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Manta: Rapid detection of structural variants and indels for clinical sequencing applications [article]

Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Anthony J. Cox, Semyon Kruglyak, Christopher T. Saunders
2015 bioRxiv   pre-print
Summary: We describe Manta, a method to discover structural variants and indels from next generation sequencing data.  ...  Manta is optimized for rapid clinical analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods  ...  INTRODUCTION Whole genome and enrichment sequencing is increasingly used for discovery of inherited and somatic genome variation in clinical contexts, however tools for rapid discovery of structural variants  ... 
doi:10.1101/024232 fatcat:mphs2xtgrbdffdekoe7lcsiily

Exploration of intermediate-sized INDELs by next-generation multigene panel testing in Han Chinese patients with breast cancer

Chihiro Hata, Hirofumi Nakaoka, Yu Xiang, Dong Wang, Anping Yang, Dahai Liu, Fang Liu, Qingfeng Zou, Ke Zheng, Ituro Inoue, Hua You
2019 Human Genome Variation  
Multigene panel testing via next-generation sequencing focuses on the detection of small-sized mutations, such as single nucleotide variants and short insertions and deletions (INDELs).  ...  We detected a novel deletion-insertion in a translational variant of PTEN (also known as PTENα) in one patient.  ...  The authors would like to thank Enago (www.enago.jp) for the English language review.  ... 
doi:10.1038/s41439-019-0080-8 pmid:31700649 pmcid:PMC6820797 fatcat:iftyw6562raxln2cmxpadryeby

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma [article]

Hannah E Roberts, Maria Lopopolo, Alistair T Pagnamenta, Eshita Sharma, Duncan Parkes, Lorne Lonie, Colin Freeman, Samantha J L Knight, Gerton Lunter, Helene Dreau, Helen Lockstone, Jenny C Taylor (+3 others)
2020 bioRxiv   pre-print
Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants).  ...  Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality.  ...  SHORT VS LONG-READ GENOME SEQUENCING FOR SOMATIC VARIANT DETECTION  ... 
doi:10.1101/2020.03.24.999870 fatcat:inrdo6gckbagndlql5e36hmcci

SvABA: genome-wide detection of structural variants and indels by local assembly

Jeremiah A. Wala, Pratiti Bandopadhayay, Noah F. Greenwald, Ryan O'Rourke, Ted Sharpe, Chip Stewart, Steve Schumacher, Yilong Li, Joachim Weischenfeldt, Xiaotong Yao, Chad Nusbaum, Peter Campbell (+5 others)
2018 Genome Research  
Structural variants (SVs), including small insertion and deletion variants (indels), are challenging to detect through standard alignment-based variant calling methods.  ...  SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs and substantially improves detection performance for variants in the 20-300 bp range, compared with existing methods  ...  We would like to thank Heng Li for helpful comments and as the primary developer of BWA-MEM, and Jared Simpson as the developer of SGA.  ... 
doi:10.1101/gr.221028.117 pmid:29535149 pmcid:PMC5880247 fatcat:k66w5luy7nc5bpguwfuqedxxjy

Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

Hannah E. Roberts, Maria Lopopolo, Alistair T. Pagnamenta, Eshita Sharma, Duncan Parkes, Lorne Lonie, Colin Freeman, Samantha J. L. Knight, Gerton Lunter, Helene Dreau, Helen Lockstone, Jenny C. Taylor (+3 others)
2021 Scientific Reports  
Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants).  ...  Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality.  ...  These consist of BAM files for Illumina genomes (tumour and normal), Nanopore genomes (tumour and normal) and Nanopore RNA seq (tumour only).  ... 
doi:10.1038/s41598-021-85354-8 pmid:33742045 fatcat:n54yqyskc5gmnhustep3ghj6vu

Development of a targeted sequencing approach to identify prognostic, predictive and diagnostic markers in paediatric solid tumours

Elisa Izquierdo, Lina Yuan, Sally George, Michael Hubank, Chris Jones, Paula Proszek, Janet Shipley, Susanne A. Gatz, Caedyn Stinson, Andrew S. Moore, Steven C. Clifford, Debbie Hicks (+12 others)
2017 OncoTarget  
Cell blends containing known single nucleotide variants (SNVs, n=528) and small insertion-deletions (indels n=108) were used to define panel sensitivities of ≥98% for SNVs and ≥83% for indels [95% CI]  ...  ABSTRACT The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours.  ...  Manta (https://github.com/ Illumina/manta) was used for the detection of structural variants.  ... 
doi:10.18632/oncotarget.23000 pmid:29340109 pmcid:PMC5762377 fatcat:vzrmktynj5bmjj6sejy24pmpee

Development of a targeted sequencing approach to identify prognostic, predictive and diagnostic markers in paediatric solid tumours [article]

Elisa Izquierdo, Lina Yuan, Sally George, Michael Hubank, Chris Jones, Paula Proszek, Janet Shipley, Susanne A. Gatz, Caedyn Stinson, Andrew S. Moore, Steven C. Clifford, Debbie Hicks (+12 others)
2017 bioRxiv   pre-print
Cell blends containing known single nucleotide variants (SNVs, n=528) and small insertion-deletions (indels n=108) were used to define panel sensitivities of ≥98% for SNVs and ≥83% for indels [95% CI]  ...  The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours.  ...  Manta (https://github.com/Illumina/manta) was used for the detection of structural variants.  ... 
doi:10.1101/165746 fatcat:ita3qxad35fslbzxq5kzia3aza

Use of an Integrated Pan-Cancer Oncology Enrichment Next-Generation Sequencing Assay to Measure Tumour Mutational Burden and Detect Clinically Actionable Variants

Valerie Pestinger, Matthew Smith, Toju Sillo, John M. Findlay, Jean-Francois Laes, Gerald Martin, Gary Middleton, Phillipe Taniere, Andrew D. Beggs
2020 Molecular Diagnosis & Therapy  
For clinical actionability, 72 tier 1 variants and 297 tier 2 variants were detected, with clinical trials identified for all patients.  ...  We carried out comprehensive molecular profiling of cancers using the Illumina TruSight Oncology 500 (TSO500) panel and compared these to whole-genome sequencing (WGS).  ...  Acknowledgements We thank Professor Ian Tomlinson (University of Edinburgh) for the contribution of oesophageal cancer DNA samples for this assay. Author Contributions  ... 
doi:10.1007/s40291-020-00462-x pmid:32306292 fatcat:6ncl6ag7v5djdlrfvw4abj2szq

Seave: a comprehensive web platform for storing and interrogating human genomic variation

Velimir Gayevskiy, Tony Roscioli, Marcel E Dinger, Mark J Cowley, Jonathan Wren
2018 Bioinformatics  
Understanding the potential impact of variants, including structural variants, requires extensive annotation from disparate sources of knowledge, and in silico prediction algorithms.  ...  Genome sequencing has had a remarkable impact on our ability to study the effects of human genetic variation, however, variant interpretation remains the major bottleneck.  ...  In medicine, there has been a rapid uptake of genome sequencing for gene discovery and diagnosis within the areas of rare disease, pharmacogenomics, non-invasive pre-natal screening and cancer care (Delaney  ... 
doi:10.1093/bioinformatics/bty540 pmid:30561546 pmcid:PMC6298057 fatcat:3morrngacrhlpl3ql2h4n3n7am

Towards accurate and reliable resolution of structural variants for clinical diagnosis

Zhichao Liu, Ruth Roberts, Timothy R. Mercer, Joshua Xu, Fritz J. Sedlazeck, Weida Tong
2022 Genome Biology  
This difficulty and diversity make the detection of SVs for clinical applications challenging and requires a framework to ensure accuracy and reproducibility.  ...  Here, we discuss current developments in the diagnosis of SVs and propose a roadmap for the accurate and reproducible detection of SVs that includes case studies provided from the FDA-led SEquencing Quality  ...  Peer review information Anahita Bishop and Barbara Cheifet were the primary editors of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team  ... 
doi:10.1186/s13059-022-02636-8 pmid:35241127 pmcid:PMC8892125 fatcat:44u3sixevndcxmblb6ionrcdmy

Seave: a comprehensive web platform for storing and interrogating human genomic variation [article]

Velimir Gayevskiy, Tony Roscioli, Marcel E Dinger, Mark J Cowley
2018 bioRxiv   pre-print
Capability for genome sequencing and variant calling has increased dramatically, enabling large scale genomic interrogation of human disease.  ...  Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists.  ...  In medicine, there has been a rapid uptake of genome sequencing for gene discovery and diagnosis within the areas of rare disease, pharmacogenomics, non-invasive pre-natal screening and cancer care (Delaney  ... 
doi:10.1101/258061 fatcat:tdh6hdykwfgyngvwst3cpzwmy4

Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study [article]

Jonathan Foox, Scott W Tighe, Charles M Nicolet, Justin M Zook, Marta Byrska-Bishop, Wayne E Clarke, Michael M Khayat, Medhat Mahmoud, Phoebe K Laaguiby, Zachary T Herbert, Derek Warner, George S Grills (+8 others)
2020 bioRxiv   pre-print
of small-scale polymorphisms and large-scale structural variants.  ...  A total of 202 datasets were generated to investigate the performance of a total of 16 sequencing platforms, including mappability of reads, coverage and error rates in difficult genomic regions, and detection  ...  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics , - Figure : : Experimental design and mapping results.  ... 
doi:10.1101/2020.07.23.218602 fatcat:xbtlnrqagbfsxolcarhj2rtfce

Use of an integrated pan-cancer oncology enrichment NGS assay to measure tumour mutational burden and detect clinically actionable variants [article]

Valerie Pestinger, Matthew Smith, Toju Sillo, John M Findlay, Jean-Francois Laes, Gerald Martin, Gary Middleton, Phillipe Taniere, Andrew D Beggs
2020 medRxiv   pre-print
, MSI, single nucleotide variants, indels, copy number/structural variation and gene fusions when compared to whole genome sequencing and orthogonal technologies.  ...  For clinical actionability 72 Tier 1 variants and 297 Tier 2 variants were identified with clinical trials identified for all patients.ConclusionsThe TruSight Oncology 500 assay accurately measures TMB  ...  SV calls for the TSO500 files were obtained using the Manta structural variant caller set in tumour only mode with a custom modification to the C++ code of the Manta SV caller to enable detection with  ... 
doi:10.1101/2020.02.01.20019992 fatcat:7mu6zohbdjbjdhx3l5y3tublau

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Ben Lawrence, Cherie Blenkiron, Kate Parker, Peter Tsai, Sandra Fitzgerald, Paula Shields, Tamsin Robb, Mee Ling Yeong, Nicole Kramer, Sarah James, Mik Black, Vicky Fan (+25 others)
2018 npj Genomic Medicine  
The somatic aneuploidy allowed pathogenic germline variants (e.g., ATM) to be expressed unopposed, with RNA expression patterns showing inactivation of downstream tumor suppressor pathways.  ...  The two clinically relevant patterns of LoH described here define a novel oncogenic mechanism and a plausible route to genomic precision oncology for this tumor type.  ...  We also thank Stefan Bohlander (University of Auckland) for his help with genomic data analysis and interpretation, Ruellyn  ... 
doi:10.1038/s41525-018-0058-3 pmid:30062048 pmcid:PMC6054670 fatcat:koja5mlcjzbh5pcrn4ya6b4doi

Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome [article]

Vera B Kaiser, Lana Talmane, Yatendra Kumar, Fiona Semple, Marie MacLennan, David R FitzPatrick, Martin S Taylor, Colin A Semple
2021 bioRxiv   pre-print
Singleton short insertions (>=5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints.  ...  Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes.  ...  Manta: rapid detection of structural variants 935 and indels for germline and cancer sequencing applications.  ... 
doi:10.1101/2021.06.10.447556 fatcat:ungqpifnkbc3fgphkkxocenqty
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