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Simultaneous structural variation discovery among multiple paired-end sequenced genomes

F. Hormozdiari, I. Hajirasouliha, A. McPherson, E. E. Eichler, S. C. Sahinalp
2011 Genome Research  
This work was supported, in part, by the Nat-  ...  Alkan for providing the initial mappings of the wholegenome shotgun (WGS) sequencing data and S. Alaei, H. Jowhari, and S. Oveis Gharan for fruitful discussions on the problem. We also thank L.  ...  Methods Simultaneous structural variation discovery among multiple genomes Given a reference genome and a collection of paired-end sequenced genomes, G 1 ,. . .  ... 
doi:10.1101/gr.120501.111 pmid:22048523 pmcid:PMC3227108 fatcat:tmrjxgsn7ndxpcadqkqyycaerm

BAdabouM: a genomic structural variations discovery tool for polymorphism analyses [article]

Tristan Cumer, François Pompanon, Frédéric Boyer
2020 bioRxiv   pre-print
Nevertheless, they remain challenging to detect in whole genome re-sequencing (WGS) data.  ...  AbstractGenomic Structural Variations (SVs) are known to impact the evolution of genomes and to have consequences on individual's fitness.  ...  247 variations in whole genome re--sequencing data.  ... 
doi:10.1101/2020.04.01.018127 fatcat:kpghv2rivvczfpvric4astbqom

Genome structural variation discovery and genotyping

Can Alkan, Bradley P. Coe, Evan E. Eichler
2011 Nature reviews genetics  
Local sequence assembly of fosmid clones with discordant read pairs has been used to systematically discover structural variation in 17 human genomes 4, 31, 63 .  ...  Array CGH, array comparative genomic hybridization; CNP, copy-number polymorphism; ESP, end-sequence pair.  ... 
doi:10.1038/nrg2958 pmid:21358748 pmcid:PMC4108431 fatcat:ujvwnpdourethb27w3xvynprhq

Toolkit for automated and rapid discovery of structural variants

Arda Soylev, Can Kockan, Fereydoun Hormozdiari, Can Alkan
2017 Methods  
The advent of high throughput sequencing (HTS) technologies and the ability to perform whole genome sequencing (WGS), makes it feasible to study these variants in depth.  ...  Structural variations (SV) are broadly defined as genomic alterations that affect >50 bp of DNA, which are shown to have significant effect on evolution and disease.  ...  Shahidi Nejad for their help in coding parts of the TARDIS software, and I. Hajirasouliha and C. Ricketts for extensive testing and bug reports.  ... 
doi:10.1016/j.ymeth.2017.05.030 pmid:28583483 fatcat:urzkaz32ffd4nf2jzoi6rngq3u

Next Generation Sequencing and Bioinformatics
차세대 염기서열 분석기법과 생물정보학

Ki-Bong Kim
2015 Journal of Life Science  
Intrinsically, the analysis of NGS data includes the alignment of sequence reads to a reference, base-calling, and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural  ...  With the ongoing development of next-generation sequencing (NGS) platforms and advancements in the latest bioinformatics tools at an unprecedented pace, the ultimate goal of sequencing the human genome  ...  I apologize for the failure to cite many of the important and relevant papers in this field due to space limitations and timing.  ... 
doi:10.5352/jls.2015.25.3.357 fatcat:rntns3jlebajzg63rtuftn55km

Completing the map of human genetic variation

2007 Nature  
Significance: We propose that the Human Genome Structural Variation Project, be based on a recently developed fosmid paired-end sequencing strategy.  ...  repeat structure, insufficient sequence quality or lack of paired-end sequence data (singletons).  ... 
doi:10.1038/447161a pmid:17495918 pmcid:PMC2685471 fatcat:ruw33etmtzdvrggl7q75tyoz7i

Genome variation discovery with high-throughput sequencing data

A. V. Dalca, M. Brudno
2010 Briefings in Bioinformatics  
The data currently generated by HTS machines require extensive computational analysis in order to identify genomic variants present in the sequenced individual.  ...  The advent of high-throughput sequencing (HTS) technologies is enabling sequencing of human genomes at a significantly lower cost.  ...  Accordingly, the discovery of SVs in a genome is typically based on pair-end sequencing approaches [19] .  ... 
doi:10.1093/bib/bbp058 pmid:20053733 fatcat:rmhcyfmaovchnndc7a7b3durni

Computational methods for discovering structural variation with next-generation sequencing

Paul Medvedev, Monica Stanciu, Michael Brudno
2009 Nature Methods  
More recently, sequencing-based methods have used mate-pair or paired-end reads for structural variant discovery 2,3,5,9 (Box 1).  ...  Finally, all three NGS platforms are capable of generating mate-pair or paired-end data, enabling their use for structural variant discovery using PEM techniques.  ... 
doi:10.1038/nmeth.1374 pmid:19844226 fatcat:acigxzhwgzgm3o6adgdmyo4prq

LUMPY: A probabilistic framework for structural variant discovery [article]

Ryan M. Layer, Ira M. Hall, Aaron R. Quinlan
2014 arXiv   pre-print
Comprehensive discovery of structural variation (SV) in human genomes from DNA sequencing requires the integration of multiple alignment signals including read-pair, split-read and read-depth.  ...  We demonstrate improved sensitivity over extant methods by combining paired-end and split-read alignments and emphasize the utility of our framework for comprehensive studies of structural variation in  ...  Background Differences in chromosome structure are a prominent source of human genetic variation.  ... 
arXiv:1210.2342v2 fatcat:khzjhimpg5a5pezqygtv6aqieq

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

A. Schlattl, S. Anders, S. M. Waszak, W. Huber, J. O. Korbel
2011 Genome Research  
Bonaccorso, Maria Vincenza Catania, Barbara Bardoni, and Marc-Emmanuel Dumas Simultaneous structural variation discovery among multiple paired-end sequenced genomes 2203 Fereydoun Hormozdiari, Iman Hajirasouliha  ...  Mottram Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance Tim Downing, Hideo Imamura, Saskia Decuypere  ...  The colorful abstract segments on each arc show common and rare structural variation events among individual genomes.  ... 
doi:10.1101/gr.122614.111 pmid:21862627 pmcid:PMC3227091 fatcat:upcmj4sgrracdco6633oysn76m

Unraveling genomic variation from next generation sequencing data

Georgios A Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim, Yves Moreau, Reinhard Schneider, Jan Aerts, Ioannis Iliopoulos
2013 BioData Mining  
We conclude with a thorough review of tools developed to efficiently store, analyze and visualize such data with emphasis in structural variation analysis and comparative genomics.  ...  As next generation sequencing (NGS) techniques have become cheaper and more advanced in throughput over time, great innovations and breakthrough conclusions have been generated in various biological areas  ...  Meander [118] It is mainly developed to visually discover and explore structural variations in a genome based on Read-Depth and Pair-end information• Linear view • It supports its own file format both  ... 
doi:10.1186/1756-0381-6-13 pmid:23885890 pmcid:PMC3726446 fatcat:l4ethjk2jjb5xlwpaw6vquwrqi

Current analysis platforms and methods for detecting copy number variation

Wenli Li, Michael Olivier
2013 Physiological Genomics  
Current analysis platforms and methods for detecting copy number variation.  ...  Control-FREEC Single-end, mate-pair or paired-end genomic sequencing Uses a sliding window approach to calculate read count (RC) in nonoverlapping windows (raw copy number polymorphism).  ...  data Can be used on reads of variable lengths Is not constrained to short read lengths Ability to analyze complex structural variations SVMerge Single, pair-end sequencing data Uses a collection  ... 
doi:10.1152/physiolgenomics.00082.2012 pmid:23132758 pmcid:PMC3544484 fatcat:l5lj7p2djndh3oaokc2zafhcae

Computational SNP discovery in DNA sequence data

Gabor T Marth
2003 Msphere  
STS Sequences Sequence-tagged site (STS) sequences, amplified and sequenced in multiple individuals, were used in the first large-scale efforts to catalog variations at the genome scale (26).  ...  In humans, single base-pair substitution-type sequence variations occur with a frequency of approx 1 in 1.3 kb when two arbitrary sequences are compared (1).  ...  At the end of this step, a POLY file is present for each of the sequence traces, containing detailed numeric information about the trace characteristics at the position of each called nucleotide. 2.  ... 
pmid:12491905 fatcat:6u7q6tarx5cyxm5ghifojik5rq

Bioinformatics for Next Generation Sequencing Data

Alberto Magi, Matteo Benelli, Alessia Gozzini, Francesca Girolami, Francesca Torricelli, Maria Luisa Brandi
2010 Genes  
These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural  ...  variant detection and genome browsing.  ...  PEM-based Methods Pair-end sequencing means to sequence both ends of a DNA fragment. In this way, the two reads belonging to a pair will have a certain distance on the genome (mapped distance).  ... 
doi:10.3390/genes1020294 pmid:24710047 pmcid:PMC3954090 fatcat:wle7h6mkhjhxxon6ovzkv3gf4q

Chapter 6: Structural Variation and Medical Genomics

Benjamin J. Raphael, Fran Lewitter, Maricel Kann
2012 PLoS Computational Biology  
The latter class, called structural variants (SVs), have received considerable attention in the past several years as they are a previously under appreciated source of variation in human genomes.  ...  We describe the genomic technologies and computational techniques currently used to measure SVs, focusing on applications in human and cancer genomics.  ...  In PEM, a paired-end sequencing protocol is used to obtain paired reads from opposite ends of a larger DNA fragment, or clone, from a individual genome.  ... 
doi:10.1371/journal.pcbi.1002821 pmid:23300412 pmcid:PMC3531322 fatcat:bocxyjea4ranbgbek7qqy3olvy
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