Competency information
Details
Annotate variation data in the context of a specific acquired or inherited disease or genetic investigation.
Considerations
- The challenges of variant identification, including single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs).
- Variation databases, e.g. dbSNP, DECIPHER.
- SNP annotation challenges.
- SNP resources in the major genome sequence repositories, e.g. Ensembl, UCSC.
- Feature identification, including SNP analysis and transcription factor binding sites.
- Missense analysis, e.g. Align GVGD, SIFT, PolyPhen, Panther, PhDSNP, MAPP.
- Splicing analysis applications, e.g. GeneSplicer, MAxEntScan NNSplice, SSFL, HSF, NetGene2.
- Classifying phenotype: London Database of Dysmorphology (LDD), Human Phenotype Ontology (HPO), ICD, Orphanet, Snomed-CT.
- Application of standard operating procedures as part of the laboratory management process.
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 1 | Outcome In the context of both human and microbes: |