Standard mutation nomenclature in molecular diagnostics: practical and educational challenges.

To translate basic research findings into clinical practice, it is essential that information about mutations and variations in the human genome are communicated easily and unequivocally. Unfortunately, there has been much confusion regarding the description of genetic sequence variants. This is largely because research articles that first report novel sequence variants do not often use standard nomenclature, and the final genomic sequence is compiled over many separate entries. In this article, we discuss issues crucial to clear communication, using examples of genes that are commonly assayed in clinical laboratories. Although molecular diagnostics is a dynamic field, this should not inhibit the need for and movement toward consensus nomenclature for accurate reporting among laboratories. Our aim is to alert laboratory scientists and other health care professionals to the important issues and provide a foundation for further discussions that will ultimately lead to solutions.

[1]  Shuji Ogino,et al.  Importance of standard nomenclature for SMN1 small intragenic (“subtle”) mutations , 2004, Human mutation.

[2]  S. Antonarakis,et al.  Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion , 2000 .

[3]  Martijn J. Schuemie,et al.  Thesaurus-based disambiguation of gene symbols , 2005, BMC Bioinformatics.

[4]  Mathew W. Wright,et al.  Guidelines for human gene nomenclature. , 2002, Genomics.

[5]  M. Stumvoll,et al.  Sex-specific effect of the Val1483Ile polymorphism in the fatty acid synthase gene (FAS) on body mass index and lipid profile in Caucasian children , 2007, International Journal of Obesity.

[6]  Victoria M. Pratt,et al.  Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel , 2004, Genetics in Medicine.

[7]  Andrew Josey.  Updates , 2003, login Usenix Mag..

[8]  Obstacles of nomenclature , 1997, Nature.

[9]  Robert L Fine,et al.  Fas-mediated apoptosis is dependent on wild-type p53 status in human cancer cells expressing a temperature-sensitive p53 mutant alanine-143. , 2003, Cancer research.

[10]  R. Ramesh,et al.  Activation of the Fas-FasL signaling pathway by MDA-7/IL-24 kills human ovarian cancer cells. , 2005, Cancer research.

[11]  S. Povey,et al.  The changing challenges of nomenclature , 1999, Cytogenetic and Genome Research.

[12]  Update on nomenclature for human gene mutations , 2022 .

[13]  C. Boehm,et al.  ACMG recommendations for standards for interpretation of sequence variations , 2000 .

[14]  K. Klinger,et al.  Laboratory standards and guidelines for population-based cystic fibrosis carrier screening , 2001, Genetics in Medicine.

[15]  Sue Povey,et al.  Genew: the Human Gene Nomenclature Database, 2004 updates , 2004, Nucleic Acids Res..

[16]  M. Gleave,et al.  Inhibition of the phosphatidylinositol 3'-kinase pathway promotes autocrine Fas-induced death of phosphatase and tensin homologue-deficient prostate cancer cells. , 2006, Cancer research.

[17]  J. D. den Dunnen,et al.  Standardizing mutation nomenclature: Why bother? , 2003, Human mutation.

[18]  Sue Povey,et al.  Genew: the Human Gene Nomenclature Database , 2002, Nucleic Acids Res..

[19]  S. Ogino,et al.  Spinal muscular atrophy: molecular genetics and diagnostics , 2004, Expert review of molecular diagnostics.

[20]  Ourania Horaitis,et al.  The challenge of documenting mutation across the genome: The human genome variation society approach , 2004, Human mutation.

[21]  S. Antonarakis.  Recommendations for a nomenclature system for human gene mutations , 1998 .