An aside: since "" interpolates variables and qq{} is the same (except you don't need to escape quotes in it) you might find this easier to read:

$Query = qq{
   EXEC $Stored_procedure $Standardisation, $Disease_cat,
        $Sex, $Sex_code, $Constraint_ref, $ICD_start_9,
        $ICD_end_9, $ICD_start_10, $ICD_end_10, $ICD_start_9_B, 
        $ICD_end_9_B, $ICD_start_10_B, $ICD_end_10_B,
        $ICD_start_9_C, $ICD_end_9_C, $ICD_start_10_C,
        $ICD_end_10_C, $yearfrom, $yearto, $min_age,
        $max_age, $region, $Instance_name, $Geo_scope,
        $number_of_years, $unique_identifier;
);
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Just makes things a little easier on the eye :)

cLive ;-)