Analysis of short tandem repeat (STR) allele frequency distributions in a Balinese population

Morell, Robert J.; Asher, James H.; Weber, James L.; Hinnant, John T.; Winata, Sunaryana; Arhya, I. Nyomen; Friedman, Thomas B.

doi:10.1093/hmg/4.1.85

Cited by 11 publications

(8 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The paper (22) is widely cited, and the presumed high mutation rates of tetranucleotides are frequently invoked to explain other observations, as in the Discussion of ref. 25.…”

Section: Discussionmentioning

confidence: 99%

Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci

Chakraborty

Kimmel²,

Stivers³

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

372

247

View full text Add to dashboard Cite

Using the generalized stepwise mutation model, we propose a method of estimating the relative mutation rates of microsatellite loci, grouped by the repeat motif. Applying ANOVA to the distributions of the allele sizes at microsatellite loci from a set of populations, grouped by repeat motif types, we estimated the effect of population size differences and mutation rate differences among loci. This provides an estimate of motif-type-specific mutation rates up to a multiplicative constant. Applications to four different sets of di-, tri-, and tetranucleotide loci from a number of human populations reveal that, on average, the non-disease-causing microsatellite loci have mutation rates inversely related to their motif sizes. The dinucleotides appear to have mutation rates 1.5-2 times higher than the tetranucleotides, and the non-disease-causing trinucleotides have mutation rates intermediate between the di-and tetranucleotides. In contrast, the disease-causing trinucleotides have mutation rates 3.9-6.9 times larger than the tetranucleotides. Comparison of these estimates with the direct observations of mutation rates at microsatellites indicates that the earlier suggestion of higher mutation rates of tetranucleotides in comparison with the dinucleotides may stem from a nonrandom sampling of tetranucleotide loci in direct mutation assays.The mutation rate () at genetic loci and the effective population size (N) are two basic parameters for understanding the genetic structure of a population. Numerous population genetic studies addressed the question of estimating these two quantities individually as well as simultaneously (1-3). For populations with large generation time and overlapping generations, direct estimation of effective population size is problematic (4). Likewise, mutation rates at most genetic loci are not large enough to be directly measured, and inference of true mutational events is also complicated by assumptions regarding biological relationships of the observed pedigrees (5, 6).One alternative is to estimate the mutation rates by indirect procedures that rely on allele frequency distributions in populations (1-3, 5, 7). In these studies it was assumed that (i) population is in a mutation-drift balance, so that the allele frequency distributions in populations could be expressed in terms of N, the product of effective population size (N), and the rate of mutation (); and (ii) that each mutation yields an allele previously not seen in the population (the infinite allele model). The first assumption is reasonable for most large populations, whereas the second may not apply to all loci. In particular, for microsatellite loci, where polymorphisms are caused by differences in the number of tandem repeats, the infinite allele model does not apply (8-10).Recent theoretical work suggests that the within-population variance of repeat unit sizes is proportional to the product of two basic parameters, N and (11, 12), and this relationship holds even when the pattern of mutational changes at microsatell...

show abstract

“…The paper (22) is widely cited, and the presumed high mutation rates of tetranucleotides are frequently invoked to explain other observations, as in the Discussion of ref. 25.…”

Section: Discussionmentioning

confidence: 99%

Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci

Chakraborty

Kimmel²,

Stivers³

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

372

247

View full text Add to dashboard Cite

show abstract

“…Therefore, we need to take into account the relative reliability of these sources. In subsequent sections, an attempt will nevertheless be made to estimate the age of Kata Kolok, informed by an evaluation of anthropological evidence (Hinnant 2000;Marsaja 2008:53-60) and genetic research stemming from the early 1990s Morell et al 1995;Winata et al 1995;Liang et al 1998;Friedman et al 2000). I argue that Kata…”

Section: Time Depth Of Kata Kolokmentioning

confidence: 99%

“…Moreover, the linguistic and anthropological documentation and description of deaf villages are still in their initial stages (Nonaka, Nyst, & Kisch 2010). The community that uses Kata Kolok is one of a few examples where analyses have been undertaken covering genetic Morell et al 1995;Winata et al 1995;Probst et al 1998;Wang et al 1998;Friedman et al 2000), anthropological (Hinnant 2000), 24 sociolinguistic (Branson et al 1999;Marsaja 2008), and in-depth linguistic analyses (Marsaja 2008;Perniss & Zeshan 2008;Schwager & Zeshan 2008;de Vos 2011;Zeshan, Marsaja, & de Vos in prep.). The study of Kata Kolok therefore offers an especially well-documented perspective on the exceptional dynamics that exist in deaf villages and their village sign languages.…”

Section: Bengkala: a Deaf Village In The North Of Balimentioning

confidence: 99%

Sign-spatiality in Kata Kolok

Vos

2013

SL&L

View full text Add to dashboard Cite

“…Polymorphisms are important because they are used to map genes through linkage analysis (Terwilliger and Ott, 1994), to presymptomatically predict disease status (Antonarakis 1989;Weber 1994), to detect submicroscopic chromosomal rearrangements (Lupski et al 1991), to identify individuals in, for example, paternity and forensic testing (Hagelberg et al 1991;Frigeau and Fourney 1993;Smith 1995;Urquhart et al 1995), and to study a wide range of biological phenomena such as evolution (Bowcock and Cavalli-Sforza 1991;Bowcock et al 1994;Jorde et al 1995), population biology (Edwards et al 1992;Deka et al 1995;Morell et al 1995), and recombination (Tanzi et al 1992;Weber et al 1993). Polymorphisms within coding and regulatory elements are also the source of relative risk for many common diseases.…”

Section: Advantages Of Whole-genome Shotgun Sequencingmentioning

confidence: 99%

“…Many highly informative human DNA polymorphisms based on short tandem repeats have already been identified, but the vast majority of the much more frequent biallelic base substitution and short insertion/deletion polymorphisms remain unknown (Kwok et al 1994(Kwok et al , 1996. Although allele frequencies vary widely, most human DNA polymorphisms are common to all populations (Bowcock and Cavalli-Sforza 1991;Jorde et al 1995;Bowcock et al 1994;Deka et al 1995;Edwards et al 1992;Morell et al 1995). DNA polymorphisms would not usually be detected through clone-by-clone sequencing because only one variant for each genomic region would be sampled.…”

Section: Advantages Of Whole-genome Shotgun Sequencingmentioning

confidence: 99%