ISO/TS 4424:2023

Genomics informatics - Data elements and their metadata for describing the tumor mutation burden (TMB) information of clinical massive parallel DNA sequencing

This document identifies data elements and metadata to represent the information about tumor mutation burden (TMB) when reporting the value for the biomarker using clinical massive parallel DNA sequencing. This document covers the TMB status and related metadata such as mutation type, sequencing types, and target areas of sequencing from human samples for clinical practice and research. This document is not intended - to define experimental protocols or methods for calculating the value of tumor mutation burden, - for the other biological species, and - for the Sanger sequencing methods.

Informatique génomique — Éléments de données et leurs métadonnées pour décrire les informations relatives à la charge tumorale mutationnelle (TMB) du séquençage massif parallèle d'ADN

General Information

• Status: Published
• Publication Date: 10-Dec-2023
• ICS: 35.240.80 - IT applications in health care technology
• Technical Committee: ISO/TC 215/SC 1 - Genomics Informatics
• Drafting Committee: ISO/TC 215/SC 1/WG 1 - Genomics data sharing
• Current Stage: 6060 - International Standard published
• Start Date: 11-Dec-2023
• Due Date: 11-Aug-2023
• Completion Date: 11-Dec-2023

Overview

ISO/TS 4424:2023 - Genomics informatics - defines standardized data elements and metadata for reporting Tumor Mutation Burden (TMB) derived from clinical massive parallel DNA sequencing (NGS). Published as a Technical Specification in 2023, it specifies what information should accompany a reported TMB value so clinicians, laboratories, researchers and health‑IT systems can interpret and reuse TMB results reliably. The document covers human clinical samples and NGS (not Sanger) and does not prescribe laboratory protocols or calculation algorithms.

Key topics and requirements

ISO/TS 4424 organizes TMB reporting into structured data fields and metadata to ensure consistent representation. Key technical areas include:

• TMB value and TMB status (summary and detailed parts of the report)
• Mutation types and variant types used for TMB calculation
• Sequencing types (e.g., whole genome, whole exome, targeted panels) and target areas/regions covered
• Reference genome version and criteria of TMB status (reporting the basis for classification)
• Germline filtering approach and any calibration or adjusted TMB values
• Biospecimen information, subject identifiers, sequencing order and dates
• Sequencing and analysis platform info, quality control metrics and other analytical metadata
• Clinical context fields such as referring diagnosis, recommended treatment, clinical trial links and supporting information
• Clear field nomenclature and optional vs required elements to support integration with electronic health records (EHRs)

Applications and users

ISO/TS 4424 is intended to improve interoperability and clinical utility of TMB as a biomarker. Primary users and stakeholders include:

• Clinical molecular laboratories and pathologists reporting TMB from NGS panels
• Bioinformaticians and analysis platform developers documenting TMB pipelines
• Electronic health record and laboratory information system (LIS) vendors implementing structured TMB reporting
• Oncologists and multidisciplinary care teams using TMB for immunotherapy decision support
• Clinical researchers and multicenter studies aggregating TMB data for secondary analysis
• Regulatory and accreditation bodies assessing TMB reporting consistency across labs

By standardizing metadata (platform, regions, filtering, reference builds), ISO/TS 4424 supports reproducible interpretation, cross‑laboratory comparison, secondary research and more reliable clinical decision support.

Related standards (if applicable)

• ISO/TS 20428 - clinical sequencing report content (related)
• ISO 8601 - date and time representation
• ISO/TS 22220 - subject identification in health care
• ISO/TS 27527 - health informatics provider identification

Keywords: ISO/TS 4424:2023, Tumor Mutation Burden, TMB, genomics informatics, NGS, massive parallel DNA sequencing, clinical sequencing report, metadata, bioinformatics, EHR interoperability.

Standards Content (Sample)

TECHNICAL ISO/TS
SPECIFICATION 4424
First edition
2023-12
Genomics informatics — Data
elements and their metadata for
describing the tumor mutation burden
(TMB) information of clinical massive
parallel DNA sequencing
Informatique génomique — Éléments de données et leurs
métadonnées pour décrire les informations relatives à la charge
tumorale mutationnelle (TMB) du séquençage massif parallèle d'ADN
Reference number
© ISO 2023
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting on
the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address below
or ISO’s member body in the country of the requester.
ISO copyright office
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Phone: [phone]
Email: [e-mail]
Website: www.iso.org
Published in Switzerland
ii
Contents Page
Foreword .v
Introduction . vi
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Abbreviated terms . 4
5 Tumor mutation burden (TMB) .5
6 Composition of elements for describing TMB on the clinical DNA NGS report .6
6.1 General . 6
6.2 Summary part . 6
6.3 Detail part . 6
7 Fields and their nomenclature of required data . 6
7.1 General . 6
7.2 Clinical sequencing order . . 7
7.2.1 General . 7
7.2.2 Clinical sequencing order code . 7
7.2.3 Date and time . 7
7.3 Information on subject of care . 8
7.3.1 General . 8
7.3.2 Subject of care identifier . 8
7.3.3 Subject of care name . 8
7.3.4 Subject of care birth date . 8
7.3.5 Subject of care sex . 8
7.3.6 Referring diagnosis . 9
7.4 Information on legally authorized person ordering clinical sequencing . 9
7.4.1 General . 9
7.5 Performing laboratory . 9
7.5.1 General . 9
7.5.2 Basic information on performing laboratory . 9
7.5.3 Information on report generator . 9
7.5.4 Information of legally confirmed person on sequencing report. 9
7.6 Biospecimen information. 9
7.6.1 General . 9
7.6.2 Type of specimen . 9
7.7 TMB status result information . . 10
7.7.1 General . 10
7.7.2 TMB value . 10
7.7.3 TMB status . 10
7.8 Recommended treatment . 10
7.8.1 General . 10
7.8.2 Medication . . 10
7.8.3 Clinical trial information . 10
7.8.4 Other recommendation . 10
7.8.5 Supporting information . 11
8 Fields and their nomenclature of optional data .11
8.1 General . 11
8.2 Reference genome version .12
8.3 TMB information .12
8.3.1 General .12
8.3.2 Criteria of TMB status .12
8.3.3 Approach of filtering germline variants . .12
iii
8.3.4 Variant types used for calculating TMB value .12
8.3.5 TMB region covered .12
8.3.6 Calibrated TMB value .12
8.4 Sequencing information . 13
8.4.1 Clinical sequencing date . 13
8.4.2 Sequencing type .13
8.4.3 Quality control metrics . 13
8.4.4 Sequencing platform information . 13
8.4.5 Analysis platform information . 14
Annex A (informative) Example structure of TMB report .16
Bibliography .20
iv
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
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electrotechnical standardization.
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described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO document should be noted. This document was drafted in accordance with the
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This document was prepared by Technical Committee ISO/TC 215, Health informatics, Subcommittee
SC 1, Genomics informatics.
Any feedback or questions on this document should be directed to the user’s national standards body. A
complete listing of these bodies can be found at www.iso.org/members.html.
v
Introduction
With the rapid advancement of next-generation sequencing (NGS) technologies, clinical sequencing
[1]
has been applied to realize personalized and precision medicine. ISO/TS 20428 was published to
standardize the clinical sequencing reports in electronic health records. After introducing NGS panel
sequencings (whole genome, whole exome, targeted gene sequencing), they are widely used in the
clinical field.
In the field of cancer treatment, various treatment strategies were tried differently from traditional
anti-cancer chemotherapies. Recently, drugs related to the immune system were developed and more
efficient for patients with specific tumor molecular characteristics. It is the immune checkpoint
blockade drug such as the first approved drug – Ipilimumab, an anti-cytotoxic T-lymphocyte antigen
[2]
(CTLA4) for non-small cell lung cancer . Tumors can use these checkpoints to protect themselves
from immune system attacks. Currently approved checkpoint therapies block inhibitory checkpoint
receptors. Blockade of negative feedback signaling to immune cells thus results in a continued immune
response against tumors. It was reported that the status of Programmed Death-Ligand 1 (PD-L1)
expression or the status of TMB (Tumor Mutation Burden) could be used as the predictive marker for
the efficacy of the immune checkpoint blockade because TMB is considered an indirect measurement of
how many tumor cell-specific peptide fragments are presenting and the increase of antigen-presenting
[3]
leads more immune reaction .
The status of TMB can be calculated and reported from detected genomic variants by NGS DNA
sequencing. According to national regulatory agencies, including US-FDA, several NGS sequencing
[4]
products are being approved for companion diagnostics . Some NGS sequencing products provide
TMB status and value on their NGS sequencing report. CLIA-certified labs or equivalent-level agencies
in countries also serve the TMB value from their own methods. It is forecasted that more clinical NGS
[5]
sequencing will be approved to report TMB.
However, there is no international standard for describing TMB status, value, and metadata. The
previous ISO/TS 20428 focused on only DNA variations compared with the reference genome. Some
research results said that TMB values and how to describe them are different even if using the same
sequencing data. The absence of a standard for TMB representation makes it difficult for clinicians and
researchers not only to use TMB results for clinical decision support but also for secondary analysing
purposes when receiving from more than one sequencing lab. Related metadata should be essential to
expand the usage of TMB values.
In this document, the data elements and their standardized metadata for TMB in electronic health
records will be described. The clinical report for TMB will provide proper information on bioinformatics
analysis to help clinical decisions.
vi
TECHNICAL SPECIFICATION ISO/TS 4424:2023(E)
Genomics informatics — Data elements and their metadata
for describing the tumor mutation burden (TMB)
information of clinical massive parallel DNA sequencing
1 Scope
This document identifies data elements and metadata to represent the information about tumor
mutation burden (TMB) when reporting the value for the biomarker using clinical massive parallel DNA
sequencing.
This document covers the TMB status and related metadata such as mutation type, sequencing types,
and target areas of sequencing from human samples for clinical practice and research.
This document is not intended
— to define experimental protocols or methods for calculating the value of tumor mutation burden,
— for the other biological species, and
— for the Sanger sequencing methods.
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content
constitutes requirements of this document. For dated references, only the edition cited applies. For
undated references, the latest edition of the referenced document (including any amendments) applies.
ISO 8601 (all parts), Date and time — Representations for information interchange
ISO/TS 22220:2011, Health informatics — Identification of subjects of health care
ISO/TS 27527, Health informatics — Provider identification
3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminology databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at https:// www .electropedia .org/
3.1
biological specimen
biospecimen
specimen
sample of tissue, body fluid, food, or other substance that is collected or acquired to support the
assessment, diagnosis, treatment, mitigation or prevention of a disease, disorder or abnormal physical
state, or its symptoms
[SOURCE: ISO/TS 20428:2017, 3.34]
3.2
clinical sequencing
next generation sequencing or later sequencing technologies with human samples for clinical practice
and clinical trials
[SOURCE: ISO/TS 20428:2017, 3.5]
3.3
deoxyribonucleic acid
DNA
molecule that encodes genetic information in the nucleus of cells
[SOURCE: ISO 25720:2009, 4.7]
3.4
DNA sequencing
determining the order of nucleotide bases (adenine, guanine, cytosine and thymine) in a molecule of
DNA
Note 1 to entry: Sequence is generally described from the 5’ end.
[SOURCE: ISO 17822:2020, 3.19]
3.5
exome
part of the genome formed by exons
[SOURCE: ISO/TS 20428:2017, 3.13]
3.6
gene
basic unit of hereditary material that encodes and controls the expression of a protein or protein
subunit
[SOURCE: ISO 11238:2018, 3.29]
3.7
gene panel
technique for sequencing the targeted genes in a genome
[SOURCE: ISO/TS 20428:2017, 3.15]
3.8
germline
series of germ cells each descended or developed from earlier cells in the series, regarded as continuing
through successive generations of an organism
[SOURCE: ISO/TS 20428:2017, 3.17]
3.9
nucleotide
base
base pair
monomer of a nucleic acid polymer such as DNA or RNA
Note 1 to entry: Nucleotides are denoted as letters (‘A’ for adenine; ‘C’ for cytosine; ‘G’ for guanine; ‘T’ for thymine
which only occurs in DNA; and ‘U’ for uracil which only occurs in RNA). The chemical formula for a specific
DNA or RNA molecule is given by the sequence of its nucleotides, which can be represented as a string over the
alphabet (‘A’, ’C’, ’G’, ‘T’) in the case of DNA, and a string over the alphabet (‘A’, ‘C’, ‘G’, ‘U’) in the case of RNA. Bases
with unknown molecular composition are denoted with ‘N’.
[SOURCE: ISO/IEC 23092-2:2020, 3.20]
3.10
quality score
Q score
Phred quality score
sequencing quality score of a given nucleotide base
Note 1 to entry: Q is defined by the following equation: Q = -10log10(e), where e is the estimated probability of
the base call being wrong.
Note 2 to entry: A quality score of 20 represents an error rate of 1 in 100, with a corresponding call accuracy of
99 %.
Note 3 to entry: Higher quality scores indicate a smaller probability of error. Lower quality scores can result in a
significant portion of the reads being unusable. Low quality scores may also indicate false-positive variant calls,
resulting in inaccurate conclusions.
[SOURCE: ISO 20397-2:2021, 3.32]
3.11
read type
type of run in the sequencing instrument
Note 1 to entry: It can be either single-end or paired-end.
Note 2 to entry: Single-end: Single read runs the sequencing instrument reads from one end of a fragment to the
other end.
Note 3 to entry: Paired-end: Paired end runs read from one end to the other end, and then start another round of
reading from the opposite end.
[SOURCE: ISO/TS 20428:2017, 3.27]
3.12
reference sequence
nucleic acid sequence with biological relevance
Note 1 to entry: Each reference sequence is indexed by a one-dimensional integer coordinate system whereby
each integer within range identifies a single nucleotide. Coordinate values can only be equal to or larger than
zero. The coordinate system in the context of this standard is zero-based (i.e. the first nucleotide has coordinate
0 and it is said to be at position 0) and linearly increasing within the string from left to right.
[SOURCE: ISO/IEC 23092-1:2020, 3.22]
3.13
sequence read
read
fragmented nucleotide sequences which are used to reconstruct the original sequence for next
generation sequencing technologies
[SOURCE: ISO/TS 20428:2017, 3.26]
3.14
sequence variation
DNA sequence variation
variation
differences of DNA sequence among individuals in a population
[SOURCE: ISO 25720:2009, 4.8]
3.15
single nucleotide variant
SNV
DNA sequence variation that occurs when a single nucleotide, A, T, C, or G, in the genome (or other
target sequence) differs between templates
[SOURCE: ISO 20395:2019, 3.35]
3.16
subject of care
any person who uses, or is a potential user of, a health care service
[SOURCE: ISO/TS 22220:2011, 3.2]
3.17
target capture
method to capture genomic regions of interest from a DNA sample prior to sequencing
[SOURCE: ISO/TS 20428:2017, 3.36]
3.18
targeted sequencing
disease-targeted gene panels
the technique used for sequencing only selected/targeted genomic regions of interest from a DNA
sample
[SOURCE: ISO/TS 22692:2020, 3.30]
3.19
whole exome sequencing
WES
technique for sequencing the exomes of the protein-coding genes in a genome
[SOURCE: ISO/TS 20428:2017, 3.38]
3.20
whole genome sequencing
WGS
technique that determines the complete DNA sequence of an organism’s genome at a single time
[SOURCE: ISO/TS 20428:2017, 3.39]
4 Abbreviated terms
This list of abbreviated terms includes all abbreviations used in this document.
ATC Anatomical Therapeutic Chemical
CTLA4 Cytotoxic T-Lymphocyte Associated Protein 4
EBI European Bioinformatics Institute
IDMP Identification of Medicinal Product
IMPID Investigational MPID
INN International Nonproprietary Names
MHC Major Histocompatibility Complex
MPID Medicinal Product Identifier
NCBI National Center for Biotechnology Information
NCCN National Comprehensive Cancer Network
NGS Next Generation Sequencing
NIH National Institutes of Health
PD-L1 Programmed Death-Ligand 1
PD-1 Programmed cell Death protein 1
SPREC Standard PREanalytical Code
TMB Tumor Mutation Burden
WES Whole Exome Sequencing
WGS Whole Genome Sequencing
WHO World Health Organization
UTN Universal Trial Number
UMI Unique Molecular Identifier
5 Tumor mutation burden (TMB)
Molecular characterization of tumors utilizing next-generation sequencing methods (NGS) is currently
in the focused area of personalized medicine. Tumor mutation burden (TMB) is considered one of
the molecular markers in the field of tumor diagnostics. Recently, clinical trials showed that immune
checkpoint inhibitors are more effective with patients with high TMB regarding response rates
[7]
and survival benefits. The simple mean of TMB is how many mutations occurred in tumor cells .
Neoantigens are novel tumor cell surface peptides presenting by Major Histocompatibility Complex
(MHC), some of which can be recognized as foreign to the body by the immune system, resulting in
increased T-cell reactivity and thereby leading to an antitumor immune response. To prevent the
excessive immune reaction, immune checkpoint proteins (ex, PD-L1, PD-1, CTLA4) were expressed on
the surface of tumor cells or T-cells. As binding these proteins between tumor cells and T-cells, the
immune reaction is decreased.
Immune checkpoint inhibitors enhance antitumor T-cell activity by inhibiting immune checkpoint
molecules. So, the status of neo-antigen or TMB can be a suitable clinical biomarker to guide treatment
decisions for immune checkpoint inhibitors. Although selecting which mutations are likely to induce
immunogenic neoantigens is not clear, TMB represents a quantifiable measure of the number of tumor
mutations that can inform treatment selection.
TMB is mostly measured by NGS – whole genome sequencing (WGS), whole exome sequencing (WES),
[8]
and targeted gene sequencing . In 2020, commercial targeted DNA sequencing for TMB was approved
as the companion diagnostics to inhibit the immune checkpoint system (PD-L1) for patients with
solid tumors in the United States. In addition, various targeted gene panel assays are being developed
for multi-purposes, including TMB assessment, and are used in various clinical trials. So, it could be
expected that more methods would be approved. Therefore, in order to increase the utility of the TMB
results from multi agencies or methods, the essential factors such as the way of describing TMB results
and metadata derived from the estimate process of TMB on the clinical report should be defined and
standardized.
6 Composition of elements for describing TMB on the clinical DNA NGS report
6.1 General
The clinical DNA NGS report, including TMB results, may mainly consist of two parts, the same as
ISO/TS 20428: the summary and detailed parts. Because the result of TMB and related data could be
calculated from the result of DNA sequencing, it is general to supply the result of TMB with the result
of clinical DNA NGS in the report. The summary part includes the subset of required fields to report
the main result of DNA sequencing, including TMB status, con
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