Copy‐number variations (CNVs) of the human sex steroid metabolizing genes UGT2B17 and UGT2B28 and their associations with a UGT2B15 functional polymorphism

UGT2B17 and UGT2B28 are among the most commonly deleted genes in humans and encode members of the uridine diphosphate (UDP)‐glucuronosyltransferase 2B (UGT2B) subfamily. They are involved, along with UGT2B15, in the catabolism of sex‐steroid hormones. Despite the recent biomedical interest in UGT2B17 and UGT2B28 copy‐number variations (CNVs) within human populations, the impact of their gene dosage has been hampered by the lack of precise molecular identification of the common deletion breakpoints within high homology sequence regions on chromosome 4. We have characterized these common deletions and report their coexistence in Caucasians, along with the p.D85Y (rs1902023:G>T) functional polymorphism of UGT2B15. Segmental duplications of 4.9 kb for UGT2B17 and 6.8 kb for UGT2B28 comprise purine‐rich recombination sites located 117 kb and 108 kb apart on both ends of the deletions. CNVs of UGT2B17 and UGT2B28 occur in Caucasians at 27% and 13.5%, respectively. While only 43% have two copies of both genes, 57% harbor at least one deletion. Their co‐occurrence on 5% of chromosomes creates a 225‐kb genomic gap. CNVs of both UGT2B17 and UGT2B28, with the co‐occurrence of UGT2B15:p.D85Y, generate seven distinct haplotypes. Restricting the analyses to CNV of the UGT2B17 gene without evaluating UGT2B28 CNV, along with the genotype of UGT2B15, may over‐ or underestimate the impact of each gene under physiological conditions or disease states. Hum Mutat 30:1–10, 2009. © 2009 Wiley‐Liss, Inc.     

Catalog of 86 single-nucleotide polymorphisms (SNPs) in three uridine diphosphate glycosyltransferase genes: <Emphasis Type="Italic">UGT2A1</Emphasis>, <Emphasis Type="Italic">UGT2B15</Emphasis>, and <Emphasis Type="Italic">UGT8</Emphasis>

We report here three high-density maps of variations found among 48 Japanese individuals in three uridine diphosphate glycosyltransferase (UGT) genes, UGT2A1, UGT2B15, and UGT8. A total of 86 single-nucleotide polymorphisms (SNPs) were identified through systematic screening of genomic regions containing these genes: 8 in 5′ flanking regions, 7 in coding regions, 67 in introns, 3 in 3′ untranslated regions, and 1 in a 3′ flanking region. We also discovered 14 variations of other types. Of the 86 SNPs, 63 (73%) were considered to be novel on the basis of comparison of our data with the Database of SNPs (dbSNP) of the National Center for Biotechnology Information. Among the seven SNPs identified in exonic sequences, five were non-synonymous changes that would result in amino-acid substitutions. The collection of SNPs derived from this study will serve as an additional resource for studies of complex genetic diseases and responsiveness to drug therapy. Received: June 12, 2002 / Accepted: June 13, 2002     

Genetic Predictors of Cervical Dysplasia in African American HIV-Infected Women: ACTG DACS 268

Abstract

Objective: To examine genome-wide associations in HIV-infected women with a history of cervical dysplasia compared with HIV-infected women with no history of abnormal Papanicolaou (Pap) tests. Design: Case-control study using data from women analyzed for the HIV Controllers Study and enrolled in HIV treatment-naïve studies in the AIDS Clinical Trials Group (ACTG). Methods: Genotyping utilized Illumina HumanHap 650 Y or 1MDuo platforms. After quality control and principal component analysis, ~610,000 significant single nucleotide polymorphisms (SNPs) were tested for association. Threshold for significance was P < 5 × 10^–8 for genome-wide associations. Results: No significant genomic association was observed between women with low-grade dysplasia and controls. The genome-wide association study (GWAS) analysis between women with high-grade dysplasia or invasive cervical cancer and normal controls identified significant SNPs. In the analyses limited to African American women, 11 SNPs were significantly associated with the development of high-grade dysplasia or cancer after correcting for multiple comparisons. The model using significant SNPs alone had improved accuracy in predicting high-grade dysplasia in African American women compared to the use of clinical data (area under the receiver operating characteristic curve for genetic and clinical model = 0.9 and 0.747, respectively). Conclusions: These preliminary data serve as proof of concept that there may be a genetic predisposition to developing high-grade cervical dysplasia in African American HIV-infected women. Given the small sample size, the results need to be validated in a separate cohort.     

Identification of single-nucleotide polymorphisms (SNPs) of human N-acetyltransferase genes NAT1, NAT2, AANAT, ARD1, and L1CAM in the Japanese population

By direct sequencing of regions of the human genome containing five genes belonging to the acetyltransferase family, arylamine N-acetyltransferase (NAT1), arylamine N-acetyltransferase (NAT2), arylalkylamine N-acetyltransferase (AANAT), L1 cell adhesion molecule (L1CAM), and the human homolog of Saccharomyces cerevisiae N-acetyltransferase ARD1, we identified 53 single-nucleotide polymorphisms (SNPs) and two insertion/deletion polymorphisms in 48 healthy Japanese volunteers. NAT1 and NAT2 are so-called drug-metabolizing enzymes. In the NAT1 gene we found two SNPs and a 3-bp insertion/deletion polymorphism that corresponded to the NAT1^*3, ^*10, and ^*18A/^*18B alleles reported in other populations. The frequencies of NAT1^* alleles in our Japanese subjects were 52.6% for NAT1^*4, 1.0% for NAT1^*3, 40.6% for NAT1^*10, 2.6% for NAT1^*18A and 3.1% for NAT1^*18B. In the NAT2 gene we found 32 SNPs and a 1-bp insertion/deletion polymorphism; 6 SNPs within the coding region were reported previously and belonged to the slow acetylator group (NAT2^*5, NAT2^*6 and NAT2^*7), and 2 of the 8 SNPs in the 5′ flanking region were reported in the dbSNP of GenBank, but the remaining 24 SNPs and the insertion/deletion polymorphism were novel. The frequencies of NAT2^* alleles in Japanese (51.3% for NAT2^*4, 1.6% for ^*5B, 26.1% for ^*6A, 2.2% for ^*6B, 1.2% for ^*7A, 10.1% for ^*7B, 7.4% for ^*12A, and 1.1% for ^*13) were significantly different from those reported in Caucasian populations. In the AANAT gene we found 4 novel SNPs: 2 in the 5′ flanking region, 1 in exon 4, and 1 in intron 3. In the two genes belonging to the N-terminal N-acetyltransferase family, we identified 9 SNPs, 7 of them novel, for ARD1, and six novel SNPs for L1CAM. Variations at these loci may contribute to an understanding of the way in which different genotypes may affect the activities of human N-acetyltransferases, especially as regards the therapeutic efficacy of certain drugs and antibiotics. Received: February 9, 2001 / Accepted: February 19, 2001     

Alu insertion polymorphisms in the African Sahel and the origin of Fulani pastoralists

Background: The origin of Western African pastoralism, represented today by the Fulani nomads, has been a highly debated issue for the past decades, and has not yet been conclusively resolved.

Aim: This study focused on Alu polymorphisms in sedentary and nomadic populations across the African Sahel to investigate patterns of diversity that can complement the existing results and contribute to resolving issues concerning the origin of West African pastoralism.

Subjects and methods: A new dataset of 21 Alu biallelic markers covering a substantial part of the African Sahel has been analysed jointly with several published North African populations.

Results: Interestingly, with regard to Alu variation, the relationship of Fulani pastoralists to North Africans is not as evident as was earlier revealed by studies of uniparental loci such as mtDNA and NRY. Alu insertions point rather to an affinity of Fulani pastoralists to Eastern Africans also leading a pastoral lifestyle.

Conclusions: It is suggested that contemporary Fulani pastoralists might be descendants of an ancestral Eastern African population that, while crossing the Sahara in the Holocene, admixed slightly with a population of Eurasian (as evidenced by uniparental polymorphisms) ancestry. It seems that, in the Fulani pastoralists, Alu elements reflect more ancient genetic relationships than do uniparental genetic systems.     

Investigation of the genetic structure of Kabyle and Chaouia Algerian populations through the polymorphism of Alu insertion markers

Abstract

Background: In Algeria, as in all North Africa, Berbers constitute the old background of the population. Today, Berber speakers account for only ～ 25% of Algerians. This decline is the product of a complex human settlement from pre-history to recent invaders.

Aim: This study aims to determine the genetic diversity level within a sample of five Algerian Berber speaking populations in order to contribute to resolving issues about the North African population settlement.

Subjects and methods: Two Algerian Berber groups (Kabyle and Chaouia), originated from five administrative regions from Algeria, were typed for 11 Alu Insertions. Analysis has been based on Fst genetic distance, AMOVA, NMDS and distance to the centroid model.

Results: No genetic differentiation has been observed between all Algerian Berbers discarding any geographical or ethnic effect. Comparative analyses based on Fst genetic distance did not show significant affinities between North Africans and either South Europeans or Middle Easterners, except genetic proximity between Algerians and Iberians. The amount of genetic diversity among Algerians and North African populations detected by the distance to the centroid model was significant compared with other North Mediterranean populations.

Conclusion: A strong genetic homogeneity has been found between Algerian Berbers. Global genetic diversity based on Alu markers is following the isolation by distance model, except for some European populations.     

Eye measurements in 7-year-old black South African children

Background: Ethnic variation often renders anthropometric reference values obtained in one population unsuitable for use in others. Fetal alcohol syndrome (FAS) diagnosis relies in part on the evaluation of certain anthropometric facial features. Measurements of these facial features in South African children have not been compared with measurements obtained in other populations.

Aim: The study seeks to determine the suitability of reference values obtained in other populations for the diagnosis of the facial phenotype associated with FAS in South African children.

Participants and methods: Palpebral fissure length (PFL), interpupillary distance (IPD), inner canthal distance (ICD) and outer canthal distance (OCD) measured in a group of black South African children were obtained from digital photographs using stereophotogrammetry, and compared with measurements published for other populations. The study population comprised 17 7-year-old boys and 17 7-year-old girls. The precision and reliability of measurements were examined with reference to published data.

Results: Eye distance measurements in the study population do not consistently reflect those in any one other population for which such measurements have been published.

Conclusion: Population-specific reference values of eye distance measurements should be established for South African children.     

Complete inherited deficiency of the fourth complement component in a child with systemic lupus erythematosus and his disease-free brother in a North African family

Although null alleles of complement C4 genes (C4A ^*Q0 andC4B ^*Q0) are frequent in the normal population, the occurrence of two null alleles on the same chromosome is very rare and therefore complete C4 deficiency is exceptional. We describe a 16-year-old North African boy who presented with systemic lupus erythematosus with renal involvement and persistent undetectable classical pathway activity and C4 protein and hemolytic activity in plasma, with normal C3 levels. Similar complement abnormalities were observed in his healthy 12-year-old brother. Complete C4 deficiency was documented in the two brothers by investigation of the family and the lack of C4A and C4B bands upon phenotyping of C4. Southern blot analysis of the C4/CYP21 gene organization in the family indicated that the deficiency resulted from a deletion of the C4B/CYP21A genes associated with nonexpression of a C4A gene. The double-null haplotype was found to be associated with homozygous A2 B17 C2C BFF C4 AQO BQO DR7 HLA haplotype. Thus, similar C4 deficiencies with HLA identity may lead to different clinical presentations.     

HLA class I and class II polymorphisms in Tunisian Berbers

Background: The HLA polymorphism is a powerful genetic tool to study population origins. By analysing allele frequencies and haplotypes in different populations, it is possible to identify ethnic groups and establish the genetic relationships among them.

Aim: The Berber (endogenous Tunisians) HLA class I and class II genotypes were analysed and compared with those of Mediterranean and Sub-Saharan African communities using genetic distances, Neighbour-Joining dendrograms, correspondence and haplotype analysis.

Subjects and methods: One hundred and five unrelated Berbers were typed for HLA class I (A, B) and class II (DRB1, DQB1) gene alleles using reverse dot-blot hybridization.

Results: High frequencies of A*0201 (24.76%), A*3402 (22.38%) and B*44 (32.85%) alleles were recorded for Berbers, the highest recorded for Mediterranean and North African populations. This study shows a close relatedness of Tunisian Berbers to other Tunisians, North Africans and Iberians.

Conclusion: The apparent relatedness of Tunisian Berbers to present-day (North African) Tunisians, Algerians and Moroccans suggests that the Arab invasion of North Africa (7^th–11^th centuries AD) did not significantly impact the genetic makeup of North Africans. Furthermore, Tunisian Berbers appear to be closely related to Iberians (Spaniards and Basques), indicating that the 7^th century AD gene flow of invaders was low in Iberians and that the main part of their genetic pool came after the Northward Saharan migration, when hyper-arid conditions were established in Sahara (before 6000 BC). Other studied populations belong to the old Mediterranean substratum, which has been present in the area since pre-Neolithic times. This study indicates a higher proportion of Iberian than Arab ancestry in Tunisian Berbers, which is of value in evaluating the evolutionary history of present-day Tunisians. Greeks seem to share genetic HLA features (Chr 6) with Sub-Saharans. The relatedness of Greeks to Sub-Saharans has been confirmed by other studies based on chromosome 7 genetic markers.     

UGT1A1 is a major locus influencing bilirubin levels in African Americans

Total serum bilirubin is associated with several clinical outcomes, including cardiovascular disease, diabetes and drug metabolism. We conducted a genome-wide association study in 619 healthy unrelated African Americans in an attempt to replicate reported findings in Europeans and Asians and to identify novel loci influencing total serum bilirubin levels. We analyzed a dense panel of over two million genotyped and imputed SNPs in additive genetic models adjusting for age, sex, and the first two significant principal components from the sample covariance matrix of genotypes. Thirty-nine SNPs spanning a 78 kb region within the UGT1A1 displayed P-values <5 × 10⁻⁸. The lowest P-value was 1.7 × 10⁻²² for SNP rs887829. None of SNPs in the UGT1A1 remained statistically significant in conditional association analyses that adjusted for rs887829. In addition, SNP rs10929302 located in phenobarbital response enhancer module was significantly associated with bilirubin level with a P-value of 1.37 × 10⁻¹¹; this enhancer module is believed to have a critical role in phenobarbital treatment of hyperbilirubinemia. Interestingly, the lead SNP, rs887829, is in strong linkage disequilibrium (LD) (r²≥0.74) with rs10929302. Taking advantage of the lower LD and shorter haplotypes in African-ancestry populations, we identified rs887829 as a more refined proxy for the causative variant influencing bilirubin levels. Also, we replicated the reported association between variants in SEMA3C and bilirubin levels. In summary, UGT1A1 is a major locus influencing bilirubin levels and the results of this study promise to contribute to understanding of the etiology and treatment of hyperbilirubinaemia in African-ancestry populations.     

Functional Single Nucleotide Polymorphisms (SNPs) in the Genes Encoding the Human Deoxyribonuclease (DNase) Family Potentially Relevant to Autoimmunity

Objective: To continue our previous investigations, we have extensively investigated the function of the 61, 41, and 35 non-synonymous single nucleotide polymorphisms (SNPs) in the human genes encoding DNASE1, DNASE1L3, and DNASE2, respectively, potentially relevant to autoimmune diseases.

Methods: The site-directed mutagenesis was employed to amino acid–substituted constructs corresponding to each SNP. The COS-7 cells were transfected with each vector and DNase activity was assayed by the single radial enzyme diffusion method. By using PolyPhen-2, changes in the DNase function of each non-synonymous SNP were predicted. Genotyping of all the non-synonymous SNPs was performed in 14 different populations including 3 ethnic groups using the polymerase chain reaction followed by the restriction fragment length polymorphism method.

Results: Expression analysis demonstrated these SNPs to be classified into four categories with regard to the effect on DNase activity: SNPs not affecting the activity level, ones reducing it, ones abolishing it, and ones elevating it. In particular, 9, 5, and 4 SNPs producing a loss-of-function variant of the enzymes in DNASE1, DNASE1L3, and DNASE2, respectively, were confirmed. SNPs producing DNase loss of function can be estimated by PolyPhen-2 to be “probably damaging” with a high accuracy of prediction. Almost all of these functional SNPs producing a loss of function or substantially low activity-harboring forms exhibited a mono-allelic distribution in all of the populations.

Conclusion: A minor allele of functional SNPs, despite the remarkably low genetic heterogeneity of the SNPs, might be a genetic risk factor for autoimmune diseases.     

Increased severity of acute graft versus host disease as a result of differential expression following a homozygous gene deletion

Acute graft versus host disease (aGvHD) is a major cause of early morbidity post‐haematopoietic stem cell transplantation with minor histocompatibility antigens being a contributing factor. One mHA encoded by the UDP glycosyltransferase 2 family polypeptide B17 (UGT2B17) gene has been shown to be immunogenic because of differential expression in the donor and recipient. We investigated the effects of a homozygous gene deletion of UGT2B17 on the severity of acute aGvHD post‐HSCT in HLA‐matched related donors. 115 donor and recipient HLA and UGT2B17 genotypes were determined using PCR‐SSO and PCR‐SSP, respectively. aGvHD grading was determined using routine criteria and dichotomized into either nonclinically significant (0–I) or clinically significant (II–IV). For all analyses, P‐values of ≤ 0.05 were considered significant. The frequency of the gene deletion within the total cohort tested was 29.1%. A significant increase in aGvHD severity (grades II‐IV) was seen in UGT2B17 recipients expressing the protein when transplanted with a UGT2B17 disparate donor (P = 0.011). We observed a significant association between UGT2B17 expressing recipients and UGT2B17 deficient donors with the severity of aGvHD. This study provides additional evidence that genomic variations may predispose to more severe aGvHD, but are not a mechanism for GvHD.     

Whole-exome sequencing of a pedigree segregating asthma

Background

Obesity has become a common human disorder associated with significant morbidity and mortality and adverse effects on quality of life. Sequence variants in two candidate genes, FTO and UCP-1, have been reported to be overrepresented in obese Caucasian population. The association of these genes polymorphisms with the obesity phenotype in a multiethnic group such as the Brazilian population has not been previously reported.

Methods

To assess the putative contribution of both FTO and UCP-1 to body mass index (BMI) and cardiovascular risk we genotyped SNPs rs9939609 (FTO) and rs6536991, rs22705565 and rs12502572 (UCP-1) from 126 morbidly obese subjects (BMI 42.9 ± 5.6 kg/m², mean ± SE) and 113 normal-weight ethnically matched controls (BMI 22.6 ± 3.5 kg/m², mean ± SE). Waist circumference, blood pressure, glucose and serum lipids were also measured. Each sample was also genotyped for 40 biallelic short insertion/deletion polymorphism (indels) for ethnic assignment and to estimate the proportion of European, African and Amerindian biogeographical ancestry in the Brazilian population.

Results

Cases did not differ from controls in the proportions of genomic ancestry. The FTO SNP rs9939609 and UCP-1 SNP rs6536991 were significantly associated with BMI (p= 0.04 and p<0.0001 respectively). An allele dose dependent tendency was observed for BMI for rs6536991 sample of controls. No other significant associations between any SNP and hypertension, hyperlipidemia and diabetes were noted after correction for BMI and no significant synergistic effect between FTO and UCP-1 SNPs with obesity were noted. There was not an association between rs9939609 (FTO) and rs6536991 (UCP-1) in with maximum weight loss after 1 year in 94 obese patients who underwent bariatric surgery.

Conclusion

Our data are consistent with FTO rs9939609 and UCP-1 rs6536991 common variants as contributors to obesity in the Brazilian population.

     

Increased inflammatory responsiveness of peripheral blood mononuclear cells (PBMCs) to in vitro NOD2 ligand stimulation in patients with ankylosing spondylitis

Abstract

Background: Ankylosing spondylitis (AS) is a common debilitating rheumatic disease in which the innate immune components especially the Interleukin (IL)-23/IL-17 axis related genes play important role in its pathogenesis. Nucleotide binding oligomerization domain-containing protein (NOD)2, as an innate receptor, is critical for IL-23 production in cells. Therefore, we aimed to stimulate NOD2 signaling and study its effects on cytokine production in peripheral blood mononuclear cells (PBMC) of these patients.

Methods: PBMCs from 18 patients with active AS and 18 healthy individuals were separated by Ficoll-Hypaque density gradient centrifugation and cultured in the presence of muramyl dipeptide (MDP), as NOD2 ligand. Quantitative expression analysis of NOD1, NOD2, RIPK2, SLC15A4, NLRP1, NLRP3, IL23A, IL17A, IL1B, and TNFA genes was performed using Real-time polymerase chain reaction (PCR). Finally, protein changes of IL23A and IL17A expression were validated using enzyme linked immunosorbent assay (ELISA).

Results: Apart from NOD1 that tend to be downregulated in the controls, all the selected genes showed overexpression in response to MDP in cells from the studied groups. Except RIPK2, all the genes had higher expression changes upon MDP stimulation in the AS population. Overexpression of IL23A and IL17A were confirmed at protein levels using ELISA. The strong positive correlation between NLRP3 and NOD2 was decreased after stimulation but new correlations between NLRP3 and IL1B, RIPK2 and SLC15A4 were observed after treatment.

Conclusions: This study indicated that AS PBMCs were hyper-responsive to MDP stimulation. This observation implies an important role of NOD2 in the pathogenesis of inflammatory diseases including AS.     

Alanine-scanning mutations of the BMP-binding domain of recombinant secretory bovine spp24 affect cytokine binding

Secreted phosphoprotein 24 kDa (spp24) is a bone morphogenetic protein (BMP)/transforming growth factor-β cytokine-binding protein. The spp24 BMP-2-binding/transforming growth factor receptor II homology-1 (TRH1) domain is a highly conserved N-to-C terminally disulfide-bonded 19-amino acid residue loop similar to those in fetuin and the BMP receptor II. TRH1 domains exhibit a characteristic BTB or β-pleated sheet/turn/β-pleated sheet secondary structure. Our objective was to identify amino acid residues in the spp24 TRH1 domain that bind BMP-2, starting with the nine invariant mammalian residues. Alanine scanning (substitution of Ala for a native residue) was conducted for Cys₁₁₀, Arg₁₁₁, Ser₁₁₂, Thr₁₁₃, Val₁₁₄, Ser₁₁₇, Val₁₂₁, Val₁₂₄, and Cys₁₂₈ of recombinant bovine spp24 (residues 24–203). Binding to rhBMP-2 was assessed by surface plasmon resonance, and the equilibrium binding constants were calculated assuming 1:1 binding between spp24 or its mutants and rhBMP-2, so that affinity = K_D = k_d/k_a. Replacing Arg₁₁₁ (a positively charged basic residue), polar residues Thr₁₁₃ and Ser₁₁₇, and the nonpolar Cys₁₂₈ with Ala had little effect on BMP-2 binding. Replacing Val₁₁₄ or Val₁₂₁ with Ala increased binding affinity, whereas replacing Cys₁₁₀, Ser₁₁₂, Val₁₂₄, or both Cys₁₁₀ and Cys₁₂₈ with Ala decreased it. The kinetics of spp24 binding to BMP-2 can be manipulated by replacing invariant TRH1 residues. Decreasing the relative degree of hydrophobicity in the β-pleated sheet secondary structural motif of the TRH1 domain by replacing key Val residues with Ala increased the affinity for BMP-2 whereas altering the composition of the α-helical turn did not. Thus, the β-pleated sheets play a greater role in BMP-2 binding than the α-helical turn.     

The Orientalisation of North Africa: New hints from the study of autosomal STRs in an Arab population

Background: Recent genomic analyses suggest that the current North African gene pool was mainly influenced by population flow coming from the East that altered the genetic structure of autochthonous Berber populations. Such genetic flow has not been extensively addressed yet using North African populations of Middle-eastern origin as reference.

Aim: To discern the Middle-eastern component in the genetic background of Tunisian Arabs and evaluate the extent of gene flow from the Middle East into North African autochthonous Berber populations.

Subjects and methods: This study has examined 113 Tunisians of well-known Arabian origin from Kairouan region, using 15 autosomal Short Tandem Repeats (STRs) loci.

Results: No deviations from Hardy-Weinberg equilibrium were observed and all loci presented high levels of heterozygosity. Principal coordinate and STRUCTURE analyses were consistent in clustering together North African and Middle Eastern populations, likely reflecting the recent gene flow from the East dating back to the Arab conquest period. This demographic migration and the Arabisation process that submerged the original Berber language and customs seems to have be accompanied by substantial gene flow and genetic admixture.

Conclusion: This study represents an additional step to obtain a comprehensive understanding of the complex demographic history of North African populations.     

Analysis of inherited genetic variations at the UGT1 locus in the French‐Canadian population

The UDP‐glucuronosyltransferase UGT1 locus is composed of nine exon 1s, each flanked by a unique promoter region, and common exons (2, 3, 4, and the alternatively spliced exons 5a and 5b). Here, we characterized the genetic architecture of the UGT1 gene in a Caucasian sample. Overall, 98 variations in regulatory domains, exons and exon–intron boundaries were genotyped in 254 unrelated subjects, including 12 unreported UGT1 polymorphisms. We determined allele frequencies, computed pairwise linkage disequilibrium (LD), and inferred haplotypes; this thorough analysis yielding a limited number of common UGT1 haplotypes. Moreover, only 17 haplotype tagging single nucleotide polymorphisms (htSNPs) are required to capture most of the allelic diversity of the locus. Four haplotype blocks were inferred: Block 9/6 (UGT1A9, UGT1A7 and UGT1A6), Block 4 (UGT1A4), Block 3/1 (UGT1A3 and UGT1A1), and Block C (3′UTR). A high level of linkage exists between Blocks 9/6 and 3/1, while the 3′UTR SNPs are genetically isolated. The most common haplotype (16.5%) presents multiple deleterious alleles, mainly 1A1*28, 1A3*2, 1A6*2, and 1A7*4. More interestingly, we reveal the co‐occurrences of multiple deleterious variations, some of which could be associated with interindividual differences in glucuronidation. Comparison with the HapMap data set demonstrated differences in haplotypic diversity between ethnic samples, but similarity between Caucasian cohorts, as observed previously. This report provides relevant data for further pharmacogenomic studies. Hum Mutat 0, 1–12, 2009. © 2009 Wiley‐Liss, Inc.     

Genetic variation in key genes associated with statin therapy in the Azores Islands (Portugal) healthy population

Background: Inter-individual variation in response to statins (efficacy and toxicity) has been described and may be due to polymorphisms implicated in drug pharmacokinetics or pharmacodynamics.

Aim: This study investigates clinically relevant pharmacogenes underlying statin response in 170 healthy Azoreans.

Methods: Eight SNPs in candidate genes—HMGCR (rs3846662, rs17238540, rs17244841), CETP (rs708272), APOE (rs7412, rs429358) and SLCO1B1 (rs2306283, rs4149056)—were genotyped.

Results: The allele frequencies were similar to those reported for European derived populations, excepting SLCO1B1 c.388A>G (rs2306283), which has a significant difference when compared with the HapMap CEU population (p?=?1?×?10^?8). The results of statin efficacy showed that 9.1% of Azoreans are APOE4 carriers. This allele has been associated with lower LDLc reduction from statin therapy and also higher LDLc levels at baseline. Regarding SLCO1B1, associated with statin toxicity, 1.8% of individuals have two reduced-function alleles (c.521CC).

Conclusion: The results contribute to overcome the lack of knowledge regarding the frequency of pharmacogenetic SNPs and their corresponding haplotypes in targeted populations, such as Azores islands. Moreover, the present work constitutes an initial step to implementing pharmacogenomics in clinical practice where physicians could use a patient’s genetic make-up to optimize statin therapy, regarding efficiency and myopathy risk.     

Three single-nucleotide polymorphisms in LPA account for most of the increase in lipoprotein(a) level elevation in African Americans compared with European Americans

Background

The extent which universally common or population‐specific alleles can explain between‐population variations in phenotypes is unknown. The heritable coronary heart disease risk factor lipoprotein(a) (Lp(a)) level provides a useful case study of between‐population variation, as the aetiology of twofold higher Lp(a) levels in African populations compared with non‐African populations is unknown.

Objective

To evaluate the association between LPA sequence variations and Lp(a) in European Americans and African Americans and to determine the extent to which LPA sequence variations can account for between‐population variations in Lp(a).

Methods

Serum Lp(a) and isoform measurements were examined in 534 European Americans and 249 African Americans from the Choices for Healthy Outcomes in Caring for End‐Stage Renal Disease Study. In addition, 12 LPA variants were genotyped, including 8 previously reported LPA variants with a frequency of >2% in European Americans or African Americans, and four new variants.

Results

Isoform‐adjusted Lp(a) level was 2.23‐fold higher among African Americans. Three single‐nucleotide polymorphisms (SNPs) were independently associated with Lp(a) level (p<0.02 in both populations). The Lp(a)‐increasing SNP (G‐21A, which increases promoter activity) was more common in African Americans, whereas the Lp(a)‐lowering SNPs (T3888P and G+1/inKIV‐8A, which inhibit Lp(a) assembly) were more common in European Americans, but all had a frequency of <20% in one or both populations. Together, they reduced the isoform‐adjusted African American Lp(a) increase from 2.23 to 1.37‐fold(a 60% reduction) and the between‐population Lp(a) variance from 5.5% to 0.5%.

Conclusions

Multiple low‐prevalence alleles in LPA can account for the large between‐population difference in serum Lp(a) levels between European Americans and African Americans.Most genetic association studies focus on within‐population, rather than between‐population, differences in disease susceptibility. Although between‐population variation accounts for only 5–15% of human genetic diversity,¹ it is invoked increasingly to explain differences in disease risk and drug response across populations.^2,3 It is unknown whether such differences result from universally common alleles, which are hypothesised to contribute to within‐population risk variation for common diseases,^4,5 or from alleles that are population specific or nearly so. The allelic spectrum of between‐population variation has important implications, as identifying susceptibility alleles that are population specific may require strategies different from those identifying alleles that are common in all populations.The coronary heart disease risk factor lipoprotein(a) (Lp(a)) level is twofold higher in African than in non‐African populations,^6,7 and provides a useful case study of between‐population variation. The cardiovascular pathogenicity of Lp(a) is established best in Caucasians^8,9 and probably involves the low‐density lipoprotein‐bound plasminogen homologue apolipoprotein(a) (apo(a)), may increase low‐density lipoprotein delivery¹⁰ and may inhibit plasminogen‐mediated thrombolysis.¹¹ The apo(a) gene (LPA; MIM 152200) explains about 90% and 80% of Lp(a) level variance in European American¹² and African American¹³ populations, respectively. A genomically unusual 5.6‐kb variable tandem repeat in LPA encodes the KIV‐2 units, whose number determines apo(a) isoform size and explains half of the LPA effect on Lp(a) level.^12,14 The inverse association between isoform size and Lp(a) level probably reflects impaired cellular secretion of larger isoforms, which has been observed in vitro.¹⁵Isoform distributions are similar across populations, and do not explain higher African Lp(a) levels.⁷ Eight LPA variants (all but one are single‐nucleotide polymorphisms (SNPs)) have been associated with the isoform‐adjusted Lp(a) level in Europeans^{16,17,18,14,19,20} or Africans.^21,18 Some investigators have speculated that unidentified trans‐acting^16,22 or environmental²³ factors may explain the between‐population difference, as none of these have been shown to contribute substantially to higher African Lp(a) levels. . However, a substantial contribution of LPA to the between‐population difference cannot be excluded and provides the simplest explanation.Previous analyses have not considered multiple LPA variants simultaneously or comprehensively, and the extensive linkage disequilibrium across the gene^15,18,14,19 is expected to confound single‐locus effect estimates. Also, few studies included both European and African or African American populations, precluding direct quantification of LPA variant contributions to the between‐population difference. We report the results of a simultaneous analysis of multiple LPA variants, isoforms and Lp(a) level in a cohort of European Americans and African Americans.