Development of ultra-short PCR assay to reveal BRAF V600 mutation status in Thai colorectal cancer tissues.

The protein kinase BRAF is one of the key players in regulating cellular responses to extracellular signals. Somatic mutations of the BRAF gene, causing constitutive activation of BRAF, have been found in various types of human cancers such as malignant melanoma, and colorectal cancer. BRAF V600E and V600K, most commonly observed mutations in these cancers, may predict response to targeted therapies. Many techniques suffer from a lack of diagnostic sensitivity in mutation analysis in clinical samples with a low cancer cell percentage or poor-quality fragmented DNA. Here we present allele-specific real-time PCR assay for amplifying 35- to 45-base target sequences in BRAF gene. Forward primer designed for BRAF V600E detection is capable of recognizing both types of BRAF V600E mutation, i.e. V600E1 (c.1799T>A) and V600E2 (c.1799_1800delTGinsAA), as well as complex tandem mutation caused by nucleotide changes in codons 600 and 601. We utilized this assay to analyze Thai formalin-fixed paraffin-embedded tissues. Forty-eight percent of 178 Thai colorectal cancer tissues has KRAS mutation detected by highly sensitive commercial assays. Although these DNA samples contain low overall yield of amplifiable DNA, our newly-developed assay successfully revealed BRAF V600 mutations in 6 of 93 formalin-fixed paraffin-embedded colorectal cancer tissues which KRAS mutation was not detected. Ultra-short PCR assay with forward mutation-specific primers is potentially useful to detect BRAF V600 mutations in highly fragmented DNA specimens from cancer patients.

Clinical presentation and molecular identification of four uncommon alpha globin variants in Thailand. Initiation codon mutation of α2-globin Gene (HBA2:c.1delA), donor splice site mutation of α1-globin gene (IVSI-1, HBA1:c.95 + 1G>A), hemoglobin Queens Park/Chao Pra Ya (HBA1:c.98T>A) and hemoglobin Westmead (HBA2:c.369C>G).

Alpha thalassemia is the most common genetic disease in the world with the prevalence of carriers ranging from 5-50% in several populations. Coinheritance of two defective α-globin genes usually gives rise to a symptomatic condition, hemoglobin (Hb) H disease. Previously, it has been suggested from several studies in different populations that nondeletional Hb H disease (--/α(T)α or --/αα(T)) is generally more severe than the deletional type (--/-α). In this report, we describe four rare nondeletional α-thalassemia mutations in Thai individuals, including initiation codon mutation (HBA2:c.1delA), donor splice site mutation (IVSI-1, HBA1:c.95 + 1G>A), Hb Queens Park (HBA1:c.98T>A) [α32(B13)Met>Lys], and Hb Westmead (HBA2:c.369C>G) [α122(H5)His>Gln]. Interactions of the first three mutations with the α(0)-thalassemia resulted in nondeletional Hb H disease; however, their clinical presentations were rather mild and some were detected accidentally. This suggests that a genotype-phenotype correlation of α-thalassemia syndrome might be more heterogeneous and so the type of mutation does not simply imply the prediction of the resulting phenotype. Our data will be of use in future genetic counseling of such conditions that are increasingly identified thanks to the improvement of molecular analysis in routine laboratories.

Genetic association study of tumor necrosis factor-alpha with sepsis and septic shock in Thai pediatric patients.

OBJECTIVES: To evaluate the association between the genetic polymorphism of the tumor necrosis factor-alpha (TNF-α) gene and the development of sepsis and septic shock in Thai pediatric patients and to investigate the clinical impacts of TNF-α polymorphisms in this population. METHODS: To perform this genetic association study, a prospective analysis of pediatric patients (age < 18 years) with clinical sepsis/septic shock was conducted. All clinical data were collected by pediatric intensive care experts, and genetic analyses were performed at a central laboratory. A single nucleotide polymorphism (SNP) located in the 5'-promoter region at position -308 was genotyped and the results were associated with clinical phenotypes. RESULTS: A total of 167 Thai individuals were investigated, 66 of which were pediatric patients with sepsis/septic shock and 101 were healthy controls. Interestingly, we could not identify an association between sepsis and -308 (G/A) polymorphism, which have previously been demonstrated to be a major SNP associated with sepsis in several Caucasian populations, since there was no frequency difference between cases and controls. CONCLUSIONS: In this report, the major TNF-α polymorphism (-308) was not associated with clinical sepsis/septic shock in Thais. This information will be important for future analyses to identify the role of TNF-α as a genetic risk for the development of immunopathology underlying several diseases in Asia.

Estudo de associação genética entre fator de necrose tumoral alfa e sepse e choque séptico em pacientes pediátricos tailandeses / Genetic association study of tumor necrosis factor-alpha with sepsis and septic shock in Thai pediatric patients

OBJETIVOS: Avaliar a associação entre o polimorfismo genético do fator de necrose tumoral alfa (TNF-α) e o desenvolvimento de sepse e choque séptico em pacientes pediátricos tailandeses e investigar o impacto clínico de polimorfismos do TNF-α nessa população. MÉTODOS: Para a realização deste estudo de associação genética, foram analisados prospectivamente pacientes pediátricos (idade < 18 anos) com sepse clínica/choque séptico. Todos os dados foram coletados por especialistas em terapia intensiva pediátrica e as análises genéticas foram realizadas em um laboratório central. Um polimorfismo de nucleotídeo único [single nucleotide polymorphism (SNP)], localizado na região promotora 5' na posição -308, foi genotipado e os resultados foram associados a fenótipos clínicos. RESULTADOS: Foram investigados 167 indivíduos tailandeses, dos quais 66 eram pacientes pediátricos com sepse/choque séptico e 101 eram controles saudáveis. Curiosamente, não foi possível identificar associação entre sepse e o polimorfismo -308 (G→A), um dos principais SNPs anteriormente associado à sepse em várias populações caucasianas, visto que não houve diferença de frequência entre casos e controles. CONCLUSÕES: Neste estudo, o principal polimorfismo do TNF-α -308 não esteve associado à sepse clínica/choque séptico na população tailandesa. Essa informação é importante para futuras análises que busquem identificar a função do TNF-α como risco genético para o desenvolvimento de imunopatologia subjacente a várias doenças no continente asiático.

OBJECTIVES: To evaluate the association between the genetic polymorphism of the tumor necrosis factor-alpha (TNF-α) gene and the development of sepsis and septic shock in Thai pediatric patients and to investigate the clinical impacts of TNF-α polymorphisms in this population. METHODS: To perform this genetic association study, a prospective analysis of pediatric patients (age < 18 years) with clinical sepsis/septic shock was conducted. All clinical data were collected by pediatric intensive care experts, and genetic analyses were performed at a central laboratory. A single nucleotide polymorphism (SNP) located in the 5'-promoter region at position -308 was genotyped and the results were associated with clinical phenotypes. RESULTS: A total of 167 Thai individuals were investigated, 66 of which were pediatric patients with sepsis/septic shock and 101 were healthy controls. Interestingly, we could not identify an association between sepsis and -308 (G→A) polymorphism, which have previously been demonstrated to be a major SNP associated with sepsis in several Caucasian populations, since there was no frequency difference between cases and controls. CONCLUSIONS: In this report, the major TNF-α polymorphism (-308) was not associated with clinical sepsis/septic shock in Thais. This information will be important for future analyses to identify the role of TNF-α as a genetic risk for the development of immunopathology underlying several diseases in Asia.