Whole-genome Linkage Analysis and Sequence Analysis of Candidate Loci in Familial Breast Cancer.

Marikkannu R, Aravidis C, Rantala J, Picelli S, Adamovic T, Keihas M, Liu T, Kontham V, Nilsson D, Lindblom A

Anticancer Res. 35 (6) 3155-3165 [2015-06-00; online 2015-05-31]

Known breast cancer-predisposing genes account for fewer than 25% of all familial breast cancer cases and further studies are required to find the remaining high- and moderate-risk genes. We set-out to couple linkage analysis using microsatellite marker data and sequence analysis of linked regions in 13 non-BRCA1/2 families in order to find novel susceptibility loci and high-penetrant genes. Genotyping with 540 fluorescently-labeled microsatellite markers located on the 23 chromosomes at 7.25 cM resolution was used for primary linkage analysis and an additional 40 markers were used for fine-mapping of loci with a logarithm of odds (LOD) or heterogeneity LOD (HLOD) score greater than one. Whole-exome sequencing data of 28 members from all 13 families were used for the bioinformatics sequence analysis on the linked regions of these families. Linkage analysis identified three loci on chromosome 18q as a putative region of interest (overall LOD=1, HLOD=1.2). Sequencing analysis of the three linked regions on 18q and mutation prediction algorithms did reveal three probable damaging variants. Overall, our study identified three weakly linked loci on 18q and three probable damaging variants of interest in the 13 families with breast cancer.

NGI Stockholm (Genomics Applications)

NGI Stockholm (Genomics Production)

National Genomics Infrastructure

PubMed 26026075

pii: 35/6/3155