J Pathol Transl Med.  2017 May;51(3):191-204. 10.4132/jptm.2017.03.14.

Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests

  • 1Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea. jihunkim@amc.seoul.kr
  • 2Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea.
  • 3Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.
  • 4Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
  • 5Department of Pathology, Yonsei University College of Medicine, Seoul, Korea.
  • 6Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.


Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS. This consensus standard proposal consists of two parts: laboratory guidelines and requirements for clinical NGS laboratories. The laboratory guidelines part addressed several important issues across multistep NGS cancer panel tests including choice of gene panel and platform, sample handling, nucleic acid management, sample identity tracking, library preparation, sequencing, analysis and reporting. Requirements for clinical NGS tests were summarized in terms of documentation, validation, quality management, and other required written policies. Together with appropriate pathologist training and international laboratory standards, these laboratory standards would help molecular pathology laboratories to successfully implement NGS cancer panel tests in clinic. In this way, the oncology community would be able to help patients to benefit more from personalized cancer medicine.


High-throughput nucleotide sequencing; Molecular pathology; Neoplasms; Quality control; Practice guidelines as topic

MeSH Terms

High-Throughput Nucleotide Sequencing
Pathology, Molecular
Practice Guidelines as Topic
Quality Control


  • Fig. 1. Varying tissue conditions to be considered for next-generation sequencing analysis. (A) Gastric carcinoma with lymphoid stroma with acceptable tumor content although many intraepithelial lymphocytes are seen. (B) The same case as (A) but this area has unacceptable tumor content due to heavy lymphoid cell infiltration. (C) This poorly differentiated carcinoma shows extensive necrosis. (D) Mucinous adenocarcinoma of the colon shows a large area of extracellular mucin.

Cited by  3 articles

Molecular biomarker testing for non–small cell lung cancer: consensus statement of the Korean Cardiopulmonary Pathology Study Group
Sunhee Chang, Hyo Sup Shim, Tae Jung Kim, Yoon-La Choi, Wan Seop Kim, Dong Hoon Shin, Lucia Kim, Heae Surng Park, Geon Kook Lee, Chang Hun Lee
J Pathol Transl Med. 2021;55(3):181-191.    doi: 10.4132/jptm.2021.03.23.

Recent Advancement of the Molecular Diagnosis in Pediatric Brain Tumor
Jeong-Mo Bae, Jae-Kyung Won, Sung-Hye Park
J Korean Neurosurg Soc. 2018;61(3):376-385.    doi: 10.3340/jkns.2018.0057.

Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors
Moonsik Kim, Changseon Lee, Juyeon Hong, Juhee Kim, Ji Yun Jeong, Nora Jee-Young Park, Ji-Eun Kim, Ji Young Park
Cancer Res Treat. 2022;55(2):429-441.    doi: 10.4143/crt.2022.891.


1. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008; 456:53–9.
2. Metzker ML. Sequencing technologies: the next generation. Nat Rev Genet. 2010; 11:31–46.
3. Aziz N, Zhao Q, Bry L, et al. College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Arch Pathol Lab Med. 2015; 139:481–93.
4. Rehm HL, Bale SJ, Bayrak-Toydemir P, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013; 15:733–47.
5. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK. WHO classification of tumours of the central nervous system. Revised 4th ed. Lyon: IARC Press;2016.
6. Burghel GJ, Hurst CD, Watson CM, et al. Towards a next-generation sequencing diagnostic service for tumour genotyping: a comparison of panels and platforms. Biomed Res Int. 2015; 2015:478017.
7. Hinrichs JW, van Blokland WT, Moons MJ, et al. Comparison of next-generation sequencing and mutation-specific platforms in clinical practice. Am J Clin Pathol. 2015; 143:573–8.
8. McCourt CM, McArt DG, Mills K, et al. Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One. 2013; 8:e69604.
9. Hicks DG, Boyce BF. The challenge and importance of standardizing pre-analytical variables in surgical pathology specimens for clinical care and translational research. Biotech Histochem. 2012; 87:14–7.
10. Howat WJ, Wilson BA. Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods. 2014; 70:12–9.
11. Do H, Dobrovic A. Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization. Clin Chem. 2015; 61:64–71.
12. Do H, Wong SQ, Li J, Dobrovic A. Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. Clin Chem. 2013; 59:1376–83.
13. Lin MT, Mosier SL, Thiess M, et al. Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. Am J Clin Pathol. 2014; 141:856–66.
14. Serizawa M, Yokota T, Hosokawa A, et al. The efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal cancer tissues. Cancer Genet. 2015; 208:415–27.
15. Marchetti A, Felicioni L, Buttitta F. Assessing EGFR mutations. N Engl J Med. 2006; 354:526–8.
16. Choi SE, Hong SW, Yoon SO. Proposal of an appropriate decalcification method of bone marrow biopsy specimens in the era of expanding genetic molecular study. J Pathol Transl Med. 2015; 49:236–42.
17. Pengelly RJ, Gibson J, Andreoletti G, Collins A, Mattocks CJ, Ennis S. A SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Med. 2013; 5:89.
18. Brownstein CA, Beggs AH, Homer N, et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 2014; 15:R53.
19. Cornish A, Guda C. A comparison of variant calling pipelines using genome in a bottle as a reference. Biomed Res Int. 2015; 2015:456479.
20. Hwang S, Kim E, Lee I, Marcotte EM. Systematic comparison of variant calling pipelines using gold standard personal exome variants. Sci Rep. 2015; 5:17875.
21. Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics. 2012; 28:2711–8.
22. Onsongo G, Baughn LB, Bower M, et al. CNV-RF is a random forest-based copy number variation detection method using next-generation sequencing. J Mol Diagn. 2016; 18:872–81.
23. Frampton GM, Fichtenholtz A, Otto GA, et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol. 2013; 31:1023–31.
24. Deans ZC, Costa JL, Cree I, et al. Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL. Virchows Arch. 2017; 470:5–20.
25. ISO 15189: 2012 Medical laboratories: requirements for quality and competence [Internet]. Geneva: International Organization for Standardization;c2012-2017. [cited 2017 Jan 31]. Available from: https://www.iso.org/obp/ui/#iso:std:iso:15189:ed-3:v2:en.
26. Nomenclature for the description of sequence variants [Internet]. Melbourne: Human Genome Variation Society;c2010-2017. [cited 2017 Jan 31]. Available from: http://www.hgvs.org/mutnomen/.
27. Li MM, Datto M, Duncavage EJ, et al. Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017; 19:4–23.
28. Use of standards in FDA regulatory oversight of next generation sequencing (NGS)-based in vitro diagnostics (IVDs) used for diagnosing germline diseases [Internet]. Rockville: US Department of Health and Services, Food and Drug Administration;c2016-2017. [cited 2017 Jan 31]. Available from: http://www.fda.gov/downloads/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/UCM509838.pdf.
29. Chin EL, da Silva C, Hegde M. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet. 2013; 14:6.
30. Cottrell CE, Al-Kateb H, Bredemeyer AJ, et al. Validation of a next-generation sequencing assay for clinical molecular oncology. J Mol Diagn. 2014; 16:89–105.
31. Hagemann IS, Cottrell CE, Lockwood CM. Design of targeted, capture-based, next generation sequencing tests for precision cancer therapy. Cancer Genet. 2013; 206:420–31.
32. Williams ES, Hegde M. Implementing genomic medicine in pathology. Adv Anat Pathol. 2013; 20:238–44.
33. Zook JM, Chapman B, Wang J, et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014; 32:246–51.
34. National Center for Biotechnology Information. GeT-RM Homo sapiens [Internet]. Bethesda: US National Library of Medicine;c2017. [cited 2017 Jan 31]. Available from: https://www.ncbi.nlm.nih.gov/variation/tools/get-rm/.
35. Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res. 2011; 21:1498–505.
36. Gargis AS, Kalman L, Berry MW, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol. 2012; 30:1033–6.
37. Gargis AS, Kalman L, Bick DP, et al. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nat Biotechnol. 2015; 33:689–93.
38. Association for Molecular Pathology. Clinical practice guidelines [Internet]. Bethesda: Association for Molecular Pathology;c2009-2017. [cited 2017 Jan 31]. Available from: https://www.amp.org/committees/clinical_practice/AMPclinicalpracticeguidelines.cfm.
39. ESMO clinical practice guidelines [Internet]. Viganello-Lugano: European Society for Medical Oncology;c2017. [cited 2017 Jan 31]. Available from: http://www.esmo.org/Guidelines.
40. Cree IA, Deans Z, Ligtenberg MJ, et al. Guidance for laboratories performing molecular pathology for cancer patients. J Clin Pathol. 2014; 67:923–31.
41. Luthra R, Chen H, Roy-Chowdhuri S, Singh RR. Next-generation sequencing in clinical molecular diagnostics of cancer: advantages and challenges. Cancers (Basel). 2015; 7:2023–36.
42. Schrijver I, Aziz N, Farkas DH, et al. Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. J Mol Diagn. 2012; 14:525–40.
43. Next generation sequence analysis (NGS). Clinical laboratory certification guidelines [Internet]. Cheongju: Ministry of Food and Drug Safety;c2016. [cited 2017 Jan 31]. Available from: http://www.mfds.go.kr/index.do?mid=1161&seq=11001&cmd=v.
44. Cheng DT, Mitchell TN, Zehir A, et al. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology. J Mol Diagn. 2015; 17:251–64.
45. Fisher KE, Zhang L, Wang J, et al. Clinical validation and implementation of a targeted next-generation sequencing assay to detect somatic variants in non-small cell lung, melanoma, and gastrointestinal malignancies. J Mol Diagn. 2016; 18:299–315.
46. Pritchard CC, Salipante SJ, Koehler K, et al. 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. 2014; 16:56–67.
47. Sikkema-Raddatz B, Johansson LF, de Boer EN, et al. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Hum Mutat. 2013; 34:1035–42.
Full Text Links
  • JPTM
export Copy
  • Twitter
  • Facebook
Similar articles
Copyright © 2023 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: koreamed@kamje.or.kr