Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel

Avila, Eduardo; Felkl, Aline Brugnera; Graebin, Pietra; Nunes, Cláudia Paiva; Alho, Clarice Sampaio

doi:10.1016/j.fsigen.2019.02.012

Cited by 25 publications

(35 citation statements)

References 41 publications

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“…Mean ACR of all median values for 27 multi‐allelic SNPs was 0.8824. Except for loci rs6812234 (0.4469) and rs2307055 (0.3913), Median ACR values of other loci were greater than 0.7832, which was more than the recommended value of 0.66 [31,45]. Median LB values ranged from 0.0124 (with the range of 0.0017–0.1449) at rs4872345 to 1.5210 (with the range of 1.0710–2.2360) at rs6812234 loci.…”

Section: Resultsmentioning

confidence: 85%

“…Median LB values ranged from 0.0124 (with the range of 0.0017–0.1449) at rs4872345 to 1.5210 (with the range of 1.0710–2.2360) at rs6812234 loci. Median LB value of rs4872345 locus was less than 0.5, reminding that the reads of this locus were less than half of the average reads of all loci [45], and this MPS panel had the demand of balancing sequencing depth. NL values of the 27 multi‐allelic SNPs were mostly near zero, and the maximum mean value was only 0.0171 (±0.0264), which appeared at rs4872345 locus and might be related to its low sequencing depth.…”

Section: Resultsmentioning

confidence: 99%

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A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies

et al. 2020

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Massively parallel sequencing (MPS) technology allows to simultaneously type multitudinous molecular genetic markers for many samples in one run with the feature of high detection resolution, and thereby arouses the increasing attention from forensic science. Herein, multiple allelic single nucleotide polymorphisms (multi‐allelic SNPs) were screened for personal identification and parentage testing, and then were genotyped using MPS platform. Unrelated individuals of Chinese Mongolian and Kazakh groups were investigated to further estimate forensic effectiveness and applicability of these multi‐allelic SNPs. The results of sequencing efficiency estimations and forensic genetic statistical parameters demonstrated that this MPS panel of multi‐allelic SNPs was expected to be work for forensic applications. Subsequently, the exploration of population genetic variation patterns among the two investigated groups and other 26 reference populations revealed that these Chinese Mongolian and Kazakh groups had the similar population genetic patterns with the populations from East Asian, but European ancestral composition in the Kazakh group was higher than that in the Mongolian group. Currently, the present results were the preliminary research to scrutinize genetic information of these two ethnic minority groups employing multi‐allelic SNPs.

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Section: Resultsmentioning

confidence: 85%

Section: Resultsmentioning

confidence: 99%

A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies

et al. 2020

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“…It has modules specific to workflows of the offered chemistries targeting specific forensic markers: STRs including multiple markers for sex-determination [68], mtDNA control region, or the full mitochondrial genome [69]. Additional modules beyond STR analysis include those interpreting data from kits targeting selected SNP sets, which can establish identity from degraded samples [70,71] or can provide investigative leads and estimate biogeographic ancestry [72]. Data organization in Converge is optimized and streamlined around case management.…”

Section: Universal Analysis Software (Verogen San Diego Ca)mentioning

confidence: 99%

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

Huszar

Gettings

Vallone

2021

Genes

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The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.

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“…This panel has been used for the investigation of diverse populations including Han Chinese [7,9], southern Chinese [10], three East Asian minorities (Tibetan, Uygur, and Hui) [11], Brazilian [12], and central Indian [13]. However, there are very limited reports on the Southeast Asian population.…”

Section: Introductionmentioning

confidence: 99%

Investigation of SNPs in the Precision ID Identity Panel using next-generation sequencing in a Myanmar population

Joo

Kwon

Moon

et al. 2022

Preprint

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Background—Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs) due to low mutation rates and small amplicon sizes. The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-SNPs, was introduced for human identification by next-generation sequencing (NGS), enabling many studies on the global population; however, few reports are available on the Southeast Asian population.Methods and Results—A total of 96 unrelated male samples from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter. The sequencing performance was evaluated by locus balance and heterozygote balance, and the results were comparable to those of the Ion Torrent platform. For 90 autosomal SNPs, minor allele frequencies ranged between 0.068 and 0.500, and combined match probability (6.994×10−34) was lower than that of 22 PowerPlex Fusion autosomal STRs (3.130×10−26). Moreover, we identified 51 cryptic variations around the target SNPs using a custom variant caller, Visual SNP. For 34 Y-SNPs, 14 Y-haplogroups were observed—mostly O2 and O1b groups. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations than the South Asian population.Conclusions—We demonstrate that the Precision ID Identity Panel can be successfully analyzed on a MiSeq using a custom data analysis pipeline and provide high discrimination power for human identification in the Myanmar population, while extending the accessibility of NGS analysis for SNPs in forensics.

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Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel

Cited by 25 publications

References 41 publications

A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies

A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

Investigation of SNPs in the Precision ID Identity Panel using next-generation sequencing in a Myanmar population

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