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PubMed2001

African-American heredity prostate cancer study: a model for genetic research.

A genome-wide scan of high-risk prostate cancer families in North America has demonstrated linkage of a particular marker to Chromosome 1q (HPC1). An even greater proportion of African-American families have shown linkage to HPC1. Therefore, investigators at the National Human Genome Research Institute (NHGRI) in collaboration with Howard University and a predominantly African-American group of urologists established the African-American Hereditary Prostate Cancer (AAHPC) Study Network to confirm the suggested linkage of HPC in African Americans with a gene on Chromosome 1. Blood samples from recruited families were sent to Howard University for extraction of DNA. The DNA was sent to NHGRI at NIH where the genotyping and genetic sequence analysis was conducted. Genotype data are merged with pedigree information so that statistical analysis can be performed to establish potential linkage. From March 1, 1998, to June 1, 1999, a total of 40 African-American families have been recruited who met the study criteria. Preliminary results suggest that racial/ethnicity grouping may affect the incidence and extent of linkage of prostate cancer to specific loci. The importance of these findings lays in the future treatment of genetic-based diseases.

Aged↗
PubMed2003

High rate of resistance to antiretroviral drugs among HIV-infected prison inmates.

BACKGROUND: Resistance to antiretroviral (ARV) drugs represents a major obstacle to the success of HIV therapy. The aim of the study was to examine the prevalence of genotypic resistance to ARV drugs in a large group of HIV-infected individuals incarcerated in penal facilities. MATERIAL/METHODS: We analyzed the reverse transcriptase and protease genes on plasma samples collected from 309 HIV-infected prison inmates in Madrid. In order to compare the prevalence of resistance at different periods and detect any trend over time, half of the samples from ARV-naive and half from pre-treated subjects were randomly collected in 1999 and in 2001. RESULTS: Overall, 63.7% of specimens harbored plasma HIV-RNA above 1000 copies/ml. Genotypic data were obtained in 94.4% of them. Primary resistance mutations among 127 drug-naive subjects were recognized in 13% in 1999 vs. 15% in 2001. In contrast, drug resistance was found in 35% and 59% of 182 pre-treated subjects in 1999 and 2001. CONCLUSIONS: Drug resistance has increased over the last two years among inmates on ARV drugs and currently affects 59% of those failing treatment. A nearly 3-fold increase has been noticed for NNRTI resistance. In comparison with HIV-positive subjects outside jail on ARV drugs, prisoners are more likely to experience virological failure, but show a lower rate of drug resistance; this affects particularly drugs with a low genetic barrier (i.e. NNRTI and 3TC).

Anti-HIV Agents↗
PubMed1992

Presymptomatic identification of carriers of the multiple endocrine neoplasia type 2A gene using flanking DNA markers.

BACKGROUND: Because the predisposition locus for multiple endocrine neoplasia type 2A (MEN2A) has been mapped to chromosome 10 by genetic linkage analysis, it has become possible to identify gene carriers by following the transmission of linked genetic markers from affected parents to offspring at risk for MEN2A. We have applied a highly accurate genetic test to presymptomatic diagnosis of gene carriers in several large kindreds with MEN2A. METHODS: DNA was extracted from 300 individuals in six kindreds with MEN2A and used for genotyping studies with DNA markers flanking the MEN2A locus. Genotype data were used to predict the inheritance of the MEN2A gene in kindred members at risk according to previously calculated map distances and the program LINKAGE: RESULTS: Ninety-five percent of individuals were informative with markers flanking the MEN2A locus. Of 130 patients at risk, 26 (20%) were predicted to be MEN2A gene carriers, 100% (77%) were noncarriers, and 4 (3%) were recombinant and their gene carrier status could not be determined. Gene carrier prediction probabilities were calculated at greater than 98% in 94% of these patients. CONCLUSIONS: We conclude that genetic testing with flanking DNA markers is a highly accurate method for the presymptomatic identification of MEN2A gene carriers and allows for diagnosis at an earlier stage than does traditional calcitonin testing.

Chromosomes, Human, Pair 10↗
PubMed2003

The development of reduced size STR amplicons as tools for analysis of degraded DNA.

New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

Blotting, Southern↗
PubMed2003

[Paternity assignment of giant panda by microsatellite genotyping].

We used genotype data across 18 microsatellite loci to establish the paternity of giant panda cubs at the Chengdu Zoo and the Chengdu Research Base of Giant Panda Breeding. The results demonstrate that the combined exclusion probability using these 18 microsatellite loci is 0.999921 while confidence is 95 % when the mother is known; if mother is unknown then the exclusion probability is 0.994109, but the confidence of this is less than 80%. Since the mother-offspring relationship is known in captive populations, the results could resolve unknown paternities in the Chengdu ex situ populations. However, to establish accurately the genetic relationships of wild giant pandas,more microsatellite loci may be required.

English Abstract↗
PubMed2005

Abdominal pigmentation variation in drosophila polymorpha: geographic variation in the trait, and underlying phylogeography.

Drosophila polymorpha is a widespread species that exhibits abdominal pigmentation variation throughout its range. To gain insight into this variation we combined phenotypic and genotypic data to test a series of nested hypotheses. First, we tested the null hypothesis that geographic variation in pigmentation is due to neutral factors. We used nested clade analysis to examine the distribution of haplotypes from a nuclear and a mitochrondrial locus. Restricted gene flow via isolation by distance, the primary inference of this phylogeographic analysis, was then used to generate and test the hypothesis of increasing average abdominal pigmentation difference with increasing geographic distance. We found no correlation between geographic distance and phenotypic distance. We then tested the hypothesis that pigmentation is affected by environmental differences among localities. We found a significant effect of habitat type on the average abdominal pigmentation phenotype of different localities. Finally, we tested the hypothesis that pigmentation in D. polymorpha is associated with desiccation resistance. We found that dark individuals of both sexes survived significantly longer in a desiccating environment than light individuals. These patterns combined lead us to hypothesize that abdominal pigmentation variation in D. polymorpha is important in mediating the organism's interactions with local ecological factors.

Abdomen↗
PubMedDate not supplied

HIV and hepatitis C virus coinfection: bad bedfellows.

Hepatitis C virus (HCV) infection is common in HIV-infected individuals and is responsible for increasing morbidity in these patients. HIV infection increases HCV replication and accelerates progression of HCV disease. HCV infection increases the risk of antiretroviral treatment. HCV genotype 1 is the predominant genotype in HCV/HIV-coinfected individuals living in the United States. State-of-the-art treatment with peginterferon alfa plus ribavirin results in lower sustained HCV virologic response rates in patients with genotype 1 infection than in those infected with other genotypes. Data from studies of HCV infection treatment in coinfected patients are discussed, as are prospects for future therapy. This article summarizes a presentation on HIV/HCV coinfection by Robert T. Schooley, MD, at the International AIDS Society-USA course in San Francisco in June 2005.

Antiviral Agents↗
PubMed2005

Sex-limited genome-wide linkage scan for body mass index in an unselected sample of 933 Australian twin families.

Genes involved in pathways regulating body weight may operate differently in men and women. To determine whether sex-limited genes influence the obesity-related phenotype body mass index (BMI), we have conducted a general nonscalar sex-limited genome-wide linkage scan using variance components analysis in Mx (Neale, 2002). BMI measurements and genotypic data were available for 2053 Australian female and male adult twins and their siblings from 933 families. Clinical measures of BMI were available for 64.4% of these individuals, while only self-reported measures were available for the remaining participants. The mean age of participants was 39.0 years of age (SD 12.1 years). The use of a sex-limited linkage model identified areas on the genome where quantitative trait loci (QTL) effects differ between the sexes, particularly on chromosome 8 and 20, providing us with evidence that some of the genes responsible for BMI may have different effects in men and women. Our highest linkage peak was observed at 12q24 (-log10p = 3.02), which was near the recommended threshold for suggestive linkage (-log10p = 3.13). Previous studies have found evidence for a quantitative trait locus on 12q24 affecting BMI in a wide range of populations, and candidate genes for noninsulin-dependent diabetes mellitus, a consequence of obesity, have also been mapped to this region. We also identified many peaks near a -log10p of 2 (threshold for replicating an existing finding) in many areas across the genome that are within regions previously identified by other studies, as well as in locations that harbor genes known to influence weight regulation.

Body Mass Index↗
PubMed2006

[HLA-B gene polymorphism detected by high-resolution sequence-based typing in Guangdong Han populations].

OBJECTIVE: To investigate the genetic polymorphism of HLA-B locus in Guangdong Han population and compare the characteristic of the allele frequency distribution with that in other populations. METHODS: A total of 562 cord blood samples from Guangzhou Cord Blood Bank were analyzed by sequence-based typing. Then the sequences encompassing exons 2, 3, and 4 for HLA-B gene were analyzed by direct sequencing of PCR products. The allele frequency distribution of HLA-B in this population was compared with that in other populations. RESULTS: A total of 59 different HLA-B alleles were detected, and among them were 6 HLA-B alleles with frequencies higher than 5%: HLA-B*4601 (14.5%), HLA-B*400101 (14.4%), HLA-B*1502 (11.5%), HLA-B*1301 (8.6%), HLA-B*5801 (8.1%) and HLA-B*380201 (6.4%); the total frequency of these six alleles was 63.5%. At the same time, there were 30 kinds of HLA-B allele with frequencies lower than 0.5%; the total frequency of these alleles was 4.9%. Maximum variation at HLA-B was seen in the HLA-B*15 allele family (nine alleles). Comparison of the HLA-B frequencies in different populations showed a close relationship of Guandong Han population with the Chinese populations from Hong Kong and Singapore, respectively. CONCLUSION: The results have shown the characteristic of HLA-B distribution and provided more accurate genotypic data that may serve as normal reference value for the Han population in Guangdong, China.

Asian People↗
PubMed2005

[Integration of pharmacogenetics in the medical practice].

Today, the initiation of any medical treatment still raises questions about its efficacy and safety. Indeed, therapeutic responses vary over time and between individuals and are influenced by age, sex, other treatments and the pathology itself. Genetic factors are thought to be responsible for 20 to 95% of these individual variations. Recent advances in biotechnology, molecular genetics and genomics allow a better understanding of drug metabolism and action. Pharmacogenetics, compiling phenotypic and genotypic data, may lead to a more personalized treatment. To allow a better approach of pharmacogenetics and pharmacogenomics, we will define these two terms and describe their actual and future clinical application.

Drug Design↗
PubMed1991

A detailed multipoint map of human chromosome 4 provides evidence for linkage heterogeneity and position-specific recombination rates.

Utilizing the CEPH reference panel and genotypic data for 53 markers, we have constructed a 20-locus multipoint genetic map of human chromosome 4. New RFLPs are reported for four loci. The map integrates a high-resolution genetic map of 4p16 into a continuous map extending to 4q31 and an unlinked cluster of three loci at 4q35. The 20 linked markers form a continuous linkage group of 152 cM in males and 202 cM in females. Likely genetic locations are provided for 25 polymorphic anonymous sequences and 28 gene-specific RFLPs. The map was constructed employing the LINKAGE and CRIMAP computational methodologies to build the multipoint map via a stepwise algorithm. A detailed 10-point map of the 4p16 region constructed from the CEPH panel provides evidence for heterogeneity in the linkage maps constructed from families segregating for Huntington disease (HD). It additionally provides evidence for position-specific recombination frequencies in the telomeric region of 4p.

Chromosome Mapping↗
PubMed2006

[Genetic polymorphism of 23 Y chromosome biallelic markers in Wuhan Han population].

To search polymorphic Y chromosome biallelic markers in Chinese Han population, and obtain their population genetic data. Genotyping of 23 biallelic markers on human Y chromosome (M7, M9, M50, M88, M89, M95, M111, M117, M119, M121, M122, M134, M159, M164, M175, M214, LINE1, MSY2, RPS4Y711, SRY465, IMS-JST164520, IMS-JST021354 and IMS-JST003305) were carried out in a sample of 160 unrelated Chinese male individuals living in Wuhan using fragment length discrepant allele specific PCR (FLDAS-PCR) and PAGE technique. In all 23 biallelic markers, genetic polymorphism were identified for 20 loci in Wuhan Han population except for M50, M159 and M164, and the ranges of gene diversity (GD) were 0.0126-0.4855. A total of 35 different haplogroups (Hg1-35) were observed and the haplogroup diversity (HD) was 0.9471. The haplogroups formed by 20 biallelic markers are highly polymorphic, and can be used in forensic science and population evolution studies.

Alleles↗
PubMed1988

A genetic linkage map of 27 loci from PND to FY on the short arm of human chromosome I.

A genetic linkage map of 27 loci on the short arm of human chromosome 1 has been developed by analysis of the 40 families in the Centre d'Etude du Polymorphisme Humain (CEPH) reference panel. Probes that recognize 14 novel RFLPs at loci designated D1S9-D1S22 were isolated from a flow-sorted chromosome 1 library. A linkage map of chromosome 1p was constructed from the genotypic data at these 14 loci, RFLPs at eight cloned genes (PND, ALPL, FUCA1, SRC2, MYCL, GLUT, TSHB, and NGFB), two previously identified RFLPs (D1S2 and D1S57), two blood group antigens (RH and FY), and the isozyme PGM1. All 27 loci form a continuous linkage group, from FY to PND, of 102 cM in males and 230 cM in females. This map provides a basis for highly informative multipoint mapping studies for most of the short arm of chromosome 1.

Animals↗
PubMed1993

An index marker map of chromosome 9 provides strong evidence for positive interference.

An index marker map of chromosome 9 has been constructed using the Centre d'Etude du Polymorphisme Humain reference pedigrees. The map comprises 26 markers, with a maximum intermarker interval of 13.1 cM and only two intervals > 10 cM. Placement of all but one marker into the map was achieved with > 10,000:1 odds. The sex-equal length is 151 cM, with male length of 121 cM and female length of 185 cM. The map extends to within 2%-3% of physical length at the telomeres, and its coverage therefore is expected to be within 20-30 cM of full map length. The markers are all of the GT/CA repeat type and have average heterozygosity .77, with a range of .60-.89. The map shows both marked contraction of genetic distance relative to physical distance in the pericentromeric region and expansion in the telomeric regions. Genotypic data were carefully examined for errors by using the crossover routine of the program DATAMAN. Five new mutations were observed among 17,316 meiotic events examined. There were two double-crossover events occurring within an interval of 0-10 cM, and another eight were observed within an interval of 10-20 cM. Many of these could be due to additional mutational events in which one parental allele converted to the other by either gene conversion or random strand slippage. When there was no correction for these possible mutational events, the number of crossovers displayed by the maternal and paternal chromosomes was significantly different (P < .001) from that predicted by the Poisson distribution, which would be expected in the absence of interference. In addition, the observed crossover distribution for paternally derived chromosomes was similar to that predicted from cytogenetic chiasma frequency observations. In all, the data strongly support the occurrence of strong positive interference on human chromosome 9 and suggest that flanking markers at an interval of < or = 20 cM are generally sufficient for disease gene inheritance predictions in presymptomatic genetic counseling by linkage analysis.

Base Sequence↗
PubMed1995

Absence of genetic linkage between polymorphisms of the insulin receptor gene and essential hypertension.

This study evaluated whether hypertensive siblings had excess sharing of RsaI and SstI alleles of the insulin receptor gene compared with a random population. Thirty families consisting of 60 affected individuals with established hypertension were genotyped for the RsaI and SstI restriction fragment length polymorphisms and the resulting genotype data was analysed using the affected pedigree member method of linkage analysis. The hypertensive siblings were found to have increased sharing of INSR alleles; however, this linkage could not be confirmed using a maximum LOD score method. Thus, the results from this study do not support a role for the INSR gene in the genesis of essential hypertension in the population studied.

Aged↗
PubMed1995

Drug-resistance patterns of saquinavir and other HIV proteinase inhibitors.

AIM: To review available drug-resistance patterns of HIV proteinase inhibitors, in particular saquinavir (formerly known as Ro 31-8959), focusing on the implications for disease management. RESULTS: Reduced sensitivity to saquinavir appears to develop slowly and at low frequency even during prolonged therapy, with an incidence of approximately 45% in 1 year of monotherapy. This reduced sensitivity is consistently associated with the presence of two independent mutations in the proteinase gene, glycine-->valine at position 48 and leucine-->methionine at position 90, with the latter predominating in vivo. Double mutants are rare, with a reported incidence of approximately 2% to date. There is no evidence that the incidence of resistance to saquinavir is increased at doses two to four times higher than those used in clinical studies. In fact, the opposite may be true. The incidence of zidovudine resistance is decreased during combination therapy with saquinavir compared to that during monotherapy, while the incidence of resistance to saquinavir is decreased by combination with zidovudine and zalcitabine. CROSS-RESISTANCE: According to the available genotype data, treatment with saquinavir is not associated with mutations at codons 46, 63 and 82, which are reported to induce cross-resistance to many other proteinase inhibitors. Saquinavir may be associated with mutations at position 84, but very rarely. CONCLUSIONS: Saquinavir appears to be well-suited to first-line monotherapy or combination therapy without prejudicing subsequent or concurrent use of other proteinase inhibitors not affected by mutations at codons 48 and 90.

Acquired Immunodeficiency Syndrome↗
PubMed1997

The role of preoperative factor V Leiden screening in different geographic populations.

Patients harboring a specific mutation in the coagulation factor V gene have been identified as being at significantly increased risk for venous thrombosis. A simple genetic test that identifies carriers of this mutation (the factor V Leiden allele) is available and may have utility in various clinical settings, including preoperative risk assessment for thromboembolic complications. In this regard, it is generally agreed that prospective studies addressing the role of preoperative factor V Leiden mutational analysis are needed to clearly define the clinical prognostic/diagnostic significance of the presence of this mutation in surgical patients. This report questions the role that population dynamics (genetic and environmental backgrounds of individual populations) plays in the analysis of factor V genotypic data in relation to postsurgical thromboembolic complications. We have determined that the frequency of individuals carrying the factor V Leiden allele is 7.9 per cent for our South Central Pennsylvania population (395 wild type, 32 heterozygotes, 2 homozygotes) using a polymerase chain reaction-restriction fragment length polymorphism technique that specifically detects the factor V Leiden mutation. This baseline population information is useful from both a clinical and a basic science viewpoint. However, considering the various unknown genetic and environmental differences between geographically distinct populations, the significance of this result, in terms of clinical management of our surgical patients, is yet to be determined.

Factor V↗