Testing for segregation distortion in the HLA complex

One of the long-standing issues in HLA research is whether there is segregation distortion in the HLA complex in human populations. In this paper we study some simple statistical models aimed at detecting segregation distortion. We present a statistic to test the Mendelian null hypothesis of equal transmission probabilities. To assess the possible contribution of multiple alleles to segregation distortion, we employ a specific log-linear model for transmission probabilities equivalent to the Bradley-Terry model in the literature of paired comparisons. We also provide a simple method for detecting a single allele effect, if present.

Predicting progress in directed mapping projects

Several recent mapping efforts have used so-called "directed" approaches to construct their maps. However, most, but not all, published methods for modeling the progress in physical mapping projects have been focused on random approaches, such as bottom-up fingerprinting and STS-content mapping. In addition, those few efforts that did model directed approaches used methods that required assuming that all insert lengths were the same. This assumption is unnecessary. Using properties of stationary processes, one can derive simple asymptotic formulas that apply equally to constant and variable clone lengths. Also, in the case of constant clone lengths, these results are equivalent to, and extend, those published results for directed mapping derived by other methods. Simulations show that these methods provide estimates well within the limits of uncertainty inherent in any mapping project.

Atypical regions in large genomic DNA sequences

Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. We describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of > 1000 nt and human sequences of > 10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. We consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

Assessing between-block heterogeneity within the post-strata of the 1990 Post-Enumeration Survey

"The 1990 [U.S.] Post-Enumeration Survey (PES) stratified the population into 1,392 subpopulations called post-strata based on location, race, tenure, sex and age, in the hope that these subpopulations were homogeneous in relation to factors affecting the Census coverage....With block-level data from the PES for sites around Detroit and Texas, we are able to examine empirically the extent to which this hope was realized. Using various measures, we find that between-block variation in erroneous enumeration and gross omission rates is about the same magnitude as, and largely in addition to, the corresponding between-post-stratum variation." Comments by Joseph L. Schafer and Donald Ylvisaker and a rejoinder by the authors are included (pp. 1,125-9).

Factors associated with human immunodeficiency virus seroconversion in homosexual men in three San Francisco cohort studies, 1984-1989

A total of 83 HIV seroconversions occurred between 1984 and 1989 in three San Francisco cohorts of homosexual and bisexual men. A nested case-control analysis was performed to assess the risk of seroconversion associated with sexual practices. Strong associations were found with total number of intercourse partners and receptive anal intercourse. Weaker, but significant associations were found with receptive oral intercourse. Individuals reporting condom use with some partners were more likely to become infected than those reporting no condom use. Some of this difference was due to increased numbers of sexual partners among those reporting some condom use, but the association remained significant in multivariate analyses. This observation indicates there is some unmeasured risk associated with those using condoms, such as more HIV seropositive partners.

Estimating the fraction of invariable codons with a capture-recapture method

A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of the number of variable codons and to previous approaches that estimate the number of variable sites (not codons) in a sequence. Computer simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that employ a capture-recapture estimate of the number of variable sites may be considerably different from corrections that assume that the number of variable sites is equal to the total number of positions in the sequence.

Robustness of the no-interference model for ordering genetic markers

Under the assumption of no chromatid interference, we derive constraints on the probabilities of the different recombination patterns among m + 1 genetic loci. An application of these constraints is a proof that the ordering of the loci that maximizes the likelihood under the assumption of no interference is, in fact, a consistent estimator of the true order even when there is interference.

Inner cell allocation in the mouse morula: the role of oriented division during fourth cleavage

Two populations of blastomeres become positionally distinct during fourth cleavage in the mouse embryo; the inner cells become enclosed within the embryo and the outer cells form the enclosing layer. The segregation of these two cell populations is important for later development, because it represents the initial step in the divergence of placental and fetal lineages. The mechanism by which the inner cells become allocated has been thought to involve the oriented division of polarized 8-cell blastomeres, but this has never been examined in the intact embryo. By using the technique of time-lapse cinemicrography, we have been able for the first time to directly examine the division planes of 8-cell blastomeres during fourth cleavage, and find that there are three, rather than two, major division plane orientations; anticlinal (perpendicular to the outer surface of the blastomere), periclinal (parallel to the outer surface of the blastomere), and oblique (at an angle between the other two). The observed frequencies of each type of division plane orientation provide evidence that the inner cells of the morula must derive from oriented division of 8-cell blastomeres, in accordance with the polarization hypothesis. Analysis of fourth cleavage division plane orientation with respect to either lineage or division order reveals that it is not associated with lineage from either the 2- or the 4-cell stage, but has a slight statistical association with fourth cleavage division order. The lack of association between division plane orientation and lineage supports the prediction that packing patterns and intercellular interactions within the 8-cell embryo during compaction play a role in determining fourth cleavage division plane orientation and thus, the positional fate of the daughter 16-cell blastomeres.

Incorporating prior information into the analysis of contingency tables

Contingency tables are often analyzed using log-linear models and in some situations prior information on the value of parameters in the log-linear model is available. In this article we describe a prior-posterior procedure that incorporates prior information directly into the analysis through a multivariate normal prior for the log-linear parameters. The mode and curvature of the posterior density are proposed as summary statistics.

Intestinal transport of monosaccharide after biliary diversion in the rat

Sugar absorption is increased in rats with a bile fistula but approaches normal values with the addition of bile salt. It has therefore been suggested that bile salts have a physiological role in decreasing intestinal absorption of monosaccharides. In experiments using rats, jejunal and ileal uptake of arbutin, a glucose analogue was increased 5 days after creating a bile fistula but normal by the 10th day after operation. Bile fistula rats ate only about one third of the intake of normal rats in the first 5 days after operation. Control animals fed the same amount as the bile fistula group showed a similar increase in jejunal and ileal arbutin uptake. In both groups, on the 5th post-operative day, addition of taurocholate depressed arbutin uptake towards normal. In normal rats, taurocholate depressed arbutin uptake in the ileum but not the jejunum. These results suggest that increased monosaccharide uptake in bile fistula rats is related to semi-starvation and is not a specific effect of bile salts.