Karen S. King

Genes mirror geography within Europe.

Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely spaced populations. Here we characterize genetic variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing; an individual’s DNA can be used to infer their geographic origin with surprising accuracy—often to within a few hundred kilometres.

The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research

Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP).

HLA-DQA1*02:01 Is a Major Risk Factor for Lapatinib-Induced Hepatotoxicity in Women With Advanced Breast Cancer

PURPOSE Hepatobiliary adverse events (AEs) have been observed in a small proportion of patients with metastatic breast cancer (MBC) treated with lapatinib. This study sought to identify gene variants associated with lapatinib-induced ALT elevation and hepatobiliary AEs. PATIENTS AND METHODS A two-stage pharmacogenetic investigation of ALT elevation was conducted in lapatinib-treated patients with MBC. Exploratory marker identification evaluated classical HLA alleles, candidate genes, and genome-wide screening in 37 cases with ALT greater than 3 times the upper limit of normal (ULN) and 286 controls with ALT ≤ 1× ULN, selected from 901 lapatinib-treated patients in 12 trials. Markers achieving prespecified association thresholds were progressed to an independent confirmatory data set of 24 ALT cases and 155 controls selected from a subsequent trial of 374 lapatinib-treated patients. RESULTS Of 58 variants associated with ALT elevation in the exploratory data set, four exceeded the prespecified significance threshold in the confirmatory analysis. These variants reside in the same MHC genomic locus and include HLA-DQA1*02:01. In the confirmatory study, DQA1*02:01 allele carriage was present in 71% of ALT cases and in 21% of controls (P < .001; odds ratio, 9.0; 95% CI, 3.2 to 27.4). As a predictor of liver safety risk in ALT cases versus noncases, DQA1*02:01 had negative and positive predictive values of 0.97 (95% CI, 0.95 to 0.99) and 0.17 (95% CI 0.10 to 0.26), respectively. CONCLUSION These results support a role for immune mechanisms in lapatinib-induced hepatotoxicity. Further work is required to determine whether testing for DQA1*02:01 allele carriage is clinically useful in managing liver safety risk during lapatinib treatment.

Global distribution of genomic diversity underscores rich complex history of continental human populations

Characterizing patterns of genetic variation within and among human populations is important for understanding human evolutionary history and for careful design of medical genetic studies. Here, we analyze patterns of variation across 443,434 single nucleotide polymorphisms (SNPs) genotyped in 3845 individuals from four continental regions. This unique resource allows us to illuminate patterns of diversity in previously under-studied populations at the genome-wide scale including Latin America, South Asia, and Southern Europe. Key insights afforded by our analysis include quantifying the degree of admixture in a large collection of individuals from Guadalajara, Mexico; identifying language and geography as key determinants of population structure within India; and elucidating a north-south gradient in haplotype diversity within Europe. We also present a novel method for identifying long-range tracts of homozygosity indicative of recent common ancestry. Application of our approach suggests great variation within and among populations in the extent of homozygosity, suggesting both demographic history (such as population bottlenecks) and recent ancestry events (such as consanguinity) play an important role in patterning variation in large modern human populations.

Pazopanib Efficacy in Renal Cell Carcinoma: Evidence for Predictive Genetic Markers in Angiogenesis-Related and Exposure-Related Genes

PURPOSE Pazopanib, an oral angiogenesis inhibitor, is approved for the treatment of advanced renal cell carcinoma (RCC). Response to pazopanib monotherapy varies between patients, and no validated biomarkers predictive of treatment outcome have been identified. We tested the hypothesis that this variability is partially dependent on germline genetic variants that may affect pazopanib exposure or angiogenesis pathways. PATIENTS AND METHODS Twenty-seven functional polymorphisms within 13 genes were evaluated in 397 patients with RCC. Genetic association with progression-free survival (PFS) and objective response rate (RR) was analyzed using the Cox proportional hazards model and proportional odds model, respectively. RESULTS Three polymorphisms in IL8 and HIF1A and five polymorphisms in HIF1A, NR1I2, and VEGFA showed nominally significant association (P ≤ .05) with PFS and RR, respectively. Compared with the wild-type AA genotype (median PFS, 48 weeks), the IL8 2767TT variant genotype showed inferior PFS (27 weeks, P = .009). The HIF1A 1790AG genotype was associated with inferior PFS and reduced RR, compared with the wild-type GG genotype (median PFS, 20 v 44 weeks; P = .03; RR, 30% v 43%, P = .02). Reductions in RR were detected for the NR1I2 -25385TT genotype, compared with the wild-type CC genotype (37% v 50%, P = .03), and for the VEGFA -1498CC genotype compared with the TT genotypes (33% v 51%). CONCLUSION Germline variants in angiogenesis- and exposure-related genes may predict treatment response to pazopanib monotherapy in patients with RCC. If validated, these markers may explain why certain patients fail antiangiogenesis therapy and they may support the use of alternative strategies to circumvent this issue.

HLA-B*57:01 Confers Susceptibility to Pazopanib-Associated Liver Injury in Patients With Cancer

Purpose: Pazopanib is an effective treatment for advanced renal cell carcinoma and soft-tissue sarcoma. Transaminase elevations have been commonly observed in pazopanib-treated patients. We conducted pharmacogenetic analyses to explore mechanistic insight into pazopanib-induced liver injury. Experimental Design: The discovery analysis tested association between four-digit HLA alleles and alanine aminotransferase (ALT) elevation in pazopanib-treated patients with cancer from eight clinical trials (N = 1,188). We conducted confirmatory analysis using an independent dataset of pazopanib-treated patients from 23 additional trials (N = 1,002). Genome-wide association study (GWAS) for transaminase elevations was also conducted. Results: The discovery study identified an association between HLA-B*57:01 carriage and ALT elevation [P = 5.0 × 10−5 for maximum on-treatment ALT (MaxALT); P = 4.8 × 10−4 for time to ALT > 3× upper limit of normal (ULN) event; P = 4.1 × 10−5 for time to ALT > 5× ULN event] that is significant after adjustment for number of HLA alleles tested. We confirmed these associations with time to ALT elevation event (P = 8.1 × 10−4 for ALT > 3× ULN, P = 9.8 × 10−3 for ALT > 5× ULN) in an independent dataset. In the combined data, HLA-B*57:01 carriage was associated with ALT elevation (P = 4.3 × 10−5 for MaxALT, P = 5.1 × 10−6 for time to ALT > 3×ULN event, P = 5.8 × 10−6 for time to ALT > 5× ULN event). In HLA-B*57:01 carriers and noncarriers, frequency of ALT > 3× ULN was 31% and 19%, respectively, and frequency of ALT > 5× ULN was 18% and 10%, respectively. GWAS revealed a possible borderline association, which requires further evaluation. Conclusions: These data indicate that HLA-B*57:01 carriage confers higher risk of ALT elevation in patients receiving pazopanib and provide novel insight implicating an immune-mediated mechanism for pazopanib-associated hepatotoxicity in some patients. Clin Cancer Res; 22(6); 1371–7. ©2015 AACR.

Concomitant use of pazopanib and simvastatin increases the risk of transaminase elevations in patients with cancer

Alanine aminotransferase (ALT) elevations were reported in oncology trials of the oral angiogenesis inhibitor pazopanib [1]. Statins, which are widely used to treat hypercholesterolemia [2], are also associated with ALT elevations. As pazopanib and statins are substrates for the same key metabolizing enzymes [e.g. cytochrome P450 3A4 (CYP3A4)] and drug transporters [e.g. P-glycoprotein (Pgp) and breast cancer resistance protein (BCRP)] [2–3], it is plausible that concomitant administration of pazopanib and statins may alter their systemic and/or hepatic exposures, leading to increased toxicities such as liver injury. Using individual patient data from 11 pazopanib clinical studies for the treatment of cancer (n = 976), we evaluated the effects of concomitant pazopanib and statin use on the incidence of ALT elevation [≥3 × upper limit of normal (ULN)]. The incidence of ALT≥ 3 × ULN was 21% in patients who received both pazopanib and any statin and 14% in patients who did not receive statins (P = 0.10; Table 1). Simvastatin and atorvastatin were the two most commonly used statins in this patient population. The incidence of ALT≥ 3 × ULN (27%) was significantly higher in simvastatin users than in patients who did not receive statins (P = 0.04; Table 1). Although the incidence of ALT≥ 3 × ULN was also higher in atorvastatin users (17%) than in patients who did not receive statins (14%), this difference did not reach statistical significance (P = 0.59). Among patients with ALT≥ 3 × ULN who received both pazopanib and simvastatin, ALT recovery to <2.5 × ULN (grade ≤1 by common toxicity criteria v3) was documented for 10/11 patients (91%) after either (i) no alteration for pazopanib and simvastatin therapy (n = 2); (ii) discontinuation of simvastatin only (n = 2); (iii) discontinuation of pazopanib only (n = 4); or (iv) discontinuation of both simvastatin and pazopanib (n = 2). There were insufficient follow-up ALT data to assess recovery for the one remaining patient after pazopanib was discontinued. The ALT recovery rate (to <2.5 × ULN) for patients receiving concomitant pazopanib and simvastatin was comparable with that seen in the larger group of pazopanib-treated study patients with renal cell carcinoma who had ALT≥ 3 × ULN (96/106, 91%) [4]. Exploratory pharmacogenetic analysis revealed that the ABCG2 (BCRP) 421C>A polymorphism may be associated with ALT elevation in patients taking pazopanib and simvastatin. Those with the variant 421C>A allele had a higher incidence of ALT≥ 3 × ULN (5/7, 71%) compared with patients with wild-type genotype (2/21, 10%; odds ratio = 19.6, 95% confidence interval 1.9–231.6; P = 0.004). This polymorphism was not associated with ALT elevations in pazopanib-treated patients without concurrent use of statins. This study showed that concomitant use of pazopanib and simvastatin increased the risk of transaminase elevations in patients with cancer. In addition to implementing the recommended dose modification guidelines for pazopanib, discontinuation of simvastatin should be considered to manage the risk of liver injury in cancer patients receiving both medications. Furthermore, hepatotoxicity/transaminase elevations have been reported in patients receiving other multi-tyrosine kinase inhibitors (e.g. imatinib, erlotinib, lapatinib, nilotinib, and sunitinib) that are also metabolized primarily by CYP3A4 [5]. The effect of concomitant administration of these tyrosine kinase inhibitors and statins on potential hepatotoxicity remains to be determined.

Genes mirror geography within Europe (Nature (2008) 456, (98-101))

This corrects the article DOI: 10.1038/nature07331

Rash in lapatinib-treated patients is not associated with human leukocyte antigen polymorphisms

Rash is a common side effect of lapatinib treatment. Since human leukocyte antigen (HLA) alleles have been implicated in multiple drug-induced cutaneous reactions, this study investigated the association of HLA alleles with lapatinib-induced rash. 1191 participants from a large lapatinib monotherapy trial underwent HLA genotyping, and allele carriage frequencies between rash cases and controls were compared. This analysis had adequate power to detect an association of common HLA alleles with rash, similar to those reported previously. No HLA alleles were significantly associated with lapatinib-induced rash, including the previously identified lapatinib hepatotoxicity biomarker HLA-DRB1*07:01 (p = 0.87). The present study is consistent with the view that lapatinib-induced rash is not the consequence of HLA-restricted, immune-mediated mechanisms.

Accurate interrogation of FCGR3A rs396991 in European and Asian populations using a widely available TaqMan genotyping method.

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