Screening for PALB2 mutations in South African women with BRCA negative familial breast cancer
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Date
2018-02
Authors
Makhetha, Mpoi F.
Journal Title
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Volume Title
Publisher
University of the Free State
Abstract
PALB2 (Partner and Localizer of BRCA2) plays a key role in the repair of damaged DNA by localizing BRCA2 and initiating the repair process. The gene has been recognized as a third breast cancer (BC) predisposition gene, together with BRCA1 and BRCA2. The absolute risk for the development of BC for mutation carriers with a familial predisposition, represents 58% at 50 years of age, similar to that of BRCA2. Although germline loss-of-function PALB2 mutations is rare, the mutation spectrum internationally and in South African (SA) is still unknown.
Eighty-six SA breast- and/or ovarian cancer (OVC) patients were selected. Patients had to be affected with either breast- and/or OVC, have a positive family history of BC (two or more affected family members, excluding the index), tested negative for pathogenic mutations in BRCA1/2, represent one of the four main SA ethnic groups and had sufficient amounts of good quality DNA stored to complete a comprehensive screen of the entire gene. The complete coding sequence together with the intron-exon boundaries were screened using qPCR-based high resolution melt analysis (HRMA). All samples deviating from the baseline was Sanger sequenced. In silico analysis using a combination of prediction programmes was performed for single base changes present in the coding regions of the gene.
A total of 20 variants was identified, of which two represented loss-of-function mutations (PALB2 c.424A>T, p.Lys142Ter and PALB2 c.508A>T, p.Arg170Ter). These mutations were situated in exon 4. Although the first mutation has been detected before, PALB2 c.508A>T, p.Arg170Ter was novel. These mutations were detected for the SA Indian (single patient), Coloured (two patients) and Afrikaner (single patient) populations. The two patients carrying these Class 5 pathogenic mutations had an extensive family history of BC and other ca types.
Two of the 18 missense variants [PALB2 c.2794G>A, p.Ala915Thr (rs374736398) and PALB2 c.3434G>T, p.Gly1145Val (novel variant)] were classified as putative Class 4 variants based on their location in the carboxy-terminal WD-40 domain, the binding site for the N-terminus of BRCA2. PALB2 c.2794G>A, p.Ala915Thr was detected for three SA patients (SA Indian and White population), whereas the novel PALB2 c.3434G>T, p.Gly1145Val variant was present in a single Coloured BC patient. In the families of the patients carrying either one of the putative Class 4 variants, BC was the dominant ca type observed. Interpretation of rare missense variants such as PALB2 c.3434G>T, p.Gly1145Val regarding impact on clinical treatment remains challenging, as no rare missense variant to date has been used to determine the clinical management of patients carrying these variants. The majority of PALB2 variants was observed for the Coloured and SA Indian populations, whereas for the other three groups, it was limited. This observation could have been due to the unique admixture of these population groups present in SA, as SA has a multi-faceted colonisation history based on the country’s location with respect to major historical trade routes. Another explanation could be the higher percentage of representation of these two population groups in the cohort, as 33.7% of the cohort was Coloured with 25.6% self-identified as SA Indian BC/OVC patients. Although 17.4% of the cohort represented Black patients, the number of variants observed for this group was very low. This indicated that the prevalence of PALB2 mutations/variants might be different for each of the SA population groups, depending on the genetic heritage of these patients. For this reason, the cohort needs to be increased in order to determine the mutation spectrum. Once this has been determined, case-control studies should be performed to determine the relative risk involved with each variant regarding the development of breast- and other ca types in SA.
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Keywords
Familial breast cancer, HRMA, Mutation screening, PALB2, Sanger sequencing, South Africa, Computer-based analysis, Dissertation (M.Med.Sc. (Human Genetics))--University of the Free State, 2018