We demonstrate that our model, cDriver, outperforms competing methods when analyzing solid tumors, hematological
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... s, and pan-cancer datasets. Applying cDriver to exome sequencing data of 21 cancer types from 6,870 individuals revealed 123 unreported tumor type-driver gene connections. These novel connections are highly enriched for chromatin-modifying proteins, hinting at a universal role of chromatin regulation in cancer etiology. Although infrequently mutated as single genes, we show that chromatin modifiers are altered in a large fraction of cancer patients. In summary, we demonstrate that integration of evolutionary signatures is key for identifying mutational driver genes, thereby facilitating the discovery of novel therapeutic targets for cancer treatment.
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WENGAN: Efficient and high quality hybrid de novo assembly of human genomes
[article]
<span title="2019-11-25">2019</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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<span class="release-stage" >pre-print</span>
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The continuous improvement of long-read sequencing technologies along with the development of ad-doc algorithms has launched a new de novo assembly era that promises high-quality genomes. However, it has proven difficult to use only long reads to generate accurate genome assemblies of large, repeat-rich human genomes. To date, most of the human genomes assembled from long error-prone reads add accurate short reads to further polish the consensus quality. Here, we report the development of a
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... l algorithm for hybrid assembly, WENGAN, and the de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms that exploit the sequence information of short and long reads to tackle assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50:16.67-62.06 Mb), few assembly errors (contig NGA50:10.9-45.91 Mb), good consensus quality (QV:27.79-33.61), and high gene completeness (BUSCO complete: 94.6-95.1%), while consuming low computational resources (CPU hours:153-1027). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 62.06 Mb (NGA50:45.91 Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50:57.88 Mb). Providing highest quality at low computational cost, WENGAN is an important step towards the democratization of the de novo assembly of human genomes. The WENGAN assembler is available at https://github.com/adigenova/wengan
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Efficient hybrid de novo assembly of human genomes with WENGAN
<span title="2020-12-14">2020</span>
<i title="Springer Science and Business Media LLC">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2bqrmk7orfmxpqzqwiiyjwide" style="color: black;">Nature Biotechnology</a>
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AbstractGenerating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel,
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... Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24–80.64 Mb), few assembly errors (contig NGA50: 11.8–59.59 Mb), good consensus quality (QV: 27.84–42.88) and high gene completeness (BUSCO complete: 94.6–95.2%), while consuming low computational resources (CPU hours: 187–1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64 Mb (NGA50: 59.59 Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88 Mb).
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Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
<span title="2015-10-12">2015</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a>
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Transposable elements are major players in genome evolution. Transposon insertion polymorphisms can translate into phenotypic differences in plants and animals and are linked to different diseases including human cancer, making their characterization highly relevant to the study of genome evolution and genetic diseases. Results: Here we present Jitterbug, a novel tool that identifies transposable element insertion sites at single-nucleotide resolution based on the pairedend mapping and
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<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26459856">pmid:26459856</a>
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... ead signatures produced by NGS alignments. Jitterbug can be easily integrated into existing NGS analysis pipelines, using the standard BAM format produced by frequently applied alignment tools (e.g. bwa, bowtie2), with no need to realign reads to a set of consensus transposon sequences. Jitterbug is highly sensitive and able to recall transposon insertions with a very high specificity, as demonstrated by benchmarks in the human and Arabidopsis genomes, and validation using long PacBio reads. In addition, Jitterbug estimates the zygosity of transposon insertions with high accuracy and can also identify somatic insertions. Conclusions: We demonstrate that Jitterbug can identify mosaic somatic transposon movement using sequenced tumor-normal sample pairs and allows for estimating the cancer cell fraction of clones containing a somatic TE insertion. We suggest that the independent methods we use to evaluate performance are a step towards creating a gold standard dataset for benchmarking structural variant prediction tools.
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Transcriptional Control of Gene Expression by MicroRNAs
<span title="">2010</span>
<i title="Elsevier BV">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iwommhyo5bdk7c3u37mhjzexfe" style="color: black;">Cell</a>
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MicroRNAs (miRNAs) control gene expression in animals and plants. Like another class of small RNAs, siRNAs, they affect gene expression posttranscriptionally. While siRNAs in addition act in transcriptional gene silencing, a role of miRNAs in transcriptional regulation has been less clear. We show here that in moss Physcomitrella patens mutants without a DICER-LIKE1b gene, maturation of miRNAs is normal but cleavage of target RNAs is abolished and levels of these transcripts are drastically
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... ced. These mutants accumulate miRNA: target-RNA duplexes and show hypermethylation of the genes encoding target RNAs, leading to gene silencing. This pathway occurs also in the wild-type upon hormone treatment. We propose that initiation of epigenetic silencing by DNA methylation depends on the ratio of the miRNA and its target RNA.
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Simultaneous alignment of short reads against multiple genomes
<span title="">2009</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a>
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Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be
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... d by alignments against the reference alone. Download GenomeMapper at a Number of known variants in 600 kb of dideoxy sequence data from [38] . b Ratio of confirmed to the sum of confirmed and missed predictions of the respective kind; indicates sensitivity of method. c False discovery rate, percentage of erroneous calls.
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Highly Specific Gene Silencing by Artificial miRNAs in Rice
<span title="2008-03-19">2008</span>
<i title="Public Library of Science (PLoS)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a>
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Endogenous microRNAs (miRNAs) are potent negative regulators of gene expression in plants and animals. Artificial miRNAs (amiRNAs)-designed to target one or several genes of interest-provide a new and highly specific approach for effective post-transcriptional gene silencing (PTGS) in plants. Methodology: We devised an amiRNA-based strategy for both japonica and indica type strains of cultivated rice, Oryza sativa. Using an endogenous rice miRNA precursor and customized 21mers, we designed
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<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0001829">doi:10.1371/journal.pone.0001829</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18350165">pmid:18350165</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2262943/">pmcid:PMC2262943</a>
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... A constructs targeting three different genes (Pds, Spl11, and Eui1/CYP714D1). Upon constitutive expression of these amiRNAs in the varieties Nipponbare (japonica) and IR64 (indica), the targeted genes are down-regulated by amiRNA-guided cleavage of the transcripts, resulting in the expected mutant phenotypes. The effects are highly specific to the target gene, the transgenes are stably inherited and they remain effective in the progeny. Conclusion/Significance: Our results not only show that amiRNAs can efficiently trigger gene silencing in a monocot crop, but also that amiRNAs can effectively modulate agronomically important traits in varieties used in modern breeding programs. We provide all software tools and a protocol for the design of rice amiRNA constructs, which can be easily adapted to other crops. The approach is suited for candidate gene validation, comparative functional genomics between different varieties, and for improvement of agronomic performance and nutritional value.
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LOCAS – A Low Coverage Assembly Tool for Resequencing Projects
<span title="2011-08-15">2011</span>
<i title="Public Library of Science (PLoS)">
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Motivation: Next Generation Sequencing (NGS) is a frequently applied approach to detect sequence variations between highly related genomes. Recent large-scale re-sequencing studies as the Human 1000 Genomes Project utilize NGS data of low coverage to afford sequencing of hundreds of individuals. Here, SNPs and micro-indels can be detected by applying an alignment-consensus approach. However, computational methods capable of discovering other variations such as novel insertions or highly
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0023455">doi:10.1371/journal.pone.0023455</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21858125">pmid:21858125</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3156226/">pmcid:PMC3156226</a>
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... sequence from low coverage NGS data are still lacking. Results: We present LOCAS, a new NGS assembler particularly designed for low coverage assembly of eukaryotic genomes using a mismatch sensitive overlap-layout-consensus approach. LOCAS assembles homologous regions in a homologyguided manner while it performs de novo assemblies of insertions and highly polymorphic target regions subsequently to an alignment-consensus approach. LOCAS has been evaluated in homology-guided assembly scenarios with low sequence coverage of Arabidopsis thaliana strains sequenced as part of the Arabidopsis 1001 Genomes Project. While assembling the same amount of long insertions as state-of-the-art NGS assemblers, LOCAS showed best results regarding contig size, error rate and runtime. Conclusion: LOCAS produces excellent results for homology-guided assembly of eukaryotic genomes with short reads and low sequencing depth, and therefore appears to be the assembly tool of choice for the detection of novel sequence variations in this scenario.
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The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
[article]
<span title="2019-07-05">2019</span>
<i title="Cold Spring Harbor Laboratory">
biorxiv/medrxiv
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Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few selected tissues and their contribution to genetic disorders is unknown. For this reason, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. Using RNA sequencing
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<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/687822">doi:10.1101/687822</a>
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... eq) data from the Genotype-Tissue Expression (GTEx) cohort comprising 49 tissues and 570 individuals, we found that new-borns on average harbour 0.5 - 1 post-zygotic and early embryonic mosaic mutations in coding exons affecting multiple tissues and organs (rate of 1.3225x 10-8 per nucleotide per individual). We further observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. Our findings suggest that EMMs are as frequent as germline de novo mutations, could therefore explain a substantial fraction of unsolved sporadic disease entities, and might play a previously under-appreciated role in cancer predisposition. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer if key functions such as cell cycle control are affected. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. In summary, the analysis of multiple tissues per individual allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and life. Our results show that embryonic mosaic mutations are frequent and likely play a role in many unsolved genetic disease cases. Hence, their detection needs to be an indispensable part of clinical diagnostics.
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The failure of B cells to induce non-canonical MYD88 splice variants correlates with lymphomagenesis via sustained NF-κB signaling
[article]
<span title="2020-06-18">2020</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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<span class="release-stage" >pre-print</span>
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Gain-of-function mutations of the TLR adaptor and oncoprotein MyD88 drive B cell lymphomagenesis via sustained NF-κB activation. In myeloid cells, sustained TLR activation and NF-κB activation lead to the induction of inhibitory MYD88 splice variants that restrain prolonged NF-κB activation. We therefore sought to investigate whether such a negative feedback loop exists in B cells. Analyzing MYD88 splice variants in normal B cells and different primary B cell malignancies, we observed that
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<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.06.18.154393">doi:10.1101/2020.06.18.154393</a>
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... splice variants in transformed B cells are dominated by the canonical, strongly NF-κB-activating isoform of MYD88 and contain at least three novel, so far uncharacterized signaling-competent splice isoforms. TLR stimulation in B cells unexpectedly reinforces splicing of NF-κB-promoting, canonical isoforms rather than the 'MyD88s', a negative regulatory isoform that is typically induced by TLRs in myeloid cells. This suggests that an essential negative feedback loop restricting TLR signaling in myeloid cells at the level of alternative splicing, is missing in B cells, rendering B cells vulnerable to sustained NF-κB activation and eventual lymphomagenesis. Our results uncover MYD88 alternative splicing as an unappreciated promoter of B cell lymphomagenesis and provide a rationale why oncogenic MYD88 mutations are exclusively found in B cells.
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711222225/https://www.biorxiv.org/content/biorxiv/early/2020/06/18/2020.06.18.154393.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext">
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The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
<span title="2020-05-27">2020</span>
<i title="Springer Science and Business Media LLC">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a>
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Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. Mosaic mutation detection in 49 normal
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-020-00746-1">doi:10.1186/s13073-020-00746-1</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32460841">pmid:32460841</a>
<a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3tim4en2crcjzklnqq37kf26ba">fatcat:3tim4en2crcjzklnqq37kf26ba</a>
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... ssues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10-8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
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Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
<span title="2018-05-31">2018</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a>
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Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes
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<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-018-1434-0">doi:10.1186/s13059-018-1434-0</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29855388">pmid:29855388</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5984361/">pmcid:PMC5984361</a>
<a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6shgjmcsrrfttkd7ovpn7f6yge">fatcat:6shgjmcsrrfttkd7ovpn7f6yge</a>
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... eutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor typespecific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.
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