Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples

Hundred unrelated father-son buccal swab sample pairs collected from consented Tanzanian population were examined to establish mutation rates using 17 Y-STRs loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTRYfiler kit used in forensics and paternity testing. Prior to 17 Y-STRs analysis, father-son pair biological relationships were confirmed using 15 autosomal STRs markers and found to be paternally related. A total of four single repeat mutational events were observed between father and sons. Two mutations resulted in the gain of a repeat and the other two resulted in a loss of a repeat in the son. All observed mutations occurred at tetranucleotide loci DYS389II, DYS385a, and DYS385b. The locus specific mutation rate varied between 0 and 1.176 x10−3 and the average mutation rate of 17Y-STRs loci in the present study was 2.353x10−3 (6.41x10−4 - 6.013x10−3) at 95% CI. Furthermore the mean fathers’ age with at least one mutation at son’s birth was 32 years with standard error of 2.387 while the average age of all fathers without mutation in a sampled population at son’s birth was 26.781 years with standard error of 0.609. The results shows that fathers’ age at son’s birth may have an effect on Y-STRs mutation rate analysis, though this age difference was statistically not significant using unpaired samples t-test (p = 0.05). As a consequence of observed mutation rates in this study, the precise and reliable understanding of mutation rate at Y-chromosome STR loci is necessary for a correct evaluation and interpretation of DNA typing results in forensics and paternity testing involving males. The criterion for exclusion in paternity testing should be defined, so that an exclusion from paternity has to be based on exclusion constellations at a minimum of two 17 Y-STRs loci.

Download Full-text

Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.1785 ◽

2016 ◽

Vol 283 (1841) ◽

pp. 20161785 ◽

Cited By ~ 4

Author(s):

Long Wang ◽

Yanchun Zhang ◽

Chao Qin ◽

Dacheng Tian ◽

Sihai Yang ◽

...

Keyword(s):

Mutation Rate ◽

Recombination Rate ◽

Mutation Rates ◽

Recombination Rates ◽

Rate Analysis ◽

A Genome ◽

Break Points ◽

New Mutations

Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent–offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination–heterozygozity correlation in peach, we caution against such an interpretation.

Download Full-text

Estimation of the Y-chromosomal short tandem repeat (Y-STR) mutation rates in Turkey

Turkish Journal of Biochemistry ◽

10.1515/tjb-2017-0240 ◽

2018 ◽

Vol 43 (2) ◽

pp. 142-150

Author(s):

Elif Mertoglu ◽

Gonul Filoglu ◽

Tolga Zorlu ◽

Ozlem Bulbul

Keyword(s):

Y Chromosome ◽

Tandem Repeats ◽

Turkish Population ◽

Mutation Rates ◽

Forensic Sciences ◽

Str Loci ◽

Kinship Relations ◽

Unchanged Form ◽

Short Tandem

Abstract Background: The Non-recombining region of the Y-chromosome (NRY) is transferred from father to son in an unchanged form without recombination in meiosis. Since Short tandem repeats on Y-chromosome (Y-STRs) in this region do not have any recombination, these regions are identical in all male individuals who are related to the father except for mutations. Therefore, these regions gain importance in identification for the forensic sciences or determination of paternity. In determination of paternity, if mismatches are observed between father and child, population-specific mutation rates should be used to determine whether it is a mutation or a true exclusion. Therefore in this study, we aim to determine the mutation rates of 17 Y-STR loci in Turkey. Material and methods: 17 Y-STR loci were typed by using AmpFlSTR® Yfiler™ Kit in 90 volunteer father-son pairs. Mutation rates were calculated and compared with other populations. Results: The mutations were found between three father-son pairs at DYS439 and DYS458 loci. In addition, a duplication in DYS389 II loci* 30, 31 was observed. The average mutation rate was determined as 1.96×10−3 for Turkish population. Conclusion: This investigation will contribute to minimize the possibility of false exclusion of the father-son and kinship relations.

Download Full-text

Dynamic of Mutational Events in Variable Number Tandem Repeats ofEscherichia coliO157:H7

BioMed Research International ◽

10.1155/2013/390354 ◽

2013 ◽

Vol 2013 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

A. V. Bustamante ◽

A. M. Sanso ◽

D. O. Segura ◽

A. E. Parma ◽

P. M. A. Lucchesi

Keyword(s):

Mutation Rate ◽

Tandem Repeats ◽

Serial Passage ◽

Variable Number ◽

Mutation Rates ◽

Similar Proportion ◽

Factors Affecting ◽

Repeat Units ◽

Differential Weighting ◽

Epidemiology Studies

VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenicE. coliO157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05to 1.8 × 10−03mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.

Download Full-text

The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time

The American Journal of Human Genetics ◽

10.1086/380911 ◽

2004 ◽

Vol 74 (1) ◽

pp. 50-61 ◽

Cited By ~ 285

Author(s):

Lev A. Zhivotovsky ◽

Peter A. Underhill ◽

Cengiz Cinnioğlu ◽

Manfred Kayser ◽

Bharti Morar ◽

...

Keyword(s):

Y Chromosome ◽

Mutation Rate ◽

Human Population ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Divergence Time ◽

Population Divergence ◽

Short Tandem

Download Full-text

Mutation rates at Y chromosome short tandem repeats in Texas populations

Forensic Science International Genetics ◽

10.1016/j.fsigen.2009.01.007 ◽

2009 ◽

Vol 3 (3) ◽

pp. 179-184 ◽

Cited By ~ 47

Author(s):

Jianye Ge ◽

Bruce Budowle ◽

Xavier G. Aranda ◽

John V. Planz ◽

Arthur J. Eisenberg ◽

...

Keyword(s):

Y Chromosome ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Mutation Rates ◽

Short Tandem

Download Full-text

Mutation rate analysis via parent–progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.1016 ◽

2016 ◽

Vol 283 (1841) ◽

pp. 20161016 ◽

Cited By ~ 25

Author(s):

Zhengqing Xie ◽

Long Wang ◽

Lirong Wang ◽

Zhiqiang Wang ◽

Zhenhua Lu ◽

...

Keyword(s):

Mutation Rate ◽

Interspecific Cross ◽

Point Mutations ◽

Mutation Rates ◽

Selfed Progeny ◽

Woody Perennials ◽

Heterozygous Individual ◽

Rate Analysis ◽

A Genome ◽

Order Of Magnitude

Mutation rates vary between species, between strains within species and between regions within a genome. What are the determinants of these forms of variation? Here, via parent–offspring sequencing of the peach we ask whether (i) woody perennials tend to have lower per unit time mutation rates compared to annuals, and (ii) hybrid strains have high mutation rates. Between a leaf from a low heterozygosity individual, derived from an intraspecific cross, to a leaf of its selfed progeny, the mutation rate is 7.77 × 10 −9 point mutations per bp per generation, similar to Arabidopsis thaliana (7.0–7.4 × 10 −9 point mutations per bp per generation). This suggests a low per unit time mutation rate as the generation time is much longer in peach. This is supported by our estimate of 9.48 × 10 −9 point mutations per bp per generation from a 200-year-old low heterozygosity peach to its progeny. From a more highly heterozygous individual derived from an interspecific cross to its selfed progeny, the mutation rate is 1.38 × 10 −8 mutations per site per generation, consistent with raised rates in hybrids. Our data thus suggest that (i) peach has an approximately order of magnitude lower mutation rate per unit time than Arabidopsis , consistent with reports of low evolutionary rates in woody perennials, and (ii) hybridization may, indeed, be associated with increased mutation rates as considered over a century ago.

Download Full-text

Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research

Frontiers in Genetics ◽

10.3389/fgene.2021.720640 ◽

2021 ◽

Vol 12 ◽

Author(s):

Carla Bini ◽

Elisabetta Cilli ◽

Stefania Sarno ◽

Mirko Traversari ◽

Francesco Fontani ◽

...

Keyword(s):

Y Chromosome ◽

Tandem Repeats ◽

18Th Century ◽

Dna Typing ◽

Geographical Location ◽

Pcr Amplification ◽

Petrous Bone ◽

Qualitative Assessment ◽

The Village ◽

Short Tandem

Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent’s criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.

Download Full-text