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. 2007 Aug 30:8:299.
doi: 10.1186/1471-2164-8-299.

Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies

Anna Gonzalez-Neira  1 , Juan Manuel Rosa-Rosa, Ana Osorio, Emilio Gonzalez, Melissa Southey, Olga Sinilnikova, Henry Lynch, Rogier A Oldenburg, Christi J van Asperen, Nicoline Hoogerbrugge, Guillermo Pita, Peter Devilee, David Goldgar, Javier Benitez
Affiliations

Genomewide high-density SNP linkage analysis of non-BRCA1/2 breast cancer families identifies various candidate regions and has greater power than microsatellite studies

Anna Gonzalez-Neira et al. BMC Genomics. .

Abstract

Background: The recent development of new high-throughput technologies for SNP genotyping has opened the possibility of taking a genome-wide linkage approach to the search for new candidate genes involved in heredity diseases. The two major breast cancer susceptibility genes BRCA1 and BRCA2 are involved in 30% of hereditary breast cancer cases, but the discovery of additional breast cancer predisposition genes for the non-BRCA1/2 breast cancer families has so far been unsuccessful.

Results: In order to evaluate the power improvement provided by using SNP markers in a real situation, we have performed a whole genome screen of 19 non-BRCA1/2 breast cancer families using 4720 genomewide SNPs with Illumina technology (Illumina's Linkage III Panel), with an average distance of 615 Kb/SNP. We identified six regions on chromosomes 2, 3, 4, 7, 11 and 14 as candidates to contain genes involved in breast cancer susceptibility, and additional fine mapping genotyping using microsatellite markers around linkage peaks confirmed five of them, excluding the region on chromosome 3. These results were consistent in analyses that excluded SNPs in high linkage disequilibrium. The results were compared with those obtained previously using a 10 cM microsatellite scan (STR-GWS) and we found lower or not significant linkage signals with STR-GWS data compared to SNP data in all cases.

Conclusion: Our results show the power increase that SNPs can supply in linkage studies.

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Figures

Figure 1
Figure 1
Multipoint nonparametric linkage analysis of 19 families. The figure includes LOD scores (top) and information content (bottom) using CEPH and ALL frequencies. Chromosome numbers are indicated below each panel.
Figure 2
Figure 2
LOD score values and information content. LOD score values (top part of each panel) and information content (bottom part of each panel) in the six candidate regions selected, taking into account: A) LD between marker loci (r2 > 0.2/0.5/0.8), and B) marker densities (0.5 cM/1 cM/2 cM).
Figure 3
Figure 3
SNP-GWS versus STR-GWS data. Comparison of SNP-GWS (black) and STR-GWS (grey) results in candidate regions. NPLOD score comparisons are at the top, and information content (IC) comparisons are at the bottom of each panel.
See this image and copyright information in PMC

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