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Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long-and short-read Multi-metagenomic sequencing Studies

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Genomics, Proteomics & Bioinformatics 2022年第2期20卷 405-417页

作者： Jacqueline Rehner Georges Pierre Schmartz Laura Groeger Jan Dastbaz Nicole Ludwig Matthias Hannig Stefan Rupf Berthold Seitz Elias Flockerzi Tim Berger Matthias Christian Reichert Marcin Krawczyk Eckart Meese Christian Herr Robert Bals Soren L.Becker Andreas Keller Rolf Muller The IMAGINE Consortium Institute of Medical Microbiology and Hygiene Saarland UniversityD-66421 HomburgGermany Clinical Bioinformatics Saarland UniversityD-66123 SaarbruckenGermany Department of Human Genetics Saarland UniversityD-66421 HomburgGermany Helmholtz Institute for Pharmaceutical Research Saarland D-66123 SaarbruckenGermany Clinic of Operative Dentistry Periodontology and Preventive DentistrySaarland UniversityD-66421 HomburgGermany Department of Ophthalmology Saarland University Medical CenterD-66421 HomburgGermany Department of Medicine Ⅱ Saarland University Medical CenterD-66421 HomburgGermany Department of Internal Medicine V–Pulmonology AllergologyIntensive Care MedicineSaarland UniversityD-66421 HomburgGermany

High-quality DNA extraction is a crucial step in metagenomic *** by different isolation kits impairs the comparison across datasets.A trending topic is,however,the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with *** thus collected bile,stool,saliva,plaque,sputum,and conjunctival swab samples and performed DNA extraction with three commercial *** each combination of the specimen type and DNA extraction kit,20-gigabase(Gb)metagenomic data were generated using short-read *** profiles of the specimen types showed close proximity to each other,we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction *** kit outperformed all selected kits on every *** reached consistently good results using the Qiagen QiAamp DNA Microbiome *** on the specimen,our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution,but DNA-based identification is superior to identification by mass ***,longread nanopore sequencing confirmed the results(correlation coefficient>0.98).Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

关键词： Whole-genome analysis Comparative genomics short-read sequencing Long-read sequencing DNA extraction Metagenomics

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Pindel-TD:A Tandem Duplication Detector Based on A Pattern Growth Approach

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 99-104页

作者： Xiaofei Yang Gaoyang Zheng Peng Jia Songbo Wang Kai Ye School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Center for Mathematical Medical the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Faculty of Science Leiden UniversityLeiden 2311 EZNetherland

Tandem duplication(TD)is a major type of structural variations(SVs)that plays an important role in novel gene formation and human ***,TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational ***,we developed a TD detection module for the Pindel tool,referred to as Pindel-TD,based on a TD-specific pattern growth ***-TD is capable of detecting TDs with a wide size range at single nucleotide *** simulated and real read data from HG002,we demonstrated that Pindel-TD outperforms other leading methods in terms of precision,recall,F1-score,and ***,by applying Pindel-TD to data generated from the K562 cancer cell line,we identified a TD located at the seventh exon of SAGE1,providing an explanation for its high ***-TD is available for non-commercial use at https://***/xjtu-omics/pindel.

关键词： Tandem duplication Pattern growth short-read sequencing Structural variation SAGE1

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