Standard Representation Of Complex Variants

Question

[Brice Tebbs]

Looking a various data in VCF files and places like dbSNP its not uncommon to find different descriptions of the same sequence change. A simple example would be a case were the sequence is ATTTTTG and one T is deleted. Which T? The first or the last?

It gets more complicated of course. The ΔF508 Deletion in CF could not only be written as (hg19).

chr7:117199646 CTTT -> T or chr7:117199646 CTT -> .

But also:

chr7:117199644 ATCT -> A

I'm working on some software for interpretation and comparison of results and am doing internal normalization of these, but I wonder if there is a specific standard I should respect/use.

Answer 1

[Fred Fleche]

Did you have a look at the Recommendations for the description of sequence variants available at the website of the Human Genome Variation Society ? http://www.hgvs.org/mutnomen/recs.html

[Chris Miller]

From the link: "for all descriptions the most 3' position possible is arbitrarily assigned to have been changed, this is important especially in single residue (nucleotide or amino acid) stretches or tandem repeats"