A new biallelic polymorphism in intron 1 of the CHRNA4 gene may cause erroneous genotyping of a closely linked CA repeat marker.

A new polymorphism in intron 1 of the neuronal nicotinic acetylcholine receptor alpha 4 subunit gene (CHRNA4) was identified. It consists of a G to T substitution located in the downstream flanking region of a previously reported CA repeat marker. This polymorphism whose frequency is about six percent in a control population occurs near the 3' end of the reverse primer generally used to type the CA repeat marker. Data are presented showing that the newly identified polymorphism causes erroneous genotyping of the CA repeat marker which can alter the results of linkage analysis for CHRNA4. The use of a different reverse primer located 34 nt downstream of the published sequence overcame errors in genotyping and identified two novel alleles of the CA repeat marker. Re-typing of the marker with the new proposed primer pair in a Caucasian control population of 107 unrelated individuals was also performed