Deletion Genotype Research Articles

Dataset for genotyping validation of cytochrome P450 2A6 whole-gene deletion (CYP2A6*4) by real-time polymerase chain reaction platforms.

This data article contains a supplementary figure and validation data relating to the research article entitled “Genotyping of wild-type cytochrome P450 2A6 and whole-gene deletion using human blood samples and a multiplex real-time polymerase chain reaction method with dual-labeled probes” (Shimizu et al., Clinica Chimica Acta 441, 71–74, 2015), which presents a multiplex real-time polymerase chain reaction method with dual-labeled probes for human P450 2A6 wild-type and whole-gene deletion. Real-time methods have dramatically improved the speed of complex genetic diagnostics compared to conventional assays based on restriction enzyme digestion. Here, we show the basic assay validation data by single and multiplex determinations in comparison with commercial TaqMan copy number assays for P450 2A6.

The association between the HLA-G 14-bp insertion/deletion polymorphism and type 1 diabetes.

Type 1 diabetes (T1D) is a multifactorial disease that has a strong genetic component. The HLA-G is a nonclassical HLA class I locus that is associated with immunomodulatory functions, including downregulation of innate and adaptive immune responses and induction of immune tolerance. However, there is currently limited information about the involvement of HLA-G in T1D susceptibility. This case-control study aims to investigate the T1D susceptibility association of alleles and genotypes of a widely investigated 14-bp insertion/deletion polymorphism in the HLA-G and to provide further evidence of the frequency distribution of class II HLA-DR-DQ-risk genotypes in T1D children and adolescents in the Brazilian population. The deletion allele and the homozygous deletion genotype are associated with susceptibility to T1D and the insertion allele and the heterozygous deletion/insertion genotype are associated with protection from T1D. We also confirm that genetic susceptibility to T1D is associated with the DRB1*03:01-DQA1*05:01-DQB1*02:01 and DRB1*04-DQA1*03:01-DQB1*03:02 haplotypes in Brazilian northeast region. The DR3-DQ2/DR4-DQ8 genotype conferred the highest detected risk for T1D. Our results identify a novel association of the 14-bp deletion allele and the homozygous deletion genotype with T1D development and provide additional evidence of the importance of HLA class II heterozygous DR3-DQ2/DR4-DQ8 genotype in T1D susceptibility.

Human Leukocyte Antigen-G (HLA-G) 14-bp deletion polymorphism is associated with decreased risk of pulmonary fibrosis in Indonesian Javanese patients with multidrug-resistant tuberculosis

Background: Human leukocyte antigen-G (HLA-G) is a nonclassical HLA class I antigen with immunomodulatory activity that usually inhibits immune responses. The role of the HLA-G polymorphism in multidrug-resistant tuberculosis (MDR-TB) is unknown. Objectives: To analyze clinical data from Indonesian Javanese patients with MDR-TB to find an association between the HLA-G polymorphism and MDR-TB. Methods: Fifty-seven Indonesian Javanese patients with MDR-TB were enrolled and monitored from May 2012 to Jan 2014. Non-TB individuals and non-MDR-TB individuals were recruited as controls. The HLA-G polymorphism status of each patient was determined by polymerase chain reaction. Patient clinical data were analyzed against polymorphism status. The presence of an association was estimated with an odds ratio (OR) and 95% confidence interval (CI) calculated via logistic regression. Results: Nineteen (33.3%), 30 (52.6%), and 8 (14.1%) MDR-TB patient participants carried a homozygous deletion (D/D), heterozygous deletion (I/D), and homozygous insertion (I/I) genotypes, respectively. Among control participants, D/D genotype carriers less frequently had a history of TB infection (OR 0.4, 95% CI 0.179-0.981, P = 0.043). The deletion allele for MDR-TB patients was associated with a decreased likelihood of developing pulmonary fibrosis (adjusted OR 0.1, 95% CI 0.014-0.639, P = 0.016). Conclusions: D/D genotype carriers are less susceptible to TB, and MDR-TB patients with a deletion allele are less likely to develop pulmonary fibrosis. Keywords: HLA-G, Indonesia, MDR-TB, polymorphism, tuberculosis

Association of glutathione S-transferase T1 and M1 polymorphisms with prostate cancer susceptibility in populations of Asian descent: a meta-analysis.

Genetic polymorphism was hypothesized to be reason of variation in prostate cancer incidence among different racial group. Based on that published data on the association of prostate cancer susceptibility with polymorphisms in genes encoding Glutathione S-transferases (GSTs) were inconclusive, the aim of this study was to more precisely address the role of GSTs polymorphisms (especially, GSTT1 and GSTM1 deletions) on prostate cancer risk in Asian descent. A meta-analysis including 8 articles with 711 cases and 1122 controls for GSTT1 and 1098 cases and 1588 controls for GSTM1 was performed. Significantly increased prostate cancer risk was found among subjects carrying GSTM1 null genotype (odds ratio (OR) = 1.403; 95% confidence interval (CI) = 1.088 - 1.808) but not among subjects carrying GSTT1 deletion genotype (OR = 0.959; 95%CI = 0.709 - 1.297). When stratified by country, the null genotype of GSTT1 neither increased nor decreased prostate cancer risk significantly in China (OR = 1.355; 95%CI = 0.895 - 2.049), Japan (OR = 0.812; 95%CI = 0.545 - 1.211), and Korea (OR = 1.056; 95%CI = 0.727 - 1.534). While significant association of elevated prostate cancer risk with GSTM1 deletion were found in China (OR = 1.665; 95%CI = 1.324 - .094) and Korea (OR = 1.914; 95%CI = 1.311 - 2.793) but not in Japan (OR = 0.980; 95%CI = 0.726 - 1.321). In summary, this meta-analysis suggested that the null genotype of GSTM1 rather than GSTT1 may be involved in the etiology of prostate cancer in Asian population.

Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea.

We developed 21,499 genome-wide insertion–deletion (InDel) markers (2- to 54-bp in silico fragment length polymorphism) by comparing the genomic sequences of four (desi, kabuli and wild C. reticulatum) chickpea [Cicer arietinum (L.)] accessions. InDel markers showing 2- to 6-bp fragment length polymorphism among accessions were abundant (76.8%) in the chickpea genome. The physically mapped 7,643 and 13,856 markers on eight chromosomes and unanchored scaffolds, respectively, were structurally and functionally annotated. The 4,506 coding (23% large-effect frameshift mutations) and regulatory InDel markers were identified from 3,228 genes (representing 11.7% of total 27,571 desi genes), suggesting their functional relevance for trait association/genetic mapping. High amplification (97%) and intra-specific polymorphic (60–83%) potential and wider genetic diversity (15–89%) were detected by genome-wide 6,254 InDel markers among desi, kabuli and wild accessions using even a simpler cost-effective agarose gel-based assay. This signifies added advantages of this user-friendly genetic marker system for manifold large-scale genotyping applications in laboratories with limited infrastructure and resources. Utilizing 6,254 InDel markers-based high-density (inter-marker distance: 0.212 cM) inter-specific genetic linkage map (ICC 4958 × ICC 17160) of chickpea as a reference, three major genomic regions harboring six flowering and maturity time robust QTLs (16.4–27.5% phenotypic variation explained, 8.1–11.5 logarithm of odds) were identified. Integration of genetic and physical maps at these target QTL intervals mapped on three chromosomes delineated five InDel markers-containing candidate genes tightly linked to the QTLs governing flowering and maturity time in chickpea. Taken together, our study demonstrated the practical utility of developing and high-throughput genotyping of such beneficial InDel markers at a genome-wide scale to expedite genomics-assisted breeding applications in chickpea.

Abstract 4336: Direct genotyping of CYP2A6 whole gene deletion: A new biomarker for prognosis of lung adenocarcinoma in Japanese smoking male

Abstract Purpose: Cytochrome P450 (CYP2A6) is known as an enzyme responsible for the metabolism of activation of tobacco-specific nitrosamines to their ultimate carcinogenic forms and metabolism of nicotine. We here report that the genetic polymorphisms of human CYP2A6*4 is associated with primary lung cancer and their overall survival. Experimental Design: We prepared genomic DNA samples from 387 Japanese patients with primary lung cancer and the genetic polymorphisms of human CYP2A6*4 (whole gene deletion) by the rapid genetic testing method we developed in this study. We analyzed the association between the CYP2A6*4 gene, NRF2 gene and overall survival. Results: Patients harboring wild-type CYP2A6*1 and whole gene deletion CYP2A6*4/*4 numbered 380 (98.2%) and 7 (1.8%), respectively. Its frequency was four-fold higher in male patients than in female (P = 0.038).Multivariate logistic regression models revealed that the genetic polymorphisms of human CYP2A6*4 were significantly related to gender and smoking behavior. Interestingly, lung cancer patients carrying CYP2A6*4/*4 (whole gene deletion), the NRF2 SNP heterozygous (c.-617C/A) and wild-type homozygous (c.-617C/C) exhibited remarkable survival over 1,500 days after surgical operation. Conclusion: CYP2A6*4/*4 whole gene is considered to be a prognostic biomarker for assessing both the gender-related risk of lung adenocarcinoma in the smoking sub-population and their overall survival. Citation Format: Yasuko Okano, Yasushi Ichikawa, Yohei Miyagi, Takashi Chishima, Yutaka Natsumeda. Direct genotyping of CYP2A6 whole gene deletion: A new biomarker for prognosis of lung adenocarcinoma in Japanese smoking male. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4336. doi:10.1158/1538-7445.AM2015-4336

The APOBEC3B deletion polymorphism is associated with prevalence of hepatitis B virus, hepatitis C virus, Torque Teno virus, and Toxoplasma gondii co-infection among HIV-infected individuals

BackgroundData regarding the influence of the APOBEC3B deletion on infectious diseases remain limited and shown discrepancies. ObjectivesTo characterize the APOBEC3B deletion polymorphism status and its association with prevalence of co-infection with blood-borne pathogens in Indonesian HIV-infected individuals. Materials and methodsA total of 597 HIV-positive blood samples were tested for the hepatitis B virus (HBV), hepatitis C virus (HCV), Torque Teno virus (TTV), GB virus-C (GBV-C), and Toxoplasma gondii. Nucleic acid was extracted from plasma samples and used for the molecular detection of HIV RNA, HBV DNA, HCV RNA, TTV DNA, and GBV-C RNA, whereas HBsAg, anti-HCV, IgM and IgG anti-T. gondii were detected through serological testing. The APOBEC3B deletion polymorphism was genotyped by polymerase chain reaction (PCR). ResultsThe deletion genotype was associated with HCV viremia (p<0.001) as well as elevated IgG anti-T. gondii (adjusted OR [aOR]=3.4). The deletion genotype was also associated with decreased levels of HBsAg (aOR=0.03), and anti-HCV (aOR=0.1). D/D was frequently found in HIV-infected individuals with CD4+T cells<14% (aOR=5.8). The intact genotype was associated with a reduced likelihood of a CD4+T cell count<200 cells/μL (aOR=0.2) but a higher prevalence of TTV co-infection (aOR=8.6). ConclusionsThe APOBEC3B deletion polymorphism was found to be associated with HBV, HCV, TTV, and T. gondii co-infection in Indonesian HIV-infected individuals.

The 19-bp deletion polymorphism of dihydrofolate reductase (DHFR) and nonsyndromic cleft lip with or without cleft palate: evidence for a protective role

Objective Nonsyndromic cleft lip with or without cleft palate (NS-CL/P) are among the most common congenital birth defects worldwide. Several lines of evidence point to the involvement of folate, as well as folate metabolizing enzymes in risk reduction of orofacial clefts. Dihydrofolate reductase (DHFR) enzyme participates in the metabolic cycle of folate and has a crucial role in DNA synthesis, a fundamental feature of gestation and development. A functional polymorphic 19-bp deletion within intron-1 of DHFR has been associated with the risk of common congenital malformations. The present study aimed to evaluate the possible association between DHFR 19-bp deletion polymorphism and susceptibility to NS-CL/P in an Iranian population.Material and Methods The current study recruited 100 NS-CL/P patients and 100 healthy controls. DHFR 19-bp deletion was determined using an allele specific-PCR method.Results We observed the DHFR 19-bp homozygous deletion genotype (D/D) vs. homozygous wild genotype (WW) was more frequent in controls than in NS-CL/P patients (25% vs. 13%), being associated with a reduced risk of NS-CL/P in both codominant (OR=0.33, P=0.027) and recessive (OR=0.45, P=0.046) tested inheritance models. We also stratified the cleft patients and reanalyzed the data. The association trend for CL+CL/P group compared to the controls revealed that the DD genotype in both codominant (OR=0.30, P=0.032) and recessive models (OR=0.35, P=0.031) was associated with a reduced risk of CL+CL/P.Conclusions Our results for the first time suggested the DHFR 19-bp D/D genotype may confer a reduced risk of NS-CL/P and might act as a protective factor against NS-CL/P in the Iranian subjects.

Label-Free Fluorescent Copper Nanoclusters for Genotyping of Deletion and Duplication of Duchenne Muscular Dystrophy.

Real applications in clinical diagnosis of label-free fluorescent copper nanoclusters (CuNCs) are demonstrated. Double-strand DNA (dsDNA) can act as an effective template for the formation of CuNCs, which can be used to distinguish the deletion or duplication genotypes of Duchenne muscular dystrophy (DMD) due to different fluorescent intensities. After PCR, the DMD amplicons reacted with copper ion by reduction of ascorbic acid and generated fluorescence. The exons of the DMD gene were taken as the model analytes for genetic diagnosis. In this sensing system, the deletion type does not show fluorescence; on the other hand, the duplication type emits higher fluorescence than normal type. Parameters of this sensing system were optimized, including PCR conditions, levels of copper ion and ascorbate, and reaction time. The DMD-dominated exons 45, 46, and 47 were detected, and the method was applied to six samples of DMD patients. The results were consistent with those of the multiplex ligation-dependent probe amplification method. This strategy was feasible to detect all exons of this disease.

Glutathione-S-Transferase Deletions and Non-arteritic Anterior Ischemic Optic Neuropathy.

In this study, we aimed at investigating the association between glutathione-S-transferase (GSTM1 and GSTT1) deletion genotypes and susceptibility to non-arteritic anterior ischemic optic neuropathy (NAION). We hope our findings may contribute to the understanding NAION pathogenesis and provide some clues for the prevention and treatment of optic diseases. The NAION group contains 113 subjects (33 males and 80 females, mean age 55.3 ± 9.8). And 98 subjects were enrolled in the control group (32 males and 66 females, mean age 56.7 ± 10.2). The individuals involved in the study were matched by gender and age to obtain two homogenous groups. GSTM1- and GSTT1- genotype and the combined genotype were investigated. The genotype distributions in NAION patients were compared with those in the controls. Significantly altered intraocular pressure (IOP) and cup-to-disc ratio (CDR) was detected between NAION patients and controls. An increased risk of NAION was observed among individuals with GSTM1- (P < 0.001). No significant difference was confirmed for GSTT1- (P = 0.290). Individuals with GSTM1-/GSTT1- have a higher susceptibility to NAION (P < 0.001); the GSTM1-/GSTT1+ genotype also had a significantly higher frequency in patients than in controls (P = 0.004). But the genotype of GSTM1+/GSTT1- seems to have no connection with NAION (P = 0.476). In conclusion, in this study, we confirmed the connection between NAION and GSTM1- genotype. But no significant association was observed between GSTT1- genotype and NAION susceptibility. In further analysis regarding combined genotype, a trend of protective effect was detected for GSTT1+ genotype. It is indicated by our result that oxidative compounds might play an important part in the pathogenesis of NAION.

Neonatal screening for α‐thalassemia by cord hemoglobin Barts: how effective is it?

It has long been recognized that the hemoglobin (Hb) Bart's in cord blood is an accurate indicator of α-thalassemia and that the level of Hb Bart's was increased accordingly with the increasing numbers of the defective α-genes. This study used an automatic capillary electrophoresis system to determine the Hb Bart's levels in cord blood. Molecular analyses were used to detect various genotypes of α-thalassemia. Sixty-nine of the total 1169 newborns were found to have an increased Hb Bart's in cord blood, in whom the diagnosis of α-thalassemia was confirmed by the DNA analysis. The remaining 1100 newborns had no detectable Hb Bart's at birth; among these, 45 carriers of silent α-thalassemia were diagnosed by DNA analysis. All the 45 cases had only the -α(3.7) deletion genotype. For newborns of one α-gene mutation, especially for 3.7-kb deletion, the method based on Hb Bart's is inadequate and is therefore not reliable for screening.

Von Hippel-Lindau status influences phenotype of liver cancers arising from PTEN loss.

BackgroundPTEN loss contributes to the development of liver diseases including hepatic steatosis and both hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC). The factors that influence the penetrance of these conditions are unclear. We explored the influence of sustained hypoxia signaling through co-deletion of Pten and Vhl in a murine model.MethodsWe used a CreER-linked Keratin 18 mouse model to conditionally delete Pten, Vhl or both in somatic cells of adult mice, evaluating the resultant tumors by histology and gene expression microarray. Existing sets of gene expression data for human HCC and CC were examined for pathways related to those observed in the murine tumors, and a cohort of human CC samples was evaluated for relationships between HIF-1α expression and clinical outcomes.ResultsBoth Pten deletion genotypes developed liver tumors, but with differing phenotypes. Pten deletion alone led to large hepatic tumors with widespread hepatosteatosis. Co-deletion of Pten and Vhl with the Keratin 18 promoter resulted in reduced steatosis and a reduced tumor burden that was characterized by a trabecular architecture similar to CC. Genes associated with hepatic steatosis were coordinately expressed in the human HCC dataset, while genes involved in hypoxia response were upregulated in tumors from the human CC dataset. HIF-1α expression and overall survival were examined in an independent cohort of human CC tumors with no statistical differences uncovered.ConclusionPten deletion in Keratin 18 expressing cells leads to aggressive tumor formation and widespread steatosis in mouse livers. Co-deletion of Vhl and Pten results in lower tumor burden with gene expression profiling suggesting a switch from a profile of lipid deposition to an expression profile more consistent with upregulation of the hypoxia response pathway. A relationship between tumor hypoxia signaling and altered hepatic steatotic response suggests that competing influences may alter tumor phenotypes.

Predictive potential role of glutathione S-transferase polymorphisms in the prognosis of breast cancer.

The current study aimed at evaluating the associa-tion between GSTM1 null/present, GSTT1 null/present, and GSTP1 IIe105Val polymorphisms and clinical response to chemotherapy and treatment outcome of breast cancers patients. Genotyping of GSTP1 rs1695, GSTT1 deletion, and GSTM1 deletion was performed by Polymerase Chain Reaction Restriction Fragment Length Polymor-phism (PCR-RFLP) assay. We found that patients with GG genotype of GSTP1 IIe105Val and null genotype of GSTM1 were more likely to have a poorer response to chemotherapy than homozygotes of the most frequent genotype; the ORs(95%CI) were 0.37(0.18-0.74) and 0.59(0.36-0.97), respectively. By the Cox proportional hazards model, patients with the GG genotype of GSTP1 IIe105Val and null genotype of GSTM1 were found to be correlated with shorter overall survival of breast cancer; the adjusted HR (95%CI) were 2.51(1.17-5.32) and 2.00(1.15-3.48), respectively. Thus, our findings provided statistical evidence that the variants of GSTP1 and GSTM1 polymorphisms could influence the response to chemotherapy and overall survival in breast cancer patients treated with chemotherapy.

Association of 5-HT3B Receptor Gene Polymorphisms with the Efficacy of Ondansetron for Postoperative Nausea and Vomiting.

PurposePostoperative nausea and vomiting (PONV) is a common problem after general anesthesia. Although 5-hydroxytryptamine type 3 (5-HT3) receptor antagonists have significantly reduced PONV, over 35% of patients treated with ondansetron can experience PONV. In this study, we investigated whether the Y129S and -100_-102AAG deletion polymorphisms of the 5-HT3B receptor gene affect the efficacy of ondansetron in preventing PONV.Materials and MethodsTwo hundred and forty-five adult patients who underwent laparoscopic cholecystectomy were enrolled. Ondansetron 0.1 mg/kg was intravenously administered 30 minutes before the end of surgery. Genomic DNA was prepared from blood samples using a nucleic acid isolation device. Both the Y129S variant and the -100_-102AAG deletion variant were screened for using a single base primer extension assay and a DNA direct sequencing method, respectively. The relationship between genetic polymorphisms and clinical outcomes of ondansetron treatment was investigated.ResultsAmong the 5-HT3B AAG deletion genotypes, the incidence of PONV was higher in patients with the homomutant than with other genotypes during the first 2 hours after surgery (p=0.02). There were no significant differences in the incidence of PONV among genotypes at 2-24 hours after surgery. In the Y129S variants of the 5-HT3B receptor gene, there were no significant differences in the incidence of PONV among genotypes during the first 2 hours and at 2-24 hours after surgery.ConclusionThe response to ondansetron for PONV was significantly influenced by the -100_-102AAG deletion polymorphisms of the 5-HT3B gene. Thus, the -100_-102AAG deletion variants may be a pharmacogenetic predictor for responsiveness to ondansetron for PONV.

The genetic biochemical markers of arterial hypertension in Adolescents.

The article deals with studying of enzyme activity of first and second lines of anti-oxidant defense in adolescents with arterial hypertension and establishing role of genetic component in realization of mechanism of development of this pathology. The main group included 20 adolescents aged from 13 to 16 years with diagnosis of arterial hypertension stage I (risk). The control group consisted of 20 healthy adolescents of corresponding age. The study was carried out to detect activity of superoxide dismutase [EC 1.15.1.1], catalase [EC 1.11.1.6], glutathione peroxidase [EC 1.11.1.9], glucose-6-phosphate dehydrogenase [EC 1.1.1.49]. The concentration of reduced glutathione was established using photoelectrocolorimeter KFK-2MP (Russia). The activity of glutathione reductase [EC 1.8.1.7] was evaluated using spectrophotometer CF-46 (LOMO, Russia). The content of nitrogen oxide was detected using V.A. Metelskaia and N.G. Gumanova technique (2005). The detection of genetically mediated risk of development of arterial hypertension and identification of gene-gene dependencies (ACE, AGT, NOS3) was implemented using technique of PCR-RFLP diagnostic ("DNA-technology", Russia). The genetic analysis identified in main group the following gene-candidates: deletion genotype DD for ACE, polymorphism M235T T->C gene AGT, version 786 C/C gene NOS3. All of then can be applied in diagnostic of arterial hypertension. In adolescents with arterial hypertension imbalance of molecular mechanisms of anti-oxidant defense was revealed. This condition is manifested by imbalance in functioning of enzymes of first line of anti-oxidant defense and accumulation of H2O2, increasing of activity of glutathione peroxidase and depressing of activity of the rest of glutathione depending enzymes. Against this background, decreasing of content of nitrogen oxide results in development of endothelial dysfunction.

Genotyping of wild-type cytochrome P450 2A6 and whole-gene deletion using human blood samples and a multiplex real-time polymerase chain reaction method with dual-labeled probes

BackgroundGenetic polymorphisms of human cytochrome P450 2A6 (CYP2A6) are one of the determinants of smoking behavior and/or tobacco-related lung cancer risk in male Japanese smokers. To help identify those at high risk, we developed a multiplex real-time polymerase chain reaction (PCR)-based genotyping method with dual-labeled probes to detect wild-type and whole-gene deletion of CYP2A6 directly from blood samples without DNA isolation. MethodsWe validated the new real-time PCR method that uses dual-labeled probes by utilizing 116 genomic DNA samples that had been genotyped previously and 33 blood samples. ResultsThe new method could discriminate CYP2A6 from highly homologous CYP2A7 and CYP2A13 genes and could also determine CYP2A6*1 (wild type) and CYP2A6*4 (whole-gene deletion) alleles in perfect accordance with previous analysis data. Amplification curve profiles were obtained by multiplex real-time PCR assay with CYP2A6*1 and CYP2A6*4 primer sets and dual-labeled probes using one-drop blood samples previously genotyped for CYP2A6*1/*1, CYP2A6*1/*4, and CYP2A6*4/*4. ConclusionsA real-time multiplex PCR assay for genotyping wild-type CYP2A6 and whole-gene deletion was developed with dual-labeled probes. The new method achieved 100% agreement with data from the conventional PCR method for 116 genomic DNA samples and samples from 33 volunteers, thereby establishing its validity.

Single tube genotyping of CYP2A6 gene deletion based on copy number determination by quantitative real-time PCR

The CYP2A6*4 allele, characterized as the whole deletion of this gene, is closely associated with nicotine dependence, cancer susceptibility, and drug responsiveness. It has long been a significant challenge for pharmacogenetics scientists to develop a reliable method to detect this molecular variant due to its high homology with its homologous genes CYP2A6 and CYP2A3 in the clinical setting. Here, we introduce a quantitative real-time PCR assay that specifically amplifies CYP2A6 by designing a specific set of primers and the probe, which effectively prevent the amplification of the CYP2A7 and CYP2A13 alleles. CYP2A6 gene copy numbers were normalized to albumin (ALB) which was co-amplified simultaneously in a single-tube duplex reaction and at a setting as the internal reference gene. The established assay was validated with a selection of previously genotyped DNA samples, which harbored none, one or two CYP2A6 gene copies. The results were in complete concordance with previously published data and no overlap between the three groups was observed. Further analysis of a cohort of 120 samples revealed high specificity and sensitivity of this assay as demonstrated by the agreement of determined gene copy numbers in all of the cases. In conclusion, this novel assay allows reliable and sensitive detection of the CYP2A6 gene deletion, which will be useful for pharmacogenetics studies and routine clinical settings.

Polymorphism, genetic effect and association with egg production traits of chicken matrix metalloproteinases 9 promoter.

Matrix metalloproteinases (MMP) are key enzymes involved in cell and tissue remodeling during ovarian follicle development and ovulation. The control of MMP9 transcription in ovarian follicles occurs through a core promoter region (−2,400 to −1,700 bp). The aim of this study was to screen genetic variations in the core promoter region and examine MMP9 transcription regulation and reproduction performance. A single cytosine deletion/insertion polymorphism was found at −1954 C+/C−. Genetic association analysis indicated significant correlation between the deletion genotype (C−) with total egg numbers at 28 weeks (p = 0.031). Furthermore, luciferase-reporter assay showed the deletion genotype (C−) had significantly lower promoter activity than the insertion genotype (C+) in primary granulosa cells (p<0.01). Therefore, the identified polymorphism could be used for marker-assisted selection to improve chicken laying performance.

European guidance for the molecular diagnosis of pseudohypoparathyroidism not caused by point genetic variants at GNAS: an EQA study.

Pseudohypoparathyroidism is a rare endocrine disorder that can be caused by genetic (mainly maternally inherited inactivating point mutations, although intragenic and gross deletions have rarely been reported) or epigenetic alterations at GNAS locus. Clinical and molecular characterization of this disease is not that easy because of phenotypic, biochemical and molecular overlapping features between both subtypes of the disease. The European Consortium for the study of PHP (EuroPHP) designed the present work with the intention of generating the standards of diagnostic clinical molecular (epi)genetic testing in PHP patients. With this aim, DNA samples of eight independent PHP patients carrying GNAS genetic and/or epigenetic defects (three patients with GNAS deletions, two with 20q uniparental disomy and three with a methylation defect of unknown origin) without GNAS point mutations were anonymized and sent to the five participant laboratories for their routine genetic analysis (methylation-specific (MS)-MLPA, pyrosequencing and EpiTYPER) and interpretations. All laboratories were able to detect methylation defects and, after the data analysis, the Consortium compared the results to define technical advantages and disadvantages of different techniques. To conclude, we propose as first-level investigation in PHP patients copy number and methylation analysis by MS-MLPA. Then, in patients with partial methylation defect, the result should be confirmed by single CpG bisulphite-based methods (ie pyrosequencing), whereas in case of a complete methylation defect without detectable deletion, microsatellites or SNP genotyping should be performed to exclude uniparental disomy 20.

Medical, psychological and social features in a large cohort of adults with Prader–Willi syndrome: experience from a dedicated centre in France

Prader-Willi syndrome (PWS) is a developmental genetic disorder characterised by a variable expression of medical, cognitive and behavioural symptoms. In adulthood, the prevalence and severity of these symptoms determine the quality of life of the affected persons. Because of their rare disease condition, data on health and social problems in adults with PWS are scarce. In this research, we present medical, psychological and social features of a large cohort of adults admitted to a specialised PWS centre in France and analyse the differences according to genotype, gender and age. Data from 154 patients (68 men/86 women), with a median age of 27 years (range 16-54), were collected during their stay in our centre. Clinical histories were completed using information from parents or main caregivers, and the same medical team performed the diagnosis of different clinical conditions. Statistical analyses were performed to determine the influence of factors such as genotype, age or gender. Paternal deletion genotype was the most frequent (65%) at all ages. Most patients had mild or moderate intellectual disability (87%). Only 30% had studied beyond primary school and 70% were in some special educational or working programme. Most of them lived in the family home (57%). The most prevalent somatic comorbidities were scoliosis (78%), respiratory problems (75%), dermatological lesions (50%), hyperlipidaemia (35%), hypothyroidism (26%), Type 2 diabetes mellitus (25%) and lymph oedema (22%). Some form of psychotropic treatment was prescribed in 58% of subjects, and sex hormones in 43%. Patients with deletion had a higher body mass index (44 vs. 38.9 kg/m(2)) and displayed higher frequency of sleep apnoeas. Non-deletion patients received insulin treatment (19% vs. 4%) and antipsychotic treatment (54.8% vs. 32.7%) more frequently. No difference was observed in the prevalence of Type 2 diabetes between the two genotype groups. Patients >27 years of age had a higher rate of comorbidities (Type 2 diabetes, hypertension, respiratory problems and lymph oedema). Gender differences were minor. Adult patients with PWS showed high prevalence of comorbid health problems that need to be monitored for early treatment. Some of them are influenced by genotype and age. Another salient problem concerns the lack of adapted structures for better social integration. Further data about the real life and health conditions of adults with PWS are necessary to further our knowledge of the natural history of the disease and to design appropriate care strategies.