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PubMed2004

Impact of GSTT1, GSTM1, GSTP1 and NAT2 genotypes on KRAS2 and TP53 gene mutations in colorectal cancer.

Which carcinogens are of influence in the development of human colorectal cancers remains a question; one answer could be the finding that specific polymorphisms in xenobiotic metabolizing enzymes are related to particular mutations in cancer genes. KRAS2 and TP53 gene mutations as well as genotypes for GSTM1, GSTP1, GSTT1 and NAT2 were determined in an exploratory series of 165 stable colorectal cancers. Mutations in KRAS2 and TP53 were found in 34% and 57.5% of cases, respectively. The KRAS2 mutation frequency was significantly lower in patients with a GSTT1 null genotype than in those with a GSTT1 non-null genotype (18% vs. 38%, p = 0.03). The overall risk of KRAS2 mutation for patients with distal colorectal cancer and GSTT1 null genotype was 0.3 (95% CI 0.1-0.9) compared to patients with distal colorectal cancer and non-null GSTT1 genotype. The overall risk of KRAS2 mutation was similarly reduced (OR = 0.4, 95% CI 0.2-0.9) for patients with distal colorectal cancer and GSTP1 mutated genotypes compared to patients with distal colorectal cancer and wild-type genotype. Patients with GSTP1 wild-type genotype appeared to be at significantly lower risk for TP53 mutation compared to patients with mutated genotypes (p = 0.023). Our results suggest that GSTT1 and GSTP1 could play a role in the occurrence of KRAS2 and TP53 mutations in colorectal cancer and generate a hypothesis on the dietary factors that could be incriminated.

Adult↗
PubMed2001

Effects of storage and viral load on hepatitis C viral genotyping.

Hepatitis C virus (HCV) genotyping is important for determining the treatment protocol for hepatitis C patients. Since amplified material from the Roche HCV Monitor kit is compatible with the Innogenetics INNO-LiPA HCV II kit (line probe assay), amplicons from the Monitor assay can be used to identify the HCV genotype. The Monitor package insert recommends using amplicons within a 7-day period (at 4 degrees C) following amplification. It was hypothesized that storage of amplicons for 4 weeks and longer (at -20 degrees C) would not affect the sensitivity of the genotyping assay. After denaturation, amplicons from two genotypes were stored for 7-386 days prior to performing the genotyping assay. Storage of amplicons did not hamper the ability to identify the genotype. Additionally, the sensitivity of the assay was evaluated by analyzing five genotypes with low viral loads. HCV genotypes were detected most consistently at viral levels of 10,000 copies/mL. In conclusion, the Innogenetics genotyping assay can use stored amplicons, thus reducing the cost of the assay by avoiding additional PCR reactions. Determining the sensitivity of this assay facilitates the efficient use of this test by incorporating a sensitivity cutoff of >or=10,000 copies/mL.

Genotype↗
PubMed2002

Preponderance of hepatitis B virus genotype B contributes to a better prognosis of chronic HBV infection in Okinawa, Japan.

The present study was designed to examine the distribution of hepatitis B virus (HBV) genotypes among patients at various stages of chronic liver disease type B in Okinawa Prefecture, Japan, where the prevalence of hepatitis B surface antigen is the highest in Japan despite the lowest mortality rate from primary liver cancer. Serum samples from 227 HBV carriers were determined for HBV genotype by polymerase chain reaction (PCR)-restriction fragment length polymorphism. Five of 227 sera were negative for HBV DNA by nested PCR and were excluded from the genotype analysis. Genotype B was predominant in asymptomatic carriers (45/67, 67%), whereas genotype C was predominant in chronic liver disease: 49% (50/103) in patients with chronic hepatitis, 63% (20/32) in patients with cirrhosis, and 60% (12/20) in patients with hepatocellular carcinoma. The distribution of genotype B decreased with increasing liver disease severity. However, this tendency was seen among patients aged less than 50 years old, whereas the prevalence of genotype B was similar among carriers with various liver diseases who were older than age 50. In conclusion, HBV genotype B was prevalent and less frequent among patients with advanced liver disease, particularly in patients aged less than 50 years. These findings suggest that the preponderance of genotype B is responsible for the low mortality rate of primary liver cancer associated with HBV seen in Okinawa Prefecture, despite having the highest HBV carrier rate in Japanese.

Adult↗
PubMed2002

Genotypes and S-gene variability of Mexican hepatitis B virus strains.

The genotypes and subtypes of 15 Mexican hepatitis B virus strains were determined by sequencing and phylogenetic analysis of the small S-gene. The most predominant strains were found to be divergent genotype/subtype F/adw4 strains (66.6%), followed by A/adw2 (20.0%), D/ayw3 (6.7%), and G/adw2 (6.7%). The S-genes of the Mexican genotype F strains and two Nicaraguan strains described previously formed a subcluster with more than 4% divergence from the other strains within this genotype. The Mexican strains within genotypes A and D showed the highest homology with strains from Europe and the United States. Ten amino acid substitutions not described previously were found in the S-genes of strains from nine chronic carriers, whereas the S gene in strains from six acute hepatitis B patients were highly conserved as compared to their respective genotypes. One genotype F strain from an HBsAg positive chronic carrier had a T to A mutation at position 647, forming a translational stop at codon 216. Two genotype F strains from HBsAg negative chronic carriers had a Val180 instead of an Ala found in the other genotype F strains. This study shows that a divergent genotype F predominates in Mexican strains analyzed, which presented amino acid substitutions not reported previously outside the a determinant.

Amino Acid Sequence↗
PubMed2003

Hepatitis B virus genotypes and serotypes in western India: lack of clinical significance.

To determine hepatitis B virus genotype and subtype distribution among HBV infected individuals with different clinical manifestations in western India, serum samples from 19 asymptomatic hepatitis B surface antigen carriers, 30 chronic hepatitis B patients, 8 acute hepatitis B patients, 5 fulminant hepatitis B patients, and with circulating HBV DNA were genotyped and subtyped on the basis of the nucleotide sequence analysis of S region of the HBV genome. Genotype D was the predominant genotype circulating in western India (57/62; 91.93%). All 19 asymptomatic hepatitis B surface antigen carriers, 8 acute hepatitis B patients, 5 fulminant hepatic failure patients and 25/30 chronic hepatitis B patients were circulating genotype D and ayw3/ayw2 subtypes. HBV genotype A was prevalent in 8% (5/62) of the total number of patients and all belonged to chronic hepatitis B category. Subtyping analysis showed that all genotype A isolates were of subtype adw2. As most of the patients from different clinical categories were infected with HBV genotype D, it is concluded that this genotype did not influence the outcome of HBV infection.

Acute Disease↗
PubMed1994

Hepatitis B virus subtypes and hepatitis C virus genotypes in patients with chronic liver disease or on maintenance hemodialysis in Indonesia.

Hepatitis B surface antigen (HBsAg) and hepatitis C virus (HCV) RNA were surveyed in patients in Yogyakarta, Indonesia, and their subtypes and genotypes were determined by serological methods and polymerase chain reaction with type-specific primers, respectively. Of 149 patients with chronic liver disease including 24 with chronic hepatitis, 86 with liver cirrhosis, and 39 with primary hepatocellular carcinoma, HBsAg was detected in 40 (27%) and HCV RNA in 48 (32%); one patient was positive both for HBsAg and HCV RNA. Thus, the cause of chronic liver disease was not identified in 62 (42%) patients. Of 58 patients on maintenance hemodialysis, four (7%) were positive for HBsAg and 44 (76%) for HCV RNA. Subtype adw was found in 34 (74%) of 46 HBsAg samples and adr in five (11%); compound subtypes, such as adyw and adyr were detected in the remaining seven (15%). Among HCV RNA samples from 48 patients with chronic liver disease, 23 (48%) were of genotype II, 17 (35%) of genotype III and one (2%) of genotype V, in a distribution strikingly different from that of 44 samples from patients on maintenance hemodialysis, 39 (89%) of which were of genotype I and only one (2%) of genotype II. Genotypes were not classifiable in seven (15%) patients with liver disease and four (9%) patients on hemodialysis despite high HCV RNA titers in them all. These results indicate that different HCV genotypes prevail in patients with distinct diseases, as well as unclassifiable HCV genotypes in Indonesia.

Adult↗
PubMed2004

High rate of spontaneous clearance of acute hepatitis C virus genotype 3 infection.

Treating acute hepatitis C with interferon alpha prevents chronicity in nearly all cases when therapy is initiated within 3 months after infection. However, 15-50% of untreated patients may clear the hepatitis C virus (HCV) spontaneously. Therefore, factors are needed to identify patients prior to therapy who have a higher or lower risk for developing a chronic course to avoid unnecessary treatment. The role of the HCV genotype for spontaneous recovery from acute hepatitis C has been discussed controversially. In the year 2002, all 1,176 new incoming prisoners in a Northern German prison for young men (age 16-24) were screened for anti-HCV antibodies and 92 tested positive. Ninety eight percent of these reported i.v.-drug abuse for a median of 32 months prior to imprisonment. HCV-RNA negative individuals (21%) were serotyped and HCV-RNA positive patients were genotyped. The prevalence of HCV genotype 3 was significantly higher among individuals who had cleared HCV spontaneously as compared to chronically infected patients (86% vs. 38%; P = 0.002). Ninety three percent of individuals exposed to HCV genotype 1 but only 63% of individuals exposed to genotype 3 experienced a chronic course of the infection (P = 0.006). Thus, acute infection in young Caucasian men with HCV genotype 3 leads more often to spontaneous clearance than infection with HCV genotype-1. Considering also the high chance of successful treatment of chronic HCV genotype 3 infection with pegylated-interferon in combination with ribavirin, we suggest not to treat acute hepatitis C genotype 3 infection early but rather to wait at least 3 months after the onset of symptoms when chronicity becomes likely.

Adolescent↗
PubMed2005

Full genome analysis of hepatitis B virus genotype E strains from South-Western Africa and Madagascar reveals low genetic variability.

The eight genotypes of hepatitis B virus (HBV), A-H, have a characteristic geographical distribution. The high prevalence of genotype E within a wide expanse of Africa makes it important to characterize this genotype. Although the preS/S region of a large number of genotype E isolates has been sequenced, to date only eight complete genotype E genomes have been published. The aim of this study, therefore, was to sequence and characterize the complete genome of genotype E isolates obtained from geographically distinct regions in Africa, including Namibia, Angola, and Madagascar. The nine newly sequenced genotype E isolates were closely related with an intra-group nucleotide divergence of 1.2%, reflecting their close geographical origin. All genotype E strains have the same characteristics, an in-frame deletion of three nucleotides (one amino acid) in the 5' pre-S1, a signature pattern of amino acids in the pre-S1 region and the serological subtype ayw4. In addition, we have identified another unique attribute of genotype E strains, the introduction of another start codon Met(83) in the pre-S1 region that may result in the translation of an elongated middle hepatitis B surface protein (MHBs).

Adult↗
PubMed2005

Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon.

Hepatitis C virus infects humans world-wide. The virus genome varies greatly and it has several genotypes. HCV infection is highly prevalent in Central Africa and Cameroon. Initial studies on the genetic variability of HCV showed infection with HCV genotypes 1, 2, and 4. We have now sequenced the NS5b and E2 regions of 156 HCV isolates collected from patients presenting for diagnosis in Yaounde and used the data to describe the distribution of HCV genotypes and subtypes in patients with hepatitis in Cameroon. Genotype 1 was more frequent than Genotypes 4 and 2. Genotypes 1 and 4 were highly heterogeneous, containing many subtypes described previously (1b, 1c, 1e, 1h, 1l, 4f, 4t, 4p, 4k) and unsubtyped groups. There was a systematic phylogenetic concordance between NS5b and E2 sequence clustering. The Genotype 2 sequences did not vary. Neither subject age nor gender influenced HCV distribution. HCV Genotypes 1 and 4 are very heterogeneous in Cameroon, perhaps due to ancient infections. The homogeneity of HCV Genotype 2 indicates its more recent introduction from western Africa.

Adult↗
PubMed2006

Hepatitis B genotypes, precore and core promoter mutants circulating in Tunisia.

Hepatitis B virus (HBV) is characterized by genetic heterogeneity, including genotypes and mutations. Eight genotypes (A-H) have been identified throughout the world with a characteristic geographical distribution. Previous studies also suggest that the viral genotypes may correlate with differences in clinical features of the infection. Two types of mutations were particularly described, precore and basal promoter mutations; they may play an important role in the clinical outcome of HBV infection. The aim of this study was to investigate the prevalence of HBV genotypes and HBV variants in Tunisia, and their eventual association with severity of liver disease. Using a molecular method, HBV genotypes, precore and basal core promoter mutations were determined in 56 asymptomatic carriers and in 82 patients with histologically verified chronic liver disease and hepatocellular carcinoma (HCC). Three genotypes (D, A, and E) were detected; the prevalence was 80%, 8%, and 9%, respectively. No significant difference was observed for genotype D with clinical status. HBV mutants were detected in 93% of cases, precore mutants were the most prevalent. Basal core promoter mutants were observed in 61% of cases, they were frequently characterized by a double mutation in 1762 and 1764. Co-infection by these two types of mutants was detected in 50% of cases. Genotype D was the most prevalent HBV genotype in Tunisia. High circulation of precore and basal core promoter mutants are common in chronic hepatitis B infection in Tunisia.

Adolescent↗
PubMed2002

Hepatitis C virus infection and genotypes among human immunodeficiency virus high-risk groups in Cameroon.

Parenteral transmission of HCV is well established but other possible routes such as heterosexual transmission are still questioned. The Central African region is characterised by a high HCV endemicity without any evidence on the route of transmission. The information on HCV genotypes that circulate in this area is also limited and controversial. HIV infection is very frequent in this region and mostly acquired via the heterosexual route. The aim of this work was to investigate the trend of HCV infection and genotypes among HIV high-risk groups from Cameroon. Four hundred eighty-two patients including 229 tuberculosis clinic attendants, 184 sexually transmitted disease clinic attendants, and 69 HIV clinical suspects from another clinic were enrolled. All plasma samples were screened for antibodies to HCV and HCV RNA. Genotypes were assigned by sequencing a 5'UTR amplified fragment. The overall prevalence of HCV markers was 11.6% and a significant increasing trend with respect to age was observed. A proportion of 64.1% (34/53) of HCV antibody positive samples was viraemic. HCV RNA was found in 3 samples that were indeterminate in RIBA 3.0. One was negative in the antibody screening test and the two others were weakly positive. The data on HCV genotypes revealed that genotype 1 was involved in 57% of viraemias, genotype 2 in 24%, while genotypes 4 and 5a accounted for 16 and 3%, respectively. In contrary to the predominance of genotype 4 reported in some African countries and even the neighbouring countries, these data demonstrate clearly that HCV infection in Cameroon is dominated by genotypes 1 and 2. No association was found between the HCV markers and the presence of HIV infection. It is concluded, therefore, that the heterosexual route plays a minor role in HCV transmission in this country.

Adolescent↗
PubMed1995

Hepatitis C genotypes in liver transplant recipients: distribution and 1-year follow-up.

Chronic hepatitis C infection (CH-C) accounts for a significant number of patients undergoing orthotopic liver transplantation (OLT). Recently, hepatitis C virus (HCV) genotype-dependent differences in disease outcome and therapeutic responses have been suggested. The objectives of our study were to determine (1) the recurrence of HCV infection after OLT; (2) distribution of HCV genotypes in patients with CH-C who required liver transplantation compared with those who did not; and (3) the 1-year transplantation outcome in patients infected with different hepatitis C genotypes. RNA was extracted from sera of 20 patients who underwent OLT for end-stage liver disease secondary to CH-C (group I) and 52 patients with CH-C who did not require OLT (group II). For viral RNA detection, reverse transcriptase and polymerase chain reaction (RT/PCR) of 5'UT region was performed on all OLT patients both before and after OLT. For genotyping, RT-PCR of the NS 5 region was performed, followed by automated sequencing of the amplification products. Nineteen OLT patients had viral RNA detected by PCR both before and after OLT. One patient had no RNA detected before OLT but became viremic after OLT. The prevalence of HCV genotype 1b was significantly higher in group I patients compared with group II (53% v 23% respectively, P = .01). Examination of outcome at 1 year after OLT showed that 9 of 10 patients with HCV genotype 1b had histological evidence of hepatitis compared with 4 of 9 patients with other genotypes (non-1b) (P = .06). However, the number of patients who had one or more episodes of rejection, underwent retransplantation, or died at 1 year after OLT were similar. Recurrence of HCV infection after OLT was shown in all studied patients. Hepatitis C genotype 1b is more prevalent in our patients who underwent transplantation compared with a group with chronic hepatitis C who did not require transplantation (P = .01). Patients infected with HCV genotype 1b may have a higher risk of histological hepatitis after transplantation.

DNA Primers↗
PubMed2001

Detection and typing of TT virus DNA genotype by the PCR-RFLP method.

TT virus (TTV) is a novel single-stranded DNA virus that was identified in patients with post-transfusion-hepatitis of non-A-G type in Japan in 1997. We developed a new detection and typing method for TTV DNA strains, by combining polymerase chain reaction (PCR) and restriction fragment length polymorphism (PCR-RFLP) techniques. TTV DNA was amplified by nested-PCR with TTV-specific mixed primers derived from the conserved open reading frame 1 (ORF1) region of the published TTV DNA sequences. Using the enzymes Hae III, Dra I, Eco RI and Pst I, we were able to distinguish between the four TTV genotypes. In 200 serum samples obtained from healthy pregnant women at an outpatient clinic, the positive rate of TTV detection was 27.0%, almost identical to the positive rate of the detection of ORF1-PCR in Japanese healthy individuals. The strains detected in the positive serum samples were genotype 1a (9.3%), genotype 1b (11.1%), genotype 2 (51.9%), genotype 3 (7.4%) and other genotypes (1.9%). This results indicate that genotype 1 and genotype 2 were the two major strains in the Japanese population. Moreover, 10 serum samples (18.5%) presented RFLP patterns in which some genotypes were mixed.

DNA Restriction Enzymes↗
PubMed1996

Genotypes with the apolipoprotein epsilon4 allele are predictors of coronary heart disease mortality in a longitudinal study of elderly Finnish men.

Earlier we reported that allelic variation in the gene coding for apolipoprotein (apoE is a significant predictor of variation in the risk of coronary heart disease (CHD) death in a longitudinal study of elderly Finnish men. Here we address the question: which of the apoE genotypes confers the risk information in these men, and whether such information persists after other CHD risk factors are considered? We followed two cohorts of elderly Finnish men aged 65 to 84 years, one in Eastern (n = 281) and the other in the Southwestern (n = 344) Finland for 5 years during which 26 (9.3%) of the men from the Eastern cohort and 40 (11.6%) of the men in the Southwestern cohort died from CHD. Baseline high density lipoprotein (HDL) cholesterol and (HDL cholesterol)2 in the Eastern cohort and age, and total and HDL cholesterol and smoking status in the Southwestern cohort were significant predictors of CHD death (P < 0.05). The apoE genotypes were significant predictors in the Southwestern cohort at P = 0.02 and in the Eastern cohort at P = 0.18. In multivariable models, information about apoE genotypes improved the prediction at P = 0.1O level of statistical significance in both cohorts. When genotypes were considered separately, the episilon2/4 combined with the epsilon4/4 in the Eastern cohort (odds ratio = 7.69, 95% CI = 1.67-35.52) and the epsilon 3/4 in the Southwestern cohort (odds ratio = 2.44, 95% CI = 1.165.10) had sigificantly greater odds of CHD death compared to the common F3/3 genotype. We conclude that apoE genotypes confer risk information about CHD death in two cohorts of elderly Finnish men in a longitudinal study, and this information persists after adjustment for other CHD risk factors. Because different genotypes were predictors in these two cohorts, we further conclude that the utility of a particular genotype as a predictor of CHD death in other populations may depend on the distribution of risk factor profiles at baseline, geographically defined environmental exposures, the CHD mortality history, and the evolutionary history of background genotypes in the population considered.

Age Factors↗
PubMed1990

Maize genotypes classified as null at the glu locus have beta-glucosidase activity and immunoreactive protein.

Maize beta-glucosidase (beta-D-glucoside glucohydrolase; EC 3.2.1.21) was extracted from coleoptiles of 15 maize genotypes (3 normals, 10 nulls, and 2 hybrids) in two fractions, the soluble and the insoluble. The enzyme activity was measured spectrophotometrically in the soluble fraction and also studied on zymograms after native gel electrophoresis and isoelectric focusing. The enzyme was purified from a normal genotype by anion-exchange chromatography and preparative electrophoresis. Antisera were raised in four rabbits, and the soluble and the insoluble extracts of each genotype were analyzed for a cross-reacting material by ELISA and immunoblotting. The results showed that extracts from both the normal and the null genotypes had beta-glucosidase activity, and the activity measured spectrophotometrically was 2- to 10-fold higher in normals than in nulls. Zymograms of the null genotypes were devoid of distinct bands that were present in those of normals and hybrids from crosses between normals and nulls. Zymograms of both the normal and the null genotypes had a diffuse, smeared zone of activity at the cathodic end of native gels. A cross-reacting antigen was present in extracts of both genotypes when assayed by ELISA and a 60-kD polypeptide (beta-glucosidase monomer) was detected by four different monospecific beta-glucosidase antisera on Western blots by immunostaining. Moreover, six of seven null genotypes had a larger amount of their 60-kD polypeptide in the insoluble fraction than in the soluble fraction. These data show that both the null and the normal genotypes have similar amounts of the enzyme protein, but the enzyme occurs mostly as insoluble or poorly soluble polymers in nulls, and the monogenic inheritance reported for the null alleles of the glu locus is likely to be for a factor encoded by another locus which affects directly or indirectly the solubility of the enzyme by increasing its polymerization into large quaternary structures.

Alleles↗
PubMed1999

The 677T genotype of the common MTHFR thermolabile variant and fasting homocysteine in childhood venous thrombosis.

Controlled data on the association of MTHFR genotypes, hyperhomocysteinaemia and their interaction with factor V G1691A with childhood thrombosis are not yet available. Therefore we conducted a case-control study comparing 141 childhood patients with venous thrombosis with 345 healthy controls. The MTHFR C677T genotypes, FV G1691A and prothrombin G20210A were evaluated; in addition, fasting homocysteine concentrations were measured in a subgroup of 60 children and 80 healthy controls. 10.4% of the healthy control population showed the MTHFR TT genotype, 34.2% the CT genotype and 55.4% the CC variant. MTHFR genotypes account for fasting homocysteine concentrations in healthy controls (CC: 5.5 micromol/l (4-7.2); CT: 7 micromol/l (3.9-9.8); TT: 12.1 micromol/l (7.7-13.3)) with an upper age-specific 95th percentile of 8.3 micromol/l. The following frequencies (patients versus controls), odds ratios (OR) and 95% confidence intervals (CI) were found for single defects: MTHFR 677TT genotype (10.6% vs. 10.4%; OR/CI: 1.02/0.54-1.93; P = 0.99) and CT genotype (43.8% vs. 34.2%; OR/CI: 2.12/1.42-3.16; P = 0.0000). A combination of FV G1691A mutation and MTHFR 677CT genotype was found in 9.9% of patients and in 2.9% of the controls (OR/CI: 3.8/1.64-8.75; P = 0.027). Fasting homocysteine median (range) concentrations in the patient group were significantly higher than in the controls (7 micromol/l (3-23) vs. 5.5 micromol/l (3-8.4): P = 0.0004), and homocysteine concentrations >8.3 micromol/l were found in 40% of patients vs. 2.5% of the controls (OR/CI: 22/2.64-183; P = 0.0003). Conclusion Data of this childhood case-control study suggest that mildly elevated fasting homocysteine concentrations >8.3 micromol/l and the CT genotype of the MTHFR C677T variant are significant risk factors for venous vascular occlusion in children.

Adolescent↗
PubMed2005

Identification and validation of QTL for Sclerotinia midstalk rot resistance in sunflower by selective genotyping.

Midstalk rot, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in sunflower (Helianthus annuus L.). Objectives of this study were to: (1) estimate the number, genomic positions and genetic effects of quantitative trait loci (QTL) for resistance to midstalk rot in line TUB-5-3234, derived from an interspecific cross; (2) determine congruency of QTL between this line and other sources of resistance; and (3) make inferences about the efficiency of selective genotyping (SG) in detecting QTL conferring midstalk rot resistance in sunflower. Phenotypic data for three resistance (stem lesion, leaf lesion and speed of fungal growth) and two morphological (leaf length and leaf length with petiole) traits were obtained from 434 F3 families from cross CM625 (susceptible) x TUB-5-3234 (resistant) under artificial infection in field experiments across two environments. The SG was applied by choosing the 60 most resistant and the 60 most susceptible F3 families for stem lesion. For genotyping of the respective F2 plants, 78 simple sequence repeat markers were used. Genotypic variances were highly significant for all traits. Heritabilities and genotypic correlations between reMidstalk rot, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in sunflower (Helianthus annuus L.). Objectives of this study were to: (1) estimate the number, genomic positions and genetic effects of quantitative trait loci (QTL) for resistance to midstalk rot in line TUB-5-3234, derived from an interspecific cross; (2) determine congruency of QTL between this line and other sources of resistance; and (3) make inferences about the efficiency of selective genotyping (SG) in detecting QTL conferring midstalk rot resistance in sunflower. Phenotypic data for three resistance (stem lesion, leaf lesion and speed of fungal growth) and two morphological (leaf length and leaf length with petiole) traits were obtained from 434 F3 families from cross CM625 (susceptible) x TUB-5-3234 (resistant) under artificial infection in field experiments across two environments. The SG was applied by choosing the 60 most resistant and the 60 most susceptible F3 families for stem lesion. For genotyping of the respective F2 plants, 78 simple sequence repeat markers were used. Genotypic variances were highly significant for all traits. Heritabilities and genotypic correlations between resistance traits were moderate to high. Three to four putative QTL were detected for each resistance trait explaining between 40.8% and 72.7% of the genotypic variance (PTS). Two QTL for stem lesion showed large genetic effects and corroborated earlier findings from the cross NDBLOSsel (resistant) x CM625 (susceptible). Our results suggest that SG can be efficiently used for QTL detection and the analysis of congruency for resistance genes across populations.

Ascomycota↗
PubMed1999

Genetic heterogeneity of autoimmune diabetes: age of presentation in adults is influenced by HLA DRB1 and DQB1 genotypes (UKPDS 43). UK Prospective Diabetes Study (UKPDS) Group.

AIMS/HYPOTHESIS: Juvenile-onset, insulin-dependent diabetes is associated with islet cell antibodies and with specific "high-risk" HLA-DRB1 and HLA-DQB1 genotypes. Patients with Type II (non-insulin-dependent) diabetes mellitus can have islet-related antibodies, but the genotypic associations at different ages of onset have not been evaluated. Our aim was to determine (i) the prevalence of DRB1 and DQB1 genotypes in patients at diagnosis of Type II diabetes at different ages from 25 to 65 years compared with the general population, and (ii) whether the presence of islet cell antibodies (ICA) or glutamic acid decarboxylase antibodies (GADA) or both by age is associated with different DRB1 and DQB1 genotypes. METHODS: The antibodies to islet cells and those to glutamic acid decarboxylase were measured in 1712 white Caucasian diabetic subjects at diagnosis of diabetes and they were genotyped for HLA DRB1*03 and DRB1*04 and the high-risk DRB1*04-DQB1* 0302 haplotype. To assess over-representation of high-risk alleles for Type I (insulin-dependent) diabetes mellitus, the prevalence of high-risk alleles in diabetic patients was expressed relative to the prevalence of low-risk alleles, non-DR3/non-DR4, that provided a reference denominator in both the diabetic patients and in 200 non-diabetic control subjects. The prevalence of ICA or GADA or both in patients with different HLA genotypes was assessed in those diagnosed in four age groups, 25-34 years, 35-44 years, 45-54 years and 55-65 years. RESULTS: In Type II diabetic patients presenting at ages 25-34, 35-44 and 45-54 years, there was an increased prevalence of DR3/DR4 compared with the general population with approximately 6.5-fold, 2.9-fold, 2.1-fold over-representation, respectively (p < 0.0001, < 0.01, < 0.05) but this was not found in those aged 55-65 years old. In the group aged 25-34 years, 32 % of patients with ICA or GADA or both had DRB1*03/DRB1*04-DQB1*0302 compared with 10% in those aged 55-65 years and expected 3% prevalence. Conversely, only 14% of those aged 25-34 years with antibodies had non-DR3/non-DR4, compared with 35 % in those aged 55-65 years. There was thus pronounced age heterogeneity in DRB1 and DQB1 predisposition to Type II diabetes. The antibodies displaced DRB1 or DQB1 genotypes in the multivariate model for requiring insulin therapy by 6 years of follow-up. CONCLUSION/HYPOTHESIS: The age of presentation of Type I diabetes in adulthood was in part dependent on the DRB1/DQB1 genotype. Islet cell antibodies and glutamic acid decarboxylase antibodies were strongly associated with DRB1*03/DRB1*04-DQB1*0302 in early adulthood but showed little relation with specific HLA genotypes after the age of 55 years.

Adult↗