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Pitfalls of automated comparative sequence analysis as a single platform for routine clinical testing for NF1
  1. L M Messiaen1,
  2. K Wimmer2
  1. 1Laboratory of Medical Genomics, 1530 3rd Avenue, S Kaul Building, Birmingham, Alabama 35249, USA
  2. 2Department of Human Genetics, Clinical Institute for Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Austria
  1. Correspondence to:
 Professor Ludwine M Messiaen
 lmessiaengenetics.uab.edu

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Mattocks et al1 have used direct DNA sequencing and comparative sequence analysis to study patients with neurofibromatosis type 1 (NF1) and claim this study “achieved the highest recorded mutation detection rate using a single technique for this gene.” As a key point, the paper states that they studied 91 subjects fulfilling the NIH NF1 diagnostic criteria and achieved a mutation detection rate of 89% using automated comparative sequence analysis. They continue by saying “This detection rate is the highest for a single technique and is therefore appropriate for routine clinical practice.”

When developing genetic tests, especially for large and complex genes such as NF1, a large cohort of patients needs to be studied in a comprehensive way in order to fully understand the spectrum of mutations present in that gene. From our experience, it is of utmost importance to analyse the complete gene for the presence of all possible alterations that may result in a premature stop codon at the mRNA level.2 A significant fraction of the mutations in the NF1 gene cause aberrant splicing, and many of them are caused by alterations outside the canonically conserved AG/GT acceptor and donor sequences and even reside deep in the large introns.2–4 Also, various exonic mutations mimicking nonsense, missense, and even silent mutations at the genomic level have been described that are splicing mutations and exert their effect by creating a novel splice donor or acceptor or affect the function of an exonic splicing enhancer (ESE) or exonic splicing silencer (ESS).2,5 Although we have now studied over 600 patients fulfilling the NIH criteria using multiple complementary techniques, we are still challenged and surprised by the diversity of mutations leading to this disorder.

There have, unfortunately, been some examples in published reports where an alteration is …

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Footnotes

  • Competing interests: none declared