Additional NGS Quality Materials

At a glance

Find publications on Next Generation Sequencing (NGS), quality management systems (QMS), quality standards, and best practices for diagnostic testing.

Background material from CLIAC Spring 2023 presentation

The Centers for Disease Control and Prevention (ob体育) and the Association for Public Health Laboratories (APHL) are collaborating on the Next Generation Sequencing (NGS) Quality Initiative. This effort also includes state and local public health laboratory partners. The NGS Quality Initiative is moving forward with a coordinated and comprehensive plan. This plan aims to develop and implement an NGS-focused quality management system (QMS) to ensure:

  • High quality
  • Reliable data for nationwide disease surveillance systems
  • Diagnostic or reference laboratory testing
  • Other public health actions which improves patient care and public health outcomes.

Goals

The Initiative is working to harmonize quality standards for NGS testing across public health and provide laboratories with confidence in reported results. The Initiative is working to create a toolkit of resources for NGS testing sites. This toolkit will help prevent duplication of efforts, increase efficiency, and save costs. The initiative supports NGS activities to meet various requirements, including CLIA. This is a prerequisite for using this transformative technology in public health laboratory diagnostic and surveillance activities.

Quality management system

The NGS Quality Initiative is happy to announce the completion of an NGS-focused QMS. This system addresses the many challenges public health and clinical laboratories face when developing and implementing NGS-based tests. It provides ready-to-implement guidance documents, customizable standard operating procedures, and other tools.

The NGS Quality Initiative's quality management system is organized and prioritized using the 12 Quality System Essentials (QSEs). These essentials are part of the Clinical & Laboratory Standards Institute (CLSI) quality framework. The Initiative has published 105 free customizable tools and resources on our webpage. They include materials for wet and dry bench personnel and leadership. We also have over 20 additional resources in development.

The Initiative will continue to update and add products to each QSE to:

  • Support training of personnel.
  • Choose appropriate protocols and analytic options.
  • Implement effective management and process controls.

Such tools are especially beneficial to laboratories performing NGS-based tests that must meet CLIA regulations and other accreditation standards. Products from this project can serve as a foundational QMS or complement existing resources. They support the development of a laboratory's current QMS.

Selected publications

These quality standards and quality management systems for diagnostic testing are based on NGS.

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Peer-reviewed publications

These guidelines, standards, and best practices are for germline and somatic variant diagnostic testing are based on NGS.

Archives of Pathology and Laboratory Medicine

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European Journal of Human Genetics

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Genetics in Medicine

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Journal of Molecular Diagnostics

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Nature Biotechnology

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Additional guidelines and documents

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FDA

The following publications are guidance for stakeholders and FDA staff.

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New York State and FDA

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Guidelines for Validation Submissions of Next Generation Sequencing (NGS) Assays under the NYS Testing Category of Genetic Testing – Molecular, New York State Department of Health (July 2015).25

Print
Content Source:
Division of Laboratory Systems (DLS)
  1. Hutchins RJ, Phan KL, Saboor A, Batra D, Booth R, Breaker E, Casas ME, Cherney B, Chang HY, Daniels J, Driggers J, Eby M, Gargis A, Gee J, Gregoricus NA, Halpin JL, Khemani R, Korth M, Kulasekarapandian Y, Langley G, Lauer A, Lubin I, Mclean JA, Mercante A, Myrick A, Okoth S, Perry KA, Ramos E, Schmerer M, Sheth M, Turnsek M, Vlachos N, Williams GM, Miller JD, and Muehlenbachs A. (2019). J Clin Microbiol. Jul 26;57(8). pii:e00261-19.
  2. Carey RB, Bhattacharyya S, Kehl SC, Matukas LM, Pentella MA, Salfinger M, and Schuetz AN. (2018). Clin Microbiol Rev. May 2;31(3). pii: e00062-17.
  3. Endrullat C, Glökler J, Franke P, and Frohme M. (2016) Appl Transl Genom. Jul 1;10:2-9.
  4. Merker JD, Devereaux K, Iafrate AJ, Kamel-Reid S, Kim AS, Moncur JT, Montgomery SB, Nagarajan R, Portier BP, Routbort MJ, Smail C, Surrey LF, Vasalos P, Lazar AJ, Lindeman NI. (2018) Arch Pathol Lab Med. 2018 Oct 30.
  5. Hegde M, Santani A, Mao R, Ferreira-Gonzalez A, Weck K, Voelkerding KV. (2017) Arch Path Lab Med. 141(6):798-805.
  6. Santani A, Murrell J, Funke B, Yu Z, Hegde M, Mao R, Ferreira-Gonzalez A, Voelkerding KV, Weck K. (2017)Arch Path Lab Med. 141(6):787-797.
  7. Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DG, Merker JD, Nagarajan R, Palicki LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV. (2015) Arch Pathol Lab Med. 139(4): 481-93.
  8. Matthijs G, Souche E, Alders M, Corveleyn A, Eck S, Feenstra I, Race V, Sistermans E, Sturm M, Weiss M, Yntema H, Bakker E, Scheffer H, Bauer P. (2016). Eur J Hum Genet. 24(10):1515
  9. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding KV, Rehm HL. (2015) Genet Med. 17(5):405-24.
  10. Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E; Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee. (2013) Genet Med. 15(9):733-47
  11. Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln S, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter A. (2018) . Journal of Molecular Diagnostics. 20(1):4-27.
  12. Santani A, Simen BB, Briggs M, Lebo M, Merker JD, Nikiforova M, Vasalos P, Voelkerding KV, Pfeifer J, Funke B. (2018). Journal of Molecular Diagnostics. Dec 31
  13. Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthy E, Zaranek AW, Zook J. (2017) Journal of Molecular Diagnostics. 19(3):417-426.
  14. Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. (2017) Guidelines for validation of next generation sequencing (NGS) based oncology panels: A joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists. Journal of Molecular Diagnostics. 19(3):341-365. 11. Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN. (2017) Journal of Molecular Diagnostics. 19(1):4-23
  15. Gargis AS, Kalman L, Bick DP, da Silva C, Dimmock DP, Funke BH, Gowrisankar S, Hegde MR, Kulkarni S, Mason CE, Nagarajan R, Voelkerding KV, Worthey EA, Aziz N, Barnes J, Bennett SF, Bisht H, Church DM, Dimitrova Z, Gargis SR, Hafez N, Hambuch T, Hyland FC, Luna RA, MacCannell D, Mann T, McCluskey MR, McDaniel TK, Ganova-Raeva LM, Rehm HL, Reid J, Campo DS, Resnick RB, Ridge PG, Salit ML, Skums P, Wong LJ, Zehnbauer BA, Zook JM, Lubin IM. (2015) Nature Biotechnology. 33(7): 689-93.
  16. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM. (2012). Nature Biotechnology, 30 (11), 1033-6. 2.
  17. Lincoln SE, Truty R, Lin C-F, Zook J, Paul J, Ramey V, Salit M, Rehm H, Nussbaum R, Lebo M. . (2019). Journal of Molecular Diagnostics. Mar;21(2):318-329.
  18. (ASHI): Standards for Accredited Laboratories Next Generation Sequencing Guidance. Section D.5.2.11 (January 2018).
  19. National Academies of Sciences, Engineering, and Medicine. 2018. . Washington, DC: The National Academies Press.
  20. Guidelines on Next Generation Sequencing from the Clinical Laboratory Standards Institute: (February 2014).
  21. Document issued on April 13, 2018.
  22. Document issued on April 13, 2018.
  23. , New York State Department of Health (April 2021).
  24. (March 2023)
  25. Guidelines for Validation Submissions of Next Generation Sequencing (NGS) Assays under the NYS Testing Category of Genetic Testing – Molecular, New York State Department of Health (July 2015).