Simultaneous detection of size and sequence polymorphisms in the transcribed trinucleotide repeat D2S196E (EST00493)

Heteroduplex analysis of minisatellite variability

Minisatellites are tandem repeat arrays of middle size (5-100 bp) repeat units widely distributed in eukaryotic genomes. They have been related to several important features of human genome biology, including gene regulation, chromosomal fragile sites, and imprinting. In this report, we have critically assessed and employed heteroduplex analysis (HA) for the identification of different human minisatellite MsH43 alleles. This minisatellite is organized as a repeat array of 5-6 bp units spanning 0.5 kbp. Our results demonstrate that this procedure is an easy, rapid, and reliable method to document allelic diversity for this locus. This work suggests that HA will also be a useful tool for studying the polymorphism of other minisatellites with small repeat units.

Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags

The construction of high-density linkage maps for use in identifying loci underlying important traits requires the development of large numbers of polymorphic genetic markers spanning the entire genome at regularly spaced intervals. As part of our efforts to develop markers for rainbow trout (Oncorhynchus mykiss), we performed a comparison of allelic variation between microsatellite markers developed from expressed sequence tag (EST) data and anonymous markers identified from repeat-enriched libraries constructed from genomic DNA. A subset of 70 markers (37 from EST databases and 33 from repeat enriched libraries) was characterized with respect to polymorphism information content (PIC), number of alleles, repeat number, locus duplication within the genome and ability to amplify in other salmonid species. Higher PIC was detected in dinucleotide microsatellites derived from ESTs than anonymous markers (72.7% vs. 54.0%). In contrast, dinucleotide repeat numbers were higher for anonymous microsatellites than for EST derived microsatellites (27.4 vs.18.1). A higher rate of cross-species amplification was observed for EST microsatellites. Approximately half of each marker type was duplicated within the genome. Unlike single-copy markers, amplification of duplicated microsatellites in other salmonids was not correlated to phylogenetic distance. Genomic microsatellites proved more useful than EST derived microsatellites in discriminating among the salmonids. In total, 428 microsatellite markers were developed in this study for mapping and population genetic studies in rainbow trout.

Detection of errors in dinucleotide repeat typing by nondenaturing electrophoresis

This study shows that consideration of minor bands (heteroduplex, shadow, and faint bands) associated with allele bands in nondenaturing polyacrylamide gel electrophoresis (PAGE) after polymerase chain reaction (PCR) is effective for detecting PCR processing errors that lead to mistyping of heterozygotes as homozygotes. Notably, we show that minor bands in native gels are highly effective for detecting allele dropout and preferential amplification in PCR amplification of dinucleotide repeats. These findings are based on an analysis of Mendelian inheritance patterns in families, and the reproduction of heterozygous band patterns by mixing homozygous DNAs before PCR, for a total of six (AC)n repeats located on human chromosome 11p15. To investigate the utility of our approach, a large population sample of 405 unrelated individuals was genotyped for each (AC)n repeat using minor bands as internal quality controls. Genotype frequencies at each of the six loci were in close agreement with Hardy-Weinberg proportions, which suggests that there were few genotyping errors. Our observations add to the evidence indicating that minor bands in native gels are of diagnostic value in the genotyping of dinucleotide repeats.

Fully mutated and gray-zone FRAXA alleles in Brazilian mentally retarded boys

We used a non-isotopic polymerase chain reaction (PCR) technique for fragile X syndrome diagnosis to screen 256 mentally retarded boys who were selected randomly from special schools. Patients identified as pre- or full-mutation carriers were further investigated by Southern blot analysis with the StB12.3 probe. The PCR-based test identified five boys with the expanded allele and 17 other patients as carriers of either premutated or gray-zone alleles. The full mutation was confirmed in four cases after Southern blotting and a fifth patient carried a normal allele. Of the 17 patients identified with a premutation allele by PCR, one individual was diagnosed as mosaic by Southern blotting, 12 individuals displayed fragments of 2.90 kb or 2.85 kb, and the remaining four individuals showed apparently normal-sized fragments. However, sizing of these 16 alleles by further PCR analysis showed them to be in the gray-zone range (40-60 repeats). Therefore, the frequency of the full mutation in this cohort of mentally retarded boys was close to 2% (5/256). The prevalence of gray-zone alleles among those mentally impaired boys who did not carry the full mutation was 6.4% (16/251) and, although more than twice the prevalence of these alleles among a cohort of unaffected Brazilian males 2.8% (71251), the difference did not reach statistical significance.

The Merck Gene Index project

The Merck Gene Index project (MGIP) fills an important niche in the Human Genome Project by directly identifying genes through sequences of their transcripts and placing in the public domain a set of EST sequences and associated clones for the uniquely expressed human genes. The MGIP promotes the unrestricted exchange of human genomic data, and facilitates progress in biomedical research by reducing duplication of efforts, speeding the identification of disease-related genes and furthering our understanding of disease processes. The project is stimulating biological research, which in turn is the driving force in drug discovery today.

Characterization and mapping of four novel human expressed polymorphic trinucleotide microsatellites

Recently, several important human genetic diseases have been shown to be due to pathological expansion of expressed trinucleotide microsatellites. Discovery of other such 'expansion diseases' will depend on characterization of more expressed loci containing trinucleotide repeats. We searched the expressed sequence tag database (dbEST) for repetitive trinucleotides and selected four loci for further studies (EST00586 EST05486, EST13299 and HHEA48B). For each locus, we have identified size polymorphism by PCR amplification and achieved chromosomal mapping using a somatic hybrid cell panel and the Stanford G3 radiation hybrid panel. Further searches of GenBank, dbEST and UniGene unraveled EST clusters for three of the loci, allowing construction of contigs and, in one instance, identification of a partial open reading frame. Three of the loci were linked to autosomal dominant human genetic diseases whose primary gene defect has not yet been established. Although it is a priori improbable that there is an etiological connection between the loci studied and the diseases, our results demonstrate that dbEST constitutes a useful starting point in the search for candidate loci for new expansion diseases.

Utilization of microsatellites for the analysis of genomic alterations in colorectal cancers in Brazil

Two different pathogenetic mechanisms are proposed for colorectal cancers. One, the so-called "classic pathway", is the most common and depends on multiple additive mutational events (germline and/or somatic) in tumor suppressor genes and oncogenes, frequently involving chromosomal deletions in key genomic regions. Methodologically this pathway is recognizable by the phenomenon of loss of heterozygosity. On the other hand, the "mutator pathway" depends on early mutational loss of the mismatch repair system (germline and/or somatic) leading to accelerated accumulation of gene mutations in critical target genes and progression to malignancy. Methodologically this second pathway is recognizable by the phenomenon of microsatellite instability. The distinction between these pathways seems to be more than academic since there is evidence that the tumors emerging from the mutator pathway have a better prognosis. We report here a very simple methodology based on a set of tri-, tetra- and pentanucleotide repeat microsatellites allowing the simultaneous study of microsatellite instability and loss of heterozygosity which could allocate 70% of the colorectal tumors to the classic or the mutator pathway. The ease of execution of the methodology makes it suitable for routine clinical typing.