ISO 24480:2024
(Main)Biotechnology — Validation of database used for nucleotide sequence evaluation
Biotechnology — Validation of database used for nucleotide sequence evaluation
This document describes a practical procedure for nucleotide sequence database evaluation and validation. This document describes minimum requirements for the validation of a nucleotide sequence database. This document is applicable only for databases consisting of entries of nucleotide sequences. This document is not applicable to the general evaluation of the entire database quality including the quality of each data entry. EXAMPLE The use of the validated database is for confirming a representative sequence specificity including primers or probes for qualification and quantification of target nucleic acids by conventional polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR), digital polymerase chain reaction (dPCR) and microarray technologies.
Biotechnologie — Validation de la base de données utilisée pour l'évaluation de la séquence nucléotidique
General Information
Standards Content (Sample)
International
Standard
ISO 24480
First edition
Biotechnology — Validation of
2024-11
database used for nucleotide
sequence evaluation
Biotechnologie — Validation de la base de données utilisée pour
l'évaluation de la séquence nucléotidique
Reference number
© ISO 2024
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ii
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 General . 3
5 Common requirements of the database . 4
6 Inclusivity database: database for inclusivity evaluation . 4
6.1 Quality criteria .4
6.2 Requirements of an inclusivity database .4
6.3 Individual data quality indicators . .5
6.3.1 Data provenance and updates .5
6.3.2 Length of the entries .5
6.3.3 Number of unidentified nucleotides (N) .5
6.4 Validation of the inclusivity database . .5
7 Exclusivity database: Database for the exclusivity evaluation . 6
7.1 Quality criteria .6
7.2 Requirements of the exclusivity database .6
7.3 Validation of the exclusivity database .6
8 Validation report . 7
Annex A (informative) Example of a data entry format . 9
Annex B (informative) Example for the validation of an inclusivity database (Inclusivity) .10
Annex C (informative) Example on validation of an exclusivity database (Exclusivity) .13
Annex D (informative) Example of use of an inclusivity database and an exclusivity database . 17
Annex E (informative) Example on dataset verification command for an inclusivity database .23
Bibliography .24
iii
Foreword
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iv
Introduction
A valid database is important for nucleotide sequence evaluation. The development of inclusivity and
exclusivity panels for diagnostics and surveillance using community genomic databases, e.g., Genbank, has
[1],[2],[3]
been evaluated . However, a specific validation procedure for the databases has yet to be provided.
Considering the current database quality, inclusivity and exclusivity are almost impossible to be validated
with ideal accuracy. Therefore, in this document a practical procedure for evaluating the quality of nucleotide
sequence database to be used for the development of inclusivity and exclusivity panels is comprehensively
described. The degree of data accuracy to be used is determined according to the user's intended test
purpose. This evaluation can become a part of the validated diagnostic or surveillance method. Ensuring the
quality of the database improves its sufficiency for validating the whole measuring system.
In polymerase chain reaction (PCR) and DNA microarray technologies, nucleotide sequence is used as
primers or probes to detect the target nucleic acids. Those technologies utilize initially the hybridization of
two single strand DNA molecules with complementary sequences. During the design process of the primers
or probes, nucleotide sequence database is used for evaluating specificity and exclusivity of probes or
primers. In general, target DNA sequences can be confirmed to match the intended sequences but not others
by similarity (homology) search on nucleotide databases with computer tools, for example BLAST.
The validated databases can be used for evaluating specificity of probe or primer sequences and ensuring
the selectivity of the qualification and quantification measurement system.
Validation of the entire nucleotide sequence database is not appropriate for the database providers because
there are wide varieties of purpose of uses by users. It is almost impossible for the users, however, to evaluate
the quality of each data entry especially in huge sequence databases. The database can reflect the fitness for
the intended test purpose of users.
This document provides the minimum requirements of a practical procedure for the validation of database
used for nucleotide sequence evaluation.
v
International Standard ISO 24480:2024(en)
Biotechnology — Validation of database used for nucleotide
sequence evaluation
1 Scope
This document describes a practical procedure for nucleotide sequence database evaluation and validation.
This document describes minimum requirements for the validation of a nucleotide sequence database. This
document is applicable only for databases consisting of entries of nucleotide sequences.
This document is not applicable to the general evaluation of the entire database quality including the quality
of each data entry.
EXAMPLE The use of the validated database is for confirming a representative sequence specificity including
primers or probes for qualification and quantification of target nucleic acids by conventional polymerase chain
reaction (PCR), quantitative polymerase chain reaction (qPCR), digital polymerase chain reaction (dPCR) and
microarray technologies.
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 20691, Biotechnology — Requirements for data formatting and description in the life sciences
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
nucleotide sequence specificity
capacity to exclusively recognize a specific nucleic acid target sequence, distinguishing it from other nucleic
acids and contaminants
Note 1 to entry: It describes the degree of similarity to specifically match to the nucleotide sequence to be searched by
distinguishing it from other nucleotide sequences, and the tendency for a primer or probe with the matched nucleotide
sequence to hybridize with its intended target and not hybridize with other non-target sequences.
Note 2 to entry: “sequence specificity” can be considered to be the combination of inclusivity (3.4) and exclusivity (3.5)
3.2
selectivity
extent to which a method can determine particular analyte(s) in a mixture(s) or matrice(s) without
interferences from other components of similar behaviour
Note 1 to entry: Selectivity is the recommended term in analytical chemistry to express the extent to which a
particular method can determine analyte(s) in the presence other components. Selectivity can be graded. The use of
the term “specificity” for the same concept is to be discouraged as this often leads to confusion.
Note 2 to entry: Sequence specificity in molecular biomarker analysis is differentiated from chemical analyte
selectivity.
[SOURCE: ISO 16577:2022, 3.3.73]
3.3
sequence similarity
proportion of matched number of units, including nucleotides and amino acids, to the number of units in
specified regions between two nucleic acids or proteins
Note 1 to entry: gap or deletion can be considered to compare the unit sequence of the regions between two nucleic
acids or proteins.
Note 2 to entry: “sequence similarity” can be evaluated simply based on a proportion of matched number of units,
whereas the term “homology” contains biological meaning in the comparison of two nucleic acids or proteins.
3.4
inclusivity
property of a nucleotide sequence to show high sequence similarity (3.3) specifically with intended target
nucleotide sequence
[4]
Note 1 to entry: The term “inclusivity” is used as same meaning of “sensitivity” in some cases .
3.5
exclusivity
property
...
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