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Case Reports
. 2024 Nov 1;44(6):617-620.
doi: 10.3343/alm.2024.0051. Epub 2024 May 31.

Identification of a False-positive Multiplex Ligationdependent Probe Amplification Result in BRCA1 Using a Copy Number Variation Algorithm Under Development for a Commercial Next-Generation Sequencing-based Homologous Recombination Deficiency Assay

Paola Concolino  1   2 , Elisa De Paolis  1   2 , Martina Rinelli  1   2 , Giulia Maneri  1   2 , Francesca Brisighelli  1   2 , Rita Trozzi  3 , Simona Duranti  4 , Luciano Giacò  5 , Maria Piane  6   7 , Alessia Preziosi  5 , Arianna Panfili  4 , Giovanni Scambia  3   8 , Camilla Nero  3 , Maria De Bonis  1   2 , Angelo Minucci  1   2
Affiliations
Case Reports

Identification of a False-positive Multiplex Ligationdependent Probe Amplification Result in BRCA1 Using a Copy Number Variation Algorithm Under Development for a Commercial Next-Generation Sequencing-based Homologous Recombination Deficiency Assay

Paola Concolino et al. Ann Lab Med. .
No abstract available

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Conflict of interest statement

CONFLICTS OF INTEREST

None declared.

Figures

Fig. 1
Fig. 1. Bioinformatic prediction of CNVs in BRCA1 and BRCA2 and validation using Sanger sequencing. (A) Bioinformatics prediction of CNVs in BRCA1 and BRCA2 genes using the prototype algorithm of SOPHiA DDM® tool. The CNV analysis indicated a wild-type status for the BRCA1 gene (left) and complete deletion of the BRCA2 gene (right). (B) Sanger sequencing result confirming the heterozygous status of the BRCA1 c.5017_5019del variant.
Fig. 2
Fig. 2. MLPA results obtained using the SALSA MLPA probemix and detailed probe sequences for BRCA1. (A) MLPA results from comparative analysis experiment obtained using Coffalyser.NET Software with SALSA MLPA probemix P002-D1 BRCA1. The final ratio of BRCA1 exon 17 probes indicates a heterozygous deletion. (B) Nucleotide sequence of BRCA1 exon 17 is highlighted in gray, with the MLPA sequence probe denoted in bold font. The three deleted nucleotides of the variant p.(His1673del) are highlighted in red. (C) MLPA results from comparative analysis experiment obtained using Coffalyser.NET Software using SALSA MLPA probemix P087-D1 BRCA1, where the final ratio of BRCA1 exon 17 probes showed no heterozygous deletion. The final ratio (FR) of each reference probe in the patient’s sample should fall between 0.80 and 1.20 for the diploid normal copy number. The following FR cut-off values were used: heterozygous deletion, 0.40<FR< 0.65; heterozygous duplication, 1.30<FR<1.65. Please note that the BRCA1 exon numbering used in both SALSA MLPA probemix product descriptions follows the traditional exon numbering, wherein no exon 4 is present. Notably, BRCA1 exon 17 reported in the MLPA kit corresponds to BRCA1 exon 16 of LRG_292.
Abbreviation: RFU, relative fluorescent units.
See this image and copyright information in PMC

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