Ann Lab Med.  2024 Nov;44(6):617-620. 10.3343/alm.2024.0051.

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

• Concolino P
• Paolis ED
• Rinelli M
• Maneri G
• Brisighelli F
• Trozzi R
• Duranti S
• Giacò L
• Piane M
• Preziosi A
• Panfili A
• Scambia G
• Nero C
• Bonis MD
• Minucci A

• KMID: 2560815
• DOI: http://doi.org/10.3343/alm.2024.0051

Figure

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  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 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

Reference

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