Convert Protein Codon to Genome Coordinates

I needed a way to check if a few codons from different proteins were covered in a next-generation sequencing panel. This sounds relatively easy to do, but proves to be a bit difficult. Here are steps to do this.

(1) Use Biomart ID converter to find the Ensembl protein ID for your protein of interest.
(2) Use Ensembl GET map/translation/:id/:region to find the genomic coordinates of the codon of interest using the following script:


ENSP00000288602 is the Ensembl protein ID for your protein of interest (example: BRAF gene)
100..100 are the start and stop codons (example: just codon 100)

The result is a JSON formatted string like this:
{"mappings":[{"assembly_name":"GRCh38","end":140834815,"seq_region_name":"7","gap":0,"strand":-1,"coord_system":"chromosome","rank":0,"start":140834813}]}

This indicates that codon 100 of the BRAF gene (for this protein transcript) is located at chr7:140834813-140834815. Ensembl uses GRCh38. If you need other builds of the genome, use liftOver for converting.

I am sure there are probably more automated ways out there to do this, but this worked for the small subset of codons I needed to check in the design panel. If you have a better way to do this, please share in the comments section.

A Vast Array of Quantitative Trait Loci

A quantitative trait locus (QTL) is a locus, usually a single nucleotide polymorphism (SNP), that influences the level of a measurable product of interest.  I have worked with expression quantitative trait loci (eQTL) in the past, but recently my eyes have been opened to the wide array of other types of QTLs that exist.  For example, here are some classes of QTLs with references:

eQTL - a DNA locus that affects expression levels of an RNA transcript (PMID: 23345460, 23374354).
meQTL - a DNA locus that affects regional methylation levels (PMID: 23431366, 21251332).
pQTL - a DNA locus that affects the level of a polypeptide or protein produced (PMID: 23676674).
sQTL - a DNA locus the influences splicing of mRNA (PMID: 21173033).

That's all I could locate for now, but I assume there may be others I am missing.  In any way, it is interesting how genetic variation at a particular locus can be associated with various changes in a measurable product of interest.  While most of these QTLs are in some way indicative of the final resulting protein product, the respective correlation of each type of QTL with resulting protein levels varies widely by both QTL type and protein of interest.  In addition, mechanisms of these QTLs are also likely to vary.  For example, some QTLs work in cis (regulate nearby products) while others work in trans (regulate products several megabases away on the same chromosome or even on another chromosome altogether).  Additionally, there are QTLs that function as master regulators which influence levels of several important products in a signaling cascade or pathway.  Anyways, thought I would share these QTL types and see if there are any other important types I am missing.  If so, please include them in the comments below (along with references) so I can update the list.