High-throughput variation detection and genotyping using microarrays.

The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray technology can enable rapid genotyping of variation specific to study samples. To facilitate their use, we have developed an automated statistical method (ABACUS) to analyze microarray hybridization data and applied this method to Affymetrix Variation Detection Arrays (VDAs). ABACUS provides a quality score to individual genotypes, allowing investigators to focus their attention on sites that give accurate information. We have applied ABACUS to an experiment encompassing 32 autosomal and eight X-linked genomic regions, each consisting of approximately 50 kb of unique sequence spanning a 100-kb region, in 40 humans. At sufficiently high-quality scores, we are able to read approximately 80% of all sites. To assess the accuracy of SNP detection, 108 of 108 SNPs have been experimentally confirmed; an additional 371 SNPs have been confirmed electronically. To access the accuracy of diploid genotypes at segregating autosomal sites, we confirmed 1515 of 1515 homozygous calls, and 420 of 423 (99.29%) heterozygotes. In replicate experiments, consisting of independent amplification of identical samples followed by hybridization to distinct microarrays of the same design, genotyping is highly repeatable. In an autosomal replicate experiment, 813,295 of 813,295 genotypes are called identically (including 351 heterozygotes); at an X-linked locus in males (haploid), 841,236 of 841,236 sites are called identically.

Patterns of genetic variation in Mendelian and complex traits.

This review discusses the prospects for understanding the genetic basis of complex traits in humans. We take the view that work done on Drosophila melanogaster can serve as a model for understanding complex traits in humans, and the literature on this model system, as well as on humans, is reviewed. The prospects for success in understanding the genetic basis of complex traits depend, in part, on the nature of the forces acting on genetic variation. We suggest that different experimental approaches should be undertaken for traits caused by common genetic variants versus those arising from rare genetic variants.

Genetic variation in rates of nondisjunction: association of two naturally occurring polymorphisms in the chromokinesin nod with increased rates of nondisjunction in Drosophila melanogaster.

Genetic variation in nondisjunction frequency among X chromosomes from two Drosophila melanogaster natural populations is examined in a sensitized assay. A high level of genetic variation is observed (a range of 0.006-0.241). Two naturally occurring variants at the nod locus, a chromokinesin required for proper achiasmate chromosome segregation, are significantly associated with an increased frequency of nondisjunction. Both of these polymorphisms are found at intermediate frequency in widely distributed natural populations. To account for these observations, we propose a general model incorporating unique opportunities for meiotic drive during female meiosis. The oötid competition model can account for both high mean rates of female-specific nondisjunction in Drosophila and humans as well as the standing genetic variation in this critical fitness character in natural populations.

Classic Weinstein: tetrad analysis, genetic variation and achiasmate segregation in Drosophila and humans.

A maximum-likelihood method for the estimation of tetrad frequencies from single-spore data is presented. The multilocus exchange with interference and viability (MEIV) model incorporates a clearly defined model of exchange, interference, and viability whose parameters define a multinomial distribution for single-spore data. Maximum-likelihood analysis of the MEIV model (MEIVLA) allows point estimation of tetrad frequencies and determination of confidence intervals. We employ MEIVLA to determine tetrad frequencies among 15 X chromosomes sampled at random from Drosophila melanogaster natural populations in Africa and North America. Significant variation in the frequency of nonexchange, or E(0) tetrads, is observed within both natural populations. Because most nondisjunction arises from E(0) tetrads, this observation is quite unexpected given both the prevalence and the deleterious consequences of nondisjunction in D. melanogaster. Use of MEIVLA is also demonstrated by reanalyzing a recently published human chromosome 21 dataset. Analysis of simulated datasets demonstrates that MEIVLA is superior to previous methods of tetrad frequency estimation and is particularly well suited to analyze samples where the E(0) tetrad frequency is low and sample sizes are small, conditions likely to be met in most samples from human populations. We discuss the implications of our analysis for determining whether an achiasmate system exists in humans to ensure the proper segregation of E(0) tetrads.

Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy.

Mitochondrial DNA of higher animals has been described as an example of extreme efficiency in genome structure and function. Where exceptionally large size molecules have been found (greater than 20 kb), most have occurred as rare variants within a species, suggesting that these variants arise infrequently and do not persist for long periods in evolutionary time. In contrast, all individuals of at least three species of bark weevil (Curculionidae: Pissodes) possess a mitochondrial genome of unusually large size (30-36 kb). The molecule owes its large size to a dramatically enlarged A + T-rich region (9-13 kb). Gene content and order outside of this region appear to be identical to that found in Drosophila. A series of 0.8-2.0-kb repeated sequences occur adjacent to the large A + T rich region and have perhaps played a role in the generation of the large size as well as an unprecedented frequency of size variant heteroplasmy. Every weevil sampled in all three species (n = 219) exhibits anywhere from two to five distinct size classes of mtDNA. The persistence of this large amount of size polymorphism through two speciation events combined with the abundant size variation within individuals suggests that these molecules may not be subject to strong selection for small overall size and efficiency of replication. This pattern of variation contrasts strongly with the conservation of gene content and arrangement in the coding region of the molecule.