BRCA1 and BRCA2 genetic testing-pitfalls and recommendations for managing variants of uncertain clinical significance

BACKGROUND

Increasing use of BRCA1/2 testing for tailoring cancer treatment and extension of testing to tumour tissue for somatic mutation is moving BRCA1/2 mutation screening from a primarily prevention arena delivered by specialist genetic services into mainstream oncology practice. A considerable number of gene tests will identify rare variants where clinical significance cannot be inferred from sequence information alone. The proportion of variants of uncertain clinical significance (VUS) is likely to grow with lower thresholds for testing and laboratory providers with less experience of BRCA. Most VUS will not be associated with a high risk of cancer but a misinterpreted VUS has the potential to lead to mismanagement of both the patient and their relatives.

DESIGN

Members of the Clinical Working Group of ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) global consortium (www.enigmaconsortium.org) observed wide variation in practices in reporting, disclosure and clinical management of patients with a VUS. Examples from current clinical practice are presented and discussed to illustrate potential pitfalls, explore factors contributing to misinterpretation, and propose approaches to improving clarity.

RESULTS AND CONCLUSION

Clinicians, patients and their relatives would all benefit from an improved level of genetic literacy. Genetic laboratories working with clinical geneticists need to agree on a clinically clear and uniform format for reporting BRCA test results to non-geneticists. An international consortium of experts, collecting and integrating all available lines of evidence and classifying variants according to an internationally recognized system, will facilitate reclassification of variants for clinical use.

Effect of Ring Asymmetry on Pseudorotation at Five-Coordinate Phosphorus in Phosphadiazetidinones

Non-equivalence of fluorine atoms has been observed in the 19F n.m.r. spectra of 1-alkyl-1,1-difluoro-N-methyl-N′-phenyl-1,2,4-phosphadiazetidin-3-ones at -40°C but not in the spectra of analogous N,N′-dimethyl compounds and a mechanism for pseudorotation in these compounds is proposed to explain this difference.

Notizen: The Fluorine-19 NMR Spectrum of Methylthiotetrafluorophosphorane

The low-temperature 19F NMR spectrum of the stereochemically non-rigid compound, CH3SPF4, shows three fluorine environments, one for the equatorial and two for the nonequivalent axial fluorine atoms. Each of the twelve lines of the upfield 19F- (axial) resonance shows further fine structure, due to coupling between 19F and the protons of the CH3S group. The center peaks of the two multiplet components reveal apparent quintet structure which, based on a computer simulation of the 19F spectrum of CH3SPF4, is rationalized in terms of accidental overlap of two quartets.

Mass Spectroscopic Studies of Phosphorus-Fluorine Compounds. Compounds containing Five-coordinate Phosphorus

The mass spectra of a number of phosphorus-fluorine compounds containing five-covalent phosphorus have been obtained. The major fragment ions for each compound are tabulated together with some probable ion assignments.

cis-trans-Isomerie in 1,5-Diaza-2,4-Diphosphorinan-6-onen cis-trans-Isomerism in 1,5-Diaza-2,4-diphosphorinan-6-ones

The methylene-bis(dialkylaminochlorophosphines) 2a and 2b react with N,N′-dimethyl- N,N′-bis(trimethylsilyl)urea 1 to give the 1,5-diaza-2,4-diphosphorinan-6-ones, 4a and 4b, each of which exists as two isomers. Sulfuration of 4a and 4b led to the stable derivatives, 5a and 5b, which, with the help of column chromatography, were separated into pure cis- and trans-isomers. The structures were established, based upon NMR-spectroscopic, chemical and analytical data.

Phosphorus-Fluorine Chemistry, XXXI

The preparation of a series of methyl-substituted piperidyl-fluorophosphoranes is described, of general formula RR′NPF4-nPhn (where RR′N = 2-Me-piperidyl-, 3-Me-piperidyl-, or 4-Me-piperi-dyl; n = 0, 1, or 2), from the cleavage of silicon-nitrogen bonds in methyl-substituted piperidyl silanes by fluorophosphoranes. The structures of the new compounds are deduced from 19F and 31P n.m.r. data.

An N.M.R. Study of some Tertiary Butyl - Phosphorus Compounds

H1 und P31 (sowie F19, soweit zutreffend) N.M.R.-Daten werden mitgeteilt für einige Verbindungen, die tertiäre Butylgruppen an Phosphor gebunden enthalten. Es wird gezeigt, daß die Verbindung (CH3)3C · P (:O) (F) [N(CH3)2] als ein Gemisch zweier Isomerer vorliegt.

Improved Synthetic Route to Unsymmetrically Substituted Phosphinimino-phosphonium Salts. Crystal Structure of Tri-n-butyl- [tris(diethylamino)phosphinimino]phosphonium Chloride

The title compound was prepared from tri-n-butyl-chlorophosphonium chloride and N-tri-methylsilyl-tris(diethylamino)-phosphinimine. A low temperature X-ray crystal structure de­termination revealed PN bond lengths of 156.1(2) and 158.0(2) pm, with a PNP angle of 149.36(17)°.

Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers

Analysis of 4,405 variants in 89,050 European subjects from 41 case-control studies identified three independent association signals for estrogen-receptor-positive tumors at 11q13. The strongest signal maps to a transcriptional enhancer element in which the G allele of the best candidate causative variant rs554219 increases risk of breast cancer, reduces both binding of ELK4 transcription factor and luciferase activity in reporter assays, and may be associated with low cyclin D1 protein levels in tumors. Another candidate variant, rs78540526, lies in the same enhancer element. Risk association signal 2, rs75915166, creates a GATA3 binding site within a silencer element. Chromatin conformation studies demonstrate that these enhancer and silencer elements interact with each other and with their likely target gene, CCND1.

Association of PHB 1630 C>T and MTHFR 677 C>T polymorphisms with breast and ovarian cancer risk in BRCA1/2 mutation carriers: results from a multicenter study

BACKGROUND

The variable penetrance of breast cancer in BRCA1/2 mutation carriers suggests that other genetic or environmental factors modify breast cancer risk. Two genes of special interest are prohibitin (PHB) and methylene-tetrahydrofolate reductase (MTHFR), both of which are important either directly or indirectly in maintaining genomic integrity.

METHODS

To evaluate the potential role of genetic variants within PHB and MTHFR in breast and ovarian cancer risk, 4102 BRCA1 and 2093 BRCA2 mutation carriers, and 6211 BRCA1 and 2902 BRCA2 carriers from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA) were genotyped for the PHB 1630 C>T (rs6917) polymorphism and the MTHFR 677 C>T (rs1801133) polymorphism, respectively.

RESULTS

There was no evidence of association between the PHB 1630 C>T and MTHFR 677 C>T polymorphisms with either disease for BRCA1 or BRCA2 mutation carriers when breast and ovarian cancer associations were evaluated separately. Analysis that evaluated associations for breast and ovarian cancer simultaneously showed some evidence that BRCA1 mutation carriers who had the rare homozygote genotype (TT) of the PHB 1630 C>T polymorphism were at increased risk of both breast and ovarian cancer (HR 1.50, 95%CI 1.10-2.04 and HR 2.16, 95%CI 1.24-3.76, respectively). However, there was no evidence of association under a multiplicative model for the effect of each minor allele.

CONCLUSION

The PHB 1630TT genotype may modify breast and ovarian cancer risks in BRCA1 mutation carriers. This association need to be evaluated in larger series of BRCA1 mutation carriers.