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SALSA MLPA Probemix P002 BRCA1

Breast and ovarian cancer, hereditary (HBOC)

Region: BRCA1 17q21.31

MLPA | CE CO IL MA
Intended use: This SALSA MLPA probemix P002 BRCA1 is an in vitro diagnostic (IVD)1 or research use only (RUO) assay for the detection of deletions or duplications in the human BRCA1 gene in order to confirm a potential cause and clinical diagnosis for hereditary breast and ovarian cancer (HBOC). This product can also be used for molecular genetic testing of at-risk family members.

This assay is for use with human genomic DNA extracted from peripheral blood and not for use with DNA extracted from formalin-fixed paraffin embedded or fresh tumour materials. Deletions or duplications detected with the P002 BRCA1 probemix must be verified by using the SALSA MLPA probemix P087 BRCA1 Confirmation assay or a different technique. In particular, copy number changes detected by only a single probe always require validation by another method. Most defects in the BRCA1 gene are point mutations, none of which will be detected by MLPA. It is therefore recommended to use this SALSA MLPA probemix in combination with sequence analysis. This assay is not intended to be used as a standalone assay for clinical decisions. The results of this test should be interpreted by a clinical molecular geneticist or equivalent.

1 Please note that this probemix is for In Vitro Diagnostic use (IVD) in the countries specified at the end of this product description. In all other countries, the product is for Research Use Only (RUO).

Clinical background: Germline defects in the BRCA1 gene are the most frequent cause of a hereditary predisposition to breast cancer. Features characteristic of hereditary, versus sporadic, breast cancer are: younger age at diagnosis, frequent bilateral disease, and more frequent occurrence of disease among male relatives. Mutations in the BRCA1 and BRCA2 genes account for about 20 to 25% of hereditary breast cancers and about 5 to 10% of all breast cancers. In addition, mutations in the BRCA1 and BRCA2 genes account for around 15% of ovarian cancers overall.
More information is available at http://www.ncbi.nlm.nih.gov/books/NBK1247/.

The great majority of germline defects in the BRCA1 gene are point mutations that can be detected by sequence analysis. Deletions and duplications of complete exons in the BRCA1 gene are the second most common cause of defects in the BRCA1 gene. These copy number changes are usually missed by amplicon-based sequencing analysis (Sanger sequencing or Next Generation Sequencing), but can be detected by the MLPA technique and hence MLPA complements sequence analysis of the BRCA1 gene. Large genomic rearrangements (LGRs) in BRCA1 may account for up to one-third of all disease-causing mutations, dependent on the population (Hansen et al. 2009). For example in Italian HBOC families the prevalence is 23% (Montagna et al. 2003), in the Netherlands 27%-36% (Hogervorst et al. 2003; Petrij-Bosch et al. 1997), while in a Danish cohort of HBOC patients the prevalence was 3.8% (Thomassen et al. 2006).

Probemix content: This SALSA MLPA probemix P002 BRCA1 contains 48 MLPA probes with amplification products between 130 and 469 nt (Table 1) including 38 probes for the BRCA1 gene region (Table 2) and 10 reference probes that detect sequences outside this region. The identity of the genes detected by the reference probes is available online (www.mlpa.com).

At least one MLPA probe is present for each exon in the major BRCA1 transcript variant 1. Eight probes are present for exon 11 (3426 nt long). Three probes are present for exon 13, which is frequently deleted or duplicated (Hogervorst et al. 2003). Three probes are present for exon 24 and two probes for exon 16. One probe is included for exon 1b, which is the first exon in transcript variants 3 and 5, and two probes detect sequences located 4.6 kb and 0.7 kb upstream of the BRCA1 gene.

This probemix contains nine quality control fragments generating amplification products between 64 and 105 nt: four DNA Quantity Fragments (Q-fragments), two DNA Denaturation Fragments (D-fragments), one benchmark fragment, and one chromosome X and one chromosome Y-specific fragment. More information on how to interpret observations on these control fragments can be found in the MLPA General Protocol and online at www.mlpa.com.

SALSA Artificial Duplication DNA SD024: In case no positive DNA sample is available in your laboratory, an artificial duplication DNA sample for this probemix (catalogue number SD024) can be ordered from MRC-Holland. This SD024 Artificial Duplication DNA will show a duplication of two or three probes when using the following probemixes: P002 and P087 BRCA1; P045, P090 and P077 BRCA2. The SD024 Artificial Duplication DNA is a mixture of human female genomic DNA and a titrated amount of plasmid containing selected probe target sequences. For further details, please consult the SD024 Artificial Duplication DNA product description, available online: www.mlpa.com. This product is for research use only (RUO).

Sample DNA
Sample DNA developed for this product:

Order Items

Probemix

Item no.
Description
Technology
Price
P002-025R
SALSA MLPA Probemix P002 BRCA1 – 25 rxn
€ 243.00
P002-050R
SALSA MLPA Probemix P002 BRCA1 – 50 rxn
€ 486.00
P002-100R
SALSA MLPA Probemix P002 BRCA1 – 100 rxn
€ 972.00

Required Reagents

Item no.
Description
Technology
Price
EK1-FAM
SALSA MLPA EK1 reagent kit – 100 rxn – FAM
€ 300.00
EK1-Cy5
SALSA MLPA EK1 reagent kit – 100 rxn – Cy5
€ 300.00
EK5-FAM
SALSA MLPA EK5 reagent kit – 500 rxn – FAM
€ 1380.00
EK5-Cy5
SALSA MLPA EK5 reagent kit – 500 rxn – Cy5
€ 1380.00
EK20-FAM
SALSA MLPA EK20 reagent kit – 2000 rxn – FAM
€ 5295.00

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CE

CE-marked products are for In Vitro Diagnostic (IVD) use only in EU (candidate) member states and members of the European Free Trade Association (EFTA).

CO

IVD-registered in Colombia.

IL

IVD-registered in Israel.

MA

IVD-registered in Morocco.