scholarly journals Body temperature predicts maximum microsatellite length in mammals

2008 ◽  
Vol 4 (4) ◽  
pp. 399-401 ◽  
Author(s):  
William Amos ◽  
Andrew Clarke
Keyword(s):  
Body Temperature ◽  
Genome Sequencing ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Temperature Dependent ◽  
Repeat Number ◽  
Stability Threshold ◽  
Marker Loci ◽  
Microsatellite Evolution ◽  
Short Tandem

A long-standing mystery in genome evolution is why short tandem repeats vary so much in length and frequency. Here, we test the hypothesis that body temperature acts to influence the rate and nature of slippage-based mutations. Using the data from both 28 species where genome sequencing is advanced and 76 species from which marker loci have been published, we show that in mammals, maximum repeat number is inversely correlated with body temperature, with warmer-blooded species having shorter ‘long’ microsatellites. Our results support a model of microsatellite evolution in which maximum length is limited by a temperature-dependent stability threshold.

scholarly journals Insertions, substitutions, and the origin of microsatellites

2000 ◽  
Vol 76 (3) ◽  
pp. 227-236 ◽  
Author(s):  
YONG ZHU ◽  
JOAN E. STRASSMANN ◽  
DAVID C. QUELLER
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Human Gene ◽  
Dna Repeats ◽  
Repeat Number ◽  
Mutation Database ◽  
Tetranucleotide Repeats ◽  
Microsatellite Evolution ◽  
Insertion Mutations ◽  
Short Tandem

This paper uses data from the Human Gene Mutation Database to contrast two hypotheses for the origin of short DNA repeats: substitutions and insertions that duplicate adjacent sequences. Because substitutions are much more common than insertions, they are the dominant source of new 2-repeat loci. Insertions are rarer, but over 70% of the 2–4 base insertion mutations are duplications of adjacent sequences, and over half of these generate new repeat regions. Insertions contribute fewer new repeat loci than substitutions, but their relative importance increases rapidly with repeat number so that all new 4–5-repeat mutations come from insertions, as do all 3-repeat mutations of tetranucleotide repeats. This suggests that the process of repeat duplication that dominates microsatellite evolution at high repeat numbers is also important very early in microsatellite evolution. This result sheds light on the puzzle of the origin of short tandem repeats. It also suggests that most short insertion mutations derive from a slippage-like process during replication.

scholarly journals Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population

Heliyon ◽  
2018 ◽  
Vol 4 (5) ◽  
pp. e00625
Author(s):  
Satoshi Hirata ◽  
Kaname Kojima ◽  
Kazuharu Misawa ◽  
Olivier Gervais ◽  
Yosuke Kawai ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Japanese Population ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Whole Genome ◽  
Population Scale ◽  
Short Tandem

scholarly journals STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data

2021 ◽  
Author(s):  
Andreas Halman ◽  
Egor Dolzhenko ◽  
Alicia Oshlack
Keyword(s):  
Genome Sequencing ◽  
Fragment Length ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
High Throughput Sequencing ◽  
Causal Variant ◽  
Sequencing Data ◽  
Pathogenic Variants ◽  
Set Up ◽  
Short Tandem

AbstractShort tandem repeats (STRs) are highly polymorphic with high mutation rates and expansions of STRs have been implicated as the causal variant in diseases. The application of genome sequencing in patients has recently allowed many new discoveries with over 50 disease causing loci known to date. There are several tools which allow genotyping of STRs from high-throughput sequencing (HTS) data. However, running these tools out of the box only allow around half of the known disease-causing loci to be genotyped, with lengths often limited to either read or fragment length which is less than the pathogenic cut-off for some diseases. While analysis tools can be customised to genotype extra loci, this requires proficiency in bioinformatics to set up, use, and analyse the resulting data, limiting their widespread usage by other researchers and clinicians.To address these issues, we have created a new software called STRipy that has an intuitive graphical interface and requires no specific skills for usage, thus significantly simplifying detection of STRs expansions from human HTS data. STRipy is able to target all known disease-causing STRs with genotyping performed with an established tool, ExpansionHunter, that is incorporated into the software. We have created additional functionality into STRipy to work with long alleles exceeding the fragment length.STRipy was validated using over 60 thousand simulated samples and was shown to work on whole genome sequencing of biological samples with pathogenic variants. Finally, we have used STRipy to acquire genotypes of pathogenic loci for thousands of samples from various populations which are provided to the user along with the data from the literature to assist with results interpretation. We believe the simplicity and breadth of STRipy will increase the testing of STR diseases in current datasets resulting in further diagnoses of rare diseases caused by STRs expansions.

Complete Paternal Uniparental Disomy of Chromosome 2 in an Asian Female Identified by Short Tandem Repeats and Whole Genome Sequencing

2019 ◽  
Vol 157 (4) ◽  
pp. 197-202 ◽  
Author(s):  
Xiaochuan Zhang ◽  
Zhaojun Ding ◽  
Ruwen He ◽  
Jiying Qi ◽  
Zijun Zhang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Uniparental Disomy ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Rare Type ◽  
Short Tandem Repeat Markers ◽  
Short Tandem

Uniparental disomy (UPD) is a rare type of chromosomal aberration that has sometimes been detected in paternity testing. We examined a 3-person family (father, mother, daughter) first by using short tandem repeat markers, which revealed 4 markers, TPOX, D2S1338, D2S1772, and D2S441, on chromosome 2 that were not transmitted in a Mendelian style. We then performed whole genome sequencing (WGS) to determine the range of the UPD. Chromosome 2 in the daughter showed a complete paternal UPD. To the best of our knowledge, this is the 4th case of complete paternal UPD of chromosome 2 with no clinical phenotype. Our study suggests that WGS, when performed to enhance the accuracy and reliability of parentage testing, can provide a powerful method to detect an UPD.

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

1997 ◽  
Vol 45 (3) ◽  
pp. 265-270 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
Mark Seielstad ◽  
Eva Mateu ◽  
David Comas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

Conditional Genotypic Probabilities for Microsatellite Loci

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1973-1980
Author(s):  
Jinko Graham ◽  
James Curran ◽  
B S Weir
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Dirichlet Distribution ◽  
Forensic Dna ◽  
Match Probability ◽  
Microsatellite Genotype ◽  
Allelic State ◽  
Forensic Assessments ◽  
Dna Profiles ◽  
Short Tandem

Abstract Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2–5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.

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