Mutation rate analysis at 19 autosomal microsatellites

2015 ◽  
Vol 36 (14) ◽  
pp. 1633-1639 ◽  
Author(s):  
Xiao-Qin Qian ◽  
Cai-Yong Yin ◽  
Qiang Ji ◽  
Kai Li ◽  
Han-Ting Fan ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Rate Analysis ◽  
Autosomal Microsatellites

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

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161785 ◽  
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.

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

2018 ◽  
Vol 2018 ◽  
pp. 1-5
Author(s):  
Fidelis Charles Bugoye ◽  
Elias Mulima ◽  
Gerald Misinzo
Keyword(s):  
Y Chromosome ◽  
Mutation Rate ◽  
Standard Error ◽  
Tandem Repeats ◽  
Dna Typing ◽  
Paternity Testing ◽  
Mutation Rates ◽  
Buccal Swab ◽  
Age Difference ◽  
Rate Analysis

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.

scholarly journals Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.

2021 ◽  
Author(s):  
Md. Shahadat Hossain ◽  
A. Q. M. Sala Uddin Pathan ◽  
Md. Nur Islam ◽  
Mahafujul Islam Quadery Tonmoy ◽  
Mahmudul Islam Rakib ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Fundamental System ◽  
Genomic Data ◽  
Rate Analysis ◽  
Neural Learning ◽  
Genome Wide ◽  
The Future ◽  
Frequent Mutations ◽  
Genomic Data Analysis ◽  
Integrated Study

Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identify 3334545 mutations (14.01 mutations per isolate), suggesting a high mutation rate. Strains from India showed the highest no. of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. Besides the most prominently occurring mutations (D416G, F106F, P314L, and UTR:C241T), we identify L93L, A222V, A199A, V30L, and A220V mutations which are in the top 10 most frequent mutations. Multi-nucleotide mutations GGG>AAC, CC>TT, TG>CA, and AT>TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C>T, A>G, and A>T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T>C, G>A, and G>T mutations, respectively. T>G\A, C>G\A, and A>T\C are not anticipated in the future. Since SARS-CoV-2 is evolving continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.

Multiplex assay development and mutation rate analysis for 13 RM Y-STRs in Chinese Han population

2016 ◽  
Vol 131 (2) ◽  
pp. 345-350 ◽  
Author(s):  
Wenqiong Zhang ◽  
Chao Xiao ◽  
Jin Yu ◽  
Tian Wei ◽  
Fei Liao ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Multiplex Assay ◽  
Assay Development ◽  
Chinese Han Population ◽  
Chinese Han ◽  
Han Population ◽  
Rate Analysis

Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure

2018 ◽  
Vol 39 (10) ◽  
pp. 1384-1392 ◽  
Author(s):  
Nguyen Dang Ton ◽  
Hidewaki Nakagawa ◽  
Nguyen Hai Ha ◽  
Nguyen Thuy Duong ◽  
Vu Phuong Nhung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mutation Rate ◽  
Whole Genome ◽  
Rate Analysis ◽  
Dioxin Exposure

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

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161016 ◽  
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.

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