Genetic Testing and Molecular Biomarkers

The aim of the study was to optimize the criteria for the BRCA1 and BRCA2 gene testing and to improve oncogenetic counseling in the Stockholm region. Screening for inherited breast cancer genes is laborious and a majority of tested samples turn out to be negative. The frequencies of mutations in the BRCA1 and BRCA2 genes differ across populations. Between 1997 and 2000, 160 families with breast and/or ovarian cancer were counseled and screened for mutations in the two genes. Twenty-five BRCA1 and two BRCA2 disease-causing mutations were found. Various factors associated with the probability of finding a BRCA1 mutation in the families were estimated. Age of onset in different generations and other malignancies were also studied. Families from our region in which both breast and ovarian cancer occur were likely to carry a BRCA1 mutation (34%). In breast-only cancer families, mutations were found only in those with very early onset. All breast-only cancer families with a mutation had at least one case of onset before 36 years of age and a young median age of onset (<43 years). Other malignancies than breast and ovarian cancers did not segregate in the BRCA1 families and surveillance for other malignancies is not needed, in general. Decreasing age of onset with successive generations was common and must be taken into account when surveillance options are considered.

The addition of a 20-base GC-clamp to a DNA fragment enabled mutations to be detected by denaturing high-performance liquid chromatography (DHPLC) in the higher melting domain of the two-domain fragment DYS271. The mutations were undetectable in the absence of the GC-clamp. The heteroduplex yield was greatly decreased by the presence of mutations in the high melting domain, presumably because this region anneals first during cooling, leading to selection of the more stable homoduplexes. Suppression of sequence-dependent melting behavior using betaine increased the heteroduplex yield almost four-fold. Mutations in the high melting domain were detected at 60°C, whereas mutations in the low melting domain were detected at 56°C. Computer modeling of the melting behavior agreed well with the experimental results, facilitating computer design of DHPLC amplicons.

β-Thalassemia major patients have chronic anemia and are dependent on blood transfusions to sustain life. Molecular characterization and prenatal diagnosis of β-thalassemia is essential in Malaysia because about 4.5% of the population are heterozygous carriers for β-thalassemia. The high percentage of compound heterozygosity (47.62%) found in β-thalassemia major patients in the Thalassaemia Registry, University of Malaya Medical Centre (UMMC), Malaysia, also supports a need for rapid, economical, and sensitive protocols for the detection of β-thalassemia mutations. Molecular characterization of β-thalassemia mutations in Malaysia is currently carried out using ARMS, which detects a single β-thalassemia mutation per PCR reaction. We developed and evaluated Combine amplification refractory mutation system (C-ARMS) techniques for efficient molecular detection of two to three β-thalassemia mutations in a single PCR reaction. Three C-ARMS protocols were evaluated and established for molecular characterization of common β-thalassemia mutations in the Malay and Chinese ethnic groups in Malaysia. Two C-ARMS protocols (cd 41-42/IVSII #654 and -29/cd 71-72) detected the β-thalassemia mutations in 74.98% of the Chinese patients studied. The C-ARMS for cd 41-42/IVSII #654 detected β-thalassemia mutations in 72% of the Chinese families. C-ARMS for cd 41-42/IVSI #5/cd 17 allowed detection of β-thalassemia mutations in 36.53% of β-thalassemia in the Malay patients. C-ARMS for cd 41-42/IVSI #5/cd 17 detected β-thalassemia in 45.54% of the Chinese patients. We conclude that C-ARMS with the ability to detect two to three mutations in a single reaction provides more rapid and cost-effective protocols for β-thalassemia prenatal diagnosis and molecular analysis programs in Malaysia.

Current guidelines recommend offering invasive testing for chromosomal disorders only to women who are aged 35 or older, or who are at similarly elevated risk (as determined by maternal serum and/or ultrasonographic screening). We conducted a decision analysis, using preference scores obtained from pregnant women, to determine whether current guidelines maximize the health-related quality of life of these women. If only miscarriage and chromosomal abnormalities are considered, the expected value of testing exceeds that of not testing for women 30 years of age or older. However, if a comprehensive range of relevant testing outcomes is considered, testing offers a higher expected value than not testing, regardless of age. Furthermore, patient preferences for specific testing outcomes play a much more substantial role in determining the course of action with the highest expected value than does the probability of any of the possible testing outcomes. The current age- and risk-based guideline for prenatal diagnosis does not maximize expected value and fails to appropriately consider individual patient preferences. For counseling purposes, how an individual values the presence and timing of fetal chromosomal information should be carefully understood.

Spinal muscular atrophy (SMA) is an autosomal recessive disorder with a newborn prevalence of 1 in 10,000, and a carrier frequency of 1 in 40-60 individuals. The SMA locus has been mapped to chromosome 5q11.2-13. The disease is caused by a deletion of the SMN gene, often encompassing other genes and microsatellite markers. The SMN gene is present in two highly homologous copies, SMN1 and SMN2, differing at five nucleotide positions. Only homozygous SMN1 mutations cause the disease. The sequence similarity between the SMN1 and SMN2 genes can make molecular diagnosis and carrier identification difficult. We developed a sensitive and reliable molecular test for SMN1 carrier identification, by setting up a nonradioactive single strand conformation polymorphism (SSCP)-based method, which allows for the quantification of the amount of the SMN1 gene product with respect to a control gene. The assay was validated in 56 obligate (ascertained) carriers and 20 (ascertained) noncarriers. The sensitivity of the test is 96.4%, and its specificity, 98%. In addition, 6 of 7 SMA patients without homozygous deletions presented with a heterozygous deletion, suggesting a concomitant undetected point mutation on the nondeleted SMN1 allele. Therefore, the present test is effective for detecting compound hemizygote patients, for testing carriers in SMA families, and for screening for SMA heterozygotes in the general population.

Screening methods for unknown DNA sequence variations are laborious, expensive, and relatively insensitive. To evaluate the sensitivity and specificity of denaturing high-pressure liquid chromatography (DHPLC) screening for unknown protein C gene (PROC) mutations, we studied 31 PROC-deficient patients. Eleven amplimers containing 4 kb of the PROC gene and spanning all exons, splice junctions, and the putative promoter and 3′-untranslated regions were amplified by PCR for each patient. Each amplimer (n = 341) was sequenced with a fluorescence-based method, and screened by DHPLC. Sequencing identified 10 unique mutations and three polymorphisms. Combining all mutations and polymorphisms, 227 amplimers were homozygous wildtype, and 63 and 51 were heterozygous and homozygous mutant, respectively. DHPLC screening correctly identified all amplimers (100% sensitivity and specificity). DHPLC is a rapid, automated, sensitive and specific screening method for unknown mutations within the PROC gene, and may be a useful screening method for unknown mutations within other genes.

Polymorphisms of the β-fibrinogen gene have been shown to affect plasma fibrinogen levels and risk of coronary artery disease (CAD). We were interested in developing an automated, PCR-based genotyping assay for the purpose of exploring relationships between CAD and CAD-associated aortic stiffness and the Bcl I allele of the β-fibrinogen gene. We have developed a rapid PCR-RFLP assay for the Bcl I polymorphism of the β-fibrinogen gene. We carried out direct PCR of genomic DNA to facilitate sequencing of the flanking region of the β-fibrinogen gene. Using this new sequence information, primers were designed which border the site of the Bcl I polymorphism. One of the primers was labeled with a fluorophore to facilitate detection of the fragments. DNA fragment analysis was carried out using an automated capillary electrophoresis instrument (ABI310). We have developed an improved PCR-RFLP high-sample-throughput assay for the semiautomated detection of the Bcl I polymorphism of the β-fibrinogen gene. This assay will support screening of large sample sizes required for population studies.

The aim of this study was to evaluate the screening policies of cystic fibrosis (CF) in the Jewish population. The prevalence of mutations that account for CF in Israel have been defined in the past by determining the frequency of CF mutations in affected individuals. This study is a population-based study and is, therefore, different from previous patient-based studies. We found that the CF mutations D1152H, W1089X, and 405 + 1G → A were present in some ethnic groups in which no CF patients carrying these mutations were reported. These facts necessitate a reevaluation of the screening policy regarding the ethnic groups in Israel. We studied 9,430 healthy Jewish Israeli individuals of 36 countries of origin. The prevalence of CF mutations was 1:19, 1:19, 1:28, and 1:42 for the Ashkenazi, Sephardi, North African, and Eastern Jews, respectively. CF mutations were identified in 374 (4.0%) individuals. These included 173 (46.3%) carriers of the W1282X mutation; 110 (29.4%) found to carry delF508; 23 (6.1%) who carried G542X; 22 (5.9%) who carried 3849 + 10Kb (C → T; 20 (5.3%) who carried D1152H; 10 (2.7%) who carried N1303K; 11 (2.9%) who carried 405 + 1G → A; 4 (1.1%) who carried W1089X; and one (0.3%) who carried S549R. No carriers were detected for the 1717-1G → A, G85E, and T360K mutations, which were tested for in 7,383, 1,558, and 41 individuals, respectively.

Familial Mediterranean fever (FMF) is a recessively inherited disorder characterized by episodes of fever with abdominal pain, pleurisy, or arthritis. The familial Mediterranean fever gene, designated MEFV, was recently cloned, and the missense mutation M694V accounting for most of the patients with this disease was identified. The objective of the present study was to establish frequencies of the M694V mutation in three groups of Jews. The subjects studied were 381 Sephardi, 256 Ashkenazi, and 65 Oriental Jews, all male subjects, previously collected for an anthropological study, independent of their FMF status. The M694V mutation in the 702 samples was assessed by amplifying genomic DNA with the use of primers that selectively amplify the normal or altered DNA sequence of the M694V mutation, by the amplification refractory mutation system (ARMS). In our sample of Sephardi Jews, the frequency of the M694V mutation is elevated (10.9%), and this is also the case for Oriental Jews (9.2%). In our sample of Ashkenazis, the M694V allele frequency is very low (0.8%).

Mutation detection in the PKD1 gene proved to be difficult because two-thirds of the gene is reiterated several times on chromosome 16. Long-range PCR has been used previously to overcome this limitation, but due to a 2.5-kb polypyrimidine tract in intron 21, the screening capacity of the PKD1 gene using this technique was hindered. Here we report the measures that we have used to overcome this limitation.

With the advent of mutational analysis for Gaucher disease, carrier screening has been incorporated into many Jewish genetic disease screening programs. Frequencies and mutations for Gaucher disease in non-Jewish populations are less well established and the detection rate of carriers are lower. Testing is problematic for resolving residual risk in a couple of mixed ethnicity. We report the testing choices made by 20 consecutive couples of mixed ethnicity where the Ashkenazi Jewish partner was identified to be a Gaucher disease gene carrier. Carrier studies of the non-Jewish partner were elected as follows: DNA studies alone, 5 (25%); enzymatic assay, 2 (10%); both, 6 (30%); no carrier studies, 7 (35%). Of the 7 couples not electing carrier studies, one was not in a pregnancy and 6 elected prenatal diagnosis in lieu of parental testing by enzymatic analysis of amniocytes. One couple elected parental carrier studies as well as prenatal diagnosis. All couples electing prenatal Gaucher determination had amniocentesis for other indications as well (4, advanced maternal age; 4, parental anxiety). We conclude that Gaucher screening is feasible for couples of mixed ethnicity if appropriate counseling and testing are offered.

X-linked adrenoleukodystrophy (ALD) is a peroxisomal disorder characterized by impaired peroxisomal β-oxidation of very-long-chain fatty acids (VLCFAs). This is probably due to reduced activation of the VLCFAs and results in demyelination of the nervous system and adrenocortical insufficiency. The ALD gene is localized on Xq28, has 10 exons and encodes a protein of 745 amino acids with significant homology to the membrane peroxisomal protein PMP70. Characterizing the disease causing mutations is of importance in prenatal diagnosis because 12-20% of women who are obligatory carriers show false-negative results when tested for VLCFA in plasma. We have analyzed DNA from blood samples of 7 Jewish (5 Sephardi and 2 Ashkenazi) and 3 Arab Israeli families suffering from ALD. Five missense-type mutations were identified: R104H, Y174C, L229P, R401Q, and G512C. A single mutation, R464X, was nonsense, and two, Y171 frameshift and E471 frameshift, were frameshift. Interestingly, a single mutation was identified in three families of Moroccan Jewish descent, probably due to a founder effect.