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PubMed2004

[X protein variations of genotype B and C hepatitis B virus isolated from the patients with hepatocellular carcinoma].

BACKGROUND & OBJECTIVE: X protein was one of the most important pathogens of hepatitis B virus (HBV), and was crucial in the carcinogenesis of HBV related hepatocellular carcinoma (HCC). It was demonstrated that the infection of genotype B or C HBV would result in different clinical manifestations and pathological characteristics in HCC patients, however, it was under elucidation whether these differences related to different genotypes of HBV X protein. This study was designed to investigate the amino acid differentiations of X proteins in standard genotype B or C HBV strains and the variations in HBV isolated from the HCC patients, and elucidate preliminarily the relationship between the genotype of HBV and carcinogenesis of HCC. METHODS: HBV X genes from the serum of twenty-two HBsAg positive HCC patients were amplified, cloned and sequenced. Genotyping of the X gene was carried out by Vector NTI6.0 software and the amino acid alignment among the standard and HCC originated X protein were done by DNAMAN software. RESULTS: Twenty-two HBV X genes were obtained and all of them could be categorized into genotype B or C. Besides of 14 amino acid differentiations within X protein between standard B and C HBV strains, HCC originated X protein of B and C genotype showed 4 consensus amino acid variations, and genotype C X protein showed additional 6 genotype-specific variations. All these differentiated and varied amino acids were located in the B, T cell epitopes and transactive or related regulatory regions. CONCLUSIONS: In addition to amino acid differentiations, X protein of genotype B or C HBV also showed genotype-specific variations in HCC patients. Amino acid differentiations and variations may result in the different immunocompetence and transactivation capacity between X proteins of genotype B and C.

Amino Acid Sequence↗
PubMedDate not supplied

Thymidylate synthetase (TS) genotype and TS/dihydropyrimidine dehydrogenase mRNA level as an indicator in determining chemosensitivity to 5-fluorouracil in advanced gastric carcinoma.

BACKGROUND: One of the target enzymes of 5-fluorouracil (5-FU) is thymidylate synthetase (TS). The DNA sequence of the TS gene includes either double or triple tandem 28-bp repeats within the promoter region, such that TS genotypes can be classified as homozygous 3R/3R heterozygous 2R/3R or homozygous 2R/2R Several recent studies have shown that TS genotype affects mRNA expression, with 3R/3R homozygotes showing higher TS mRNA expression compared to the other genotypes. PURPOSE: We analyzed the TS genotype and TS and dihydropyrimidine dehydrogenase (DPD) mRNA expression levels in 22 advanced gastric carcinoma patients, and analyzed results with respect to patient 5-FU chemosensitivity, as detected by the tetrazolium-based colorimetric (MTT) assay and survival outcome. PATIENTS AND METHODS: Between September 2001 and April 2002, 22 Japanese patients with advanced gastric carcinoma were evaluated. Informed written consent was obtained from all patients and the study was approved by the ethical committee at our University Hospital Fresh surgical specimens from carcinoma lesions were enzymatically dissociated and incubated with 5-FU at a concentration of 50 microg/ml for 48 hours to determine the inhibition rate as detected by MTT assay. Normal and tumor tissue and peripheral blood samples were collected and stored at -80 degrees C until assay for TS genotype and TS and DPD mRNA level The TS genotype was assessed by PCR assay using peripheral monocytes, since monocyte genotypes represent the genotype of normal and tumor tissues. Quantification of TS and DPD mRNA levels was performed using real-time PCRP Survival outcome was assessed according to the disease-free survival period in cases with similar clinical backgrounds. RESULTS: TS genotyping revealed 19 3R/3R homozygotes and 3 2R/3R heterozygotes. After analysis of normal and tumor tissues, samples from homozygote 3R/3R cases showed higher TS mRNA expression than heterozygote 2R/3R cases, which was statistically significant at p<0.05. We also observed a statistically significant correlation in TS mRNA levels between normal and tumor tissues, while no significant correlation was observed for DPD mRNA levels between normal and tumor tissues. While no relationship between 5-FU chemosensitivity and TS genotype or mRNA expression was observed, cases with high DPD mRNA expression were resistant to 5-FU and exhibited poor survival outcomes. CONCLUSION: While TS genotype affected TS mRNA expression in both normal and tumor tissues in advanced gastric cancer, there is no relationship between TS genotype or mRNA expression level and 5-FU chemosensitivity. CONCLUSION: Our finding, that DPD mRNA expression appears to be a factor in determining 5-FU chemosensitivity and the survival outcome of advanced gastric cancer patients, is comparable with previous reports.

Aged↗
PubMed2004

[The difference in distribution of HCV genotypes between patients infected with HCV by transfusion and non-transfusion routes].

OBJECTIVE: To investigate the HCV genotypes distribution in northern and southern cities in China and the difference between patients infected with HCV by transfusion and non-transfusion routes. METHODS: The HCV genotypes of the patients with chronic hepatitis C from 9 cities belonging to different regions were genotyped by the PCR products of 5 prime untranslated region NTR digested with restriction endonucleases, and the HCV genotypes distribution among different cities or between the patients infected with HCV through transfusion and other routes was analyzed. RESULTS: The HCV genotypes of 214 in 219 cases were determined; 197 patients were infected with monogenotype HCV. The major epidemic genotypes of HCV isolates in China were 1b (76.64%) and 2a (18.22%), but 5.14% of patients were infected with HCV belonging to genotype 3b and this was the first report that there is genotype 4a in China. The HCV genotype distribution was not different in northern and southern areas, but was significantly different between patients infected with HCV through transfusion and non-transfusion routes (P=0.036). In patients infected trough transfusion, the rates of monogenotype HCV infection and genotype 1b were 93.88% and 76.87%, respectively, which were higher than those (86.57% and 58.21%) in the patients infected with HCV through non-transfusion routes. The rate of patient infected with mixed genotype HCV strains in non-transfusion group was 13.43%, which was higher than that (6.12%) of patients in transfusion group. CONCLUSION: The HCV genotype distribution in northern and southern regions were similar, but was significantly different between the patients infected through transfusion and other routes.

5' Untranslated Regions↗
PubMed2006

YMDD mutations and genotypes of hepatitis B virus in northern China.

The objective of this research was to determine the relationship between YMDD mutations and the genotypes of hepatitis B virus (HBV) during lamivudine treatment. HBV genotypes were determined by nested PCR with 6 pairs of HBV genotype-specific primers (A to F) in serum specimens from 142 hepatitis B patients receiving lamivudine antiviral therapy. YMDD mutations were detected by fluorescent hybridization bioprobe PCR and melting curve assay (FH-PCR-MC). Among 142 serum specimens, 13 samples were genotype B (9.2%), 125 samples were genotype C (88%), 4 samples were genotype D (2.8%), and 80 YMDD mutations were found. The YMDD mutation rates were 69.2 and 54.4% in genotype B and genotype C, respectively. There was no significant difference in the YMDD mutation rate between genotypes B and C. Nine genotype B sera with YMDD mutations were found, including 2 YIDD mutations and 7 YVDD (M + V) mutations. Sixty-eight genotype C sera with YMDD mutations were found, including 34 mutations I (M + I) and 17 mutations V (M + V). There was a significant difference in the YMDD mutation types between genotypes B and C. Our results suggested that the YMDD mutation rate was 56.3% in patients treated with lamivudine for 2-4 years. YIDD was the main mutation type. The YMDD mutation rate showed no significant difference between HBV types B and C (P > 0.05), while the YMDD mutation types showed a significant difference between HBV types B and C in Northern China (chi2 test = 4.6, P < 0.05).

Antiviral Agents↗
PubMed2006

Genotype distribution amongst hepatitis C patients in The Netherlands.

BACKGROUND: The prevalence of the genotypes of the hepatitis C virus (HCV) differs according to geographical location. In the United States and in European countries, the majority of patients are infected with genotype 1, 2 or 3. There is a lack of data on the distribution of HCV genotypes in The Netherlands. METHODS: The current survey determined the distribution of HCV genotypes amongst recently genotyped patients seen by physicians treating hepatitis C in The Netherlands. RESULTS: Almost half of the 351 patients (49.3%) were infected with genotype 1. Genotype 3 was the second most dominant genotype with a prevalence of 29.3%. Genotypes 2 and 4 were found in 9.7 and 10.5% of the patients, respectively. For 61.5% of the patients (n=216), the subtype was available. For genotype 1 the prevalence of subtype 1a and 1b was very similar, while for genotype 3 a large majority of patients were infected with subtype 3a. CONCLUSION: This survey gives the first estimation of the distribution of HCV genotypes amongst unselected HCV patients in The Netherlands.

Epidemiologic Studies↗
PubMed2006

[kgp genotypes of Porphyromonas gingivalis in subgingival plaque in puberty gingivitis].

OBJECTIVE: To assess the prevalence of specific kgp genotypes in puberty gingivitis and investigate their possible association with disease severity. METHODS: Subgingival plaque samples were collected from 72 pubertal children aged from 14 to 17 years, which were divided into two groups, gingivitis group and healthy (control) group. Clinical parameters were recorded beforehand. PCR technique was used to amplify the region encoding the catalytic domain of gingipain K (KGP). The PCR products were digested with restriction enzymes Mse I. RESULTS: The kgp-A genotype was digested in fragments of 102 bp, 288 bp and 402 bp, and kgp-B genotype was unrestricted with 792 bp. Virulent strain P. gingivalis W83 was manifested by kgp-A genotype while a virulent strain P. gingivalis ATCC 33277 was manifested by kgp-B genotype. All P. gingivalis positive subjects were subgingivally colonized by only one kgp genotype. The prevalence of kgp-A genotype in puberty gingivitis group and gingival healthy group was 79.0% and 22.2% respectively. The distribution differences of genotypes between the two groups were statistically different (P = 0.028). There was no statistically significant difference in the clinical parameters between pubertal subjects harboring P. gingivalis of kgp-A genotype and kgp-B genotype (P > 0.05). CONCLUSIONS: Most subjects with puberty gingivitis were harbored by the same kgp genotype as that of virulent strain P. gingivalis W83. It may be necessary to continue to monitor individuals who are positive for P. gingivalis of kgp-A genotype since their risk of developing periodontal diseases may be increased in the future.

Adolescent↗
PubMedDate not supplied

[The nature of the genotype and heredity].

The term "genotype" is used for both hereditary information and its substantial bearer. The most important property of the information is relatively of its content which means very weak dependence on properties of the information substantial bearer (genotype of the second meaning) and very strong dependence on properties of the information recipient. Hereditary information (genotype in the first meaning) is addressed to the ontogenesis system, that is, to phenotype. From this it follows: 1) The genotype content is determined not so much by properties of its substantial bearer as by properties of the phenotype to which it is addressed; 2) Certainty of the genotype content depends not so much on stability of its elements, genes, as on stability of the phenotype of adaptive norm; 3) Genotype possess certain content only for a phenotype inherited from the ontogeny of other (maternal) organism or from a previous ontogenetic stage of the same organism; 4) Genotype (and this is true for any hereditary information of an organism) can not be localized in the primary structures of the nucleic acids. It is an aspect of phenotype and not a part thereof and, in this sense, does not possess independent being; 5) Each element of the phenotype, including genotype, relative to its other elements, is both recipient and bearer of hereditary information; 6) Genotype, as genetic code, is specialized but, not the only, "organ" of storing and transferring of hereditary information; 7) There is no two identical genotypes existing in nature; 8) The only operational definition of the genotype is its treating as genetic information localized in one or several loci; 9) Rather strong relation between certain symbols of genetic code (genes) and certain phenotypic characters reflects stability of reactional system of adaptive norm; 10) High semantic university of some symbols of genetic code indicates deep phylogenetic unity of all existing organisms; 11) Biological sense of structural separateness of the genotype within phenotype is creating and supporting of an information pool undestroyable during ontogenetic development; 12) All and only living systems possess reciprocally determining processes of individual and historic development; 13) Heredity, as an ability of descendants to reproduce safely in their ontogeneses the properties of their ancestors is an integral undecomposable (more exactly, decomposable but for operational purposes) property of the life. There is no and could not be any "heredity substance, as there is no and could not be an "information substance".

Animals↗
PubMed1998

Cytomegalovirus glycoprotein B genotyping in ocular fluids and blood of AIDS patients with cytomegalovirus retinitis.

PURPOSE: To determine the frequency of cytomegalovirus glycoprotein B (gB) genotypes in clinical samples of ocular fluids of patients with acquired immune deficiency syndrome (AIDS) who have cytomegalovirus retinitis and to compare these with the cytomegalovirus gB genotype in paired peripheral blood leukocytes. METHODS: Glycoprotein B genotypes of cytomegalovirus genomic DNA were determined in 29 ocular and 9 paired blood samples of 27 patients, by polymerase chain reaction amplification followed by restriction fragment length polymorphism analysis. RESULTS: In the 29 ocular samples, 30 gB genotypes were determined: Glycoprotein B1 was found in 8 samples (27%), gB2 in 9 samples (30%), gB3 in 6 samples (20%), and gB4 in 3 samples (10%). In one sample, a mixed genotype was observed. In addition to these previously characterized gB genotypes, a new gB variant was observed in the ocular fluid of four patients. Partial sequence analysis revealed that this new gB genotype is closely related to gB3, and it was therefore named gB3'. In the blood samples, only gB1, gB2, and gB3 genotypes were observed. In the nine paired samples of ocular fluid and blood, four showed a difference in gB genotype between these compartments. CONCLUSIONS: The distribution of cytomegalovirus glycoprotein B genotypes gB1-gB4 in ocular fluids of patients with AIDS who have cytomegalovirus retinitis was determined in this study. The predominance of gB2, as described by others, was not confirmed. The glycoprotein B genotype in the eye can be different from the genotype found in the blood of the same patient. A new gB variant, gB3', was found in the ocular samples of 4 of 27 patients, but not in the blood samples tested.

AIDS-Related Opportunistic Infections↗
PubMed1999

Molecular genotyping of HIV-1 in 61 patients with AIDS from Lomé, Togo.

To study the distribution of HIV types and genotypes, in Lomé, Togo, a random population of patients who met the clinical criteria of the Bangui definition of AIDS and were positive with two independent screening assays for antibodies to HIV-1 group M, HIV-2, and HIV-1 group O was selected. HIV RNA from serum samples was reverse-transcribed and amplified with degenerate primers annealing to conserved regions of the HIV-1, HIV-2, and HIV-O gag gene. Amplicons were directly sequenced using an automated sequencer. A 262-271-bp (strain-dependent) fragment of the gag gene from each patient was phylogenetically analyzed and compared to the corresponding gag sequences of published HIV-1 sequences of known African genotypes. Genotype A was found in 48 of 60 patient amplicons (80%), subdivided into two clusters. Ten patients (16.7%) were HIV-1 genotype G; one was genotype D and one genotype H. HIV-1 genotype B was not found. Amplicons from two patients contained sequence ambiguities, requiring cloning and sequencing of the gag insert. One patient (T52) was apparently infected with HIV-1 genotypes A and G; whereas HIV-1 from patient T139 was of genotype A, with 2/10 clones having a three-codon insertion at nucleotide position 1142 of the gag gene. HIV-1 genotype A is dominant in Togo; genotype G is frequent and genotype B has not been found.

Acquired Immunodeficiency Syndrome↗
PubMed2006

Distribution of hepatitis C virus genotypes among hemodialysis patients in Tehran--a multicenter study.

Hepatitis C virus has substantial heterogeneity of genotypes throughout the world. The aim of this study was to determine the frequency of HCV genotypes, risk factors and clinical implications in cases of hemodialysis living in Tehran. A total of 155 patients treated by hemodialysis, who had been identified to be anti-HCV positive at 45 medical centers in Tehran, were enrolled. Genotyping was using restriction fragment length polymorphism (RFLP) on HCV-RNA positive samples. HCV-RNA was detected in 66 (42.6%) patients. Genotyping of HCV-RNA positive serum samples demonstrated that subtypes 3a and 1a were predominant accounting for 30.3 and 28.8%, respectively. The distribution of other HCV genotypes showed genotype 1b, 18.2%; genotype 4, 16.7%; mixed genotypes 1a and 1b, 3%; and genotype 3b, 3%. Genotype 2 was not detected in this study. Statistically significant differences were identified between HCV infected and non-HCV infected patients regarding history of hemodialysis unit changes more than two times (P = 0.01), and history of hemodialysis for more than 20 years (P = 0.02). However, blood transfusion, mean duration of hemodialysis therapy and the history of solid organ transplantation did not differ between these two groups. This study indicates that the dominant HCV genotypes among patients treated by hemodialysis living in Tehran were 3a and 1a, and considering previous reports from the general population, genotype 4 was strongly associated with hemodialysis. The duration of treatment by hemodialysis and, in turn, more hemodialysis unit changes will lead to more frequent HCV infections.

Cross-Sectional Studies↗
PubMed2002

Prevalence of HBV genotypes in asymptomatic carrier residents and their clinical characteristics during long-term follow-up: the relevance to changes in the HBeAg/anti-HBe system.

Randomly selected 50 asymptomatic hepatitis B virus (HBV) carrier residents who had been followed annually were enrolled in this study. The subject group comprised 25 males and 25 females with a mean age at the start of follow-up of 44.1+/-10.4 years. The mean follow-up period was 15.5+/-2.7 years. Genotyping revealed 27 (54%) of genotype B and 23 (46%) of genotype C. The prevalence of genotype B was clearly higher in asymptomatic HBV carrier redidents, which was contrary to the previous reports on chronic liver disease. At the start of follow-up, the ratio of carriers positive for anti-HBe was significantly higher in genotype B than genotype C (P<0.001). Furthermore, the ratio of carriers with reduced HBV-DNA levels was significantly higher in genotype B than genotype C (P<0.01), suggesting that most genotype B carriers had already undergone seroconversion from HBeAg to anti-HBe and were clinically stable at the start of follow-up. The subsequent follow-up observations demonstrated that levels of HBV-DNA and ALT were lower in genotype B than genotype C. Seroconversion from HBeAg to anti-HBe was less likely to occur in genotype C carriers, especially on 40-year-old generation, and these subjects were more likely to develop chronic liver disease.

Journal Article↗
PubMed2025

Human papillomavirus (HPV) genotypes extended prevalence in the female population from a city in Northern Chile.

BACKGROUND: Cervical cancer is primarily associated with the presence of human papillomavirus (HPV), with high-risk genotypes HPV-16 and HPV-18 being the focus of vaccination programs in developing countries such as Chile. Preventive screening for cervical cancer in women aged 25 to 64 years remains centered on cytological techniques and is primarily performed based on clinical suspicion of cervical lesions. However, extended screening for HPV genotypes using DNA amplification methods is not routinely applied to the Chilean female population yet. This study aimed to determine the prevalence of high- and low-risk HPV genotypes in women without known risk factors in a city in northern Chile. METHODS: Cervicovaginal brushing samples were obtained from 390 women from Antofagasta city, Northern Chile, aged between 25 and 64 years; genomic DNA was extracted, and multiplex real-time PCR analysis was used to identify a larger group of high- and low-risk HPV genotypes. RESULTS: Among 390 samples, HPV prevalence was 36.9%, of which 54.9% were high-risk genotypes, 18.7% were low-risk genotypes, and 26.4% showed mixed infection with both high- and low-risk genotypes. High-risk genotypes 16, 58, 39, and 31 were the most frequently identified among HPV-positive samples. Furthermore, a significant association was observed between HPV presence and both age and suspicion of cervical alteration, and women testing positive for other sexually transmitted infections (STIs) were more likely to acquire HPV. CONCLUSIONS: Implementing a screening program that incorporates extended HPV genotyping in Chile, including testing for high-risk genotypes 16, 18, 31, 39, and 58, is crucial to optimize control, early detection, and vaccination efforts for Chilean circulating HPV genotypes that are not covered by the actual vaccine, thus contributing to a more effective reduction in the burden of disease associated with the virus.

Humans↗
PubMed2005

Angiotensin-converting enzyme insertion/deletion genotype, exercise, and physical decline.

CONTEXT: Physical performance in response to exercise appears to be influenced by the angiotensin-converting enzyme (ACE) insertion (I)/deletion (D) genotype in young adults, but whether this relationship could help explain variation in older individuals' response to exercise has not been well studied. OBJECTIVE: To determine whether the ACE genotype interacts with significant physical activity to affect the incidence of mobility limitation in well-functioning older adults. DESIGN, SETTING, AND PARTICIPANTS: The Health Aging and Body Composition (Health ABC) Cohort Study, conducted in the metropolitan areas of Memphis, Tenn, and Pittsburgh, Pa. A total of 3075 well-functioning community-dwelling adults aged 70 through 79 years were enrolled from 1997 to 1998 and had a mean of 4.1 years of follow-up. MAIN OUTCOME MEASURE: Incident mobility limitation defined as the report of difficulty walking a quarter of a mile (0.4 km) or walking up 10 steps on 2 consecutive semiannual interviews (n = 1204). RESULTS: Physically active participants (those reporting expending > or =1000 kcal/wk in exercise, walking, and stair climbing) were less likely to develop mobility limitation regardless of genotype. However, activity level interacted significantly with the ACE genotype (P = .002). In the inactive group, the ACE genotype was not associated with limitation (P = .46). In the active group, those with the II genotype were more likely to develop mobility limitation after adjusting for potential confounders compared with those with ID/DD genotypes (adjusted rate ratio, 1.45, 95% confidence interval, 1.08-1.94). The gene association was especially strong among participants reporting weightlifting. Exploration of possible physiological correlates revealed that among active participants, those with the II genotype had higher percentage of body fat (P = .02) and more intermuscular thigh fat (P = .02) but had similar quadriceps strength as those with ID/DD. CONCLUSIONS: Among older individuals who exercised, those with the ACE DD or ID genotypes were less likely to develop mobility limitation than those with the II genotype. Regardless of genotype, individuals who exercised were less likely to develop mobility limitation than those who did not exercise.

Aged↗
PubMed1996

Distribution of HCV genotypes among blood donors, patients with chronic liver disease, hepatocellular carcinoma, and patients on maintenance hemodialysis in Korea.

Hepatitis C virus (HCV) is a single-stranded RNA virus related to the Flaviviridae family, and striking nucleotide sequence diversity has been reported among HCV isolates from different geographic areas. To study the distribution HCV genotypes among disease group in Korea, we subtyped HCV using the method of Okamoto et al. [(1992a): Journal of General Virology 73:673-679] and the reverse hybridization method (INNO-LiPA) on 138 patients who were HCV polymerase chain reaction (PCR)-positive: 30 blood donors, 30 with hepatocellular carcinoma (HCC), 33 with chronic hepatitis, 15 with liver cirrhosis, and 30 patients on maintenance hemodialysis in Korea. In 30 blood donors, HCV genotype 1b was most dominant (80%), followed by genotype 2a (13.3%), and 2b (6.7%). In 30 HCC cases, HCV genotype 1b was less frequent (60%), compared to blood donors, followed by genotype 2a (33.3%), and unclassified (6.7%). In 33 chronic hepatitis cases, HCV genotype 1b was also dominant (63.6%), followed by genotype 2a (30.3%), and 1a (6.1%). In 15 patients with liver cirrhosis, HCV genotype 1b was also dominant (60%), followed by genotype 2a (33.3%), and 1a (6.7%). In 30 patients on maintenance hemodialysis, HCV genotype 1b was dominant (86.7%), followed by genotype 2a (13.3%). In conclusion, among 138 HCV PCR-positive patients, type 1b was the prevailing type (71%), followed by type 2a (23.9%), type 1a (2.1%), type 2b (1.5%), and unclassified (1.5%) in Korea. The prevalence of type 1b in blood donors (80%) was higher than in patients with liver disease (61.5%) and the prevalence of type 1b was the lowest in patients with HCC (60%).

Base Sequence↗
PubMed2002

Rh genotyping: avoiding false-negative and false-positive results among individuals of African ancestry.

High homology, variant alleles, and silent alleles have made the development of completely reliable genotyping assays for the RHD and RHC alleles difficult. An RHD pseudogene (RHDPsi) possessing a 37-bp insertion within exon 4 is common among serologically RhD-negative individuals of African descent and generates false-positive results in previously reported RhD genotyping assays. Genotyping RhC is problematic due to exon 2 homology between RHD and RHC; however, an RHC-specific 109-bp insertion within intron 2 has been reported useful for genotyping. Primers flanking the exon 4 insertion point were used for detection of RHD and RHDPsi among a total of 231 serotyped individuals: 134 African American, 85 Caucasian, and 12 RhD serotype-negative/genotype-positive, D-sensitized women. Primers flanking the RHC-specific intron 2 insertion were used to genotype 282 serotyped individuals (128 African American, 154 Caucasian) and were compared to RHC genotyping using the exon 1 RhC-specific nt48 cytosine polymorphism. Complete correlation was observed between genotyping with the RHDPsi primer pair and serotyping among 219 individuals and 10/12 previous RHD false-positive genotyping results were resolved. RHDPsi was detected in 19% (n = 4/21) of RhD seronegative African Americans and 4.4% (n = 5/113) of RhD seropositive African Americans. When using the 109-bp intron 2 insertion for genotyping of RHC, a 23.9% (n = 11/46) false-negative rate was observed among African American RhCc serotyped heterozygotes. Utilization of the exon 1 nt48 cytosine for indirect genotyping of RHC yielded a 7.2% (n = 4/55) and 56.3% (n = 45/80) false-positive rate among Rhcc Caucasians and African Americans, respectively. We conclude that these additional reactions, though not sufficient alone, can be useful supplements to existing Rh genotyping assays.

Alleles↗
PubMed2004

Testing for association with a case-parents design in the presence of genotyping errors.

Genotyping errors can create a problem for the analysis of case-parents data because some families will exhibit genotypes that are inconsistent with Mendelian inheritance. The problem with correcting Mendelian inconsistent genotype errors by regenotyping or removing families in which they occur is that the remaining unidentified genotype errors can produce excess type I (false positive) error for some family-based tests for association. We address this problem by developing a likelihood ratio test (LRT) for association in a case-parents design that incorporates nuisance parameters for a general genotype error model. We extend the likelihood approach for a single SNP to include short haplotypes consisting of 2 or 3 SNPs. The extension to haplotypes is based on assumptions of random mating, multiplicative penetrances, and at most a single genotype error per family. For a single SNP, we found, using Monte Carlo simulation, that type I error rate can be controlled for a number of genotype error models at different error rates. Simulation results suggest the same is true for 2 and 3 SNPs. In all cases, power declined with increasing genotyping error rates. In the absence of genotyping errors, power was similar whether nuisance parameters for genotype error were included in the LRT or not. The LRT developed here does not require prior specification of a particular model for genotype errors and it can be readily computed using the EM algorithm. Consequently, this test may be generally useful as a test of association with case-parents data in which Mendelian inconsistent families are observed.

Adult↗
PubMed1995

Hepatitis B virus infection: precore mutants and its relation to viral genotypes and core mutations.

The precore-core gene of hepatitis B virus (HBV) was directly sequenced from serum samples of 42 patients with chronic B hepatitis (19 hepatitis B e antigen [HBeAg]+ and 23 anti-HBE+). Viral genotypes were determined by comparison with 11 reference sequences and by restriction analysis. Genotype A was identified in 16 cases, genotype D in 24 cases, and other genotypes in 2 cases. Precore mutations, mainly M1 (stop at codon 28), were differently distributed among the viral genotypes: 3 cases (18.8%) with genotype A and 18 cases (75%) with genotype D. In sequences with precore mutants, the encapsidation signal was more stable (negative stabilization energy) than in sequences without precore mutants. In genotype A, the M1 mutation coexisted with a second mutation (C-->T at position 1858 in codon 15), and both mutations were paired in the secondary structure of the RNA encapsidation signal, which justified the rare presence of precore mutants in this genotype. The analysis showed different distribution of mutations depending on the viral genotype; patients with genotype D were more likely to have persistent HBV infection by selection of precore mutants. Multiple amino acid substitutions were detected in the core region, mainly in two subsequences that have been previously described as epitopes (flanked by codons 11 to 27 and 74 to 83); the presence of these mutations was significantly related to the presence of precore variants which abolished the expression of HBeAg.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed2005

Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources.

The promise of whole genome amplification (WGA) is that genomic DNA (gDNA) quantity will not limit molecular genetic analyses. Multiple displacement amplification (MDA) and the OmniPlex PCR-based WGA protocols were evaluated using 4 and 5 ng of input gDNA from 60 gDNA samples from three tissue sources (mouthwash, buffy coat, and lymphoblast). WGA DNA (wgaDNA) yield and genotyping performance were evaluated using genotypes determined from gDNA and wgaDNA using the AmpFlSTR Identifiler assay and N = 49 TaqMan SNP assays. Short tandem repeat (STR) and SNP genotyping completion and concordance rates were significantly reduced with wgaDNA from all WGA methods compared with gDNA. OmniPlex wgaDNA exhibited a greater reduction in genotyping performance than MDA wgaDNA. Reduced wgaDNA genotyping performance was due to allelic (all protocols) and locus (OmniPlex) amplification bias leading to heterozygote and locus dropout, respectively, and %GC sequence content (%GC) was significantly correlated with TaqMan assay performance. Lymphoblast wgaDNA exhibited higher yield (OmniPlex), buffy coat wgaDNA exhibited higher STR genotyping completion (MDA), whereas mouthwash wgaDNA exhibited higher SNP genotyping discordance (MDA). Genotyping of wgaDNA generated from < or = 5 ng gDNA, e.g., from archaeological, forensic, prenatal diagnostic, or pathology samples, may require additional genotyping validation with gDNA and/or more sophisticated analysis of genotypes incorporating observed reductions in genotyping performance.

Adult↗