Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition

1. Laura B. Ramsey1,
2. Gitte H. Bruun2,
3. Wenjian Yang1,
4. Lisa R. Treviño1,
5. Selina Vattathil3,
6. Paul Scheet3,
7. Cheng Cheng4,5,
8. Gary L. Rosner6,
9. Kathleen M. Giacomini7,
10. Yiping Fan8,
11. Alex Sparreboom1,5,9,
12. Torben S. Mikkelsen10,
13. Thomas J. Corydon2,
14. Ching-Hon Pui11,
15. William E. Evans1,5,9 and
16. Mary V. Relling1,5,9,12

1. ¹Pharmaceutical Sciences Department, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
2. ²Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark;
3. ³Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
4. ⁴Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
5. ⁵College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA;
6. ⁶Department of Oncology Biostatistics, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland 21231, USA;
7. ⁷Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94102, USA;
8. ⁸Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
9. ⁹Department of Clinical Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA;
10. ¹⁰Department of Pediatric Oncology and Hematology, Aarhus University Hospital, DK-8200 Aarhus N, Denmark;
11. ¹¹Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA

Abstract

Methotrexate is used to treat autoimmune diseases and malignancies, including acute lymphoblastic leukemia (ALL). Inter-individual variation in clearance of methotrexate results in heterogeneous systemic exposure, clinical efficacy, and toxicity. In a genome-wide association study of children with ALL, we identified SLCO1B1 as harboring multiple common polymorphisms associated with methotrexate clearance. The extent of influence of rare versus common variants on pharmacogenomic phenotypes remains largely unexplored. We tested the hypothesis that rare variants in SLCO1B1 could affect methotrexate clearance and compared the influence of common versus rare variants in addition to clinical covariates on clearance. From deep resequencing of SLCO1B1 exons in 699 children, we identified 93 SNPs, 15 of which were non-synonymous (NS). Three of these NS SNPs were common, with a minor allele frequency (MAF) >5%, one had low frequency (MAF 1%–5%), and 11 were rare (MAF <1%). NS SNPs (common or rare) predicted to be functionally damaging were more likely to be found among patients with the lowest methotrexate clearance than patients with high clearance. We verified lower function in vitro of four SLCO1B1 haplotypes that were associated with reduced methotrexate clearance. In a multivariate stepwise regression analysis adjusting for other genetic and non-genetic covariates, SLCO1B1 variants accounted for 10.7% of the population variability in clearance. Of that variability, common NS variants accounted for the majority, but rare damaging NS variants constituted 17.8% of SLCO1B1's effects (1.9% of total variation) and had larger effect sizes than common NS variants. Our results show that rare variants are likely to have an important effect on pharmacogenetic phenotypes.

Footnotes

• ↵12 Corresponding author.
  E-mail mary.relling{at}stjude.org.
• [Supplemental material is available for this article.]
• Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/ .

• Received July 27, 2011.
• Accepted November 1, 2011.

• Copyright © 2012 by Cold Spring Harbor Laboratory Press

Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition