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

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.

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

BioChip Journal ◽

10.1007/s13206-015-9210-7 ◽

2015 ◽

Vol 9 (2) ◽

pp. 164-172 ◽

Cited By ~ 3

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

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Characterization of DNA Methylation in Short Tandem Repeats in Human Genome

ISEE Conference Abstracts ◽

10.1289/isee.2014.p2-520 ◽

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

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Systematic analysis of short tandem repeats in 38,095 exomes provides an additional diagnostic yield

10.1101/2020.10.19.20211144 ◽

2020 ◽

Author(s):

Bart P.G.H. van der Sanden ◽

Jordi Corominas ◽

Michelle de Groot ◽

Maartje Pennings ◽

Rowdy P.P. Meijer ◽

...

Keyword(s):

Genetic Testing ◽

Movement Disorder ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Diagnostic Yield ◽

Genetic Disorders ◽

Systematic Analysis ◽

Str Analysis ◽

Manual Curation ◽

Short Tandem

AbstractPurposeThe expansion of specific short tandem repeats (STRs) can lead to approximately 30 different human genetic disorders. Despite extensive application of exome sequencing (ES) in routine diagnostic genetic testing, STRs are not routinely identified from these data.MethodsWe assessed diagnostic utility by applying ExpansionHunter to 2,867 exomes from movement disorder patients and 35,228 other clinical exomes.ResultsWe identified 36 movement disorder patients with a possible aberrant STR length. Validation by PCR and/or repeat-primed PCR technologies confirmed the presence of aberrant expansion alleles for 11 (31%). For seven of these patients the genotype was compatible with the phenotypic description, and resulted in a molecular diagnosis. We subsequently tested the remainder of our diagnostic ES cohort, including over 30 clinically and genetically heterogeneous disorders. Optimized manual curation yielded 140 samples with a likely aberrant STR length. Validations confirmed 70/140 (50%) aberrant expansion alleles, of which 48 were in the pathogenic range and 22 in the premutation range.ConclusionsOur work provides guidance for the implementation of STR analysis in clinical ES. Our results show that systematic STR evaluation may increase diagnostic ES yield by 0.2%, and recommend to make STR evaluation a routine part of ES interpretation in genetic testing laboratories.

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Disputed paternity presumption in Burkina Faso: determination of the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00221-3 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Missa Millogo ◽

Serge Theophile Soubeiga ◽

Bapio Valerie Jean Telesphore Bazie ◽

Theodora Mahoukede Zohoncon ◽

Abdoul Karim Ouattara ◽

...

Keyword(s):

Burkina Faso ◽

Tandem Repeat ◽

Short Tandem Repeat ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Str Analysis ◽

Resource Limited ◽

Biological Fathers ◽

Short Tandem

Abstract Background In resource-limited countries, ABO, HLA, MNS, Kells, and hemoglobin electrophoresis are classic tests for the resolution of paternity disputes due to their affordable cost. The limitations of these tests in cases of disputed paternity require the use of Short Tandem Repeats (STR) for their certification. This study aimed to determine the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays in Burkina Faso, West Africa. Results Of the fourteen trios studied, the ABO-rhesus/hemoglobin electrophoresis analysis revealed ten probable inclusion cases, three exclusion cases, and one undetermined paternity. DNA STR analysis found five inclusions of paternity out of the ten probable inclusions with ABO-rhesus/hemoglobin electrophoresis assay versus nine exclusions of paternity. Conclusion This study showed that the implementation of the analysis of short tandem repeat is required to resolve increasing disputed filiation cases in Burkina Faso.

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

PeerJ ◽

10.7717/peerj.7031 ◽

2019 ◽

Vol 7 ◽

pp. e7031 ◽

Cited By ~ 5

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.

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Isolation and characterization of short tandem repeats in an invasive swimbladder nematode, parasitic in Atlantic freshwater eels, Anguillicola crassus

Molecular Ecology Notes ◽

10.1111/j.1471-8286.2007.01773.x ◽

2007 ◽

Vol 7 (6) ◽

pp. 1051-1053 ◽

Cited By ~ 5

Author(s):

SÉBASTIEN WIELGOSS ◽

MATTHIAS SANETRA ◽

AXEL MEYER ◽

THIERRY WIRTH

Keyword(s):

Short Tandem Repeats ◽

Tandem Repeats ◽

Isolation And Characterization ◽

Anguillicola Crassus ◽

Freshwater Eels ◽

Short Tandem

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Genetic and structural characterization of 20 autosomal short tandem repeats in the Chinese Qinghai Han population and its genetic relationships and interpopulation differentiations with other reference populations

Forensic Sciences Research ◽

10.1080/20961790.2018.1485199 ◽

2018 ◽

Vol 3 (2) ◽

pp. 145-152 ◽

Cited By ~ 3

Author(s):

Zhanhai Wang ◽

Bin Lu ◽

Xiaoye Jin ◽

Jiangwei Yan ◽

Haotian Meng ◽

...

Keyword(s):

Structural Characterization ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Genetic Relationships ◽

Han Population ◽

Autosomal Short Tandem Repeats ◽

Short Tandem

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Characterization of Short Tandem Repeats from Thirty-One Human Telomeres

Genome Research ◽

10.1101/gr.7.9.917 ◽

1997 ◽

Vol 7 (9) ◽

pp. 917-923 ◽

Cited By ~ 24

Author(s):

Marjorie Rosenberg ◽

Lester Hui ◽

Junli Ma ◽

Harris C. Nusbaum ◽

Kevin Clark ◽

...

Keyword(s):

Short Tandem Repeats ◽

Tandem Repeats ◽

Short Tandem

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Genetic analysis of 12 X-short tandem repeats loci in a northern Thai population

Medicine Science and the Law ◽

10.1177/0025802420965000 ◽

2020 ◽

pp. 002580242096500

Author(s):

Supakit Khacha-ananda ◽

Phatcharin Mahawong

Keyword(s):

Genetic Polymorphism ◽

Allele Frequency ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Thai Population ◽

Weinberg Equilibrium ◽

Hardy Weinberg Equilibrium ◽

Forensic Genetic ◽

Short Tandem ◽

Forensic Parameters

Short tandem repeats (STRs) are widely used as DNA markers in paternity testing and criminal investigations because of their high genetic polymorphism among individuals in population. However, many factors influence genetic variations of STRs. Therefore, understanding STR information within individual populations could provide database and scientifically reliable STR genotyping for forensic genetic purposes. We aimed to examine allele frequencies of X-STRs, including some forensic parameters, in a northern Thai population. A retrospective descriptive study was conducted by collecting X-STR data from unrelated individuals living in a northern region of Thailand. The allele frequency and forensic parameters – for example polymorphism information content (PIC), power of discrimination in females and males (PDf and PDm), mean exclusion chance (MEC) and haplotype frequency – were calculated. The Hardy–Weinberg equilibrium was analysed. A total of 132 alleles were observed, with corresponding allele frequency ranging from 0.0064 to 0.4904. The PIC of all loci was >0.6, representing high genetic polymorphism, except DXS8378 and DXS7423. Notably, DXS10135 was the most diverse loci with the highest PD and MEC, while DXS7423 was the least polymorphic marker with the lowest PD and MEC. The highest haplotype diversity in male data was on linkage group III (DXS10101-DXS10103-HPRTB) by 0.9895. The genetic distance analysis demonstrated that the northern Thai population had a close relationship with Taiwanese (DA = 0.023). There are no significant deviations among the Hardy–Weinberg equilibrium except DXS10148. This study has established a northern Thai X-STRs reference database to be used as a tool for forensic genetic purposes.

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