Promoting standards in biological research

Most research advances are built upon pre-existing data and findings. This paradigm implies that researchers must be able to reproduce data on which they base their own research. Yet a number of promising pre-clinical researches do not go into clinics because of the inability to reproduce the work (Freedman and Inglese). For this, it has become essential to set standards and good practices in life sciences research.

Initiatives promoting standards in biology

A number of initiatives have been created to set and promote standards in biology research. Some society are proposing standards to cover all areas of basic research and clinics, while others are focusing on specific research fields. Here are some of the most advanced organizations which develop standards for biological research data quality, annotation, and exchange.

FGED: Functional genomics data society

The Functional Genomics Data Society (FGED) was founded in 1999, motivated by the growing importance of microarrays in genomics and transcriptomics research. This society works with other organization to support the effective sharing and reproducibility of functional genomics data, mainly by facilitating the creation and use of standards and software tools for better annotation and sharing of data.

 

The FGED as defined the following standards:

  • MIAME– The formulation of the minimum information about a microarray experiment required to interpret and verify the results.
  • MINSEQE– The development of the Minimum Information about a high-throughput SEQuencing Experiment standard for Ultra High-Throughtput Sequencing experiments.
  • MAGE-TAB–  A simple spreadsheet-based, MIAME-supportive format for microarray experimental data called MAGE-TAB, based on a richer a data exchange and object modeling format known as MAGE.
  • Annotare– A stand-alone desktop application to help bench biologists annotate biomedical investigations and their resulting data.
  • Ontology– The development of ontologies for microarray experiment description and biological material (biomaterial) annotation in particular.
  • Collaborative standards- Engaging with and supporting the efforts of other relevant standards organizations.

 

As for MINSEQE, the FGED basic recommendations when making data available include the description of the biological system, samples, and experimental variables, the sequence read data for each assay, the final processed data of the study, the general information about the experiment, and experimental and data processing protocols.

CLSI: Clinical and Laboratory Standards Institute

The Clinical and Laboratory Standards Institute (CLSI) is an international organization that develops and fosters clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. The CLSI publishes standards for a wide range of biological specialties such as clinical chemistry and toxicology, hematology, method evaluation, microbiology, etc. It also provides guidance for obtaining accreditation and certifications as set by the International Organization for Standardization (ISO).

 

CLSI website homepage.
CLSI website homepage.

 

Future breakthroughs in biology will most likely depend on today’s experiments. Establishing standards in next-generation sequencing experiments is a modern challenge, as the use of this technology is wide-spreading across all fields of biology. The use of standardized protocols and data annotation will ensure reproducibility and successful clinical development of next-generation therapies.

Reference

Hoen et al. (2013). Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nature Biotechnology.

Gargis et al. (2012). Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature Biotechnology.

Freedman and Inglese. (2014). The Increasing Urgency for Standards in Basic Biological Research. Cancer Research.