Triplex forming oligonucleotides: sequence-specific tools for gene targeting.

Sequence-specificity is the key to effective genetic targeting. With specificity, targeted genes can be manipulated in multiple ways; without it, gene therapy agents become loose canons within cells. Triplex forming oligonucleotides (TFOs) bind in the major groove of duplex DNA with high specificity and affinity. Because of these characteristics, TFOs have been proposed as homing devices for genetic manipulation in vivo. Here we review work demonstrating the ability of TFOs and related molecules to alter gene expression and mediate genome modification in mammalian cells. Recent studies have established that TFOs can mediate targeted gene knock out in mice, laying the foundation for the potential application of these molecules in human gene therapy.

Analyses of the COGA data set in one ethnic group with examinations of alternative definitions of alcoholism.

We used GENEHUNTER and GENEHUNTER-PLUS to search for linkage with the markers in the Collaborative Study on the Genetics of Alcoholism (COGA) data set in a single ethnic group. Analyses of a complex disorder such as alcoholism depend on the definition of affection status. The COGA study provides two definitions of alcoholism (variables ALDX1 and ALDX2). To identify more severely affected alcoholics that might be more homogeneous genetically, we developed two other ways of characterizing subjects as alcohol dependent: (1) by combining the symptom variable values equally into a 24-point scale and (2) by weighting optimally the symptoms and other descriptive variables into a single score using logistic regression. We applied these definitions within a single ethnic group to map alcoholism-related loci. We found two regions on chromosome 1 that have adjacent markers significant at p-values < or = 0.05. ALDX1 provided the highest Z-scores compared to the alternatives.

A more powerful method to evaluate p-values in GENEHUNTER.

The determination of statistical significance in genetic linkage studies is complicated by many factors, such as missing individuals or uninformative markers, and the validity of theoretical results is often questionable. Although many simulation-based methods have been proposed to determine empirically the statistical significance, they are either not generally applicable to complex pedigree structures, or not able to preserve the observed genetic information content at each locus in the pedigrees. We have developed and implemented a general and computationally efficient randomization procedure in GENEHUNTER that applies to arbitrary pedigree structure and preserves the observed information content at each locus. We applied this method to the Problem 1 data set of the Genetic Analysis Workshop 11. The performance of this new method was similar to the method implemented in GENEHUNTER-PLUS, and both outperformed the conservative approach in GENEHUNTER.