scholarly journals New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

2013 ◽  
Vol 15 (3) ◽  
pp. 343-353 ◽  
Author(s):  
K. Song ◽  
J. Ren ◽  
G. Reinert ◽  
M. Deng ◽  
M. S. Waterman ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Comparison ◽  
Next Generation ◽  
New Developments ◽  
Alignment Free ◽  
Comparison Measures ◽  
Generation Sequencing

scholarly journals Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

2013 ◽  
Vol 20 (2) ◽  
pp. 64-79 ◽  
Author(s):  
Kai Song ◽  
Jie Ren ◽  
Zhiyuan Zhai ◽  
Xuemei Liu ◽  
Minghua Deng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Comparison ◽  
Next Generation ◽  
Alignment Free ◽  
Generation Sequencing

scholarly journals Prostate cancer heterogeneity assessment with multi-regional sampling and alignment-free methods

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Ross G Murphy ◽  
Aideen C Roddy ◽  
Shambhavi Srivastava ◽  
Esther Baena ◽  
David J Waugh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Cancer Heterogeneity ◽  
Alignment Free ◽  
Treatment Indications ◽  
Patient Heterogeneity ◽  
Genomic Locations ◽  
Generation Sequencing

Abstract Combining alignment-free methods for phylogenetic analysis with multi-regional sampling using next-generation sequencing can provide an assessment of intra-patient tumour heterogeneity. From multi-regional sampling divergent branching, we validated two different lesions within a patient’s prostate. Where multi-regional sampling has not been used, a single sample from one of these areas could misguide as to which drugs or therapies would best benefit this patient, due to the fact these tumours appear to be genetically different. This application has the power to render, in a fraction of the time used by other approaches, intra-patient heterogeneity and decipher aberrant biomarkers. Another alignment-free method for calling single-nucleotide variants from raw next-generation sequencing samples has determined possible variants and genomic locations that may be able to characterize the differences between the two main branching patterns. Alignment-free approaches have been applied to relevant clinical multi-regional samples and may be considered as a valuable option for comparing and determining heterogeneity to help deliver personalized medicine through more robust efforts in identifying targetable pathways and therapeutic strategies. Our study highlights the application these tools could have on patient-aligned treatment indications.

scholarly journals Next generation sequencing reads comparison with an alignment-free distance

2014 ◽  
Vol 7 (1) ◽  
pp. 869 ◽  
Author(s):  
Emanuel Weitschek ◽  
Daniele Santoni ◽  
Giulia Fiscon ◽  
Maria De Cola ◽  
Paola Bertolazzi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Free Distance ◽  
Alignment Free ◽  
Generation Sequencing

scholarly journals FALCON-meta: a method to infer metagenomic composition of ancient DNA

2018 ◽  
Author(s):  
Diogo Pratas ◽  
Armando J. Pinho ◽  
Raquel M. Silva ◽  
João M. O. S. Rodrigues ◽  
Morteza Hosseini ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ancient Dna ◽  
Computational Cost ◽  
Next Generation ◽  
Link Type ◽  
Alignment Free ◽  
Sample Composition ◽  
Metagenomic Sample ◽  
Consequent Increase ◽  
Generation Sequencing

The general approaches to detect and quantify metagenomic sample composition are based on the alignment of the reads, according to an existing database containing reference microbial sequences. However, without proper parameterization, these methods are not suitable for ancient DNA. Quantifying somewhat dissimilar sequences by alignment methods is problematic, due to the need of fine-tuned thresholds, considering relaxed edit distances and the consequent increase of computational cost. Additionally, the choice of the thresholds poses the problem of how to quantify similarity without producing overestimated measures. We propose FALCON-meta, a compression-based method to infer metagenomic composition of next-generation sequencing samples. This unsupervised alignment-free method runs efficiently on FASTQ samples. FALCON-meta quickly learns how to give importance to the models that cooperate to predict similarity, incorporating parallelism and flexibility for multiple hardware characteristics. It shows substantial identification capabilities in ancient DNA without overestimation. In one of the examples, we found and authenticated an ancient Pseudomonas bacteria in a Mammoth mitogenome.FALCON-meta can be accessed at https://github.com/pratas/falcon.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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