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, ...
[download]

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
+_id ...
[download]

in your select, then you really shouldn't ask for anything but the primary.gene_id from the left side of the join.