Comparison of mRNA splicing assay protocols across multiple laboratories: Recommendations for best practice in standardized clinical testing

Phillip J. Whiley, Miguel De La Hoya, Mads Thomassen, Alexandra Becker, Rita Brandão, Inge Sokilde Pedersen, Marco Montagna, Mireia Menéndez, Francisco Quiles, Sara Gutiérrez-Enríquez, Kim De Leeneer, Anna Tenés, Gemma Montalban, Demis Tserpelis, Toshio Yoshimatsu, Carole Tirapo, Michela Raponi, Trinidad Caldes, Ana Blanco, Marta SantamariñaLucia Guidugli, Gorka Ruiz De Garibay, Ming Wong, Mariella Tancredi, Laura Fachal, Yuan Chun Ding, Torben Kruse, Vanessa Lattimore, Ava Kwong, Tsun Leung Chan, Mara Colombo, Giovanni De Vecchi, Maria Caligo, Diana Baralle, Conxi Lázaro, Fergus Couch, Paolo Radice, Melissa C. Southey, Susan Neuhausen, Claude Houdayer, Jim Fackenthal, Thomas Van Overeem Hansen, Ana Vega, Orland Diez, Rien Blok, Kathleen Claes, Barbara Wappenschmidt, Logan Walker, Amanda B. Spurdle, Melissa A. Brown

Research output: Contribution to journalArticle

41 Scopus citations

Abstract

BACKGROUND: Accurate evaluation of unclassified sequence variants incancer predisposition genesis essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting. METHODS: We conducted a multicenter investigation to compare mRNA splicingassay protocols usedbymembers of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2) gene variants known to alter splicing (BRCA1: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and BRCA2: c.426-12-8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501 + 3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design. results: PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with BRCA1, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., BRCA2 c.8632 + 1G>A Δ19,20 and BRCA1 c.135-1G>T A5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., BRCA2 c.426-12-8delGTTTT ins18bp). conclusions: We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.

Original languageEnglish (US)
Pages (from-to)341-352
Number of pages12
JournalClinical chemistry
Volume60
Issue number2
DOIs
StatePublished - Feb 2014

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

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    Whiley, P. J., De La Hoya, M., Thomassen, M., Becker, A., Brandão, R., Pedersen, I. S., Montagna, M., Menéndez, M., Quiles, F., Gutiérrez-Enríquez, S., Leeneer, K. D., Tenés, A., Montalban, G., Tserpelis, D., Yoshimatsu, T., Tirapo, C., Raponi, M., Caldes, T., Blanco, A., ... Brown, M. A. (2014). Comparison of mRNA splicing assay protocols across multiple laboratories: Recommendations for best practice in standardized clinical testing. Clinical chemistry, 60(2), 341-352. https://doi.org/10.1373/clinchem.2013.210658