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PubMed1999

Cytochrome P450 2D6 genotype and steady state plasma levels of risperidone and 9-hydroxyrisperidone.

The role of the polymorphic cytochrome P450 2D6 (CYP2D6) in the metabolism of risperidone to its major active metabolite, 9-hydroxyrisperidone (9-OH-risperidone), has been documented after single oral doses of the drug. In this study, the influence of the CYP2D6 polymorphism on the steady-state plasma concentrations of risperidone and 9-OH-risperidone was investigated. Thirty-seven schizophrenic patients on monotherapy with risperidone, 4-8 mg/day, were genotyped by RFLP and PCR for the major functional variants of the CYP2D6 gene. Steady state plasma levels of risperidone and 9-OH-risperidone were analysed by HPLC. Based on the genotype analysis, three patients were classified as ultrarapid metabolizers (UM) with an extra functional CYP2D6 gene, 16 were homozygous extensive metabolizers (EM), 15 heterozygous EM and three poor metabolizers (PM). The median steady-state plasma concentration-to-dose (C/D) ratios of risperidone were 0.6, 1.1, 9.7 and 17.4 nmol/l per mg in UM, homozygous EM, heterozygous EM and PM, respectively, with statistically significant differences between PM and the other genotypes (P < 0.02). The C/D of 9-OH-risperidone also varied widely but was not related to the genotype. The risperidone/9-OH-risperidone ratio was strongly associated with the CYP2D6 genotype, with the highest ratios in PM (median 0.79). Heterozygous EM also had significantly higher ratios than homozygous EM (median value 0.23 versus 0.04; P < 0.01) or UM (median 0.03; P < 0.02). No significant differences were found in the C/D of the sum of the plasma concentrations of risperidone and 9-OH-risperidone between the genotype groups. In conclusion, the steady-state plasma concentrations of risperidone and the risperidone/9-OH-risperidone ratio are highly dependent on the CYP2D6 genotype. However, as risperidone and 9-OH-risperidone are considered to have similar pharmacological activity, the lack of relationship between the genotype and the sum of risperidone and 9-OH-risperidone indicates that the CYP2D6 polymorphism may be of limited importance for the clinical outcome of the treatment.

Adult↗
PubMed2002

Greater trunk muscle torque reduces postmenopausal bone loss at the spine independently of age, body size, and vitamin D receptor genotype in Japanese women.

Bone mineral density (BMD) is affected by muscle strength. Recently, vitamin D receptor (VDR) genotype was reported to affect muscle strength as well as BMD in Caucasian women. The aim of this study was to evaluate independent effects of muscle strength of the trunk on BMD at the spine and its change over time in Japanese women. We followed 119 healthy postmenopausal women for 4 years and determined the change in BMD at the spine by dual energy X-ray absorptiometry. Isometric peak torque and isokinetic concentric and eccentric peak torque of the trunk flexors and extensors were measured. The VDR genotype was determined by the PCR-RFLP method based on Apa I and Taq I endonuclease digestions defining the absence/existence of the restriction sites as A/a and T/t, respectively. The subjects were 60.1 +/- 6.6 years old, had 0.808 +/- 0.159 g/cm2 of BMD at baseline. The mean annual change in BMD (delta BMD) was -5.6 +/- 10.4 mg/cm2 during the follow-up period. The VDR genotype, defined by Taq I enzyme, significantly related to BMD at baseline and delta BMD showing that the subjects with genotype TT had the lowest BMD at baseline and lost bone most rapidly. However, its effect on muscle strength was not significant. All the trunk muscle strength indices showed significant positive effects on delta BMD, that is, the effects in increasing the gain and reducing the loss of BMD, after controlling for the effects of age, body size and the VDR genotype. The eccentric trunk extensor torque had a significant positive effect on delta BMD in a dose-dependent manner. The effect of this torque was the greatest among all the muscle indices. The net effect of the trunk extensor torque on delta BMD was greater than that of the VDR genotype. The trunk muscle strength was suggested to affect BMD change independently of age, body size, and the VDR genotype. Exercise programs to increase the strength of the trunk muscles would be beneficial for the prevention of osteoporosis regardless of the VDR genotypes.

Absorptiometry, Photon↗
PubMed2000

Genotype and phenotype of cytochrome P450 2D6 in human immunodeficiency virus-positive patients and patients with acquired immunodeficiency syndrome.

OBJECTIVE: To examine the distribution of the cytochrome P450 (CYP) CYP2D6 phenotype and its relation to genotype, concomitant medication, and disease state in human immunodeficiency virus (HIV)-positive patients. DESIGN: A cross sectional study with a longitudinal component compared individual genotypes for CYP2D6 to the CYP2D6 phenotype. METHODS: Sixty-one predominately male Caucasian, HIV-positive patients were recruited and CYP2D6 genotypes [extensive metabolizer (EM) or poor metabolizer (PM)] determined by polymerase chain reaction (PCR)-based amplification, followed by restriction fragment-length analysis. The patients were also phenotyped using dextromethorphan (DM) to determine their respective enzyme activity and assigned either a CYP2D6 EM or PM phenotype. Complete medical and treatment histories were compiled. A total of 44 patients were tested longitudinally. RESULTS: Fifty-nine patients (97%) possessed an EM genotype, consistent with previously observed distributions in demographically similar populations. In healthy seronegative populations, genotype and phenotype have been shown to be essentially interchangeable measures of CYP2D6 activity. In this cohort, 2 of the 59 patients with an EM genotype expressed a PM phenotype. In addition, 4 EM patients were less extensive DM metabolizers than any of the patients receiving medication known to inhibit CYP2D6. This apparent shift toward the PM phenotype from the EM genotype was associated with the presence of active illness. CONCLUSION: Changes may occur in HIV-positive patients such that their CYP2D6 activity approaches that of PMs, despite having an EM genotype. Neither active disease nor drug interactions alone explain the shift.

Acquired Immunodeficiency Syndrome↗
PubMed2004

The use of phenotypic markers to identify Brassica oleracea genotypes for routine high-throughput Agrobacterium-mediated transformation.

Doubled haploid (DH) genotypes from a genetic mapping population of Brassica oleracea were screened for ease of transformation. Candidate genotypes were selected based on prior knowledge of three phenotypic markers: susceptibility to Agrobacterium tumefaciens, shoot regeneration potential and mode of shoot regeneration. Mode of regeneration was found to be the most significant of the three factors. Transgenic plants were successfully obtained from genotypes that regenerated multiple shoots via a distinct swelling or callus phase. The absence of tissue culture blackening (associated with genotypes that formed callus) was found to be critical for transformation success. Transgenic shoots were obtained from genotypes that regenerated via an indirect callus mode, even when susceptibility to Agrobacterium was low. The most efficient genotype (DH AG1012) produced transgenic shoots at an average rate of 15% (percentage of inoculated explants giving rise to transgenic plants). The speed and efficiency of regeneration enabled the isolation of transgenic shoots 5-6 weeks after inoculation with A. tumefaciens. This line was also self-compatible, enabling the production of seed without the need for hand-pollination. A genetically uniform DH genotype, with an associated genetic map, make DH AG1012 highly desirable as a potential model B. oleracea genotype for studying gene function. The possibility of applying the same phenotypic tissue culture markers to other Brassica species is discussed.

Biomarkers↗
PubMed2003

The serum angiotensin-converting enzyme and angiotensin II response to altered posture and acute exercise, and the influence of ACE genotype.

The deletion (D) rather than insertion (I) allele of the angiotensin-converting enzyme (ACE) gene is associated with greater ACE activity. We examined: (1) the influence of posture change (recumbent to seated) and acute exercise on serum ACE and angiotensin II (Ang II) activity; (2) the relationship between ACE and Ang II levels; and (3) the influence of ACE genotype on changes in ACE and Ang II levels with posture and exercise. Recreationally active young male Caucasians (10 each of II, ID and DD genotypes) rested for 35 min supine then 15 min upright, took 20 min bicycle ergometric exercise at 70% maximum oxygen uptake, then rested for 40 min. Samples were taken throughout for ACE activity and Ang II levels. Supine ACE levels were dependent upon ACE genotype [24.8 (5.7), 26.9 (4.5), 45.5 (6.4) nmol His-Leu ml(-1) min(-1); II, ID, DD, respectively; P<0.00005] and thereafter. ACE activity rose with assumption of a seated posture [from 32.4 (10.9) nmol His-Leu ml(-1) min(-1) to 35.0 (11.5) nmol His-Leu ml(-1) min(-1), P<0.00001], the absolute rise being independent of genotype [3.22 (1.92), 1.6 (1.6), 2.4 (2.3) nmol His-Leu ml(-1) min(-1); II, ID, DD; P=0.22], unlike percentage change [12.8 (6.8), 5.6 (5.5), 5.3 (5.0)%; II, ID, DD; P<0.01, and P=0.004 for II vs presence of the D allele]. A further genotype-independent rise occurred with exercise [+2.9 (3.7) units, P<0.0003]. An associated rise in Ang II levels [30.3 (15.9), or 2587.9 (489.76)%, P<0.00001] was independent of ACE genotype or activity. Upright posture increases ACE activity, and this may be influenced by ACE genotype. ACE activity and Ang II levels rise independently with exercise in a non-genotype-dependent fashion.

Adaptation, Physiological↗
PubMed2003

Foliar quality influences tree-herbivore-parasitoid interactions: effects of elevated CO2, O3, and plant genotype.

This study examined the effects of carbon dioxide (CO2)-, ozone (O3)-, and genotype-mediated changes in quaking aspen (Populus tremuloides) chemistry on performance of the forest tent caterpillar (Malacosoma disstria) and its dipteran parasitoid (Compsilura concinnata) at the Aspen Free-Air CO2 Enrichment (FACE) site. Parasitized and non-parasitized forest tent caterpillars were reared on two aspen genotypes under elevated levels of CO2 and O3, alone and in combination. Foliage was collected for determination of the chemical composition of leaves fed upon by forest tent caterpillars during the period of endoparasitoid larval development. Elevated CO2 decreased nitrogen levels but had no effect on concentrations of carbon-based compounds. In contrast, elevated O3 decreased nitrogen and phenolic glycoside levels, but increased concentrations of starch and condensed tannins. Foliar chemistry also differed between aspen genotypes. CO2, O3, genotype, and their interactions altered forest tent caterpillar performance, and differentially so between sexes. In general, enriched CO2 had little effect on forest tent caterpillar performance under ambient O3, but reduced performance (for insects on one aspen genotype) under elevated O3. Conversely, elevated O3 improved forest tent caterpillar performance under ambient, but not elevated, CO2. Parasitoid larval survivorship decreased under elevated O3, depending upon levels of CO2 and aspen genotype. Additionally, larval performance and masses of mature female parasitoids differed between aspen genotypes. These results suggest that host-parasitoid interactions in forest systems may be altered by atmospheric conditions anticipated for the future, and that the degree of change may be influenced by plant genotype.

Animals↗
PubMed1999

Genotypes of TT virus (TTV) compared between liver disease patients and healthy individuals using a new PCR system capable of differentiating 1a and 1b types from others*.

TT virus (TTV) lacks obvious pathogenicity; almost all of the infected hosts are symptom-free. A possibility remains, however, that certain strains can cause liver disease while most others are non-pathogenic. Genotypes 1 a and 1 b have been proposed to contain such pathogenic strains. To test this possibility, we constructed a PCR system capable of detecting TTV of the 1 a and 1 b genotypes differentially from the other genotypes, and compared the frequencies of these genotypes between patients with liver disease of unknown etiology (n=42) and healthy individuals (n=50). The assay comprised 3 steps: i) PCR to amplify a 3.2-kb fragment using universal primers; ii) 2nd-round PCR, starting from the 3.2-kb amplicon, for a approximately 280-nt fragment by use of genotype 1-specific primers; and iii) digestion of the approximately 280-nt amplicon with MboI and BanI to discriminate between 1 a and 1 b. Eventually, 40 (95%) of the patients and 47 (94%) of the controls were positive for the 3.2-kb amplicon, and the 1 a, 1 b, 1 a+1 b, and non-1 genotypes of TTV were found in 2 (5%) vs 4 (9 percent), 5 (13%) vs 4 (9%), 1 (3%) vs 1 (2%) and 32 (80%) vs 38 (81%) of the 40 patients and 47 controls, respectively: the distribution was almost identical between the two groups. The hypothesis that the genotype 1 of TTV may be more closely associated with liver disease than other genotypes was not supported by this study.

Base Sequence↗
PubMed2003

ABO blood type, Lewis and Secretor genotypes, and chronic atrophic gastritis: a cross-sectional study in Japan.

BACKGROUND: the H type I structure, synthesized by the secretor (Se) enzyme in gastric foveolar cells, and its metabolite, Lewis b (le(b)) antigen, mediate the adhesion of Helicobacter pylori ( H. Pylori) to the gastric epithelium, whereas H. Pylori does not bind to modified forms of Le(b) specific for blood types A and B. Such host factors as Le and Se genotypes and ABO blood type may affect the establishment of H. Pylori infection and, once infected, the risk of chronic atrophic gastritis. METHODS: we investigated the cross-sectional relation of abo blood type and Le and Le genotypes to gastric atrophy, assessed by serum pepsinogen levels, in japanese residents from two sources. RESULTS: among the 151 h. Pylori-positive participants of the h. Pylori eradication program, odds ratios (ors) for gastric atrophy, adjusted for age, sex, and smoking, were elevated for blood types a (or = 5.35; 95% confidence interval (ci), 2.11-13.58) and b (or = 4.79; 95% ci, 1.77-12.93) relative to type o. Ors for blood types a and b were also elevated in h. Pylori-negative subjects. These associations were not observed among 250 h. Pylori-positive health check-up examinees. The le genotype was not associated with gastric atrophy in either study population. The se/ se genotype was associated with statistically nonsignificant elevation of gastric atrophy risk in both populations. CONCLUSIONS: the present data showed a strong association of blood types a and b with gastric atrophy in one, but not the other, study population. Discrepant results between the two populations warrant further investigation. Background: the h type i structure, synthesized by the secretor (se) enzyme in gastric foveolar cells, and its metabolite, lewis b (le(b)) antigen, mediate the adhesion of helicobacter pylori ( h. Pylori) to the gastric epithelium, whereas h. Pylori does not bind to modified forms of le(b) specific for blood types a and b. Such host factors as le and se genotypes and abo blood type may affect the establishment of h. Pylori infection and, once infected, the risk of chronic atrophic gastritis. Methods: we investigated the cross-sectional relation of abo blood type and le and se genotypes to gastric atrophy, assessed by serum pepsinogen levels, in japanese residents from two sources. Results: among the 151 h. Pylori-positive participants of the h. Pylori eradication program, odds ratios (ors) for gastric atrophy, adjusted for age, sex, and smoking, were elevated for blood types a (or = 5.35; 95% confidence interval (ci), 2.11-13.58) and b (or = 4.79; 95% ci, 1.77-12.93) relative to type o. Ors for blood types a and b were also elevated in h. Pylori-negative subjects. These associations were not observed among 250 h. Pylori-positive health check-up examinees. The le genotype was not associated with gastric atrophy in either study population. The se/ se genotype was associated with statistically nonsignificant elevation of gastric atrophy risk in both populations. Conclusions: the present data showed a strong association of blood types a and b with gastric atrophy in one, but not the other, study population. Discrepant results between the two populations warrant further investigation.

Adult↗
PubMed2003

Possible influence of glutathione S-transferase GSTT1 null genotype on age of onset of sporadic colorectal adenocarcinoma.

INTRODUCTION: Glutathione S-transferase enzymes mediate exposure to cytotoxic and genotoxic agents and may be involved in cancer susceptibility. Both glutathione S-transferase mu 1 (GSTM1) and GST theta 1 (GSTT1) genes have a null variant allele in which the entire gene is absent. The association of glutathione S-transferase null genotype and risk of developing colorectal cancer is not yet fully clarified. METHODS: We tested whether the null genotypes for GSTM1 and GSTT1 genes altered the risk for sporadic colorectal adenocarcinoma in Brazilian patients. Genomic DNA from 102 sporadic colorectal adenocarcinoma patients and 300 controls was analyzed by polymerase chain reaction. RESULTS: Frequencies of GSTM1, GSTT1, and null combined genotypes were similar in patients and controls (49.9 vs. 44.6 percent, 16.6 vs. 17.3 percent, and 8.8 vs. 8 percent, respectively). We found a 1.03-fold (95 percent confidence interval, 0.96-1.10) and 1.08-fold (95 percent confidence interval, 0.99-1.18) increased risk associated with GSTM1 and GSTT1 null genotypes, respectively (P = 0.45 and P = 0.08) and a 1.18-fold (95 percent confidence interval, 0.47-2.90) increased risk associated with the combined null genotype (P = 0.74). The GSTT1 null genotype was more common in patients who were diagnosed before the age of 60 years than in those who were diagnosed at an older age (28.8 vs. 4 percent, respectively; P = 0.0008). CONCLUSIONS: The results suggest that inherited absence of this carcinogen detoxification pathway may not be associated with sporadic colorectal adenocarcinoma in the present cases. However, a higher frequency of GSTT1 null genotype in patients diagnosed before the age of 60 years suggests that this genotype could influence the age of disease onset in Brazil.

Adenocarcinoma↗
PubMed2005

Cyclin D1 genotype and expression in sporadic hemangioblastomas.

Central nervous system (CNS) hemangioblastomas are highly-vascularized tumors occurring in sporadic form or as a manifestation of von Hippel-Lindau disease (VHL). The VHL protein (pVHL) regulates various target genes, one of which is the CCND1 gene, encoding cyclin D1, a protein that plays a critical role in the control of the cell cycle. Overexpression of cyclin D1 is found in many cancers. The CCND1 gene contains a common G --> A polymorphism (870G > A) that enhances alternative splicing of the gene. CCND1 genotype is associated with clinical outcome in a number of cancers although prognostic significance varies with tumor type. In VHL disease, CCND1 genotype has been suggested as a genetic modifier that influences susceptibility to hemangioblastomas. In order to analyze whether CCND1 genotype plays a role in sporadic CNS hemangioblastomas, we investigated CCND1 genotype in tumor tissue of 17 sporadic and also in five VHL-related CNS hemangioblastomas. In addition, in these tumors the extent and localization of cyclin D1 expression was investigated by immunohistochemistry. We found no deviation in CCND1 genotype distribution and allele frequencies from expected values. Also, there was no correlation between age at onset and CCND1 genotype. The expression of cyclin D1 as detected by immunohistochemistry was highly variable within and between tumors, without a clear correlation with CCND1 genotype. We conclude that, whereas variable but sometimes high cyclin D1 expression is a feature of sporadic hemangioblastomas, CCND1 genotype is unlikely to be an important genetic modifier in the oncogenesis of these tumors.

Adult↗
PubMed2026

Effect of founder breeds on genotype imputation accuracy in Canchim cattle.

UNLABELLED: Genotype imputation is a technique used to infer unobserved genotypes based on reference panels, allowing increased marker density and cost-effective optimization for genomic selection. This study aimed to evaluate whether the inclusion of genotypes from the founder breeds Nelore (NE) and Charolais (CH) improves the imputation accuracy in the composite beef cattle breed Canchim (CA). The populations studied consisted of 804 NE, 897 CH, and 392 CA animals, all genotyped using high-density panels (777,962 SNP &#x2013; single nucleotide polymorphisms). CA animals had their genotypes masked to simulate a medium-density panel (54,609 SNP). Fourteen imputation scenarios were evaluated, varying according to breed, sex, year of birth, and lineage. Imputation accuracy was determined based on the percentage of correctly imputed genotypes (PERC) and the squared Pearson&#x2019;s correlation between observed and imputed genotypes (R2). PERC values ranged from 66.52% to 97.39% and R&#xb2; from 0.6352 to 0.9780. The scenarios that included NE, CH, and CA (males or animals born before 2004) as the reference population for imputing CA females or CA animals born after 2004 showed the highest imputation accuracies. Therefore, the use of founder breeds in the reference population improves the accuracy of genotype imputation in CA cattle. The results indicate that a multibreed reference population, incorporating founder breeds, could provide a more robust and informative genetic basis for imputing composite cattle. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13353-026-01060-z.

Animal breeding↗
PubMed2002

Molecular characterisation of two mumps virus genotypes circulating during an epidemic in Lithuania from 1998 to 2000.

An epidemic of mumps in Lithuania started in December 1998 and continued until May 2000. The total registered number of cases was about 11.000 of a total of 3,7 million inhabitants in Lithuania (29,7 cases/10,000). Virus-containing samples were collected from 80 patients treated at the hospital of Kaunas from October 1999 until the end of the epidemic. Out of the 80 patients with parotitis, meningitis was observed in 11 patients and orchitis in 22 of 69 male patients. Twenty-seven virus strains were genotyped by nucleotide sequencing of the small hydrophobic (SH) protein gene, and the 57 amino acid sequences of the gene were deduced. Twenty-five virus strains belonged to the C genotype and two were of the D genotype. By phylogenetic analysis the virus strains causing meningitis grouped in a separate cluster, designated C1, within the C genotype. Another group of ten of the 25 genotype C strains exhibited an amino acid triplet at amino acid positions 28 to 30 of the protein, consisting of valine, alanine and serine, instead of the previously recognised valine, valine and serine combination of genotype C. The amino acid alanine at position 29 was found in combination with the amino acid serine at position 48. This variant was designated C2 and it was associated with parotitis. The amino acid alanine at position 29 and serine in position 48 of the C2 genotype may constitute a marker of low neurovirulence compared to other genotype C strains.

Adolescent↗
PubMed2006

Respiratory syncytial virus group A and B genotypes and disease severity among Cuban children.

BACKGROUND: Respiratory syncytial virus (RSV) is the leading cause of serious lower tract infections in infants. Comorbid conditions such as chronic diseases and prematurity have been associated with greater severity illness, but virus genotypes and disease severity is still unknown. METHODS: Forty selected strains of RSV group A and B from Cuban infants with acute respiratory disease (ARD) over five seasons were studied. Viral RNA was extracted and polymerase chain reaction (PCR) was carried out using direct primers directed to parts of the nucleoprotein (N) and fusion (F) genes, respectively. Amplicons were digested using restriction fragment length polymorphism (RFLP) to define the association between virus and disease severity. Disease severity was assessed as very mild, mild, moderate, and severe. RESULTS: Three of six known N genotypes were detected. NP4 and NP3 were found more frequently; moreover, it was difficult to establish a relationship between N genotypes and disease severity. Five genotypes in F gene were found: F1, F2, F5, F9 and F11; F9 and F11 were associated with very mild disease, but F1 genotype appears to be associated with moderate to severe disease. CONCLUSIONS: At least five combinations of N and F genotypes circulated in the studied infants in Cuba. Patients with F1NP4 genotype showed moderate to severe disease. Relationship between genotypes and disease severity was established.

Cuba↗
PubMed2003

Smoking-dependent association between paraoxonase 1 M/L55 genotype and coronary atherosclerosis in males: an autopsy study.

High-density lipoprotein-associated paraoxonase 1 (PON1) enzyme can retard the oxidation of lipids. The methionine for leucine substitution at position 55 (M/L55) of the PON1 protein is associated with lower (MM genotype) or higher (ML or LL genotype) expression of the gene affecting serum level of PON1. We studied the association of the PON1 M/L55 genotype with the extent of atherosclerosis in an autopsy series of Finnish males. Areas of the coronary arteries and the aorta covered with fatty streaks and fibrotic and complicated lesions were measured from a total of 700 cases. Carriers of the MM genotype (14.4% of subjects) had larger percentual areas of fatty streaks in their left anterior descending coronary artery (P=0.014) and right coronary artery (P=0.004), as well as in thoracic (P<0.001) and abdominal aorta (P=0.010) compared to carriers of the LL or ML genotype. A PON1 genotype-by-smoking interaction was observed on the area of fatty streaks in left anterior descending coronary artery (P=0.011) and right coronary artery (P=0.005); the association between fatty streaks and MM genotype was evident only among non-smokers, whereas in smokers this association was abolished. The areas of more advanced atherosclerotic lesions did not vary significantly between the genotype groups. These data suggest that the genetic variation of PON1 affects the formation of early atherosclerotic lesions and that the effect is modified by smoking.

Adult↗
PubMed2005

Glutathione S-transferase genotypes and cancer risk.

Over 500 studies have examined the association of genetic variants of glutathione S-transferases with various malignancies yielding inconsistent results. The genotyping was based on PCR assays that identified the GSTM1 and GSTT1 null (-/-) genotypes but did not distinguish homozygous wild-type +/+ and heterozygous +/- individuals. Complete GSTM1 and GSTT1 genotyping can be accomplished by recently developed assays [Cancer Res. 64 (2004) 1233-1236; Pharmacogenetics 10 (2000) 557-565] that allow the definition of +/+, +/-, and -/- genotypes by separate identification of the respective GSTM1 and GSTT1 wild-type and null alleles. Application of the new GSTM1 assay to a breast cancer case-control study revealed that the relative risk of breast cancer for the +/+ genotype compared to the -/- genotype was 2.83 (95% confidence interval 1.45-5.59; P=0.002), suggesting a protective effect of the GSTM1 deletion [Cancer Res. 64 (2004) 1233-1236]. Regardless of the explanation for the association between the +/+ genotype and increased breast cancer risk, these results warrant application of true GSTM1 and GSTT1 genotyping to additional or previously analyzed groups with breast cancer or other malignancies.

Breast Neoplasms↗
PubMed2006

Individual single tube genotyping and DNA pooling by allele-specific PCR to uncover associations of polymorphisms with complex diseases.

BACKGROUND: The genotyping for the study of the SNPs in different complex diseases require a great number of patients. In this sense, the determination of allele frequencies and genotypes requires a rapid and economical procedure. METHODS: The genotype has been carried out by allele-specific PCR in single tube with the discrimination of the products of PCR by its T(m). For this purpose a GC tail was added to 5' extreme of the specific primer. The allele frequencies were also calculated by DNA pooling and QRT-PCR using allele-specific primers. RESULTS: The use of the genotyping in single tube through allele-specific PCR and melting curves has led us to the accurate genotype of three polymorphisms of vdr (cdx-2), osteoprotegerin (A-163G) and ppar-gamma (C-681G) genes in 225 postmenopausal women to be associated to osteoporosis. Only the cdx-2 polymorphism was associated with a reduced bone mineral density (BMD). These data were similar to those obtained when the allele frequencies were calculated using QRT-PCR in DNA pools. CONCLUSIONS: Individual genotyping with allele-specific PCR in single tube and melting curve analysis is a fast, trustworthy and economic method to study any SNP. We propose the following approach to determine the possible association of SNPs with complex and multifactorial diseases like osteoporosis, in which hundreds of individuals should be analyzed: construct control and problem groups, make DNA pools, and calculate pooled allelic frequencies. Genotyping each individual further permits to determine the genotypic distribution when differences in allelic frequencies are observed, thus allowing more complex statistical analyses (including other variables like age, weight, etc.).

CDX2 Transcription Factor↗
PubMed2006

High-throughput genotyping with infrared fluorescence allele specific hybridization (iFLASH): a simple, reliable and low-cost alternative.

OBJECTIVES: To develop and validate a novel genotyping approach, named infrared Fluorescence Allele Specific Hybridization (iFLASH), which combines the principles of allele specific oligonucleotide (ASO) hybridization with the advanced possibilities of infrared imaging. DESIGN AND METHODS: As an example, we genotyped the 55L > M and the 192Q > R common genetic variants of the paraoxonase-1 gene in 92 DNA samples using the iFLASH technique, and validated the outcomes with the restriction fragment length polymorphism (RFLP) and TAQman genotyping assays. RESULTS: There was a 100 percent agreement in genotype outcome among the three methods. CONCLUSIONS: Although we found complete unity in genotype outcome, the iFLASH assay has essential advantages over the RFLP and TAQman genotyping assays. First, the iFLASH technique is capable of handling up to 1536 samples per assay, which makes it a suitable technique for high-throughput genotyping. Secondly, because the costs per assay are lower, high-throughput genotyping with iFLASH is affordable.

Alleles↗
PubMed2006

Osmotic regulation of 10 wheat (Triticum aestivum L.) genotypes at soil water deficits.

Drought is a worldwide problem, seriously influencing plant (crop) productivity. Wheat is a stable food for 35% of the world population, moreover about 60% of land area on the globe belongs to arid and semi-arid zone. Wheat drought resistance is a multi-gene-controlling quantitative character and wheat final production in field is realized mainly by physiological regulation under the condition of multi-environmental factor interaction. Exploring drought resistance physiological mechanisms for different wheat genotypes is of importance to finding new drought resistance gene resources and conventional breeding and the basis for wheat drought resistance biotechnological breeding and platform. Osmotic adjustment regulation is the main component for physiological machinery of wheat drought resistance. By pot-cultivating experiments, investigation of osmotic adjustment comparison for 10 wheat genotypes at soil water deficits (75% FC, 55% FC, 45% FC, respectively), was conducted. The main results were as followed: (1) K(+) content in 10 wheat genotypes at three levels of soil water stress and at the same soil water deficit was very different. Five of these 10 wheat genotypes had higher K K(+) content under the condition of 75% FC. (2) Five of these 10 wheat genotypes possessed greater soluble sugar content at 55% FC soil water level. (3) Proline (Pro) content in five wheat genotypes was higher at 75% FC. (4) Five of these 10 wheat genotypes had lower malondialdehyde (MDA) content at 45% FC at seedling stage. Osmotic adjustment of wheat different genotypes was discussed in terms of different content of osmotic solutes.

Carbohydrates↗