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Essential Elements for Establishing Clinical Next-generation Sequencing Testing

민원기|이우창|전사일|박경진
대한진단검사의학회 (Korean Society For Laboratory Medicine)|2019.04|Laboratory Medicine Online|제9권 제2호|pp. 37-44|DOI https://doi.org/10.3343/lmo.2019.9.2.37

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Next-generation sequencing (NGS)Quality control (QC)Reference material (RM)

초록

Over the past decade, next-generation sequencing (NGS) has evolved at an astonishing pace and has revolutionized clinical medicine as well as genomics research. The rapid advancements in NGS technologies have been accompanied by accumulating evidence of the analytical and clinical validity, and clinical utility of NGS. NGS is used worldwide. This review provides medical technicians and laboratory physicians with the essential elements for establishing clinical NGS testing. Here the authors briefly describe the advantages and drawbacks of currently available NGS platforms, potential sources of error in NGS workflow, and reference materials.

Abstract

Over the past decade, next-generation sequencing (NGS) has evolved at an astonishing pace and has revolutionized clinical medicine as well as genomics research. The rapid advancements in NGS technologies have been accompanied by accumulating evidence of the analytical and clinical validity, and clinical utility of NGS. NGS is used worldwide. This review provides medical technicians and laboratory physicians with the essential elements for establishing clinical NGS testing. Here the authors briefly describe the advantages and drawbacks of currently available NGS platforms, potential sources of error in NGS workflow, and reference materials.

참고문헌 (29)

  1. Levy SE, "Advancements in next-generation sequencing", Annu Rev Genomics Hum Genet, 17, pp.95~115 (2016)
  2. Goodwin S, "Coming of age : ten years of next-generation sequencing technologies", Nat Rev Genet, 17, pp.333~351 (2016)
  3. Minear MA, "Noninvasive prenatal genetic testing : current and emerging ethical, legal, and social issues", Annu Rev Genomics Hum Genet, 16, pp.369~398 (2015)
  4. 박경진, "A Population-Based Genomic Study of Inherited Metabolic Diseases Detected Through Newborn Screening", Annals of Laboratory Medicine, 36(6), pp.561~572 (2016), 대한진단검사의학회
  5. Bodian DL, "Utility of whole-genome sequencing for detection of newborn screening disorders in a population cohort of 1, 696 neonates", Genet Med, 18, pp.221~230 (2016)
  6. Pritchard CC, "Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens", J Mol Diagn, 16, pp.56~67 (2014)
  7. Lih CJ, "Analytical validation and application of a targeted next-generation sequencing mutation-detection assay for use in treatment assignment in the NCI-MPACT trial", J Mol Diagn, 18, pp.51~67 (2016)
  8. Saunders CJ, "Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units", Sci Transl Med, 4, pp.154ra135~ (2012)
  9. Segal JP, "Next-generation proficiency testing", J Mol Diagn, 18, pp.469~470 (2016)
  10. Aziz N, "College of American Pathologists’ laboratory standards for next-generation sequencing clinical tests", Arch Pathol Lab Med, 139, pp.481~493 (2015)
  11. Aird D, "Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries", Genome Biol, 12, pp.R18~ (2011)
  12. Benjamini Y, "Summarizing and correcting the GC content bias in high-throughput sequencing", Nucleic Acids Res, 40, pp.e72~ (2012)
  13. Jennings LJ, "Guidelines for validation of next-generation sequencing-based oncology panels : a joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists", J Mol Diagn, 19, pp.341~365 (2017)
  14. Robasky K, "The role of replicates for error mitigation in next-generation sequencing", Nat Rev Genet, 15, pp.56~62 (2014)
  15. Jones S, "Personalized genomic analyses for cancer mutation discovery and interpretation", Sci Transl Med, 7, pp.283~ (2015)[DOI]
  16. Kebschull JM, "Sources of PCR-induced distortions in high-throughput sequencing data sets", Nucleic Acids Res, 43, pp.e143~ (2015)
  17. "Illumina"[URL]
  18. Pabinger S, "A survey of tools for variant analysis of next-generation genome sequencing data", Brief Bioinform, 15, pp.256~278 (2014)
  19. Oliver GR, "Bioinformatics for clinical next generation sequencing", Clin Chem, 61, pp.124~135 (2015)
  20. Chiara M, "Evaluation of quality assessment protocols for high throughput genome resequencing data", Front Genet, 8, pp.94~ (2017)
  21. Gargis AS, "Good laboratory practice for clinical next-generation sequencing informatics pipelines", Nat Biotechnol, 33, pp.689~693 (2015)
  22. Santani A, "Development and validation of targeted next-generation sequencing panels for detection of germline variants in inherited diseases", Arch Pathol Lab Med, 141, pp.787~797 (2017)
  23. Hardwick SA, "Reference standards for next-generation sequencing", Nat Rev Genet, 18, pp.473~484 (2017)
  24. Schmitt MW, "Detection of ultra-rare mutations by next-generation sequencing", Proc Natl Acad Sci U S A, 109, pp.14508~14513 (2012)
  25. Sims DJ, "Plasmid-based materials as multiplex quality controls and calibrators for clinical next-generation sequencing assays", J Mol Diagn, 18, pp.336~349 (2016)
  26. Kudalkar EM, "Multiplexed reference materials as controls for diagnostic next-generation sequencing : a pilot investigating applications for hypertrophic cardiomyopathy", J Mol Diagn, 18, pp.882~889 (2016)
  27. "Illumina"[URL]
  28. Duncavage EJ, "A model study of in silico proficiency testing for clinical next-generation sequencing", Arch Pathol Lab Med, 140, pp.1085~1091 (2016)
  29. Davies KD, "Multi-institutional FASTQ file exchange as a means of proficiency testing for next-generation sequencing bioinformatics and variant interpretation", J Mol Diagn, 18, pp.572~579 (2016)

관련 논문AI추천

Application of Next Generation Sequencing in Laboratory MedicineLi Marilyn M., Schubert Jeffrey, Wu Jinhua, Xu Feng, Zhong Yiming대한진단검사의학회 · Annals of Laboratory Medicine2021 · 제41권 제1호Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests최진, 고영혜, 김나영, 김지훈, 박웅양, 성창옥, 심효섭, 원재경, 장세진, 천성민, 최윤라대한병리학회 · Journal of Pathology and Translational Medicine2017 · 제51권 제3호Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships한진영, Justin M. Zook, Lisa V. Kalman, Marc L. Salit, Mickey Williams, Vivekananda Datta대한진단검사의학회 · Annals of Laboratory Medicine2016 · 제36권 제6호Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing김자영, 박상태대한배뇨장애요실금학회 · International Neurourology Journal2016 · 제20권 제1호Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors김문식, 김주희, 김지은, 박지영, 이창선, 정지윤, 홍주연대한암학회 · Cancer Research and Treatment2023 · 제55권 제2호Korean Society for Genetic Diagnostics Guidelines for Validation of Next-Generation Sequencing-Based Somatic Variant Detection in Hematologic Malignancies김선희, 김종원, 김혜진, 김희진, 윤재원, 이승태대한진단검사의학회 · Annals of Laboratory Medicine2019 · 제39권 제6호

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