An Introduction to MPEG-G: The First Open ISO/IEC Standard for the Compression and Exchange of Genomic Sequencing Data

Abstract

The development and progress of high-throughput sequencing technologies have transformed the sequencing of DNA from a scientific research challenge to practice. With the release of the latest generation of sequencing machines, the cost of sequencing a whole human genome has dropped to less than $600. Such achievements open the door to personalized medicine, where it is expected that genomic information of patients will be analyzed as a standard practice. However, the associated costs, related to storing, transmitting, and processing the large volumes of data, are already comparable to the costs of sequencing. To support the design of new and interoperable solutions for the representation, compression, and management of genomic sequencing data, the Moving Picture Experts Group (MPEG) jointly with working group 5 of ISO/TC276 "Biotechnology" has started to produce the ISO/IEC

Implementation of Privacy and Security for a Genomic Information System Based on Standards

“…For its purpose, we mainly focused on ISO/IEC 23092 features [ 2 , 3 ], as this is a genomic information format which has been developed using privacy by design principles since its inception. Such features, among others, are as follows: protection of information and privacy rules associated with genomic information, including metadata, a hierarchical structuring of the information, starting from the complete file and finishing on the blocks containing genomic information itself, and the possibility of associating security information with a high level of granularity.…”

“…We already described a preliminary version of this system in [ 1 ], but it is still under improvement, as we explain in this paper. Although the proposed system architecture is standards-agnostic, most of the modules implemented in this version are based on the ISO/IEC 23092 standard, also known as MPEG-G (Genomic Information Representation) [ 2 , 3 ], as we further describe in the following sections.…”

“…The aim of the work presented in this paper is to describe how genomic information can be managed in a secure way using a modular architecture (GIPAMS [ 1 ]) based on standardized information formats, specifically ISO/IEC 23092 [ 2 , 3 ]. Moreover, we explain some implementation details (programming languages, tools, etc.)…”

“…ISO/IEC 23092 Information Technology - Genomic Information Representation [ 2 , 3 ] is a standard devoted to the representation of compressed genomic information including appropriate security and privacy features [ 12 , 13 , 14 ] since its inception following a Security and Privacy by Design approach [ 15 ]. It is composed of six parts, most of them already published.…”

Genozip 14 - advances in compression of BAM and CRAM files

“…We benchmarked Genozip 14 against two versions of CRAM: CRAM 3.0, which is the default version in samtools, and CRAM 3.1, the latest CRAM version, for which the current version of samtools (1.15.1) produces the warning “ This is a technology demonstration that should not be used for archival data ”. We acknowledge that other BAM compression systems exist, such as DeeZ (Hach et al ., 2014) and MPEG-G (Voges et al ., 2021). However, they have been shown to be significantly inferior to both CRAM 3.1 and Genozip 13 (Bonfield, 2022), therefore we did not include them in our benchmark.…”