Draft Genetic Test Review

Breast Cancer
Analytic Validity
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ANALYTIC VALIDITY

ANALYTIC VALIDITY  

Question 1: What is the specific clinical disorder being studied?

Testing for BRCA1/2 mutations is qualitative.  There are three possible categories of results for full DNA sequencing: 1) positive for deleterious mutation, 2) negative for deleterious mutation, and 3) genetic variant (three types – suspected deleterious, favor polymorphism and uncertain clinical significance).  Testing targeted at specific mutations (e.g., a mutation identified in an index case or the three mutations common in Ashkenazi Jewish women) will yield only positive or negative results; all of the mutations being tested are known to have clinical significance. Myriad Genetic Laboratories (Myriad) further breaks down these results into categories as follows: (www.myriadtests.com/provider/doc/tech_specs_brac.pdf, under Technical Specifications).

“Positive for a deleterious mutation”: Includes all mutations (nonsense, insertions, deletions) that prematurely terminate (truncate) the protein product of BRCA1 at least 10 amino acids from the C-terminus, or the protein product of BRCA2 at least 110 amino acids from the C-terminus (based on documentation of deleterious mutations in BRCA1 and BRCA2).  In addition, specific missense mutations and non-coding intervening sequence (IVS) mutations are recognized as deleterious on the basis of data derived from linkage analysis of high risk families, functional assays, biochemical evidence and/or demonstration of abnormal messenger ribonucleic acid (mRNA) transcript processing.

“Genetic variant, suspected deleterious”: Includes genetic variants for which the available evidence indicates likelihood, but not proof, that the mutation is deleterious.  The specific evidence supporting such an interpretation will be summarized for individual variants on each such report.

“Genetic variant, favor polymorphism”: Includes genetic variants for which available evidence indicates that the variant is highly unlikely to contribute substantially to cancer risk.  The specific evidence supporting such an interpretation will be summarized for individual variants on each such report.

“Genetic variant of uncertain significance”: Includes all missense mutations and mutations that occur in analyzed intronic regions whose clinical significance has not yet been determined, as well as chain-terminating mutations that truncate BRCA1 and BRCA2 distal to amino acid positions 1853 and 3308, respectively.

“No deleterious mutation detected”: Includes non-truncating genetic variants observed at a frequency of approximately 2 percent of a suitable control population (providing that no data suggest clinical significance), as will as all genetic variants for which published data demonstrate absence of substantial clinical significance.  Also includes mutations in the protein-coding region that neither alter the amino acid sequence nor are predicted to significantly affect exon splicing, and base pair alterations in non-coding portions of the gene that have been demonstrated to have no deleterious effect on the length or stability of the mRNA transcript.  Data on polymorphic variants are available upon request.  There may be uncommon genetic abnormalities in BRCA1 and BRCA2 that will not be detected by BRACAnalysisä (see last paragraph of this question).  This analysis, however, is believed to rule out the majority of abnormalities in these genes, which are believed to be responsible for most hereditary susceptibility to breast and ovarian cancer.

“Specific variant/mutation not identified”: Specific and designated deleterious mutations or variants of uncertain clinical significance are not present in the individual being tested.  If one (or rarely two) specific deleterious mutations have been identified in a family member, a negative analysis for the specific mutation(s) indicates that the tested individual is at the general population risk of developing breast or ovarian cancer.

Change of interpretation and issuance of amended reports: If and whenever there is a change in the clinical interpretation of a specific reported variant, an amended test report will automatically be provided by Myriad Genetic Laboratories.

Limitations of DNA Sequencing

• DNA sequencing is able to detect only point and small mutations

• Promoter regions are not analyzed 

• Large genomic rearrangements and some types of errors in RNA transcript processing are not detected by the usual polymerase chain reaction (PCR)-based methodologies, including Myriad’s sequencing technique.  These defects represent an estimated 10 to 15 percent of all disease-causing mutations in the general population (Puget et al., 1999; Unger et al., 2000) and up to 36 percent in the Dutch population. (Petrij-Bosch et al., 1997) .   
• There may be limited portions of either BRCA1 or BRCA2 for which sequence determination can be performed only in the forward or reverse direction

• Unequal allele amplification may result from rare polymorphisms under primer sites

• Question 18 examines the issue of clinical validity in more detail.  It has been estimated that between 63 and 67 percent of expected deleterious mutations showing linkage to BRCA1 are identified by PCR-based mutation-detection assays. (Ford et al., 1998; Gayther and Ponder, 1997)   In August of 2002, Myriad added a panel to its comprehensive analysis that identifies five deleterious large recurrent rearrangements in the BRCA1 gene.  This panel detects four large deletions in exons 8 and 9, exon 13, exon 22, and exons 14-20, and one duplication in exon 13.