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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

K. Ye, M. H. Schulz, Q. Long, R. Apweiler, Z. Ning
2009 Bioinformatics  
Results: We present Pindel, a pattern growth approach, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads.  ...  Availability: The binary code and a short user manual can be freely downloaded from  ...  Walter and Y. Zhang for comments. Funding: NGI/EBI fellowship 050-72-436 from Netherlands Genomics Initiative. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp394 pmid:19561018 pmcid:PMC2781750 fatcat:vw232fnc3bdzbhhxusoutswoui

iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data

Takahiro Mimori, Naoki Nariai, Kaname Kojima, Mamoru Takahashi, Akira Ono, Yukuto Sato, Yumi Yamaguchi-Kabata, Masao Nagasaki
2013 BMC Systems Biology  
We applied iSVP to the whole-genome sequence data of a CEU HapMap sample, and detected a large number of deletions, including notable peaks around 300 bp and 6,000 bp, which corresponded to Alus and long  ...  It achieved highly accurate deletion calling with >90% precision and >90% recall on the 30× read data for a broad range of size.  ...  Acknowledgements We would like to thank the anonymous referees for their constructive comments and suggestions, which improved the quality of the manuscript.  ... 
doi:10.1186/1752-0509-7-s6-s8 pmid:24564972 pmcid:PMC4029547 fatcat:3pwbvhzklne5ng2qr5dsj3arey

Machine learning-based detection of insertions and deletions in the human genome [article]

Charles Curnin, Rachel L. Goldfeder, Shruti Marwaha, Devon Bonner, Daryl Waggott, Matthew T. Wheeler, Euan A. Ashley
2019 bioRxiv   pre-print
Insertions and deletions (indels) make a critical but under-studied contribution to human genetic variation.  ...  Here, we present a machine learning-based approach to the detection of indel breakpoints.  ...  E.A.A is a founder of Personalis, Inc. and Deepcell Inc. EAA is an advisor to Sequence Bio and Genome Medical. Corresponding author Correspondence to Euan Ashley euan@stanford.edu  ... 
doi:10.1101/628222 fatcat:ypcfguycsnc2te6ga6umzf43km

Cloudbreak: Accurate and Scalable Genomic Structural Variation Detection in the Cloud with MapReduce [article]

Christopher W. Whelan, Jeffrey Tyner, Alberto L'Abbate, Clelia Tiziana Storlazzi, Lucia Carbone, Kemal Sönmez
2013 arXiv   pre-print
We describe a conceptual framework for SV detection algorithms in MapReduce based on computing local genomic features, and use it to develop a deletion and insertion detection algorithm, Cloudbreak.  ...  The detection of genomic structural variations (SV) remains a difficult challenge in analyzing sequencing data, and the growing size and number of sequenced genomes have rendered SV detection a bona fide  ...  Acknowledgments We would like to thank Izhak Shafran at the Center for Spoken Language Understanding for advice, support, and shared computational resources, and Bob Handsaker for helpful conversations  ... 
arXiv:1307.2331v2 fatcat:iztkom4hqbbpvobjpl3krabbm4

A comprehensive catalogue of somatic mutations from a human cancer genome

Erin D. Pleasance, R. Keira Cheetham, Philip J. Stephens, David J. McBride, Sean J. Humphray, Chris D. Greenman, Ignacio Varela, Meng-Lay Lin, Gonzalo R. Ordóñez, Graham R. Bignell, Kai Ye, Julie Alipaz (+33 others)
2009 Nature  
Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer  ...  A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers.  ...  Acknowledgements The authors acknowledge the support of C. Henry, S. Kahn, D. Evers, G. Smith, K. Hall and the technical and administrative support staff at Illumina.  ... 
doi:10.1038/nature08658 pmid:20016485 pmcid:PMC3145108 fatcat:atgbvmp7yrh5vjyj277dwijl5e

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploidCapsella bursa-pastoris

Gavin M. Douglas, Gesseca Gos, Kim A. Steige, Adriana Salcedo, Karl Holm, Emily B. Josephs, Ramesh Arunkumar, J. Arvid Ågren, Khaled M. Hazzouri, Wei Wang, Adrian E. Platts, Robert J. Williamson (+4 others)
2015 Proceedings of the National Academy of Sciences of the United States of America  
Approximately 20 million 2x105nt Illumina read pairs (4.3GBase) from two European accessions (12.4 and 16.9) were 3' trimmed to remove sequences with a quality <30 and contigs were then generated by the  ...  A marginal degree of further scaffolding was then undertaken with the Soap de Novo assembler (BGI, v 1.05) using the same paired-end data and a Kmer length of 51.  ...  Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.  ... 
doi:10.1073/pnas.1412277112 pmid:25691747 pmcid:PMC4352811 fatcat:gjd5fcxdlbcyfhxxcndai7f2ty

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

Colin S Cooper, Rosalind Eeles, David C Wedge, Peter Van Loo, Gunes Gundem, Ludmil B Alexandrov, Barbara Kremeyer, Adam Butler, Andrew G Lynch, Niedzica Camacho, Charlie E Massie, Jonathan Kay (+60 others)
2015 Nature Genetics  
Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men.  ...  This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule  ...  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871 (2009). 34.. Campbell, P. J. et al.  ... 
doi:10.1038/ng.3221 pmid:25730763 pmcid:PMC4380509 fatcat:7mtd3ni3djdtljrdotol6gwg7a

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome

Walter Sanseverino, Elizabeth Hénaff, Cristina Vives, Sara Pinosio, William Burgos-Paz, Michele Morgante, Sebastián E. Ramos-Onsins, Jordi Garcia-Mas, Josep Maria Casacuberta
2015 Molecular biology and evolution  
Here we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, structural variation and transposon insertion polymorphisms.  ...  This is a strong limitation as structural variation and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding.  ...  Acknowledgements We thank Jordi Morata for his help dating retrotransposon insertions. This work was  ... 
doi:10.1093/molbev/msv152 pmid:26174143 fatcat:vytk6yovevacbiy2qxu4ajkjx4

AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis thaliana Genome

Agnieszka Zmienko, Malgorzata Marszalek-Zenczak, Pawel Wojciechowski, Anna Samelak-Czajka, Magdalena Luczak, Piotr Kozlowski, Wojciech M Karlowski, Marek Figlerowicz
2020 The Plant Cell  
Here, we performed a genome-wide analysis and identified large indels (50-499 bp) and CNVs (500 bp and larger) present in these accessions.  ...  We then successfully used the CNVs as markers in an analysis of population structure and migration patterns.  ...  and CNV-Insert size distributions in paired-end libraries.  ... 
doi:10.1105/tpc.19.00640 pmid:32265262 pmcid:PMC7268809 fatcat:ow7aacaixnbnrib3ai6gjhz5hm

A comprehensive benchmarking of WGS-based structural variant callers [article]

Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Sei Chang, Angela Lu, Nicholas Darci-Maher, Russell Littman, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin (+2 others)
2020 bioRxiv   pre-print
Dissecting SVs from whole genome sequencing (WGS) data presents a substantial number of challenges and a plethora of SV-detection methods have been developed.  ...  Our study investigates the ability of the methods to detect deletions, thus providing an optimistic estimate of SV detection performance, as the SV-detection methods that fail to detect deletions are likely  ...  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25 , 2865-2871 (2009). 40. Lin, Y.-Y. et al.  ... 
doi:10.1101/2020.04.16.045120 fatcat:vvj2cj4pzzeyxgiixt43sgi5oi

Ultra-deep sequencing reveals dramatic alteration of organellar genomes in Physcomitrella patens due to biased asymmetric recombination

Masaki Odahara, Kensuke Nakamura, Yasuhiko Sekine, Taku Oshima
2021 Communications Biology  
AbstractDestabilization of organelle genomes causes organelle dysfunction that appears as abnormal growth in plants and diseases in human.  ...  The rearrangements were location-dependent and mostly derived from the asymmetric products of microhomology-mediated recombination.  ...  This work was supported by SUMITOMO Foundation (170946 to M.O.), the Japan Society for the Promotion of Science (16K18588 and 19K22405 to M.O.), and the Strategic Research Foundation Grant-aided Project  ... 
doi:10.1038/s42003-021-02141-x pmid:34045660 fatcat:gmrqxuh4ozcm5ewdtheyllxjdu

Collateral damage: Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme [article]

Morag A Lewis, Neil A Ingham, Jing Chen, Selina Pearson, Francesca Di Domenico, Sohinder Rekhi, Rochelle Allen, Matthew Drake, Annelore Willaert, Victoria Rook, Johanna Pass, Thomas Keane (+4 others)
2021 bioRxiv   pre-print
Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline.  ...  Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and many phenotypes are easy to miss if not specifically looked for.  ...  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-71 (2009). 70. McLaren, W. et al.  ... 
doi:10.1101/2021.06.30.450312 fatcat:qvpurhdd5zcqjnhe5sw5oejcsy

Haplotype-resolved and integrated genome analysis of ENCODE cell line HepG2 [article]

Bo Zhou, Steve S. Ho, Stephanie U. Greer, Noah Spies, John M. Bell, Xianglong Zhang, Xiaowei Zhu, Joseph G. Arthur, Seunggyu Byeon, Reenal Pattni, Ishan Saha, Giltae Song (+5 others)
2018 bioRxiv   pre-print
We performed deep whole-genome sequencing, mate-pair sequencing and linked-read sequencing to identify a wide spectrum of genome characteristics in HepG2: copy numbers of chromosomal segments, SNVs and  ...  A large number of SVs were phased, sequence assembled and experimentally validated. Several chromosomes show striking loss of heterozygosity.  ...  Idan Gabdank, Nathaniel Watson, Zachary A. Myers, and Dr. Cricket Sloan for data  ... 
doi:10.1101/378497 fatcat:47rquomydbgdnilbhq77zwbqyi

The Spontaneous Mutation Rate in the Fission YeastSchizosaccharomyces pombe

Ashley Farlow, Hongan Long, Stéphanie Arnoux, Way Sung, Thomas G. Doak, Magnus Nordborg, Michael Lynch
2015 Genetics  
However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract  ...  We undertook an 1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates  ...  Army Research Office and the National Institutes of Health (grant R01GM101672 to M.L.).  ... 
doi:10.1534/genetics.115.177329 pmid:26265703 pmcid:PMC4596680 fatcat:uow6us4cvbgmpamsrak6pkn4d4

TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data

Jesper Eisfeldt, Francesco Vezzi, Pall Olason, Daniel Nilsson, Anna Lindstrand
2017 F1000Research  
Ye K, Schulz MH, Long Q, et al.: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.  ...  Here we present TIDDIT, a time efficient variant caller, that uses discordant read pairs as well as the depth of coverage and split reads to detect and classify a large spectrum of SVs.  ...  Acknowledgments The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure (NGI), and Uppmax for providing assistance in massive parallel sequencing  ... 
doi:10.12688/f1000research.11168.1 pmid:28781756 pmcid:PMC5521161 fatcat:263bo6ntzjbmhg6aju5syuqp34
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