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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop.
Osoegawa K, Vayntrub TA, Wenda S, De Santis D, Barsakis K, Ivanova M, Hsu S, Barone J, Holdsworth R, Diviney M, Askar M, Willis A, Railton D, Laflin S, Gendzekhadze K, Oki A, Sacchi N, Mazzocco M, Andreani M, Ameen R, Stavropoulos-Giokas C, Dinou A, Torres M, Dos Santos Francisco R, Serra-Pages C, Goodridge D, Balladares S, Bettinotti MP, Iglehart B, Kashi Z, Martin R, Saw CL, Ragoussis J, Downing J, Navarrete C, Chong W, Saito K, Petrek M, Tokic S, Padros K, Beatriz Rodriguez M, Zakharova V, Shragina O, Marino SR, Brown NK, Shiina T, Suzuki S, Spierings E, Zhang Q, Yin Y, Morris GP, Hernandez A, Ruiz P, Khor SS, Tokunaga K, Geretz A, Thomas R, Yamamoto F, Mallempati KC, Gangavarapu S, Kanga U, Tyagi S, Marsh SGE, Bultitude WP, Liu X, Cao D, Penning M, Hurley CK, Cesbron A, Mueller C, Mytilineos J, Weimer ET, Bengtsson M, Fischer G, Hansen JA, Chang CJ, Mack SJ, Creary LE, Fernandez-Viña MA. Osoegawa K, et al. Hum Immunol. 2019 Apr;80(4):228-236. doi: 10.1016/j.humimm.2019.01.009. Epub 2019 Feb 6. Hum Immunol. 2019. PMID: 30738112 Free PMC article. Review.
Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score …
Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the …
FastQ Screen: A tool for multi-genome mapping and quality control.
Wingett SW, Andrews S. Wingett SW, et al. F1000Res. 2018 Aug 24;7:1338. doi: 10.12688/f1000research.15931.2. eCollection 2018. F1000Res. 2018. PMID: 30254741 Free PMC article.
FastQ Screen is intended to be used routinely as a quality control measure and for analysing samples in which the origin of the DNA is uncertain or has multiple sources....
FastQ Screen is intended to be used routinely as a quality control measure and for analysing samples in which the origin of th …
Review of Clinical Next-Generation Sequencing.
Yohe S, Thyagarajan B. Yohe S, et al. Arch Pathol Lab Med. 2017 Nov;141(11):1544-1557. doi: 10.5858/arpa.2016-0501-RA. Epub 2017 Aug 7. Arch Pathol Lab Med. 2017. PMID: 28782984 Free article. Review.
This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE: - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet …
This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. …
Overview of Genotyping Technologies and Methods.
Kockum I, Huang J, Stridh P. Kockum I, et al. Curr Protoc. 2023 Apr;3(4):e727. doi: 10.1002/cpz1.727. Curr Protoc. 2023. PMID: 37026777
A general process of the steps involved in genotyping, from DNA preparation to quality control, is described with relevant protocols referenced. Different types of DNA variants are illustrated, including mutations, SNP, insertions, deletions, microsatellites, and co …
A general process of the steps involved in genotyping, from DNA preparation to quality control, is described with relevant pro …
SeQual-Stream: approaching stream processing to quality control of NGS datasets.
Castellanos-Rodríguez Ó, Expósito RR, Touriño J. Castellanos-Rodríguez Ó, et al. BMC Bioinformatics. 2023 Oct 27;24(1):403. doi: 10.1186/s12859-023-05530-7. BMC Bioinformatics. 2023. PMID: 37891497 Free PMC article.
BACKGROUND: Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. ...RESULTS: In this paper we present SeQual-Stream, a streaming tool that allows performing multiple quality control operations on genomic da …
BACKGROUND: Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. ...RESULTS: In …
Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA.
Willey JC, Morrison TB, Austermiller B, Crawford EL, Craig DJ, Blomquist TM, Jones WD, Wali A, Lococo JS, Haseley N, Richmond TA, Novoradovskaya N, Kusko R, Chen G, Li QZ, Johann DJ Jr, Deveson IW, Mercer TR, Wu L, Xu J. Willey JC, et al. Cell Rep Methods. 2021 Nov 3;1(7):100106. doi: 10.1016/j.crmeth.2021.100106. eCollection 2021 Nov 22. Cell Rep Methods. 2021. PMID: 35475002 Free PMC article.
The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis protocols and quality control metrics for use in DNA testing to enhance scientific research and precision medicine. This study r …
The primary objective of the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) project is to develop standard analysis pr …
Nucleic Acid Isolation and Quality Control.
Dong L, Yoshizawa J, Li X. Dong L, et al. Methods Mol Biol. 2019;1897:325-343. doi: 10.1007/978-1-4939-8935-5_28. Methods Mol Biol. 2019. PMID: 30539456 Review.
It also summarizes currently popular methods of quality control (QC) for genomic DNA, RNA, and next generation sequencing (NGS) libraries....
It also summarizes currently popular methods of quality control (QC) for genomic DNA, RNA, and next generation sequencing ( …
NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.
Mendoza-Parra MA, Saleem MA, Blum M, Cholley PE, Gronemeyer H. Mendoza-Parra MA, et al. Methods Mol Biol. 2016;1418:243-65. doi: 10.1007/978-1-4939-3578-9_13. Methods Mol Biol. 2016. PMID: 27008019
However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a …
However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets …
A versatile platform for combinatorial antibody library cloning and NGS-based quality control with high accuracy.
Zhang Z, D'Hondt S, Van der Kant R, Hermans G, Geukens N, Pinheiro VB, Schymkowitz J, Rousseau F, Dewilde M. Zhang Z, et al. Nucleic Acids Res. 2025 Oct 14;53(19):gkaf1001. doi: 10.1093/nar/gkaf1001. Nucleic Acids Res. 2025. PMID: 41099698 Free PMC article.
Additionally, we established a PCR-free next-generation sequencing (NGS) platform to assess the quality of assembled VHH libraries. Overall, these advancements provide a more efficient approach for constructing high-diversity multi-CDR combinatorial libraries with h …
Additionally, we established a PCR-free next-generation sequencing (NGS) platform to assess the quality of assembled VHH libra …
Quality Control and Analysis of NGS RNA Sequencing Data.
Quinn EM, McManus R. Quinn EM, et al. Methods Mol Biol. 2015;1326:217-32. doi: 10.1007/978-1-4939-2839-2_18. Methods Mol Biol. 2015. PMID: 26498624
This chapter describes an example workflow for the quality control and analysis of raw RNA sequencing reads for the purposes of differential gene expression analysis, followed by pathway/enrichment analysis of significantly different genes. ...
This chapter describes an example workflow for the quality control and analysis of raw RNA sequencing reads for the purposes o …
880 results