Abacavir is an effective antiretroviral drug used to treat HIV-1 infection. Approximately 5% of patients treated with abacavir develop a hypersensitivity reaction that requires discontinuation of the drug. In an initial pharmacogenetic study conducted in a predominantly White male population, multiple markers in the human leukocyte antigen (HLA)-B chromosomal region were associated with hypersensitivity to abacavir. The HLA-B*5701 association has now been confirmed in White males in a subsequent, larger study (n=293, p=4.7 x 10(-18)) and is also observed in White females (n=56, p=6.8 x 10(-6)) and Hispanics (n=104, p=2.1 x 10(-4)). HLA-B*5701 was not associated with hypersensitivity in Blacks (n=78, p=0.27). HLA-B*5701 alone lacks sufficient predictive value to identify patients at risk for hypersensitivity to abacavir across diverse patient populations. Efforts are ongoing to identify markers with sufficient sensitivity and specificity to be clinically useful. Even after a marker set is identified, appropriate clinical identification and management of hypersensitivity to abacavir must remain the cornerstone of clinical practice.

A loxP-transposon retrofitting strategy for generating large nested deletions from one end of the insert DNA in bacterial artificial chromosomes and P1 artificial chromosomes was described recently [Chatterjee, P. K. & Coren, J. S. (1997) Nucleic Acids Res. 25, 2205-2212]. In this report, we combine this procedure with direct sequencing of nested-deletion templates by using primers located in the transposon end to illustrate its value for position-specific single-nucleotide polymorphism (SNP) discovery from chosen regions of large insert clones. A simple ampicillin sensitivity screen was developed to facilitate identification and recovery of deletion clones free of transduced transposon plasmid. This directed approach requires minimal DNA sequencing, and no in vitro subclone library generation; positionally oriented SNPs are a consequence of the method. The procedure is used to discover new SNPs as well as physically map those identified from random subcloned libraries or sequence databases. The deletion templates, positioned SNPs, and markers are also used to orient large insert clones into a contig. The deletion clone can serve as a ready resource for future functional genomic studies because each carries a mammalian cell-specific antibiotic resistance gene from the transposon. Furthermore, the technique should be especially applicable to the analysis of genomes for which a full genome sequence or radiation hybrid cell lines are unavailable. I dentifying polymorphic sites in the genome is a basic aspect of molecular genetics and genomics. The process is needed for a variety of purposes, ranging from the development of polymorphic marker sets useful as a tool for genetic analysis of a chromosomal region or full genome scan, to the initial identification of variants or mutations in a newly discovered gene (1, 2). In most cases, the identity of base differences and their location relative to a gene or other polymorphic sites is either useful or required. Recent estimates of the number of singlenucleotide polymorphisms (SNPs) needed for whole genome association studies in humans vary from several thousand to several hundred thousand (1, 3); thus, efficient and cost-effective methods for identifying a large number of SNPs with the required characteristics of dense yet even spacing, and of known order over large uncharacterized regions of the genome, is of interest. A comparison of two methods to develop a densely ordered map of SNPs covering a 4-Mb region of the human genome was recently reported (4). In one approach, large-insert bacterial clones, bacterial artificial chromosomes (BACs) (5) and P1 artificial chromosomes (PACs) (6), spanning this region were fragmented and reconstructed in 2-kb plasmid libraries, which were then sequenced. This shotgun procedure is efficient in identifying SNPs; however, to approach a map of 30-kb average SNP spacing, bidirectional sequencing of approximately 500 randomly chosen subclones per 100 kb of genomic sequence was required. Multiple BAC and PAC clones mapping to the region...

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Introduction Alzheimer's disease (AD) is a continuum with neuropathologies manifesting years before clinical symptoms; thus, AD research is attempting to identify more disease‐modifying approaches to test treatments administered before full disease expression. Designing such trials in cognitively normal elderly individuals poses unique challenges. Methods The TOMMORROW study was a phase 3 double‐blind, parallel‐group study designed to support qualification of a novel genetic biomarker risk assignment algorithm (BRAA) and to assess efficacy and safety of low‐dose pioglitazone to delay onset of mild cognitive impairment due to AD. Eligible participants were stratified based on the BRAA (using TOMM40 rs 10524523 genotype, Apolipoprotein E genotype, and age), with high‐risk individuals receiving low‐dose pioglitazone or placebo and low‐risk individuals receiving placebo. The primary endpoint was time to the event of mild cognitive impairment due to AD. The primary objectives were to compare the primary endpoint between high‐ and low‐risk placebo groups (for BRAA qualification) and between high‐risk pioglitazone and high‐risk placebo groups (for pioglitazone efficacy). Approximately 300 individuals were also asked to participate in a volumetric magnetic resonance imaging substudy at selected sites. Results The focus of this paper is on the design of the study; study results will be presented in a separate paper. Discussion The design of the TOMMORROW study addressed many key challenges to conducting a dual‐objective phase 3 pivotal AD clinical trial in presymptomatic individuals. Experiences from planning and executing the TOMMORROW study may benefit future AD prevention/delay‐of‐onset trials.

The objective of pharmacogenetic research is to identify a genetic marker, or a set of genetic markers, that can predict how a given person will respond to a given medicine. To search for such marker combinations that are predictive of adverse drug events, we have developed and applied two complementary methods to a pharmacogenetic study of the hypersensitivity reaction (HSR) associated with treatment with abacavir, a medicine that is used to treat HIVinfected patients. Our results show that both of these methods can be used to uncover potentially useful predictive marker combinations. The pairwise marker combination method yielded a collection of marker pairs that featured a spectrum of sensitivities and specificities. Recursive partitioning results led to the genetic delineation of multiple risk categories, including those with extremely high and extremely low risk of HSR. These methods can be readily applied in pharmacogenetic candidate gene studies as well as in genome-wide scans.