Human Genetic and Genomic Testing Using Traditional and High-Throughput Nucleic Acid Sequencing Methods
This CLSI guideline provides step-by-step recommendations for designing, validating, and implementing next-generation sequencing (NGS) and Sanger sequencing tests in clinical laboratories. As sequencing technologies expand from single-gene to whole-genome applications, MM09 offers essential guidance for hereditary disorder diagnostics, tumor testing, HLA typing, noninvasive prenatal testing, and circulating tumor DNA sequencing.
MM09 helps laboratories translate regulatory requirements into clinical practice through instructional worksheets and real-world examples, ensuring quality and compliance in sequencing-based testing.
Sequencing-based clinical tests have evolved from single-gene tests to whole-genome tests. Next-generation sequencing (NGS) technologies have largely replaced Sanger sequencing and are firmly established in the medical management of hereditary disorders, as well as in tumor testing. Newer clinical NGS applications include human leukocyte antigen typing, noninvasive prenatal testing, sequencing of circulating tumor DNA in peripheral blood, and RNA sequencing. Although NGS applications have undergone major technical simplifications, clinical implementation continues to be complex. Clinical and Laboratory Standards Institute guideline MM09—Human Genetic and Genomic Testing Using Traditional and High-Throughput Nucleic Acid Sequencing Methods provides recommendations for design, development, validation, results reporting, and continual quality management of NGS-based tests, as well as Sanger sequencing–based tests. In conjunction with instructional worksheets and educational examples, MM09 provides step-by-step guidance to help medical laboratories translate regulatory requirements into clinical practice.
Overview of Changes
This guideline replaces the previous edition of the approved guideline, MM09-A2, published in 2014. MM09-A2 introduced NGS as a new technology. This edition has been updated beyond an introduction of NGS technology to provide practical use case and implementation guidance, as well as instructions that cover each step of the clinical NGS test development lifecycle. Several changes were made in this edition, including: • Providing step-by-step recommendations on designing, developing, validating, and implementing a clinical NGS test • Adding clear and specific instructions on performing steps in the clinical NGS test lifecycle • Presenting an application-driven approach • Providing educational use case examples, supplemented by instructional worksheets • Updating appendixes with additional details on steps in the test development process and specific applications
Scope
This guideline covers nucleic acid sequencing applications currently in clinical use: medical management of hereditary disorders, solid tumor and hematological malignancy testing, human leukocyte antigen (HLA) typing, noninvasive prenatal testing (NIPT), liquid biopsy, and RNA sequencing (RNAseq) applications. Most of the content in this guideline focuses on next-generation sequencing (NGS), which is the predominant platform in current use. Sanger sequencing continues to be used for certain clinical applications, so guidance on Sanger sequencing is also included. This guideline also provides introductory information on the management of computational and/or bioinformatics aspects of NGS, because these concepts are fundamental yet somewhat novel for the clinical testing community. Detailed guidance on bioinformatics will be provided in a forthcoming CLSI document. MM09 does not cover microbial or infectious diseases applications. Detailed guidance on NGS-based infectious diseases testing is provided in CLSI document MM24. This guideline also does not cover validation of confirmatory testing or mitochondrial DNA testing for inherited disorders. This guideline is intended for developers of sequencing-based clinical tests (both Sanger sequencing and NGS), including manufacturers of commercially distributed in vitro diagnostic (IVD) devices and developers of laboratory-developed tests (LDTs). IVD device manufacturers might be subject to additional quality system requirements. For example, design controls are not included in this guideline, but they are well described in existing literature.
Product Details
MM09Ed3
978-1-68440-174-1
160
MM09Ed3E
978-1-68440-175-8
160
Authors
Birgit Funke, PhD, FACMG
John D. Pfeifer, MD, PhD
Sami S. Amr, PhD, FACMG
Arthur Martin Baca, MD, PhD
Mark J. Bowser, MS, MPH, MLS(ASCP)CM
Jillian Buchan, MS, PhD, FACMB
Maria Laura Cremona, PhD, FACMG, CGMB
Dora Dias-Santagata, PhD, FACMG
Jianli Dong, MD, PhD, FACMG
Bert Gold, PhD, FACMG, CGMB
Elizabeth Duffy Hynes, BS
Jianling Ji, MD, MS
Sabah Kadri, PhD
Robert F. Klees, PhD
Niklas Krumm, MD, PhD
Annette Leon, PhD, MS, FACMG, CGMBS, CCS
You Li, PhD
Meredith Halks Miller, MD
Dimitri Monos, PhD
Kara Norman, PhD
Honey V. Reddi, PhD, FACMG
Avni Santani, PhD, FACMG
Timothy R. Schwartz, PhD
Junaid Shabbeer, PhD, FACMG
Birgitte Simen, PhD
Cynthe Sims, PhD, HCLD(ABB)
Zivana Tezak, PhD
Francisca Reyes Turcu, PhD
Patrik Vitazka, MD, PhD, FACMG
Richard Y. Zhao, PhD
Abstract
Sequencing-based clinical tests have evolved from single-gene tests to whole-genome tests. Next-generation sequencing (NGS) technologies have largely replaced Sanger sequencing and are firmly established in the medical management of hereditary disorders, as well as in tumor testing. Newer clinical NGS applications include human leukocyte antigen typing, noninvasive prenatal testing, sequencing of circulating tumor DNA in peripheral blood, and RNA sequencing. Although NGS applications have undergone major technical simplifications, clinical implementation continues to be complex. Clinical and Laboratory Standards Institute guideline MM09—Human Genetic and Genomic Testing Using Traditional and High-Throughput Nucleic Acid Sequencing Methods provides recommendations for design, development, validation, results reporting, and continual quality management of NGS-based tests, as well as Sanger sequencing–based tests. In conjunction with instructional worksheets and educational examples, MM09 provides step-by-step guidance to help medical laboratories translate regulatory requirements into clinical practice.
Overview of Changes
This guideline replaces the previous edition of the approved guideline, MM09-A2, published in 2014. MM09-A2 introduced NGS as a new technology. This edition has been updated beyond an introduction of NGS technology to provide practical use case and implementation guidance, as well as instructions that cover each step of the clinical NGS test development lifecycle. Several changes were made in this edition, including: • Providing step-by-step recommendations on designing, developing, validating, and implementing a clinical NGS test • Adding clear and specific instructions on performing steps in the clinical NGS test lifecycle • Presenting an application-driven approach • Providing educational use case examples, supplemented by instructional worksheets • Updating appendixes with additional details on steps in the test development process and specific applications
Scope
This guideline covers nucleic acid sequencing applications currently in clinical use: medical management of hereditary disorders, solid tumor and hematological malignancy testing, human leukocyte antigen (HLA) typing, noninvasive prenatal testing (NIPT), liquid biopsy, and RNA sequencing (RNAseq) applications. Most of the content in this guideline focuses on next-generation sequencing (NGS), which is the predominant platform in current use. Sanger sequencing continues to be used for certain clinical applications, so guidance on Sanger sequencing is also included. This guideline also provides introductory information on the management of computational and/or bioinformatics aspects of NGS, because these concepts are fundamental yet somewhat novel for the clinical testing community. Detailed guidance on bioinformatics will be provided in a forthcoming CLSI document. MM09 does not cover microbial or infectious diseases applications. Detailed guidance on NGS-based infectious diseases testing is provided in CLSI document MM24. This guideline also does not cover validation of confirmatory testing or mitochondrial DNA testing for inherited disorders. This guideline is intended for developers of sequencing-based clinical tests (both Sanger sequencing and NGS), including manufacturers of commercially distributed in vitro diagnostic (IVD) devices and developers of laboratory-developed tests (LDTs). IVD device manufacturers might be subject to additional quality system requirements. For example, design controls are not included in this guideline, but they are well described in existing literature.
Modernizing Guidance for Clinical Sequencing: Human Genetic and Genomic Testing Using Traditional and High-Throughput Nucleic Acid Sequencing Methods Webinar
