We have undertaken a systematic study of primary human breast tumor DNA to identify and characterize frequently occurring somatic mutations. Loss of heterozygosity (LOH) has been the most frequent mutation in our panels of primary breast tumor DNA. It is currently thought that LOH reveals recessive mutations within the affected region of the genome. One goal of our studies has been to physically define the target genes revealed by LOH in primary breast tumors. We have focused our efforts on chromosome 17, finding five regions of the chromosome which are independently affected by LOH in breast tumors. Two apparent target loci are on chromosome 17p; one is the TP53 gene. The other is an as-yet undefined locus telomeric to the TP53 gene. Loss of expression of the nmel gene on chromosome 17q in tumors was linked to patients with a poor prognosis (p = 0.018). Although a significant trend (p = 0.05) was found between LOH of the nmel gene and loss of nmel expression, no point mutations were found within the coding region of the nmel gene by single strand conformational polymorphism (SSCP) or nucleotide sequence analysis. These and other results suggest to us that there may be potential tumor suppressor genes both centromeric and telomeric to the nmel locus on chromosome 17q.