We are delighted to announce that three and a half years of hard work by the collaborative team that brought you the Matched Annotation from NCBI and EMBL-EBI (MANE) dataset has culminated in a full article in the April 14 issue of Nature! We invite you to read the online article to learn more about the goals of the MANE collaboration, MANE offerings and how to access them, and the methods used in generating MANE data. And of course, now you have a paper to cite MANE data!
Morales, J., Pujar, S., Loveland, J.E. et al. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature (2022). DOI: 10.1038/s41586-022-04558-8
Launched in October 2018, MANE is a collaboration between the National Library of Medicine’s (NLM) National Center for Biotechnology Information (NCBI) and the EMBL’s European Bioinformatics Institute (EMBL-EBI), the two major groups who provide whole-genome annotation for a broad range of organisms including human. Our initial offering, MANE Select, is intended to be used as a universal standard to report clinical variants and for browser display in genome resources. Starting from MANE v0.92, we added MANE Plus Clinical transcripts for a small set of genes where MANE Select alone was not sufficient to report known clinical variants (Figure 1).
Figure 1. The Sequence Viewer showing the MANE Project track and the NCBI Genes track for the human SCN5A gene region on chromosome 3. The MANE track has the MANE Select Transcript, NM_000335, and the MANE Plus Clinical transcript, NM_001099404, providing two standard transcripts to represent the gene.
We are very close to our goal of assigning a MANE Select for all human protein coding genes. With 19,062 MANE Select and 58 MANE Plus Clinical transcripts, the current release (MANE v1.0) includes coverage of 99% of human protein-coding genes and 99.8% of genes of clinical relevance, including genes in the American College of Medical Genetics and Genomics (ACMG) Secondary Findings list (SF) v3.0. MANE v1.0 is currently available on FTP and will soon be available in updated RefSeq and Ensembl/GENCODE annotations and the associated resources. We plan to complete the MANE Select set in the next few months.
The availability of MANE transcripts and proteins means that you no longer must choose between the two annotations for applications that require a representative transcript per gene. Even more important is that having a universal transcript with synonymous RefSeq and Ensembl identifiers will promote consistency in clinical variant reporting, facilitate efficient exchange of clinical variant data, and reduce clinical harm that may be caused by errors in variant interpretation. Ultimately, this will help drive innovations and discovery in human health and diagnostics.
In the past year, several key resources have incorporated MANE Select accessions in their webpages, including gnomAD (v3.1.2), ClinVar, ClinGen, DECIPHER, and UniProtKB/Swiss-Prot. We encourage other resources to follow suit and help drive the widespread adoption of this key dataset by the clinical genomics and research community.
Your feedback is critical to maintaining the quality of this resource. Please send suggestions, questions, and specific requests about new or existing MANE transcripts to MANEfirstname.lastname@example.org.
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