Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms

Weber, James L.

doi:10.1016/0888-7543(90)90195-z

Cited by 1,258 publications

(810 citation statements)

References 19 publications

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“…Our resuits thus indicate that DNA sequencing of compound microsatellites can permit differentiation of alleles that although identical in size, are not identical in sequence. These loci represent a substantial proportion of all microsatellites [11% in one collection of dinucleotide repeats (Weber 1990)] and thus represent an untapped reservoir of potentially useful genetic variation. By designating alleles based on sequence and not on size, this previously unrecognized variation may increase the power of microsatellites in genetic mapping efforts.…”

Section: Discussionmentioning

confidence: 99%

Homoplasy for size at microsatellite loci in humans and chimpanzees.

Garza

Freimer²

1996

Genome Res.

106

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Homoplasy (convergence in the size of different alleles) at microsatellite loci was examined by sequencing multiple alleles of two compound microsatellites and single copies of alleles of the same size at two other compound loci in both chimpanzees and humans. At one of the two loci for which multiple alleles were sequenced, extensive homoplasy for size was uncovered both within and between species. At the three loci for which alleles of the same size were examined in the two species, sequencing demonstrated different internal structures. These results confirm theoretical predictions that a certain fraction of mutations at microsatellite loci should produce alleles that are identical in size but differ by a number of mutations. The sequence data reveal a previously unrecognized class of variation at microsatellites and open up the possibility that DNA sequencing may allow the extraction of more information from these loci, thus increasing their power as variable markers for genetic mapping studies. Conversely, the data also indicate that the assumption that alleles of the same size are identical in sequence, which is implicit in several methods of analysis, is violated in some cases. Therefore, caution should be used when employing microsatellites in phylogenetic and other studies in which the individuals being examined are separated by a great number of generations from a common ancestor.

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Section: Discussionmentioning

confidence: 99%

Homoplasy for size at microsatellite loci in humans and chimpanzees.

Garza

Freimer²

1996

Genome Res.

106

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“…They hypothesized that, because microsatellite isolation protocols generally select loci with unusually long repeat lengths in the source species, any tendency for microsatellites to mutate towards shorter lengths would result in these loci exhibiting fewer repeats in related species. Likewise, because longer alleles tend to be more variable than shorter alleles (Weber, 1990), microsatellites in the source species should be more polymorphic and exhibit higher heterozygosity. This critique led to several studies that compared microsatellite allele lengths and variability reciprocally between two species using loci developed in both species van Treuren et al, 1997;Cooper et al, 1998;Crawford et al, 1998;Hutter et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis

et al. 2004

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SummaryMicrosatellite primers are often developed in one species and used to assess neutral variability in related species. Such analyses may be confounded by ascertainment bias (i.e. a decline in amplification success and allelic variability with increasing genetic distance from the source of the microsatellites). In addition, other factors, such as the size of the microsatellite, whether it consists of perfect or interrupted tandem repeats, and whether it is autosomal or X-linked, can affect variation. To test the relative importance of these factors on microsatellite variation, we examine patterns of amplification and allelic diversity in 52 microsatellite loci amplified from five individuals in each of six populations of Cyrtodiopsis stalk-eyed flies that range from 2 . 2 % to 11 . 2% mitochondrial DNA sequence divergence from the population used for microsatellite development. We find that amplification success and most measures of allelic diversity declined with genetic distance from the source population, in some cases an order of magnitude faster than in birds or mammals. The median and range of the repeat array length did not decline with genetic distance. In addition, for loci on the X chromosome, we find evidence of lower observed heterozygosity compared with loci on autosomes. The differences in variability between X-linked and autosomal loci are not adequately explained by differences in effective population sizes of the chromosomes. We suggest, instead, that periodic selection events associated with X-chromosome meiotic drive, which is present in many of these populations, reduces X-linked variation.

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“…It is accepted that this size increase is due to an increase in the number of CGG repeats in carrier and affected individuals. As is the case for other similar sequences in the genome called microsatellites [26], the number of C G G repeats is polymorphic i.e. i t varies normally in the population (from 6 to 50 copies of the CGG with a mean of 29) [27].…”

Section: The Fragile X Mutations: a New Type Of Pathogenic Mutationsmentioning

confidence: 99%

The fragile X syndrome: implications of molecular genetics for the clinical syndrome

Rousseau

1994

Eur J Clin Investigation

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Abstract. The fragile X syndrome of mental retardation is one of the most common genetic diseases. Characterization of the mutations involved has greatly improved our knowledge of the transmission of fragile X syndrome and new DNA-based diagnostics tools significantly outperform cytogenetic testing both for establishing the diagnosis and for determining carrier status. Fragile X mutations consist of an expansion of a CGG trinucleotide repeat localized in a gene (FMR-1) that is abnormally methylated in all affected individuals. They are classified as premutations (asymptomatic) and full mutations (associated with the disease). Several different DNA analysis protocols are used for fragile X genotyping but only a few have been tested on large samples of individuals. There are several clinical indications for direct DNA genotyping for fragile X including mental retardation, learning disability or hyperactivity in children with or without a family history of mental retardation, the establishment of carrier diagnosis in fragile X families and prenatal screening of children from carrier women.

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Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms

Cited by 1,258 publications

References 19 publications

Homoplasy for size at microsatellite loci in humans and chimpanzees.

Homoplasy for size at microsatellite loci in humans and chimpanzees.

Microsatellite variation among divergent populations of stalk-eyed flies, genus Cyrtodiopsis

The fragile X syndrome: implications of molecular genetics for the clinical syndrome

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