Clarification on interchromosomal event annotations

[mhayes]

Hi,

I am not sure if this is the correct forum for this question, so I apologize in advance.

When I see interchromosomal rearrangements (e.g. translocations) annotated in databases and publications, the following information is usually given:

chrA, chrA breakpoint, strand A, chrB, chrB breakpoint, strand B

The participating chromosomes are provided as well as the breakpoints. The strands that form the translocation are also provided.

My question is, for a given rearrangement, does it matter which chromosome is annotated as chrA or chrB? Since these are interchromosomal events, I assume there is no inherent ordering among the participating chromosomes. Is it customary to just arbitrarily assign one of the participating chromosomes as the "beginning" of the rearrangement?

Also, let's say we have the following fusion between the plus strands of chromosomes 3 and 4:

chr3, 323246186, +, chr4, 118501916, +

Couldn't I also annotate this as shown below?

chr4, 118501916, -, chr3, 323246186, -

Thanks.