Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia

Khubrani, Yahya M.; Jobling, Mark A.; Wetton, Jon H.

doi:10.1016/j.fsigen.2019.102164

Cited by 31 publications

(27 citation statements)

References 40 publications

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“…While in Novroski’s and Churchill’s reports, the number of SB alleles of D22S1045 were increased due to FR variations, but in Chinese populations ( 45 , 49 and our study), no sequence variation (neither repeat nor flanking region) was observed at the D22S1045 locus. Overall, the sequence variations observed herein were consisted with the observations reported in previous literature 34 , 37 , 39 , 45 , 50 .…”

Section: Discussionsupporting

confidence: 89%

“…A pair-ended sequencing will be performed after the library preparation and then the raw data will be imported to UAS to analyse automatically. Validations using the ForenSeq Signature system have demonstrated its advantages in forensic practice relative to other library preparation kits [29][30][31][32][33] , but the knowledge of alleles and genotype frequencies of these 58 STRs is still inadequate for accurate lineage analysis [34][35][36][37][38][39] and is not sufficient for population genetic studies, which limits its utility in forensic casework.…”

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confidence: 99%

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Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Peng

Zhang

Ren

et al. 2020

Sci Rep

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Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases. Several genetic markers have been introduced to forensic genetics to clarify the problems of kinship analysis and personal identification. Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are commonly used genetic markers in present forensic cases 1,2. STRs, usually 2-6 bp in length, are commonly typed with the amplified fragment length polymorphism (Amp-FLP) strategy combining fluorescently labelled multiplex PCR and capillary electrophoresis (CE) 3. Allele calling can thus be inferred from fragment length by comparison with a locus specific allelic ladder that has been previously sequenced, where the number of repeat units is distinct 2. Thus, each allele is regarded as a lengthbased (LB) allele using this approach. With the advancement of sequencing technologies over the last decade, the existence of sequence structure variations in alleles with the same length has been uncovered 4. SNPs, which could be amplified with smaller amplicons, are bi-allelic genetic markers with lower mutation rates compared with STRs 5. Several autosomal SNP marker sets and detection methods, such as single-base extension, chip-based microarrays, and allele-specific hybridization arrays, have been developed to compensate for the relatively weaker discrimination power of single loci caused by the bi-allelic nature of the human genome 5-7. However, these methods are not widely used in forensic practice due to the requirement of higher DNA inputs or the limited ability to detect a vast number of SNP loci in a single reaction 8. Different from detection methods mentioned above, massively paralle...

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Section: Discussionsupporting

confidence: 89%

mentioning

confidence: 99%

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Peng

Zhang

Ren

et al. 2020

Sci Rep

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“…Furthermore, the detail DoCs for all samples were presented in Supplementary Table S2 and Supplementary Figure S1-S3, which indicated that the DoCs for all samples were balanceable, with no differences for females and males. Our sequencing results were in accordance with other forensic MPS-related studies [40,41,43,45,[111][112][113][114][115]. No matter in females or males, the DoCl and DoCs had no differences at the same locus, and the DoC were unbalanced in different types of genetic markers.…”

Section: Resultssupporting

confidence: 90%

“…With the observations of the sequence variations which derived high polymorphisms of some autosomal STR loci in Hainan Li population and other populations that the variations also existed [84,[111][112][113][114][115][116][117][118][119][120][121][122][123][124], it indicated that the sequence variation-derived high polymorphisms widely existed in different populations, and the genetic diversity of the same locus in different populations were diverse under some circumstances. It could be explained by the relatively isolations between populations from the cultural, geographical and social differences, and genetic mutations accumulated over many years in populations.…”

Section: Str Sequence Variations Observed By the Sequence-based Methodsmentioning

confidence: 99%

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Fan

Wang

et al. 2021

Int J Legal Med

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Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai-language speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics, however, the forensic associated studies on Hainan Li population are still insufficient.Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DAPA, it demonstrated that the STRs and iiSNPs in DAPA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three Datasets, which included the genetic data of (Ⅰ). iiSNPs (27 populations, 2640 individuals), (Ⅱ). Y-STRs (42 populations, 8281 individuals), and (Ⅲ). Yhaplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives.In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.

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“…The application of MPS in casework requires accessible datasets from the global population designed to enrich the allele frequencies of sequence‐based STR genotypes, as recommended by the International Society for Forensic Genetics (ISFG) (Parson et al, 2016; Phillips, Devesse, et al, 2018; Phillips, Gettings, et al, 2018). Several MPS‐STR population datasets have been reported in recent years (Churchill et al, 2017; Delest et al, 2020; Hussing et al, 2019; Khubrani et al, 2019; Kim et al, 2016, 2018; Novroski et al, 2016; Peng et al, 2020; Phillips, Devesse, et al, 2018; Phillips, Gettings, et al, 2018; Wang et al, 2020; Wendt et al, 2017). Tibetans are one of China's 56 ethnic groups and are indigenous to the Qinghai‐Tibet Plateau.…”

Section: Introductionmentioning

confidence: 99%

RETRACTED: Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population

Zhang

Song

et al. 2021

Molec Gen & Gen Med

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Background Massively parallel sequencing (MPS) is a promising supplementary method for forensic casework in short tandem repeats (STRs) genotyping, owing to several advantageous features in comparison to traditional capillary electrophoresis (CE). However, the application of MPS in casework requires accessible datasets from the worldwide population to enrich the allele frequencies of sequence‐based STR genotypes. Methods In this study, we report the characterization of sequence‐based allele frequencies of 58 STRs from a Tibetan population comprising 120 unrelated individuals using the ForenSeq™ DNA Signature Prep Kit. A concordance study evaluating MPS and CE allele data was performed to ensure that MPS is compatible with current CE‐based forensic databases. The diversity of observed alleles, allele frequencies, and forensic parameters per locus by length (LB), sequence without flanking region (RSB), and sequence with flanking region (FSB) were analyzed and compared. Results The concordance study demonstrated a concordance rate exceeding 99%. The combined random match probability (RMP) for the 26 A‐STRs was 2.04 × 10–29, 1.93 × 10–31, and 9.56 × 10–33 for LB, RSB, and FSB, respectively. Similar trends were observed in other forensic parameters resulting from the increase in the number of unique alleles available. A total of 111 and 113 unique haplotypes in the Y‐STR loci were observed when using length‐based and sequence‐based alleles, respectively. In addition, we identified 35 novel alleles at 25 loci and 25 polymorphisms in the flanking regions at 17 STRs. Conclusions Our data suggest that MPS‐ and CE‐derived alleles are compatible. MPS‐based analysis of the STR data substantially increased the allele diversity and improved the forensic parameters, which clearly demonstrated the advantages of MPS in comparison to CE. With more pooled data and larger‐scale validation, MPS could play a valuable role in forensic genetics and might be an additional tool for routine casework.

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Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia

Cited by 31 publications

References 40 publications

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

RETRACTED: Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population

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