Localization of Multiple Melanoma Tumor–Suppressor Genes on Chromosome 11 by Use of Homozygosity Mapping-of-Deletions Analysis

Abstract

Loss-of-heterozygosity (LOH) studies have implicated one or more chromosome 11 tumor-suppressor gene(s) in the development of cutaneous melanoma as well as a variety of other forms of human cancer. In the present study, we have identified multiple independent critical regions on this chromosome by use of homozygosity mapping of deletions (HOMOD) analysis. This method of analysis involved the use of highly polymorphic microsatellite markers and statistics to identify regions of hemizygous deletion in unmatched melanoma cell line DNAs. Regions of loss were defined by the presence of an extended region of homozygosity (ERH) at > or =5 adjacent markers and having a statistical probability of < or =.001. Significant ERHs were similar in nature to deletions identified by LOH analyses performed on uncultured melanomas, although a higher frequency of loss (24 [60%] of 40 vs. 16 [34%] of 47) was observed in the cell lines. Overall, six small regions of overlapping deletions (SROs) were identified on chromosome 11 flanked by the markers D11S1338/D11S907 (11p13-15.5 [SRO1]), D11S1344/D11S11385 (11p11.2 [SRO2]), D11S917/D11S1886 (11q21-22.3 [SRO3]), D11S927/D11S4094 (11q23 [SRO4]), AFM210ve3/D11S990 (11q24 [SRO5]), and D11S1351/D11S4123 (11q24-25 [SRO6]). We propose that HOMOD analysis can be used as an adjunct to LOH analysis in the localization of tumor-suppressor genes.

A network of clinically and functionally relevant genes is involved in the reversion of the tumorigenic phenotype of MDA-MB-231 breast cancer cells after transfer of human chromosome 8

“…These are indicative for allelic loss in the unmatched tumor cells (Goldberg et al, 2000). These markers were concentrated in the 8p12-p21 region previously determined to be frequently deleted in BC (Seitz et al, 2000).…”

High-Resolution Mapping of Structural Mutations in Prostate Cancer With Single Nucleotide Polymorphism Arrays

“…Current generations of SNP arrays provide high enough marker density to make it feasible to identify regions of LOH by the absence of heterozygous loci (which we call inferred LOH), rather than by comparison to the paired normal. For example, the homozygosity mapping of deletions (HOMOD) method was developed to use highly polymorphic microsatellite markers to identify regions of hemizygous deletion in unpaired tumor 5 cell lines [16], and a simple method of inferring LOH using the product of the probability of homozygosity in neighboring SNPs was able to identify 80% of LOH in 10K SNP array data from one sample [3,17]. SNP markers are less polymorphic than microsatellite markers, however, and the haplotype structure may render closely located SNP dependent in their genotype calls.…”

“…One advantage of a model-based approach over the existing tumor-only LOH inference methods [3,16] is its extensibility. The basic HMM was developed using average heterozygosity rates, but readily extended it to incorporate the SNP-specific heterozygosity rates and haplotype information as they became available.…”

“…We compared tumor-only inferred LOH to the observed LOH calls determined by paired analysis of tumor and normal genotypes, using 10K SNP array data from autosomes of 14 lung and breast cancer and EBV-transformed normal cell line pairs [15] ( Figure 3A). Here, 17,511 of 17,922 markers observed as LOSS in tumor/normal pairs were called LOSS in unpaired tumors by the HMM (for a sensitivity of 97.7%), and 15,962 of 16,364 markers that were observed as RET in tumor/normal pairs were called RET in unpaired tumors (for a specificity of 97.5%) (Supplemental Table 1A). …”

A 2·6 Mb interval on chromosome 6q25.2–q25.3 is commonly deleted in human nasal natural killer/T‐cell lymphoma

“…ND, not done. (Goldberg et al, 2000). The method involves the use of highly polymorphic microsatellite markers and statistics to define the presence of an extended region of homozygosity (ERH) at ‡ 5 adjacent markers, having a statistical probability of £ 0AE001.…”