High-resolution melting analysis is a more effective approach for screening TSC genes mutations.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder with a prevalence of 1 in 95,136 in Taiwan. TSC is characterized by hamartomatous lesions in multiple organ systems. Genetic defects in TSC1 and TSC2 genes are the main causes of TSC. A molecular screening protocol using denaturing high-performance liquid chromatography (dHPLC) followed by DNA sequencing is currently performed to locate the genetic lesions in many clinical laboratories. The current screening approach is time consuming and inefficient. In this study, we analyzed all coding exons of TSC1 and TSC2 genes of 30 TSC patients and 47 unaffected family members using the traditional dHPLC protocol and our recently developed diagnostic platform based on high-resolution melting analysis (HRM) followed by bidirectional DNA sequencing. Data indicated that 20 mutations, including 5 mutations in TSC1 (2 sporadic, 1 familial mutation, and 2 of uncertain origin) and 15 mutations in TSC2 (14 sporadic and 1 familial mutation), 8 single-nucleotide polymorphisms (SNPs, including 3 SNPs found in irrelevant individuals without TSC phenotypes studied in the control group), and 3 variants with undetermined significance were identified, including 4 novel mutations. The sensitivities of HRM and dHPLC for TSC mutation screening were estimated as 95% and 75%, respectively. The specificities of HRM and dHPLC for TSC mutation screening were evaluated as 91% and 98%. In addition, results suggested our novel HRM screening protocol to be more economical. In conclusion, we successfully developed a superior approach for TSC genes mutation screening for clinical application.

Three missense mutations, including a novel 860C>T transition, and allelic enhancement phenomenon associated with ABO blood subgroups A in Taiwan.

BACKGROUND: It was estimated that approximately 25 percent of Taiwanese residents were ABO blood group A. Many subgroups of A, however, revealed ambiguous serologic typing results. This study aimed to delineate the molecular basis of the A3, Ax, and weak A phenotypes. STUDY DESIGN AND METHODS: Serologic analyses including adsorption and elution assay, serum transferases activity assay, and saliva test were performed to determine the unique phenotypes of these samples. DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism were performed to further investigate the relationships between the genetic characteristics and phenotypic features of these samples. RESULTS: Three single-nucleotide transitions (745C>T, 820G>A, and a novel 860C>T) were found in nine A3/A3B cases. In addition, the Ax and A3B subjects shared the same 860C>T mutation. This A(x) allele with 860C>T transition expressed A3B phenotype in A(x)/B101 heterozygote but Ax phenotype in A(x)/O01 heterozygote. This allelic enhancement was also observed in the weak A family with Aw05 allele, which was previously not found in Taiwan. CONCLUSION: This allelic enhancement phenomenon was prone to cause serologic discrepancy between parents and children. Genotyping could help us to resolve this problem. Thus, a novel mutation is reported among Taiwanese blood donors.

Hypermethylation of the CpG islands in the promoter region flanking GSTP1 gene is a potential plasma DNA biomarker for detecting prostate carcinoma.

OBJECTIVES: To investigate the possibility of identifying DNA hypermethylation in the circulation of prostate cancer patients. METHODS: Plasma DNA samples were extracted from 36 prostate cancer patients and 27 benign prostate hyperplasia (BPH) cases. After extensive methylation-sensitive restriction enzyme digestion, the DNA samples were subjected to the real-time quantitative PCR amplification. Dissociation curve analysis was applied to determine if hypermethylation occurred in the promoter region flanking the GSTP1 gene, a well-documented epigenetic event among prostate cancer cells, in these plasma DNA samples. RESULTS: 11 of 36 prostate cancer patients showed positive peak pattern, indicating methylation changes occurred. Concordant data were obtained from the corresponding paraffin-embedded tissue samples available from the Tumor Bank. Twenty-five of the 27 BPH cases showed negative results, suggesting no methylation changes happened in the CpG islands in these cases. CONCLUSIONS: We have successfully identified prostate cancer genome hypermethylation in the peripheral circulation in prostate cancer patients with this protocol. This method can effectively distinguish BPH from prostate neoplasm. Although a larger number of samples are necessary to validate the capability of the protocol in practice, using plasma DNA sample is an ideal non-invasive approach for prostate neoplasm detection.

Human chromosome 21-specific DNA markers are useful in prenatal detection of Down syndrome.

Trisomy 21 is the most common chromosomal aberration in live births. In this study we employed human chromosome 21-specific short tandem repeat (STR) DNA markers to determine the numbers of chromosome 21 present in fetal cells. Forty amniotic fluid samples from pregnancies complicated with fetal Down syndrome and 98 samples from euploid pregnancies were analyzed for D21S11 and interferon-alpha receptor (IFNAR) gene intervening sequence. Fluorescent dye-labeled primers were used in PCR amplification of these 2 markers. The PCR amplicon was analyzed with an automatic DNA sequence analyzer. The results showed that 35 of 40 fetal Down syndrome samples analyzed for IFNAR showed 3 distinct peaks, while 24 of 30 cases analyzed for D21S11 showed 3 distinct peaks. Two Down syndrome samples showed two uneven peaks. By analyzing 98 euploid pregnancies as controls, the ratios of area under the peaks were determined to be 1.31 +/- 0.22 and 1.96 +/- 0.18 (mean +/- SD) for the euploid pregnancies and pregnancies complicated by fetal Down syndrome with 2 peaks, respectively. Our data showed that altogether 39 of 40 (97.5%) Down syndrome cases were correctly identified based on either the 3-peak pattern in one or more of the DNA markers or the relative peak area ratio calculation. In conclusion, polymorphic STR DNA markers are useful for determining the numbers of chromosome 21 in fetal cells. The high sensitivity and automation of the procedures suggest a good prospect for use of this method in prenatal detection of fetal Down syndrome. However, this is a preliminary investigation and a large-scale study is necessary to validate the clinical application of this protocol.

The use of real-time quantitative PCR to detect circulating prostate-specific membrane antigen mRNA in patients with prostate carcinoma.

Prostate-specific antigen (PSA) has long been criticized for its lack of specificity in screening for the occurrence of prostate cancer. In this study, we tried to measure levels of another biomarker, prostate-specific membrane antigen (PSM), in the peripheral circulation from subjects with either prostate cancer or benign prostatic hyperplasia (BPH). Total RNA was extracted from blood samples of 70 patients with prostate cancer and 19 with BPH. Reverse transcription was performed to convert mRNA to cDNA. The cDNA was analyzed with a novel real-time quantitative polymerase chain reaction (PCR) protocol to measure PSM mRNA levels in the circulation. Melting curve analysis was adapted to assure that correct amplification data were obtained. Results showed that 41 of 70 prostate cancer patients had positive results, whereas 9 of 19 BPH cases were negative. Therefore, the sensitivity and specificity were determined to be 58.6% and 47.4%, respectively. For comparison, traditional nested PCR was performed to investigate whether the new method was superior. The sensitivity and specificity of nested PCR were determined to be 27.1% and 57.9%, respectively. The detection limits of these two methods were 0.0005 ng (for the real-time quantitative PCR method) and 0.5 ng of PSM-cDNA (for the nested PCR method). In conclusion, we have successfully developed a novel, noninvasive real-time quantitative PCR method to detect the PSM mRNA levels in the peripheral circulation of prostate cancer subjects. This method may provide references for urologists diagnosing prostate cancer or monitoring the patient's condition after treatment.

Lack of STK11 gene expression in homozygous twins with Peutz-Jeghers syndrome.

Clinical features of Peutz-Jeghers syndrome (PJS), an autosomal dominant disorder, include clusters of melanotic spots on the lips and limbs, polyposis of the gastrointestinal (GI) tract, and propensity to develop neoplasms of the GI tract, ovaries, testes, and other sites. We report twin sisters with PJS who were found to be homozygous, based on analyses of 9 DNA markers containing short tandem repeats (STR). Aberrant expression of a putative tumor suppressor gene, STK11, which encodes a serine threonine kinase, has been suggested as the etiologic factor in PJS. In both of the twin sisters with PJS, mRNA analyses by RT-PCR demonstrated a complete lack of STK11 gene expression. These results provide direct evidence that STK11 gene expression is abnormal in PJS. Detecting abnormal expression of the STK11 gene may serve as a molecular approach to the diagnosis of PJS and may facilitate genotype-phenotype correlations in PJS patients.

Elevated maternal midtrimester serum free beta-human chorionic gonadotropin levels in vegetarian pregnancies that cause increased false-positive Down syndrome screening results.

OBJECTIVE: The aim of this study was to examine whether midtrimester maternal serum free beta-human chorionic gonadotropin and alpha-fetoprotein levels for Down syndrome screening differed in vegetarian pregnancies and omnivore pregnancies and to evaluate whether maternal serum vitamin B(12) concentration affected these maker levels. STUDY DESIGN: Ninety-eight vegetarian and 122 omnivore singleton pregnancies were studied. Reference levels of free beta-human chorionic gonadotropin and alpha-fetoprotein were based on a population of 6312 singleton euploid pregnancies that had been surveyed previously. Serum free beta-human chorionic gonadotropin and alpha-fetoprotein levels were measured by enzyme immunoassay or radioimmunoassay. Multiples of the median values were calculated to determine whether different diet habits affected serum biomarker levels. Maternal serum vitamin B(12) levels were determined with radioimmunoassay. RESULTS: The free beta-human chorionic gonadotropin multiples of the median values were elevated significantly in the vegetarian pregnancies group (1.28 multiples of the median) compared with that of the reference population (1.00 multiples of the median) (P<.001). A negative association between the serum free beta-human chorionic gonadotropin multiples of the median values and the concentration of maternal serum vitamin B(12) was observed in the vegetarian pregnancies. No correlation was found between the alpha-fetoprotein multiples of the median values and the maternal serum vitamin B(12) concentration. CONCLUSION: The current data showed that the midtrimester maternal serum free beta-human chorionic gonadotropin levels increased in vegetarian pregnancies and led to an elevated false-positive rate in screening for Down syndrome compared with pregnant women with regular diet and resulted in unnecessary invasive procedures. It is necessary to establish vegetarian pregnancy alpha-fetoprotein and beta-human chorionic gonadotropin reference levels to correct increased false-positive screening results.

Prenatal diagnosis of alpha-thalassemia of Southeast Asian deletion with non-radioactive southern hybridization.

BACKGROUND: Alpha-thalassemia is a common hereditary disease in Taiwan. Affected patients always carry a heavy burden of morbidity and early death. Prenatal diagnosis has reduced the disease burden on families and the health care system. This study evaluated a new non-radioactive Southern blotting hybridization method for prenatal diagnosis of this disease. METHODS: Seventy two chorionic villi samples (CVS) and 30 amniocyte samples from 102 pregnancies of couples who were both heterozygous for alpha-thalassemia-1 of the Southeast Asian (SEA) type deletion were studied. A non-radioactive Southern blotting hybridization method using a dig-alkaline phosphate detection system was developed for use in this study. RESULTS: Non-radioactive Southern blotting hybridization data showed that 19 (26%) CVS and five (17%) amniotic fluid samples had 10 Kb and 4Kb fragments, indicating homozygosity of the alpha-thalassemia-1 SEA type deletion. DNA samples were extracted from most of the aborted tissue of the 24 fetuses with a diagnosis of homozygous for the alpha-thalassemia-1 SEA type deletion. Homozygosity for alpha-thalassemia-1 SEA type deletion was reconfirmed by Southern blotting hybridization in all of these samples. CONCLUSIONS: The non-radioactive Southern hybridization protocol used in this study allows efficient and accurate early prenatal diagnosis of alpha-thalassemia-1 SEA type deletion. It can be routinely used for testing couples who both carry the alpha-thalassemia-1 SEA type deletion.

The use of real-time quantitative polymerase chain reaction to detect hypermethylation of the CpG islands in the promoter region flanking the GSTP1 gene to diagnose prostate carcinoma.

PURPOSE: We developed a real-time, quantitative, methylation sensitive polymerase chain reaction (PCR) protocol to analyze hypermethylation of the CpG islands in the promoter region of the pi class glutathione-S-transferase gene GSTP1 in prostate cancer tissue. MATERIALS AND METHODS: A total of 21 prostate cancer and 72 benign prostate hyperplasia (BPH) tissue samples were analyzed. Genomic DNA was digested with restriction enzyme, followed by real-time quantitative PCR amplification. Cycle threshold values were used to determine whether cancer genome was present in these tissues. A cutoff cycle threshold value of 35 was arbitrarily assigned. Samples with a cycle threshold of 35 or less were considered positive for prostate cancer. Conventional nested PCR was also performed for comparison. RESULTS: The mean cycle threshold values plus or minus standard deviation in prostate cancer and BPH cases were 30.12 +/- 2.88 and 37.77 +/- 2.72, respectively. All prostate cancer samples analyzed showed positive results, while 5 of the 72 BPH samples tested positive. Conventional nested PCR data indicated that 19 of 21 prostate cancer cases were positive for the methylation change, while 71 of 72 BPH cases tested negative. The test limitations of real-time PCR and the nested PCR protocols were determined to be 0.048 and 0.64 ng. DNA, respectively. CONCLUSIONS: We established a novel protocol for detecting the methylation change in the 5' regulatory sequence flanking the GSTP1 gene. The sensitivity of this protocol was superior to that of conventional nested PCR. The data also suggest that this novel protocol may accurately discriminate prostate carcinoma from BPH.