Forensic Spanish allele and haplotype database for a 17 X-STR panel

Prieto-Fernández, Endika; Núñez, Carolina; Baeta, Miriam; Jiménez-Moreno, Susana; Martı́nez-Jarreta, Begoña; Pancorbo, Marian M. de

doi:10.1016/j.fsigen.2016.06.016

Cited by 12 publications

(1 citation statement)

References 24 publications

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“…14 Moreover, there have been many reports involving diversity in STRs on the sex chromosomes, such as allele frequency among races and ethnicities. [15][16][17][18][19][20] It has been assumed that variations in allele frequency or genetic distributions might differ among individuals living in different geographic locations. Therefore, this study aimed to examine the allele frequency, some forensic parameters and the diversity and dispersion of STR alleles on chromosome X in a northern Thai population in order to establish an allele frequency database.…”

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confidence: 99%

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

Khacha-ananda

Mahawong

2020

Med Sci Law

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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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Section: Introductionmentioning

confidence: 99%

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

Khacha-ananda

Mahawong

2020

Med Sci Law

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Analysis of four novel X-chromosomal short tandem repeats within 71 kb of the Xp22.3 region

2017

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DNA testing using X-chromosomal short tandem repeat (X-STR) polymorphisms has been used in maternity/paternity and complex kinship cases. Analyses of repeat sequences, surveys on racial statistics, and development of practical applications for DNA testing continue to be reported. In this study, we identified four novel tetranucleotide STR loci located in the X chromosome, which is the basis of X-STR research. These four tetranucleotide STRs were located within 71 kb of the chromosome Xp22.3 region. Using sequence analysis of the structure of repeat sequences, we identified simple repeat sequences of TAAA, CTTT, TATC, and GATA with rare insertions. We then calculated forensic statistical parameters using base length analysis. In the Japanese population, the polymorphism information content was 0.597-0.687, power of discrimination in females was 0.829-0.884, and power of discrimination in males was 0.635-0.729. As these tetranucleotide STRs are closely linked, we conducted haplotype analysis and detected that three loci (LC149476, LC149479, and LC149480) were in linkage disequilibrium. We demonstrated that the simultaneous analysis of these loci may be useful in complex kinship cases. Because these four loci can be detected by multiplex PCR, the detection of alleles at these loci can be rapidly and easily achieved. We conclude that the X-STR loci detected in this study may be useful tools in complex kinship cases and may increase the reliability of genetic testing.

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Establishment of 11 linked X-STR loci within 1.1 Mb to assist with kinship testing

et al. 2017

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This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci. The distance between each pair of loci ranged from 24,998 to 244,701 bp with an average of approximately 110.8 kb. The number of observed alleles ranged from 7 to 30 for these 10 loci with a polymorphic information content ranging from 0.593 to 0.930. The LOD score from a pairwise linkage study ranged from 4.40 to 23.73, indicating that these 11 loci were highly linked, as expected. In line with standard forensic practice, all 11 loci can be amplified in one multiplex reaction, and comprehensive allelic ladders for all the loci have been constructed. These newly established 11 linked STR loci on the human X chromosome were found to be highly polymorphic and have the potential to aid in kinship testing where the X chromosome loci currently plays a role.

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Forensic Spanish allele and haplotype database for a 17 X-STR panel

Cited by 12 publications

References 24 publications

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

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

Analysis of four novel X-chromosomal short tandem repeats within 71 kb of the Xp22.3 region

Establishment of 11 linked X-STR loci within 1.1 Mb to assist with kinship testing

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