p53 Pro72Arg polymorphism and prostate cancer in men of African descent

BACKGROUND

p53 is a transcription factor that regulates the cell cycle, DNA repair, and apoptosis. A variant at codon 72, rs1042522, results in altered activities for p53 and is, notably, differentially distributed among different ethnic populations. However, associations of this variant with cancer in men of African descent have not been explored. Herein, we tested the hypothesis that rs1042522 was associated with prostate cancer (PCa) risk.

MATERIALS AND METHODS

Genotypes were determined by PCR-RFLP methods in a study population of African descent consisting of 266 PCa patients and 196 male controls.

RESULTS

Our results indicate that the p53 polymorphism may be associated with increased risk of PCa. Genotypes were significantly and marginally associated with PCa risk using the dominant and log-additive genetic models (OR=1.53, 95% CI: 1.02-2.29, P=0.04; OR=1.33, 95% CI: 0.99-1.78, P=0.06, respectively). After adjusting for age, the associations with PCa remained, but results were not statistically significant (OR=1.48, 95% CI: 0.95-2.31, P=0.08; OR=1.30, 95% CI: 0.95-1.80, P=0.10, respectively).

CONCLUSIONS

The present study demonstrates that population-dependent differences in allele frequencies associated with health disparities provide a valuable framework for the interrogation of complex diseases in all populations.

Agouti-related protein promoter variant associated with leanness and decreased risk for diabetes in West Africans

OBJECTIVE

The role of the central melanocortin system in the development of obesity has been extensively studied. Single-nucleotide polymorphisms (SNPs) within several candidate genes have been associated with food intake and obesity-related phenotypes; however, few of these associations have been replicated. SNPs in the agouti-related protein (AGRP) gene coding (Ala67Thr, 199G/A) and promoter (-38C/T) have been reported to be associated with body mass index (BMI), fat mass (FM) and percent body fat, in populations of European and African descent. In this study, we evaluated the association between the functional AGRP -38C/T promoter SNP and weight-related traits, namely BMI, FM and fat-free mass (FFM), as well as diabetes status.

DESIGN

An association study of the AGRP -38C/T SNP and indices of obesity and diabetes status.

SUBJECTS

A well-characterized population of 538 West Africans from Ghana and Nigeria recruited in the AADM (Africa America Diabetes Mellitus) study (mean age 52 years, 41.3% males, 71% diabetic).

MEASUREMENTS

Genotyping of the AGRP -38C/T SNP, BMI, FM, FFM and fasting plasma glucose.

RESULTS

Women carrying two copies of the variant T allele had significantly lower BMI (OR=0.47; 95% CI, 0.25-0.87). Also, men with at least one copy of the variant T allele were over two times less likely to be diabetic than other men (OR=0.44; 95% CI, 0.22-0.89).

CONCLUSION

Our results replicate previous findings and implicate the AGRP -38C/T SNP in the regulation of body weight in West Africans.

A genome-wide scan for quantitative trait loci linked to obesity phenotypes among West Africans

OBJECTIVE

To identify quantitative trait loci (QTL) for three obesity phenotypes: body mass index (BMI), fat mass (FM) and percent body fat (PBF) in West Africans with type 2 diabetes (T2DM).

DESIGN

An affected sibling pair (ASP) design, in which both siblings had T2DM. Obesity was analyzed as a quantitative trait using a variance components approach.

SUBJECTS

Sib-pairs affected with T2DM from the Africa America Diabetes Mellitus (AADM) study, comprising 321 sibling pairs and 36 half-sibling pairs.

MEASUREMENTS

Weight was measured on an electronic scale to the nearest 0.1 kg, and height was measured with a stadiometer to the nearest 0.1 cm. Body composition was estimated using bioelectric impedance analysis (BIA). Genotyping was carried out at the Center for Inherited Disease Research (CIDR) with a panel of 390 trinucleotide and tetranucleotide repeats.

RESULTS

The obesity-related phenotype showing the strongest linkage evidence was PBF on chromosome 2 (LOD 3.30 at 72.6 cM, marker D2S739). Suggestive linkage to FM was found on chromosomes 2 (LOD 2.56 at 80.4 cM) and 5 (LOD 2.25 at 98 cM, marker D5S1725). The highest LOD score for BMI was 1.68 (chromosome 4, 113.8 cM). The areas of linkage for the three phenotypes showed some clustering as all three phenotypes were linked to the same regions of 2p13 and 5q14, and our study replicated linkage evidence for several regions previously reported in other studies.

CONCLUSION

We obtained evidence for several QTLs on chromosome 2, 4 and 5 to three obesity phenotypes. This study provides data on the genetics of obesity in populations that are currently under represented in the global effort directed at understanding the pathophysiology of excess adiposity in free living individuals.

Conceptualizing human variation

What is the relationship between the patterns of biological and sociocultural variation in extant humans? Is this relationship accurately described, or best explained, by the term 'race' and the schema of 'racial' classification? What is the relationship between 'race', genetics and the demographic groups of society? Can extant humans be categorized into units that can scientifically be called 'races'? These questions underlie the discussions that address the explanations for the observed differences in many domains between named demographic groups across societies. These domains include disease incidence and prevalence and other variables studied by biologists and social scientists. Here, we offer a perspective on understanding human variation by exploring the meaning and use of the term 'race' and its relationship to a range of data. The quest is for a more useful approach with which to understand human biological variation, one that may provide better research designs and inform public policy.

Ethnic differences in asthma and associated phenotypes: collaborative study on the genetics of asthma

BACKGROUND

In the Collaborative Study on the Genetics of Asthma, 314 families with 2584 subjects were characterized for asthma and allergy.

OBJECTIVE

The purpose of this investigation was to examine clinical heterogeneity observed in asthma and allergic characteristics among 3 ethnic groups (African American, white, and Hispanic family members).

METHODS

Pulmonary function parameters and asthma associated phenotypes were compared among the ethnic groups.

RESULTS

In comparison with the other groups, African American sibling pairs had a significantly lower baseline FEV(1) percent of predicted (P =.0001) and a higher rate of skin test reactivity to cockroach allergen (P =.0001); Hispanic sibling pairs had significantly more skin reactivity overall (P =.001); and white sibling pairs had significantly lower total serum IgE (P <.05). In addition, there were significantly more relatives with asthma among the African American families than among the white and the Hispanic families (P =.001).

CONCLUSION

Although different environmental backgrounds should be considered, these clinical differences could be due to differences in genetic susceptibility among the ethnic groups, such as those suggested by our previous genome screen.

Extent of linkage disequilibrium between the androgen receptor gene CAG and GGC repeats in human populations: implications for prostate cancer risk

While studies have implicated alleles at the CAG and GGC trinucleotide repeats of the androgen receptor gene with high-grade, aggressive prostate cancer disease, little is known about the normal range of variation for these two loci, which are separated by about 1.1 kb. More importantly, few data exist on the extent of linkage disequilibrium (LD) between the two loci in different human populations. Here we present data on CAG and GGC allelic variation and LD in six diverse populations. Alleles at the CAG and GGC repeat loci of the androgen receptor were typed in over 1000 chromosomes from Africa, Asia, and North America. Levels of linkage disequilibrium between the two loci were compared between populations. Haplotype variation and diversity were estimated for each population. Our results reveal that populations of African descent possess significantly shorter alleles for the two loci than non-African populations (P<0.0001). Allelic diversity for both markers was higher among African Americans than any other population, including indigenous Africans from Sierra Leone and Nigeria. Analysis of molecular variance revealed that approx. 20% of CAG and GGC repeat variance could be attributed to differences between the populations. All non-African populations possessed the same common haplotype while the three populations of African descent possessed three divergent common haplotypes. Significant LD was observed in our sample of healthy African Americans. The LD observed in the African American population may be due to several reasons; recent migration of African Americans from diverse rural communities following urbanization, recurrent gene flow from diverse West African populations, and admixture with European Americans. This study represents the largest genotyping effort to be performed on the two androgen receptor trinucleotide repeat loci in diverse human populations.

Cyp17 promoter variant associated with prostate cancer aggressiveness in African Americans

Androgens play an important role in the etiology of prostate cancer. The CYP17 gene encodes the cytochrome P450c17alpha enzyme, which is the rate-limiting enzyme in androgen biosynthesis. A T to C polymorphism in the 5' promoter region has recently been associated with prostate cancer. However, contradictory data exists concerning the risk allele. To investigate further the involvement of the CYP17 variant with prostate cancer, we typed the polymorphism in three different populations and evaluated its association with prostate cancer and clinical presentation in African Americans. We genotyped the CYP17 polymorphism in Nigerian (n = 56), European-American (n = 74), and African-American (n = 111) healthy male volunteers, along with African-American men affected with prostate cancer (n = 71), using pyrosequencing. Genotype and allele frequencies did not differ significantly across the different control populations. African-American men with the CC CYP17 genotype had an increased risk of prostate cancer (odds ratio, 2.8; 95% confidence interval, 1.0-7.4) compared with those with the TT genotype. A similar trend was observed between the homozygous variant genotype in African-American prostate cancer patients and clinical presentation. The CC genotype was significantly associated with higher grade and stage of prostate cancer (odds ratio, 7.1; 95% confidence interval, 1.4-36.1). The risk did not differ significantly by family history or age. Our results suggest that the C allele of the CYP17 polymorphism is significantly associated with increased prostate cancer risk and clinically advanced disease in African Americans.

Genome-wide linkage analyses of total serum IgE using variance components analysis in asthmatic families

Variance components models were used to analyze total IgE levels in families ascertained though the Collaborative Study of the Genetics of Asthma (CSGA) using a genome-wide array of polymorphic markers. While IgE levels are known to be associated with clinical asthma and recognized to be under strong genetic control (here the heritability was estimated at 44-60% in the three racial groups), specific genes influencing this trait are still largely unknown. Multipoint analysis of 323 markers yielded little indication of specific regions containing a trait locus controlling total serum IgE levels (adjusted for age and gender). Although a number of regions showed LOD statistics above 1.5 in Caucasian families (chromosome 4) and in African-American families (chromosomes 2 and 4), none yielded consistent evidence in all three racial groups. Analysis of total IgE adjusted for gender, age and Allergy Index (a quantitative score of skin test sensitivity to 14 common aeroallergens) was conducted on these data. In this analysis, a much stronger signal for a trait locus controlling adjusted log[total IgE] was seen on the telomeric end of chromosome 18, but only in Caucasian families. This region accounted for most of the genetic variation in log[total IgE], and may represent a quantitative trait locus for IgE levels independent of atopic response. Oligogenic analysis accounting simultaneously for the contribution of this locus on chromosome 18 and other chromosomal regions showing some evidence of linkage in these Caucasian families (on chromosomes 2, 4 and 20) failed to yield significant evidence for interaction.

In search of susceptibility genes for type 2 diabetes in West Africa: the design and results of the first phase of the AADM study

PURPOSE

The purpose of this study is to map type 2 diabetes susceptibility genes in West African ancestral populations of African-Americans, through an international collaboration between West African and US investigators.

DESIGN AND METHODS

Affected sib-pairs (ASP) along with unaffected spouse controls are being enrolled and examined in West Africa, with two sites established in Ghana (Accra and Kumasi) and three in Nigeria (Enugu, Ibadan, and Lagos). Eligible participants are invited to study clinics to obtain detailed epidemiologic, family, and medical history information. Blood samples are drawn from each participant to measure glucose, insulin, C-peptide, total cholesterol, LDL, HDL, triglycerides, albumin, creatinine, urea, uric acid, total calcium and to detect autoantibodies to glutamic acid decarboxylase (GAD). DNA is isolated from frozen white blood cells obtained from 20 ml of EDTA whole blood samples.

RESULTS

With full informed consent, 162 individuals from 78 families have been enrolled and examined since the Africa America Diabetes Mellitus (AADM) study began in June of 1997. Logistics of field examinations and specimen shipping have been successfully established. At the end of the third year of field activity (September 2000) the AADM study will have enrolled and performed comprehensive examination on 400 ASP with type 2 diabetes, for a minimum of 800 cases and 200 controls from Ghana and Nigeria. At the current participation rate, the goal of 400 sib-pairs and 200 controls will be met before the scheduled closing date.

CONCLUSIONS

The AADM study will create a comprehensive epidemiologic and genetic resource that will facilitate a powerful genome-wide search for West African susceptibility genes to type 2 diabetes.

Early age of disease onset in African American type 1 diabetes patients is associated with DQB1*0201 allele

The goal of this study is to assess the association of HLA-DQ alleles with the age of onset of type 1 diabetes in African American patients. Using PCR oligonucleotide typing, HLA-DQA1 and DQB1 alleles were determined. DQA1*0301, DQB1*0201, and DQB1*0302 were significantly increased in African American patients. However, the DQB1*0602 allele was decreased in these patients. In addition, DQA1*0401 and DQB1*0402, were associated with protection in African Americans. When stratified by age of onset, prepubertal patients showed an absence of the protective allele DQB1*0602 and a significant increase in DQB1*0201 compared to postpubertal patients. The high frequency of the HLA-DQ susceptibility allele in pre-pubertal patients suggest that the biology of disease in this group may differ from type 1 diabetes with a later age of onset.

BRCA1 mutations in African Americans

The breast cancer predisposing gene, BRCA1, was analyzed for germline mutations in 45 African American families at high-risk for hereditary breast cancer. Patients were considered high-risk if they had a family history of the disease, early onset breast cancer, bilateral breast cancer, or breast and ovarian cancer. The entire BRCA1 coding and flanking intron regions have been examined by single stranded conformation polymorphism analysis followed by sequencing of variant bands. Eleven different BRCA1 germline mutations/variations were identified in 7 patients from the 45 high-risk families. Two pathogenic, protein-truncating mutations were detected in exon 11. A ten base pair tandem duplication, 943ins10, was present in a woman with breast and ovarian cancer whose first-degree relatives had prostate cancer. A four base pair deletion, 3450del4, was detected in a breast cancer patient with five cases of breast cancer in the family; two of the proband's sisters with breast cancer also carried the same mutation. Four amino acid substitutions (Lys1183Arg, Leu1564Pro, Gln1785His, and Glu1794Asp) and four nucleotide substitutions in intron 22 (IVS22+78 C/A, IVS22+67 T/C, IVS22+8 T/A and IVS22+7 T/C) were observed in patients and not in control subjects. One early onset breast cancer patient carried five distinct BRCA1 variations, two amino acid substitutions and three substitutions in intron 22. An amino acid substitution in exon 11, Ser1140Gly, was identified in 3 different unrelated patients and in 6 of 92 control samples. The latter probably represents a benign polymorphism.

Genetic regulation of Dermatophagoides pteronyssinus-specific IgE responsiveness: a genome-wide multipoint linkage analysis in families recruited through 2 asthmatic sibs. Collaborative Study on the Genetics of Asthma (CSGA)

BACKGROUND

Dermatophagoides pteronyssinus (Der p) is one of the most frequently implicated allergens in atopic diseases. Although HLA could play an important role in the development of the IgE response to the Der p allergens, genetic regulation by non-HLA genes influences certain HLA-associated IgE responses to complex allergens.

OBJECTIVE

To clarify genetic control for the expression of Der p-specific IgE responsiveness, we conducted a genome-wide search for genes influencing Der p-specific IgE antibody levels by using 45 Caucasian and 53 African American families ascertained as part of the Collaborative Study on the Genetics of Asthma (CSGA).

METHODS

Specific IgE antibody levels to the Der p crude allergen and to the purified allergens Der p 1 and Der p 2 were measured. Multipoint, nonparametric linkage analysis of 370 polymorphic markers was performed with the GENEHUNTER program.

RESULTS

The best evidence of genes controlling specific IgE response to Der p was obtained in 2 novel regions: chromosomes 2q21-q23 (P = .0033 for Caucasian subjects) and 8p23-p21 (P = .0011 for African American subjects). Three regions previously proposed as candidate regions for atopy, total IgE, or asthma also showed evidence for linkage to Der p-specific IgE responsiveness: 6p21 (P = .0064) and 13q32-q34 (P = 0.0064) in Caucasian subjects and 5q23-q33 (P = 0.0071) in African American subjects.

CONCLUSIONS

No single locus generated overwhelming evidence for linkage in terms of established criteria and guidelines for a genome-wide screening, which supports previous assertions of a heterogeneous etiology for Der p-specific IgE responsiveness. Two novel regions, 2q21-q23 and 8p23-p21, that were identified in this study merit additional study.

Genetic influences of chromosomes 5q31-q33 and 11q13 on specific IgE responsiveness to common inhaled allergens among African American families. Collaborative Study on the Genetics of Asthma (CSGA)

BACKGROUND

We have recently conducted a genome-wide screening for genes influencing Dermatophagoides pteronyssinus-specific IgE responsiveness as a part of the Collaborative Study on the Genetics of Asthma (CSGA), which showed evidence for linkage in some regions, including chromosomes 5131-q33 and 11q13 in African American families.

OBJECTIVES

To clarify relative contributions of these regions to atopy in the same African American population, we have conducted further genetic linkage studies of specific IgE responses toward common inhaled allergens.

METHODS

We studied 328 individuals in 58 African American families participating in the CSGA. Specific IgE responses toward Dermatophagoides farinae, cat, dog, American cockroach, rye grass, and Bermuda grass, as measured by skin tests, were used for multipoint linkage analysis with polymorphic markers on chromosomes 5q31-q33 and 11q13.

RESULTS

Specific IgE response toward American cockroach showed evidence for linkage to chromosomes 5q31-q33 (P = .0050) and 11q13 (P = .017). Specific IgE response toward dog showed evidence for linkage with chromosome 5q31-q33 (P = .0043). Evidence for linkage with chromosome 11q13 was obtained for specific IgE responses toward Dermatophagoides farinae (P = .012), cat (P = .035), and Bermuda grass (P = .017). The presence of a positive ST response for at least 1 of 30 common allergens showed evidence for linkage to chromosomes 5q31-q33 (P = .017) and 11q13 (P = .00058).

CONCLUSIONS

These data support that genes on both chromosomes 5q31-q33 and 11q13 confer susceptibility to upregulated IgE-mediated immune responses in this African American population. The putative genes on chromosomes 5q31-q33 and 11q13, however, showed contrasting effects on atopy, which may result from strong gene-environmental interactions.

Plasma lipid alterations in African-American women with breast cancer

The purpose of this study was to examine the relationship between plasma lipid and lipoprotein levels, stage of disease and breast cancer risk in African-American women. The study population comprised 163 African-American women: patients (n = 58) and controls (n = 105), with mean ages of 57.2 years and 47.7 years respectively. Approximately 71% and 56% of the women with breast cancer and the control population, respectively, were postmenopausal. Those with cancer had significantly higher education levels, P < or = 0.01, and higher triglyceride levels compared to the controls, P < or = 0.001, but lower body mass index (BMI) levels, P < or = 0.01. There were no statistically significant differences observed in total cholesterol, high-density-lipoprotein-containing cholesterol and low-density-lipoprotein-containing cholesterol between the patients and controls. After adjustments for age, education, BMI, and menopausal status, triglycerides remained significantly and positively associated with breast cancer risk. The significant correlation between the high levels of triglycerides and breast cancer risk (odds ratio = 5.12) may be attributed to differences in lipid metabolism between the women with breast cancer and controls, or to the consequences of breast cancer.

HLA associations in end-stage renal disease due to membranous glomerulonephritis: HLA-DR3 associations with progressive renal injury. Southeastern Organ Procurement Foundation

Membranous glomerulonephritis (MGN) is the most common cause of idiopathic glomerulonephritis in American adults. African-Americans develop end-stage renal disease (ESRD) due to chronic glomerulonephritis four times more often than whites. To determine whether HLA phenotype associations existed in the subset of MGN patients with ESRD we analyzed HLA frequencies, by race, in patients with MGN entered in the Southeastern Organ Procurement Foundation registry between 1982 and 1992. HLA frequencies from 250 renal transplant patients with MGN (190 whites and 60 African-Americans) were compared with 4,506 race-matched cadaveric kidney donor controls (4,039 whites and 467 African-Americans). Race-specific odds ratios (ORs) were calculated and fitted into a log-linear model to determine associations between MGN and HLA frequencies. The reported values were considered significant (P < 0.05) after Bonferroni correction for multiple comparisons. HLA-DR3 and HLA-DR5 frequencies were increased in cases of both races compared with race-matched controls (race-combined ORs, 2.22 and 1.61, respectively; all P < 0.02). Interracial analyses revealed that HLA-DR7 frequency was decreased solely in whites with MGN (OR, 0.53; P < 0.04). The results of this study indicate that HLA-DR3 and HLA-DR5 are positively associated with ESRD due to MGN in patients of both races and that HLA-DR7 is negatively associated with MGN in whites. These analyses confirm the published reports of HLA-DR3 association with MGN in Chinese, French, British, Chilean, and American white populations. The novel association of HLA-DR5 may reflect the fact that the MGN cases in this study all had ESRD.(ABSTRACT TRUNCATED AT 250 WORDS)

Vitiligo is associated with HLA-DR4 in black patients. A preliminary report

We have determined the HLA-DR and HLA-DQ phenotypes of 24 black patients with vitiligo and compared these with phenotypes of 143 local black controls. HLA-DR4 was significantly increased in patients, 38% vs 11% for controls. HLA-DQw3 was also increased in patients, 58% vs 32% for controls and may be explained in part by linkage disequilibrium with HLA-DR4. When patients were subgrouped according to family history of autoimmune disease and compared with controls, the increase in HLA-DR4 and HLA-DQw3 segregated with a positive family history. HLA-DRw6 in patients with a negative family history of autoimmune disease (64%) was significantly greater than the 10% in patients with a positive family history. When patients were subgrouped according to age at onset of disease, HLA-DR4 was increased in those with early onset of disease (younger than 20 years) while HLA-DRw6 was greater in patients who were older at onset of disease. These findings support the hypothesis of an immunogenetic influence on the expression of vitiligo in black patients with vitiligo.

Prednisone when used as treatment for rejection correlates with poor outcome

Since January 1974, 195 of 202 (95%) renal transplants have been performed on blacks at the Howard University Hospital Transplant Center. Hypertension is the most common cause of end-stage renal disease (ESRD) at this center (57%). The immunosuppressive regimens utilized were divided into four eras. The first era (1974-1980) consisted of the prophylactic administration of prednisone, Imuran (AZA), and Minnesota antilymphocyte globulin (MAG) with high prednisone dosage used to treat rejection. One-year, two-year, and five-year patient survival rates were 59% 54%, and 41%, respectively. Graft survival rates for the same period were 53%, 47%, and 36%. In the second era (1980-1983), the same immunoprophylaxis was used but only MAG was used to reverse rejection. One-year and two-year patient survival rates were 90% and 84%. Graft survival rates for the same period were 72% and 64%. When era 1 is compared with era 2, statistically significant improvement in patient survival is evident (P less than 0.005). Graft survival rates are statistically significant for one-year graft survival (P less than 0.05). In the third era (1983-1986), cyclosporine was the principal immunosuppressive agent used along with prednisone. Rejection in this era was treated by adjusting the cyclosporine dose to keep the level between 100 ng to 150 ng per mL and in addition to high prednisone. One-year patient survival and graft survival rates were 83% and 55%, respectively. The fourth era began April 1986 and was initiated because of previous bad experiences with high doses of prednisone to treat rejection in era 1.(ABSTRACT TRUNCATED AT 250 WORDS)

Regressive logistic models for ordered and unordered polychotomous traits: application to affective disorders

Regressive models are extended to disease phenotypes with two or more affection classes through the use of polychotomous logistic regression. The classes of affection may be ordered (ranked as on a liability continuum), or unordered. Data on affective disorders are used for illustration.

Unique HLA-D region heterogeneity in American blacks

American blacks and whites show heterogeneity in serologically detected and lymphocyte-defined HLA-D region antigen frequencies. Also, alterations in linkage relationships are seen in DR and DQ specificities. Since homozygous typing cells probably identify a cluster of specificities that are usually found in linkage disequilibrium in a given population, it is not surprising that blacks have unique HLA-D types. The significance of the observed differences in the function of class II molecules is being investigated.

Association of HLA and autoantibody in transfused sickle cell disease patients

This study evaluates autoantibody production in sickle cell disease patients and determines whether genes in the major histocompatibility complex are associated with autoantibody responses. Rheumatoid factor was significantly increased for both male and female patients and was less prevalent in highly transfused patients. Significant increases were also detected in the incidences of antinuclear antibody for females and antismooth muscle antibody for males. Low incidence of antinuclear antibody was significantly associated with HLA-DR3. Significant associations were also found between the incidence of antinuclear antibody and both HLA-A28 and B15.