Figure 4:
Answers across respondents (503 ‘non-clinical’ and 285 ‘clinical’) to
question 8: “Which reference sequences do you use for reporting
variants (select all that apply)”:
- RefSeq transcripts or proteins
- GRCh37/hg19 genome
- LRG transcripts or LRG proteins
- Ensembl/GENCODE transcripts or proteins
- GRCh38/hg38 genome
- Use both RefSeq and Ensembl
- Use both 37 and 38 genome references
In general, the ‘clinical’ respondents used:
- RefSeq transcripts or proteins rather than Ensembl/GENCODE (73% vs
24%),
- GRCh37/hg19 (71% vs 19% for GRCh38) and
- LRG transcripts or proteins (27%).
Whereas the ‘non-clinical’ community replies were more equally spread
across using:
- GRCh38 and GRCh37 (46% vs 42%), and
- RefSeq or Ensembl/GENCODE (46% vs 52%) and
- little usage of LRG (4%).
Declarations
Ethics approval and consent to participate n/a
Consent for publication - n/a
Availability of data and
materials
The datasets generated and/or analysed during the current study are
available here. https://tinyurl.com/embl-ebi-transcript-survey
Conflicts of interest
statement
PF is a member of the scientific advisory boards of Fabric Genomics,
Inc., and Eagle Genomics, Ltd.
Author’s contributions
- Joannella: survey design; survey analysis; survey promotion
- Aoife: survey design; survey design feedback, survey figures
- Jane: survey design, survey design feedback
- Adam: survey design, survey design feedback
- Emily P: survey review; survey
- Sarah H: bioinformatics analysis
- Irina M. A: bioinformatics analysis
- Paul F: survey dissemination - twitter; survey design feedback,
manuscript input
- Fiona: wrote this manuscript; survey design; survey analysis;
publication text; survey promotion