ISO/TS 22692:2020
(Main)Genomics informatics— Quality control metrics for DNA sequencing
Genomics informatics— Quality control metrics for DNA sequencing
This document identifies quality metrics for the detection of DNA variants using next generation sequencing (NGS) technology. It also defines the data types, relationships, optionality, cardinalities and terminology bindings of the data. This document provides a basis for sharing and for the application of "high quality" genomic data and contributes to the realization of the precision medicine and the development of relevant industries. This document is intended to serve as a catalogue of sequencing data elements used to address quality metrics for various clinical, industrial and commercial applications. The exchange of these data allows researchers, commercial entities, and regulatory bodies to assess for the purpose of selective utilization of the data by setting application-specific quality criteria This document is not intended for — sequencing methods other than NGS, such as the Sanger sequencing, — targets other than genome, such as transcriptome or proteome, or — specimens of species other than humans.
Informatique génomique — Mesures de contrôle de la qualité pour le séquençage de l'ADN
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TECHNICAL ISO/TS
SPECIFICATION 22692
First edition
2020-10
Genomics informatic — Quality
control metrics for DNA sequencing
Informatique génomique — Mesures de contrôle de la qualité pour le
séquençage de l'ADN
Reference number
©
ISO 2020
© ISO 2020
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
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii © ISO 2020 – All rights reserved
Contents Page
Foreword .v
Introduction .vi
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Abbreviated terms . 5
5 Quality control metrics for sample preparation . 5
5.1 General . 5
5.2 Sample sequencing type . 5
5.2.1 Sequencing type . 5
5.2.2 Target gene. 5
5.3 Sample information . 5
5.3.1 Specimen type . 5
5.3.2 Sampling date . 6
5.3.3 Specimen origin . 6
5.4 Summary of sample preparation related metrics . 6
6 Quality control metrics for library preparation . 6
6.1 General . 6
6.2 DNA extraction method . 6
6.2.1 DNA extraction kit . 6
6.3 DNA quality . 7
6.3.1 General. 7
6.3.2 DNA purity. 7
6.3.3 DNA integrity . 7
6.4 Library construction . 7
6.4.1 Library input amount . 7
6.4.2 Library insert size . 7
6.4.3 Library construction kit . 7
6.5 Summary of library preparation related metrics . 7
7 Quality control metrics for sequencing . 8
7.1 General . 8
7.2 Sequencing information . 8
7.2.1 Sequencing instrument . 8
7.2.2 Read length . 8
7.2.3 Sequencing direction . . 8
7.2.4 Running mode . 8
7.3 Running quality information . 9
7.3.1 Error rate . 9
7.3.2 Percent data quality >Q30 . 9
7.4 Summary of sequencing related metrics . 9
8 Quality control metrics for data processing . 9
8.1 General . 9
8.2 Data quality measurement . 9
8.2.1 Total reads . 9
8.2.2 Mean coverage . 9
8.2.3 Uniformity .10
8.2.4 Duplication rate .10
8.2.5 On-target rate .10
8.2.6 Q30 rate .10
8.3 Sequencing alignment.10
8.3.1 Mapping algorithm.10
8.3.2 Local realignment software and version .10
8.4 Variant calling .10
8.4.1 Variant calling software and version .10
8.4.2 Variant call quality score . .10
8.4.3 Allelic read percentage & ratio .10
8.5 Variant filtering and annotation.11
8.5.1 General.11
8.5.2 Germline filter criteria .11
8.5.3 Mutation and annotation database .11
8.6 Summary of data processing related metrics .11
Annex A (informative) Example layout of quality control metrics .12
Bibliography .14
iv © ISO 2020 – All rights reserved
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
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www .iso .org/ directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of
any patent rights identified during the development of the document will be in the Introduction and/or
on the ISO list of patent declarations received (see www .iso .org/ patents).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO's adherence to the
World Trade Organization
...
TECHNICAL ISO/TS
SPECIFICATION 22692
First edition
2020-10
Genomics informatic — Quality
control metrics for DNA sequencing
Informatique génomique — Mesures de contrôle de la qualité pour le
séquençage de l'ADN
Reference number
©
ISO 2020
© ISO 2020
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
CP 401 • Ch. de Blandonnet 8
CH-1214 Vernier, Geneva
Phone: +41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland
ii © ISO 2020 – All rights reserved
Contents Page
Foreword .v
Introduction .vi
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Abbreviated terms . 5
5 Quality control metrics for sample preparation . 5
5.1 General . 5
5.2 Sample sequencing type . 5
5.2.1 Sequencing type . 5
5.2.2 Target gene. 5
5.3 Sample information . 5
5.3.1 Specimen type . 5
5.3.2 Sampling date . 6
5.3.3 Specimen origin . 6
5.4 Summary of sample preparation related metrics . 6
6 Quality control metrics for library preparation . 6
6.1 General . 6
6.2 DNA extraction method . 6
6.2.1 DNA extraction kit . 6
6.3 DNA quality . 7
6.3.1 General. 7
6.3.2 DNA purity. 7
6.3.3 DNA integrity . 7
6.4 Library construction . 7
6.4.1 Library input amount . 7
6.4.2 Library insert size . 7
6.4.3 Library construction kit . 7
6.5 Summary of library preparation related metrics . 7
7 Quality control metrics for sequencing . 8
7.1 General . 8
7.2 Sequencing information . 8
7.2.1 Sequencing instrument . 8
7.2.2 Read length . 8
7.2.3 Sequencing direction . . 8
7.2.4 Running mode . 8
7.3 Running quality information . 9
7.3.1 Error rate . 9
7.3.2 Percent data quality >Q30 . 9
7.4 Summary of sequencing related metrics . 9
8 Quality control metrics for data processing . 9
8.1 General . 9
8.2 Data quality measurement . 9
8.2.1 Total reads . 9
8.2.2 Mean coverage . 9
8.2.3 Uniformity .10
8.2.4 Duplication rate .10
8.2.5 On-target rate .10
8.2.6 Q30 rate .10
8.3 Sequencing alignment.10
8.3.1 Mapping algorithm.10
8.3.2 Local realignment software and version .10
8.4 Variant calling .10
8.4.1 Variant calling software and version .10
8.4.2 Variant call quality score . .10
8.4.3 Allelic read percentage & ratio .10
8.5 Variant filtering and annotation.11
8.5.1 General.11
8.5.2 Germline filter criteria .11
8.5.3 Mutation and annotation database .11
8.6 Summary of data processing related metrics .11
Annex A (informative) Example layout of quality control metrics .12
Bibliography .14
iv © ISO 2020 – All rights reserved
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
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.
The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www .iso .org/ directives).
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of
any patent rights identified during the development of the document will be in the Introduction and/or
on the ISO list of patent declarations received (see www .iso .org/ patents).
Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.
For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO's adherence to the
World Trade Organization
...
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