Forensic Autosomal Short Tandem Repeats and Their Potential Association With Phenotype

Wyner, Nicole; Barash, Mark; McNevin, Dennis

doi:10.3389/fgene.2020.00884

Cited by 57 publications

(40 citation statements)

References 79 publications

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“…importance in terms of genetic markers (forensic applications) and perhaps even their functional role in regulation [33]. Despite this interest, little is known about the correction of their sequencing.…”

Section: Plos Onementioning

confidence: 99%

Sequencing DNA with nanopores: Troubles and biases

2021

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Oxford Nanopore Technologies’ (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate. While many papers have studied read correction methods, few have addressed the detailed characterization of observed errors, a task complicated by frequent changes in chemistry and software in ONT technology. The MinION sequencer is now more stable and this paper proposes an up-to-date view of its error landscape, using the most mature flowcell and basecaller. We studied Nanopore sequencing error biases on both bacterial and human DNA reads. We found that, although Nanopore sequencing is expected not to suffer from GC bias, it is a crucial parameter with respect to errors. In particular, low-GC reads have fewer errors than high-GC reads (about 6% and 8% respectively). The error profile for homopolymeric regions or regions with short repeats, the source of about half of all sequencing errors, also depends on the GC rate and mainly shows deletions, although there are some reads with long insertions. Another interesting finding is that the quality measure, although over-estimated, offers valuable information to predict the error rate as well as the abundance of reads. We supplemented this study with an analysis of a rapeseed RNA read set and shown a higher level of errors with a higher level of deletion in these data. Finally, we have implemented an open source pipeline for long-term monitoring of the error profile, which enables users to easily compute various analysis presented in this work, including for future developments of the sequencing device. Overall, we hope this work will provide a basis for the design of better error-correction methods.

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Section: Plos Onementioning

confidence: 99%

Sequencing DNA with nanopores: Troubles and biases

2021

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“…The amelogenin locus can also reveal persons inflicted with amelogenesis imperfecta, a disorder that affects the enamel on teeth. Variants at vWA and TPOX are associated with venous thromboembolism (Meraz‐Ríos et al, 2014), D8S1179, D5S818, and D2S1338 with gastric cancer, and TH01, D18S51, and D2S1338 with psychiatric disorders (Wyner et al, 2020). Any of the genomic markers that are used for forensic identification (i.e., STRs, SNPs, interspersed repeat sequences) can reveal persons who have mosaicisms, either natural or artificial.…”

Section: “Omics” and Privacy—past Present And Futurementioning

confidence: 99%

Privacy implications of the new “omic” technologies in law enforcement

Roffey

Scudder

2021

WIREs Forensic Science

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Omic" technologies have opened a new revolution in law enforcement and are now solving decades-old cold cases as well as current investigations. The Golden State Killer case is probably the most notable of the cold case investigations that has been solved by one of the new "omic" technologies, namely forensic genetic genealogy. The resolution of this case epitomizes the power of the "omic" technologies to solve crime while simultaneously unearthing serious legal and ethical concerns around the individuals' privacy in the use of their genetic information. The legislation that is currently used by the state, territory, and Commonwealth jurisdictions in Australia to regulate the use of DNA for criminal investigation is now two decades old and does not address the application of "omic" technologies to criminal investigation. The Australian government is reviewing current privacy laws, and this review could include the use of "omic" technologies. In the absence of specific legislation, law enforcement must continue to develop processes to consider privacy, law, and ethics around the use of "omic" technologies for criminal investigation and the identification of human remains.

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“…Genetic polymorphism analysis of STR loci has been utilized worldwide in many fields, including paternity detection, genetic mapping, disease linkage investigation, evolutionary biology, and the genetics of population. Our previous data showed that two autosomal STRs (TH01 and TPOX) were related to impulsive aggression, and the two other autosomal STRs (Penta D and Penta E) were involved in initiative aggression (Wyner et al., 2020 ; C. Yang et al., 2018 ). However, so far there have been no data to suggest the correlation between STRs on the autosomal chromosomes and male schizophrenia.…”

Section: Introductionmentioning

confidence: 99%

The association of 20 short tandem repeat loci of autosomal chromosome with male schizophrenia

Yang

Zou

et al. 2022

Brain and Behavior

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Introduction Schizophrenia's heritability and familial transmission have been known for several decades. The male‐specific Y chromosome plays an important role in schizophrenia. Short tandem repeats (STRs)have been recognized as risk genes in the development of schizophrenia. Here, we investigated the association between male schizophrenia and Y‐chromosomal STRs loci. Methods We recruited 355 patients with schizophrenia and 473 healthy males for physical examination and amplified them with a PowerPlex 21 System fluorescence‐labeled composite amplification System. Then, the resultant products were separated by electrophoresis and further detected. Finally, differences in allele and genotype frequency distributions of STR loci were observed. Results Our results showed that all 20 STR loci were in accordance with Hardy–Weinberg's law ( p > .05). There were statistically significant differences in alleles of D13S317 and D5S818 loci and genotype frequency distribution between the two groups (alleles: p = .039, p = .022, respectively; genotype: p = .0004, p = .011, respectively). However, there was no difference in the other autosomal 18 STR loci between the two groups ( p > .05). Univariate analysis showed that the frequency distribution differences of allele 11 and genotype 10‐11 at the D13S317 locus between the two groups were significant (compared to the controls, p = 0.005, odds ratio (OR) = 1.37, 95%b confidence interval (CI) = 1.10–1.71, compared to the controls, p = .0000002, OR = 3.92, 95% CI = 2.27–6.77, respectively). The frequency distribution differences of allele 7 and genotype 7‐10 at D5S818 between the two groups were significant (compared to the controls, p = .0006, OR = 3.42, 95% CI = 1.63–7.16, compared to the controls, p = .0011, OR = 8.24, 95% CI = 1.83–37.05, respectively). Conclusion Polymorphisms of the D13S317 and D5S818 loci may be predisposing factors for schizophrenia.

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Forensic Autosomal Short Tandem Repeats and Their Potential Association With Phenotype

Cited by 57 publications

References 79 publications

Sequencing DNA with nanopores: Troubles and biases

Sequencing DNA with nanopores: Troubles and biases

Privacy implications of the new “omic” technologies in law enforcement

The association of 20 short tandem repeat loci of autosomal chromosome with male schizophrenia

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