Development of a mutation hotspot detection kit for the phenylalanine hydroxylase gene by ARMS-PCR combined with fluorescent probe technology

To develop a screening kit for detecting mutation hotspots of the phenylalanine hydroxylase (PAH) gene. Thirteen exons of the PAH gene were sequenced in 84 cases with phenylketonuria (PKU) diagnosed during neonatal genetic and metabolic disease screening in Shaanxi province, and their mutations were analyzed. We designed and developed a screening kit to detect nine mutation sites covering more than 50% of the PAH mutations found in Shaanxi province (c.728G>A, c.1197A>T, c.331C>T, c.1068C>A, c.611A>G, c.1238G>C, c.721C>T, c.442-1G>A, and c.158G>A) by using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) combined with fluorescent probe technology. Peripheral blood and dried blood samples from PKU families were used for clinical verification of the newly developed kit. PAH gene mutations were detected in 84 children diagnosed with PKU. A total of 159 mutant alleles were identified, consisting of 100 missense mutations, 28 shear mutations, 24 nonsense mutations, and 7 deletion mutations. Exon 7 had the highest mutation frequency (32.08%). Among them, the mutation frequency of p.R243Q was the highest, accounting for 20.13% of all mutations, followed by p.R111X, IVS4-1G>A, EX6-96A>G, and p.R413P; these five loci accounted for 47.17% (75/159) of all mutations. In addition, we identified three previously unreported PAH gene mutations (p.C334X, p.G46D, and p.G256D). Fifteen mutation sites were identified in the 47 PAH carriers identified by next-generation sequencing (NGS), which were verified by the newly developed kit, with an agreement rate of 100%. This newly developed kit based on ARMS-PCR combined with fluorescent probe technology can be used to detect common PAH gene mutations.

Molecular Evaluation of HIF-1α Gene Variation and Determination of Its Frequency and Association with Breast Cancer Susceptibility in Saudi Arabia

AIM

Hypoxia-inducible factor 1 (HIF-1α) is responsible in regulating oxygen homeostasis in tissues and is a central effector of the hypoxic response besides its protein overexpression has been shown to have prognostic relevance in several cancers including breast cancer. Several reports indicated that HIF-1α gene variation C1772T (Pro582Ser) is associated with increased breast susceptibility but results remained controversial. Therefore, we performed the molecular evaluation of HIF-1α gene variation and determined its frequency and association with Breast Cancer susceptibility in Saudi Arabia.

METHODS

This study was conducted on histologically confirmed Breast cancer patients and gender matched healthy women. HIF-1α C1772T (Pro582Ser) genotyping was done by Amplification refractory mutation system PCR method. The HIF-1α gene genotypes were correlated with different clinicopathological characteristics of breast cancer patients.

RESULTS

A significant difference was observed in genotype distribution of HIF-1α gene variation C1772T (Pro582Ser) between breast cancer cases and gender matched healthy controls (P=0.010). Our findings showed that the HIF- 1α variant was associated with an increased risk of Breast cancer for HIF-1α CC vs CT genotype OR = 2.20, 95% CI = (1.28 -3.77), P = 0.004) in codominant inheritance model. The significant association was reported for HIF1A for genotypes CC vs (CT+ TT) OR = 1.98, 95% CI = (1.17-3.34), P = 0.010) in dominant inheritance model tested. In case of recessive inheritance model, a non-significant association of HIF-1 alpha gene variants was reported for (CC+ CT) vs TT) OR = 1.03, 95% CI = (0. 064-16.79), P = 0.97). During the allelic comparison, a non-significant association was reported between A vs C allele among Breast cancer patients. A significant association of HIF- 1α polymorphism was reported with stage as well as distant metastasis of the disease.

CONCLUSION

A significant difference was observed in genotype distribution of HIF-1α gene variation C1772T (Pro>Ser) between breast cancer cases and gene matched healthy controls (P=0.010). HIF-1α- CT heterozygosity and CC genotype increased the susceptibility .The HIF-1α polymorphism was reported to be significantly associated with the distant metastasis of Breast cancer. Further studies with larger data set and well-designed models are required to validate our findings.

Association between clinical characteristics and the diagnostic accuracy of circulating single-molecule amplification and resequencing technology on detection epidermal growth factor receptor mutation status in plasma of lung adenocarcinoma

BACKGROUND

Lung cancer is the leading cause of cancer-related mortality in the world. Circulating single-molecule amplification and resequencing technology (cSMART) can successfully detect epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer (NSCLC). However, few studies have investigated the association between clinical characteristics and the diagnostic accuracy of cSMART technique in lung adenocarcinoma.

METHODS

We enrolled 95 patients, which included paraffin embedded tumor tissues and matched plasma samples. Retrospectively analyzed the correlation between clinical characteristics and sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of cSMART.

RESULTS

Of the 95 lung adenocarcinoma cancer patients, 49 (51.5%) and 40 (42.1%) harbored EGFR mutations respectively in tissue and plasma. In younger than 60 years group, sensitivity, specificity and consistency for cSMART were 81.0%, 100%, and 90.9% (P<.001). In metastasis group, sensitivity, specificity, and consistency for cSMART were 92.9%, 77.8%, and 87.0% (P=.001). By univariate analysis, younger than 60 years (OR=5.938; 95% confidence interval: 1.835-19.210; P=.001); metastasis group (OR=4.482; 95% confidence interval: 1.432-14.024; P=.007) were significantly correlated with a higher accuracy. By multivariate analysis, younger than 60 years (P=.003) and metastasis (P=.004) were confirmed as independent factors for diagnostic accuracy of EGFR mutation in plasma through cSMART.

CONCLUSION

cSMART is feasible for detection EGFR mutation in plasma when tissue is unavailable. Age and metastasis might be considered as independent factors in diagnostic accuracy of cSMART in lung adenocarcinoma.