title: Exon sequencing and high resolution haplotype analysis of ABC transporter genes implicated in drug resistance.
abstract: BACKGROUND
  The ATP-binding cassette (ABC) proteins are a superfamily of efflux pumps implicated as a mechanism for multidrug resistance in cytotoxic chemotherapy, immunosuppressive therapy, HIV and epilepsy. Genetic variation in P-glycoprotein, the product of the ABCB1 gene, is proposed to mediate de novo drug resistance, but associations between polymorphisms in ABCB1 and pharmacoresistance have produced conflicting results. Potential explanations for the inconsistency of results include inadequate characterization of gene structure, variation and linkage disequilibrium (LD) in ABCB1, as well as overlap in substrate specificity between ABCB1 and the various other drug transporters.
  
  
  RESULTS
  We undertook a fundamental analysis of gene structure, variation and LD in ABCB1 and four other drug transporter genes implicated in pharmacoresistance: ABCC1, ABCC2, ABCC5 and ABCB4. Manual annotation of the five genes revealed nine shorter alternative transcripts with new untranslated regions and one novel region of coding sequence, demonstrating that on-line annotations are incomplete. Sequencing of exons in 47 Caucasian individuals identified 75 novel single nucleotide polymorphisms (SNPs) previously undescribed in any public database, including 14 new coding sequence SNPs. Genotyping of 502 SNPs in 842 Caucasian individuals across the five genes revealed large blocks of high LD, and low haplotype diversity across all five genes that could be characterized by between 67 and 114 tagging SNPs, depending on the tagging criteria.
  
  
  CONCLUSIONS
  The study illustrates that publicly available data resources on genomic organization of genes and common variation can have important gaps and limitations, and establishes a comprehensive set of tagging SNPs for future association studies in pharmacoresistance.
authors.affiliation: Imperial College, London, UK.
authors.forename: Guy
authors.initials: G
authors.lastname: Leschziner
authors.forename: Delilah
authors.initials: D
authors.lastname: Zabaneh
authors.forename: M
authors.initials: M
authors.lastname: Pirmohamed
authors.forename: Andrew
authors.initials: A
authors.lastname: Owen
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Alison J
authors.initials: AJ
authors.lastname: Coffey
authors.forename: David J
authors.initials: DJ
authors.lastname: Balding
authors.forename: David B
authors.initials: DB
authors.lastname: Bentley
authors.forename: Michael R
authors.initials: MR
authors.lastname: Johnson
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics*; D000483:Alleles; D018432:Drug Resistance, Multiple / Q000235:genetics; D005091:Exons; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D000089762:Multidrug Resistance-Associated Protein 2; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000235:genetics*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D044465:White People
chemical_list: D018528:ATP-Binding Cassette Transporters; D000089762:Multidrug Resistance-Associated Protein 2; D027425:ATP-Binding Cassette, Sub-Family C Proteins; C000715087:ABCC2 protein, human; C421109:multidrug resistance-associated protein 1