The human genome initiative--do databases reflect current progress?

Current Concepts in Embryonic Craniofacial Development

Embryology mirrors phylogeny. The phenotypic expression of the genome is the result of differential gene transcription, the critically timed turning on and off of specific genes by transcription factors to produce cyto-, histo-, and morpho-differentiation that fleetingly reflects evolutionary stages of development during ontogeny. Hox genes regulate transcription of other structural genes and are responsible for patterning of the facial primordia. Cephalic development involves extremely complex morphogenetic mechanisms built on conserved elements that have undergone enormous evolutionary changes. Transient expression of phylogenetic origins characterize ontogeny and are reflected in defective development that may be due to inappropriate expression of Hox genes or distorted or disrupted epignetic processes. The mechanisms by which genetic information is transformed into morphological patterning by the actions of growth factors, morphogenes, and receptors are currently being identified. Biochemical, immunological, and allometric analyses of embryos and fetuses in experimental and descriptive studies are elucidating details of units of craniofacial morphogenesis--faciogenesis, palatogenesis, gnathogenesis, odontogenesis. Three-dimensional model computer-assisted reconstruction of sectioned embryos and fetuses provides a further technique for understanding the complex configurations of tissue migratory patterns and growth sites that account for normal and abnormal craniofaciogenesis.

The construction of a tetraploid cotton genome wide comprehensive reference map

Integration of multiple genomic maps provides a higher density of markers and greater genome coverage, which not only facilitates the identification and positioning of QTLs and candidate genes, but it also provides a basic structure for the genome sequence assembly. However, the diversity in markers and populations used in individual mapping studies limits the ability to fully integrate the available data. By concentrating on marker orders rather than marker distances, published map data could be used to produce a comprehensive reference map (CRM) that includes a majority of known markers with optimally estimated order of those markers across the genome. In this study, a tetraploid cotton genome-wide CRM was constructed from 28 public cotton genetic maps. The initial CRM contained 7,424 markers and represented over 93% of the combined mapping information from the 28 individual maps. The current output is stored and displayed through CottonDB (http://www.cottondb.org), the public cotton genome database.

Analysis of DNA sequences

Recent developments in the statistical analysis of DNA sequences are reviewed. The pace with which sequence data are being generated and analysed has increased with the growth of the human genome project. Two areas of activity are emphasized: attention to error rates in recorded sequences, and heterogeneity in structure of sequences. There is now empirical evidence suggesting error rates in the range 0.1%-1%, and such rates will affect evolutionary studies since these are about the rates at which DNA sequences from different individuals are expected to differ. Heterogeneity for such quantities as base composition, or lengths between successive subsequences of specified types, may be sufficient to account for observed long-range correlations between bases. The need for statistical models and analyses of DNA sequence data will continue, and will offer interesting challenges.

The future of genetic epidemiology

Starting from a broad definition of genetic epidemiology, current developments in association, segregation, and linkage analysis of complex inheritance are considered together with integration of genetic and physical maps and resolution of genetic heterogeneity. Mitochondrial inheritance, imprinting, uniparental disomy, pregressive amplification, and gonadal mosaicism are some of the novel mechanisms discussed, with speculation about the future of genetic epidemiology.

Algorithms for a location database

The algorithms that drive the ldb location database are described. The program captures data on genetic and physical maps and combines information from different sources into a summary map. To assure portability it was developed in Fortran on a SUN SPARCStation under Unix. The algorithms, which combine rule-based seriation with a minimum deviance bootstrap, allow investigators and chromosome committees to produce a composite location in Mb that integrates partial maps. The program and manual are now available from the authors.

Integration of gene maps: chromosome 1

A composite map of 177 loci has been constructed in two steps. The first combined pairwise logarithm-of-odds scores on 127 loci into a comprehensive genetic map. Then this map was projected onto the physical map through cytogenetic assignments, and the small amount of physical data was interpolated for an additional 50 loci each of which had been assigned to an interval of less than 10 megabases. The resulting composite map is on the physical scale with a resolution of 1.5 megabases. In the future these methods may be used to incorporate locations from linkage, contigs, radiation hybrids, restriction fragments, and somatic cell maps. Dense, reliable, and well-documented maps are essential for long-range sequencing and to localize and clone disease genes.