Lordy, don't change the column names. You can
alias the name with AS in most SQL dialects:
SELECT p.gene_id, s.gene_id AS SecGene, ...
If the gene_id in the second table is a
foreign key into the primary table, you really
want it to have the same name, for your and
everyone elses sanity. I gotta ask, is the
gene_id field the field that you use to tie
the two tables together? If so, and you have:
... FROM primary LEFT JOIN secondary ON primary.gene_id=secondary.gene
in your select, then you really shouldn't ask
for anything but the primary.gene_id
from the left
side of the join.