Characterization of human short tandem repeats (STRs) for individual identification using the Ion Torrent

2015 ◽  
Vol 9 (2) ◽  
pp. 164-172 ◽  
Author(s):  
Seri Lim ◽  
Jong Pil Youn ◽  
Sang Ok Moon ◽  
Youn Hyung Nam ◽  
Seung Bum Hong ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Individual Identification ◽  
Ion Torrent ◽  
Short Tandem

Characterization of DNA Methylation in Short Tandem Repeats in Human Genome

2014 ◽  
Vol 2014 (1) ◽  
pp. 2478
Author(s):  
Lifang Hou* ◽  
Zhou Zhang ◽  
Yinan Zheng ◽  
Wei Zhang ◽  
Xu Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7031 ◽  
Author(s):  
Thanh Hoa Le ◽  
Khue Thi Nguyen ◽  
Nga Thi Bich Nguyen ◽  
Huong Thi Thanh Doan ◽  
Takeshi Agatsuma ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Coding Region ◽  
Protein Coding ◽  
Lung Fluke ◽  
Short Tandem

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 5′ end of nad4 overlapped with the 3′ end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu. These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies.

scholarly journals Characterization of Short Tandem Repeats from Thirty-One Human Telomeres

1997 ◽  
Vol 7 (9) ◽  
pp. 917-923 ◽  
Author(s):  
Marjorie Rosenberg ◽  
Lester Hui ◽  
Junli Ma ◽  
Harris C. Nusbaum ◽  
Kevin Clark ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data

2018 ◽  
Vol 39 (4) ◽  
pp. 291-300
Author(s):  
San-Xu Liu ◽  
San-Xu Liu ◽  
Wei Hou ◽  
Xue-Yan Zhang ◽  
Chang-Jun Peng ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Macaque Genome ◽  
Tibetan Macaque ◽  
Identification And Characterization ◽  
Short Tandem

scholarly journals Forensic efficiency estimate and phylogenetic analysis for Chinese Kyrgyz ethnic group revealed by a panel of 21 short tandem repeats

2018 ◽  
Vol 5 (6) ◽  
pp. 172089 ◽  
Author(s):  
Yuxin Guo ◽  
Chong Chen ◽  
Tong Xie ◽  
Wei Cui ◽  
Haotian Meng ◽  
...  
Keyword(s):  
Ethnic Group ◽  
Phylogenetic Trees ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Forensic Genetics ◽  
Genetic Relationships ◽  
Individual Identification ◽  
Forensic Sciences ◽  
Dna Index ◽  
Short Tandem

Short tandem repeats (STRs) with a high level of polymorphisms and convenient detection method play an indispensable role in human population and forensic genetics. Recently, we detected the 21 autosomal non-combined DNA index system (non-CODIS) STR loci in a Kyrgyz ethnic group, calculated their forensic parameters and analysed its genetic relationships with reference populations from China. In total, 168 alleles were observed at 21 non-CODIS STRs with corresponding allelic frequencies from 0.0016 to 0.4788. No significant deviations at these STRs were observed from the Hardy–Weinberg equilibrium. The values of cumulative power of discrimination and probability of exclusion for all the 21 non-CODIS STRs were 0.99999999999999999998835 and 0.9999994002, respectively. Furthermore, the analyses of phylogenetic trees, genetic distances and interpopulation differentiations demonstrated that the Kyrgyz group had relatively close genetic relationships with the Uygur and Kazak groups. These 21 non-CODIS STRs were characterized by high genetic diversities in the Kyrgyz group and could be applied as a robust tool for individual identification and kinship testing in forensic sciences.

scholarly journals Identification and Characterization of Nine Novel X-Chromosomal Short Tandem Repeats on Xp21.1, Xq21.31, and Xq23 Regions

2021 ◽  
Vol 12 ◽  
Author(s):  
Qinrui Yang ◽  
Jinglei Qian ◽  
Chengchen Shao ◽  
Yining Yao ◽  
Zhihan Zhou ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Mapping Function ◽  
Str Analysis ◽  
The Family ◽  
Further Development ◽  
Multiplex System ◽  
Short Tandem ◽  
Forensic Parameters

The application of X-chromosomal short tandem repeats (X-STRs) has been recognized as a powerful tool in complex kinship testing. To support further development of X-STR analysis in forensic use, we identified nine novel X-STRs, which could be clustered into three linkage groups on Xp21.1, Xq21.31, and Xq23. A multiplex PCR system was built based on the electrophoresis. A total of 198 unrelated Shanghai Han samples along with 168 samples from 43 families was collected to investigate the genetic polymorphism and forensic parameters of the nine loci. Allele numbers ranged from 5 to 12, and amplicon sizes ranged from 146 to 477 bp. The multiplex showed high values for the combined power of discrimination (0.99997977 in males and 0.99999999 in females) and combined mean exclusion chances (0.99997918 and 0.99997821 in trios, 0.99984939 in duos, and 0.99984200 in deficiency cases). The linkage between all pairs of loci was estimated via Kosambi mapping function and linkage disequilibrium test, and further investigated through the family study. The data from 43 families strongly demonstrated an independent transmission between LGs and a tight linkage among loci within the same LG. All these results support that the newly described X-STRs and the multiplex system are highly promising for further forensic use.

Sign in / Sign up

Export Citation Format

Share Document