Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics
Abstract
:1. Introduction
2. Materials and Methods
3. Results
4. Discussion
4.1. Contributions by Country
4.2. Contributions by Year
4.3. Articles Type, Journal, and Access
4.4. Articles Focus and Current Knowledge
4.4.1. Precision ID GlobalFiler NGS STR Panel
4.4.2. Precision ID Identity Panel
4.4.3. Precision ID Ancestry Panel
4.5. Sequencing Instrument and Automation
4.6. Limitations
4.7. Future Perspectives
4.8. Ethical Considerations
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Reference | Sequencing Panel | Sequencing Instrument | Main Points |
---|---|---|---|
Wang et al., 2017 [35] | Precision ID GlobalFiler NGS STR Panel | Ion Torrent PGM | Evaluation of the kit on Ion PGM. Population data for Chinese Han were obtained. Minor contributor of mixture could be detected in 19:1 mixture. Good results were obtained from multiple casework-type samples. |
Müller et al., 2018 [36] | Early Access Precision ID GlobalFiler NGS STR Panel | Ion S5 System | Inter-laboratory evaluation (two laboratories) of prototype kits, Early Access Precision ID GlobalFiler Mixture ID and GlobalFiler NGS STR Panel. Higher sensitivity was revealed with manual library preparation (full profiles at 62 pg) compared to automated. |
Tao et al., 2019 [37] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Evaluation of the kit on Ion S5. Population data for Uyghur (inner Asia) were obtained. Full profiles were generated down to 62.5 pg and from 1:3 mixtures. Discordances with GlobalFiler CE kits were observed at Penta D due to high interlocus imbalance. Urea concentrations higher than 1000 ng/μL inhibited profiling. |
Faccinetto et al., 2019 [38] | Precision ID GlobalFiler NGS STR Panel v2 | Ion GeneStudio S5 System | Internal validation of the kit. Complete profiles were obtained with 12 pg of DNA. Partial profiles were generated from 1:80 mixtures. More stutters and noise artefacts were observed in the NGS kit compared to CE with the GlobalFiler kit, which also produced more reliable calls from mixtures. |
Shyla et al., 2019 [39] | Precision ID GlobalFiler NGS STR Panel v2 | HID Ion GeneStudio S5 System | Application of the kit for a complex paternity case with three incompatibilities. Uniparental disomy from the mother was proven. |
Pajnič, Pogorelc and Zupanc, 2019 [40] | Precision ID GlobalFiler NGS STR Panel (v2) | Ion S5 System | Human remains from World War 2 were processed for kinship analysis, on top of ESI 17 and NGM kits STR typing. The added information obtained with the GlobalFiler NGS kit proved useful. |
Fattorini et al., 2019 [41] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Isometric artefacts were identified from analysis of heat-degraded samples. These should be evaluated carefully as they could be interpreted as mixtures. |
Oldoni et al., 2019 [42] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | A microhaplotype panel for Ion S5 was compared to GlobalFiler NGS and CE kits for mixture deconvolution. The GlobalFiler NGS kit performed better than CE for mixtures, and the microhaplotype panel performed even better, with 50 pg sensitivity and full profiles attainable from three–five people mixtures. |
Barrio et al., 2019 [43] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 XL System | Spanish population data were reported. Comparison of the GlobalFiler NGS results with the PowerPlex Fusion 6C STR kit showed high concordance. Increased discrimination power was obtained with sequence data. |
Ragazzo et al., 2020 [44] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Evaluation of the kit for mixture interpretation from saliva and urine samples. The GlobalFiler CE kit performed better at detecting the minor contributor, but the NGS kit provided increased discrimination. |
Wang et al., 2020 [45] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 XL System | Chinese Han and Tibetan population data were reported. Increased variation was revealed from sequence data compared to CE data. Discordances at Penta E and interlocus imbalance were highlighted. |
Pajnič, Obal and Zupanc, 2020 [46] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Human remains from World War 2 were processed for kinship analysis, on top of autosomal STR and Y-STR kits. The added information obtained with the GlobalFiler NGS kit proved useful to increase posterior probability. |
Dash et al., 2021 [47] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Central Indian population samples were evaluated for microvariant alleles, which appeared to be rare. |
Kitayama et al., 2022 [48] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 XL System | Japanese population data were reported. Discrepancy at locus D2S441 was observed with CE data from the GlobalFiler STR kit. |
Ohuchi et al., 2022 [49] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Japanese population data were obtained for database generation. Care in evaluation of sequence errors and stutters was advised. |
Guo et al., 2022 [50] | Precision ID GlobalFiler NGS STR Panel v2 | Ion Genexus Sequencer | Evaluation of the kit on Ion Torrent Genexus, a new automated technology for library preparation and sequencing coupled with analysis software for quick and easy profile generation. Sensitivity down to 100 pg of DNA was shown, while the minor contributor was identified in a 1:4 mixture. |
Pajnič et al., 2022 [51] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Isometric artefacts were identified from analysis of heat-degraded samples. Additionally, 5.9 artefacts per test were observed, 5.2% with higher coverage than the original allele. These artefacts are stochastic and represent a particular issue with Ion Torrent technology. |
Fonseca and Fridman, 2022 [52] | Precision ID GlobalFiler NGS STR Panel v2 | Ion GeneStudio S5 System | The kit was used to analyze sequence variation between monozygotic twins for differentiation purposes. Two SNPs were identified in the flanking regions, which highlights the possibility of using this kit to differentiate identical twins. |
Kocsis, Matrai and Egyed, 2023 [53] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Evaluation of discordances at locus Penta E between the GlobalFiler NGS STR kit, PowerPlex Fusion 6C, and PowerPlex 18D Systems CE kits. Sanger sequencing was performed. |
Sharma and Wurmbach, 2024 [54] | Precision ID GlobalFiler NGS STR Panel v2 | Ion S5 System | Kit evaluation on Ion S5. Optimal recovery PCR method was used. Full profiles were obtained from 50 pg of DNA, and degraded samples with Degradation Index (DI) > 60. 1:30–1:20 mixtures were identified using read count. High locus imbalance was observed at locus Penta D. Most artefacts were detected at D12S391. |
Eduardoff et al., 2015 [55] | HID-Ion AmpliSeq Identity Panel v2.2 | Ion Torrent PGM | Evaluation of the Identity kit between three laboratories; 25–100 pg of DNA were found to deliver acceptable results. |
Gill et al., 2015 [56] | HID-Ion AmpliSeq Identity Panel v2.2 | Ion Torrent PGM | The LRmix program was used for deconvolution of two–three people mixtures. Two people mixtures gave good results, while three people cases had variable success. |
Guo et al., 2016 [57] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Evaluation of the kit following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Data for Han Chinese were obtained. Cross-reactivity with primates was observed. Full deconvolution was obtained with 1:9 mixtures. |
Ochiai et al., 2016 [58] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Only Y-chromosome SNPs were considered. Data for Japanese and Malay were produced. Missing results and minor misreading were highlighted. |
Buchard et al., 2016 [59] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | The panel was validated in an accredited laboratory for relationship testing. Thresholds were set and a Python script for analysis was devised. A 1:24 mixture of two people was identified by the script. |
Kampmann et al., 2016 [60] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Buccal swab samples on FTA cards were successfully processed. |
Pilli et al., 2016 [61] | HID-Ion AmpliSeq Identity Panel v2.3 | Ion Torrent PGM | Human DNA was extracted and successfully typed from lice for both STRs (AmpFℓSTR NGM Select kit) and SNPs (Identity Panel). More successful results were obtained with NGS SNP testing. |
Meiklejohn and Robertson, 2017 [62] | Precision ID Identity Panel | Ion Torrent PGM | Evaluation of the kit on Ion PGM. Two types of genotyping analysis software were used, the Ion Torrent HID SNP Genotyper and CLC Genomics Workbench, achieving 100% concordance. |
van der Heijden et al., 2017 [63] | Precision ID Identity Panel | Ion Torrent PGM and Ion S5 System | Comparison between manual library preparation with Ion PGM sequencing, automated library preparation (Biomek 3000) with Ion PGM sequencing, and automated library preparation (Ion Chef) with Ion S5 sequencing. The Ion Chef/Ion S5 workflow gave the best results but was more expensive. Somali population data were generated. |
Garcia, Soto and Yurrebaso, 2017 [64] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Forensic evaluation of the kit on Ion PGM. Population data for Basques were obtained. |
Juras et al., 2017 [65] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Human remains from neolithic graves were processed for kinship analysis. Illumina mtDNA sequencing was also performed. The SNP NGS kit was inefficient with poorly preserved ancient samples and was only useful with well-preserved samples. |
Apaga et al., 2017 [32] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Comparison of shared markers between ForenSeq kit on MiSeq and Identity Panel on Ion PGM. Different performances were highlighted. Some SNPs with observed discordances require attention. |
Bleka et al., 2017b [66] | HID-Ion AmpliSeq Identity Panel v2.2 | Ion Torrent PGM | Two–three people mixtures were analyzed to evaluate deconvolution performance of the quantitative model EuroForMix compared to the qualitative model LRmix. The discrimination power appeared improved. |
Bleka et al., 2017a [67] | HID-Ion AmpliSeq Identity Panel v2.2 | Ion Torrent PGM | Two–three people mixtures were analyzed to evaluate the deconvolution performance of the quantitative model EuroForMix compared to the qualitative model LRmix. The discrimination power appeared improved. |
Cho et al., 2017 [68] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | DNA was successfully typed from cell-free DNA from pregnant mothers’ serum as a method to perform pre-natal DNA test. |
Liu et al., 2018 [69] | Precision ID Identity Panel | Ion Torrent PGM | Tibetan, Uyghur, and Hui population data were generated. Y haplogroups were compared with worldwide populations. |
Li et al., 2018 [70] | HID-Ion AmpliSeq Identity Panel v2.3 | Ion Torrent PGM | Southern Chinese (Han) population data and forensic parameters were evaluated. Poor allelic balance was shown for seven markers, and 0.82% of miscalled reads were found. Y haplogroups were also investigated. |
Sun et al., 2019 [71] | Precision ID Identity Panel | Ion Torrent PGM | Chinese Han (Hebei province) population data and forensic parameters were evaluated. Y haplogroups were investigated and microhaplotypes identified. |
Christiansen et al., 2019 [72] | Precision ID Identity Panel | Ion S5 System | Paternal SNPs were successfully typed from cell-free DNA from pregnant mothers’ plasma to perform pre-natal DNA test. False calls were found, indicating the need for at least duplicate testing as these false calls were not reproducible. Paternal SNP dropouts could be reduced by using smaller amplicons. |
Turchi et al., 2019 [73] | Precision ID Identity Panel | Ion Torrent PGM | The panel was successful with challenging samples and degraded and low-quantity DNA. Informative profiles were obtained from 1.2 to 1 ng of DNA with DI > 9. Most challenging samples could benefit from the generation of consensus profile of two to three replicates, from using <25–26 PCR cycles, and applying 50 reads coverage threshold. |
Bottino, Silva and Moura-Neto, 2019 [74] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | The article reports forensic evaluation and investigation of Y haplogroups for Brazilians. Only twelve individuals were typed, but they appeared to represent the expectations for the general Brazilian population. |
Avila et al., 2019b [75] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Forensic evaluation and population data for Brazilians were produced. Y haplogroups were also investigated. The kit appeared suitable for both identity and kinship testing. Comparison with worldwide population was performed. Improvements in inter- and intralocus balance were highlighted as required. |
Avila et al., 2019a [76] | HID-Ion AmpliSeq Identity Panel | Ion Torrent PGM | Brazilian casework samples were processed with the PowerPlex Fusion STR kit and Identity Panel SNP kit. The statistical strength of NGS results was higher than STRs. Epithelial cells generated lower-quality results. Manual review of NGS data appeared fundamental. |
Turchi et al., 2020 [77] | Precision ID Identity Panel | Ion Torrent PGM | The kit was successful with challenging samples and degraded and low-quantity DNA. Good results were obtained down to 12 pg of degraded DNA. The most challenging samples could benefit from three replicates testing and 50 reads coverage threshold. |
Tiedge et al., 2020 [78] | Precision ID Identity Panel | Ion S5 System | PowerPlex Fusion 6C STRs and Identity Panel SNPs were typed from prints developed using the columnar thin-film (CTF) method. No inhibition from CTF was shown for both methods, but more information was obtained from the NGS kit for low-quality/quantity DNA. A maximum of 27 PCR cycles was recommended. |
Gray et al., 2020 [79] | Precision ID Identity Panel | Ion S5 System | STR (PowerPlex Fusion 6C) and SNP (Identity Panel) profiles were obtained from mosquitos after feeding on blood. All SNPs were obtained after 48 h from feeding (single source) or 24 h (mixtures), while all STRs were obtained after 24 h (single source) or 20 h (mixtures). However, STR was more efficient for mixture interpretation. |
Sun et al., 2020 [80] | Precision ID Identity Panel | Ion Torrent PGM | Tumor tissue was profiled to identify the body source. More than 99% accuracy was obtained using 69–89 threshold when counting the number of loci with two alleles shared. |
Chen et al., 2020 [81] | Precision ID Identity Panel | Ion Torrent PGM | A Perl-based pipeline was developed to deconvolute mixtures of two people. The method worked well even when mixed samples were first-degree relatives. The 1:19 mixtures showed poor results compared to 1:4 and 1:9, which were also worse than 1:1.5 and 1:4 results. |
Tiedge et al., 2021 [82] | Precision ID Identity Panel | Ion S5 System | Fingerprints exposed to different environmental conditions and collected via CTF were typed. All samples yielded complete profiles and no inhibition from CTF was shown; 23 PCR cycles were used with 0.5–1 ng DNA and 29 for DNA input < 0.5 ng. |
Dash et al., 2022 [83] | Precision ID Identity Panel | Ion GeneStudio S5 System | Central Indian population data were produced. Y-chromosome SNPs were investigated and interpopulation comparison was performed. |
Yin, Zhang and Xing, 2022 [84] | Precision ID Identity Panel | HID Ion GeneStudio S5 System | R algorithm was devised and tested for mixture deconvolution. The deconvolution accuracy was high for balanced mixture ratios or unbalanced with known minor contributor, and the ratio was estimated correctly from 1:1 to 1:6 ranges. |
Yang, Lee and Lee, 2023 [85] | Precision ID Identity Panel | HID Ion S5/Ion GeneStudio S5 | Korean population data were produced and compared with other populations. Visual SNP caller was used to obtain microhaplotypes. The use of 16 microhaplotypes improved the discrimination power. Y-haplogroups were investigated. Population databases for the use of this kit for forensic application are still lacking. |
Joo et al., 2023 [86] | Precision ID Identity Panel | Illumina MiSeq System | Myanmar population data were produced and compared with other populations. The kit was used on the MiSeq instrument. Microhaplotypes were found using Visual SNP caller. |
Li et al., 2023 [87] | Precision ID Identity Panel | Ion S5 XL System | ForenSeq DNA Signature Prep Kit on MiSeq FGx, Precision ID Identity Panel on Ion S5 XL, and MGIEasy Signature Identification Library Prep Kit on MGISEQ-2000 were sequenced and compared. All performed differently, with no platform performing consistently better for all parameters considered. Six SNPs had discordant calls. |
Pajnič, Leskovar and Cresnar, 2023 [88] | Precision ID Identity Panel | Ion GeneStudio S5 System | The Identity Panel was used together with the Investigator EssplexPlus SE QS kit for full siblings’ prediction from Early Middle Ages skeletons. The prediction was inconclusive with STRs only but successful with SNPs. |
Fattorini et al., 2023 [89] | Precision ID Identity Panel | Ion S5 System | World War 2 bone remains delivering no results on STR testing were processed with the Identity Panel. The average DNA quantity was 6.8 pg; 93.8% of libraries produced results for 63/90 autosomal markers; 40% of results did not match the donor or were mixed profiles, possibly due to contamination. |
Kiesler, Gettings and Vallone, 2015 [90] | HID-Ion AmpliSeq Identity Panel v4.0 and Ancestry Panel v4.0 | Ion Torrent PGM | Evaluation of Identity and Ancestry Panels on NIST samples for the establishment of reference material. Some markers (0.25% for Identity and 2.02% for Ancestry Panel) showed coverage below recommended values of 300 X. Some markers in both panels showed allelic imbalance and strand bias (ratio of positive strand reads to negative strand reads). Discordant replicates were observed on two occasions in the Ancestry Panel. |
Tasker et al., 2017 [91] | HID-Ion AmpliSeq Identity Panel and Ancestry Panel | Ion Torrent PGM | DNA was typed from touch/blood samples recovered from bomb fragments for ancestry inference. The InnoTyper 21 Kit for insertions/null markers was also used and appeared good for challenging samples. The success of the SNP NGS kits was variable. |
Scheible et al., 2021 [92] | Precision ID Ancestry and Identity Panels | Illumina MiniSeq System | Workflow for Ancestry and Identity Panels was tested on Illumina MiniSeq; 93.9% of SNPs were successfully genotyped from positive controls, buccal swabs, and dust samples. |
Meiklejohn et al., 2023 [93] | Precision ID Ancestry and Identity Panels | Illumina MiniSeq System | SNPs from dust samples were typed on the MiniSeq instrument. The FastID software was used for mixture deconvolution; 72% of the alleles were recovered, and 93% of known occupants were detected in at least one sample, while 54% had non-occupant alleles. |
Themudo et al., 2016 [94] | HID-Ion AmpliSeq Ancestry Panel | Ion Torrent PGM | Ancestry Panel profiles were obtained from Greenlanders. The training set was used as reference for subsequent, more successful assignment of ancestry. |
Garcia et al., 2017 [95] | Precision ID Ancestry Panel | Ion Torrent PGM | Forensic evaluation of the Ancestry Panel on Ion PGM. Population data for Basques were obtained and used for ancestry inference, which showed clustering with Europeans. |
Truelsen et al., 2017 [96] | Precision ID Ancestry Panel | Ion Torrent PGM | Middle East populations (Turks and Iranians) were analyzed to investigate genetic differentiation using GenoGeographer program. Differentiation was not possible. |
Pereira et al., 2017 [97] | Precision ID Ancestry Panel | Ion Torrent PGM | Evaluation of the panel with casework samples (blood and buccal swabs on FTA cards) from Somalia and Denmark was reported. Some markers consistently performed poorly. |
Santangelo et al., 2017 [98] | Precision ID Ancestry Panel | Ion Torrent PGM | Ancestry and admixture investigation of three Ecuadorians ethnic groups (Kichwa, Mestizo, and Afro-Ecuadorian) was reported. |
Hollard et al., 2017 [99] | HID-Ion AmpliSeq Ancestry Panel | Ion Torrent PGM | Ancestry kit, Yfiler Plus, mtDNA HV1 sequencing, and Irisplex SNPs were used to analyze ancestry and phenotype from a carbonized corpse that failed CE STR testing. A combined approach appeared preferable. |
Wang et al., 2018 [100] | Precision ID Ancestry Panel | Ion Torrent PGM | Forensic evaluation, population data, and ancestry inference for Chinese Tibeto-Burman were reported. The panel performed well and was suitable for both ancestry and identification. |
Nakanishi et al., 2018 [101] | Precision ID Ancestry Panel | Ion Torrent PGM | Japanese populations from mainland and Okinawa were analyzed to evaluate the possibility to distinguish them via ancestry investigation. Differentiation was not possible. |
Jin et al., 2018 [102] | Precision ID Ancestry Panel | Ion S5 System | Development of guidelines for the implementation of a biogeographic ancestry inference service based on Admixture Prediction produced in the Ion Torrent Suite for Precision ID Ancestry Panel. The panel appeared effective for ancestry prediction. |
He et al., 2018 [103] | Precision ID Ancestry Panel | Ion Torrent PGM | Chinese populations (Uyghur and Hui) were analyzed to investigate population data and ancestry. Individuals could be differentiated both by ancestry and individually. A limitation was observed in distinguishing homogeneous populations. |
Al-Asfi et al., 2018 [104] | Precision ID Ancestry Panel | Ion Torrent PGM | Evaluation of the kit on Ion PGM. Ancestry prediction was accurate at 125 pg and 30 pg using 21 and 25 PCR cycles, respectively. Partial profiles (85%) were obtained from 15 pg of DNA, while <6 pg produced less than 50% concordance; 1 ng was suggested as minimum input for high-confidence ancestry assignment. |
Lee et al., 2018 [105] | Precision ID Ancestry Panel | Ion S5 XL System | Seven Asian populations (Southern Chinese, Beijing Chinese, Japanese, Koreans, Vietnamese, Nepalese, Indians, and Pakistani) were profiled, and ancestry was investigated. All Northeast (China, Japan, and Korea) and Southeast Asians (Vietnamese) were predicted as East Asians, while Southwest Asians (Nepal, India, and Pakistan) were predominantly assigned to South Asia. |
Young et al., 2019 [106] | Precision ID Ancestry Panel | Ion GeneStudio S5 System | Ancestry Panel, 24 SNP HIrisplex System, and QIAGEN 140-SNP forensic identification multiplex kits were used on different touched items. Accurate calls were obtained from 70% of samples for all three panels combined. |
Daniels-Higginbotham et al., 2019 [107] | Precision ID Ancestry Panel | Illumina MiSeq FGx System | 19th century skeletal remains were sequenced using MiSeq FGx to identify ancestry. AmpFℓSTR Yfiler PCR Amplification Kit and Y-typing of four important SNP variants were also used to upload results on the FamilyTreeDNA website. |
Shan et al., 2019 [108] | Precision ID Ancestry Panel | N/A | Ancestry investigation from Punjabi Pakistani samples was reported. The GenoGeographer software was used. The population appeared admixed and non-distinguishable from South Central Asia and Middle East populations. |
Al-Dosari et al., 2019 [109] | Precision ID Ancestry Panel | Ion Torrent PGM | Comparison between manual and automated library preparation to type casework samples. No significant differences were found, but the automated method was faster and avoided pipetting errors. A full profile was obtained from 0.12 ng of DNA. |
Mogensen et al., 2020 [110] | Precision ID Ancestry Panel | N/A | The GenoGeographer software was assessed for ancestry assignment using publicly available data from multiple populations. Ancestry was not assigned to 22.4% of the individuals. Of the assigned individuals, 8.2% had discordant assignment, and 8.2% had ambiguous assignment. Prediction would be improved with more SNPs and more data in databases. |
Cooley et al., 2021 [111] | Precision ID Ancestry Panel | Ion S5 System and Ion Torrent PGM | Comparison of Ion OneTouch 2/Ion PGM and Ion Chef/Ion S5 systems using forensic-type samples. The Ion Chef/Ion S5 method was faster and generated higher coverage and SNP quality, even if both systems predicted concordant ancestries. |
Truelsen et al., 2021 [112] | Precision ID Ancestry Panel | Ion S5 System | Samples from 14 European, Middle Eastern, African, and Asian countries were sequenced with the Ancestry and EUROFORGEN panels to perform ancestry prediction with GenoGeographer. The Ancestry Panel was sufficient to distinguish North Africans from European and Middle Eastern, with improved separation when combining the two panels. Separation of Middle Eastern from Europeans and South-Central Asians was difficult even with both kits combined. |
He et al., 2021 [113] | Precision ID Ancestry Panel | Ion S5 XL System | Population genetics, admixture, ancestry, and forensic parameters were evaluated in Southern Chinese Sinitic/Tai-Kadai individuals. |
Shan et al., 2021 [114] | Precision ID Ancestry Panel | Ion S5 System | Pakistani individuals (Baloch, Pashtun, and Punjabi subpopulations) samples were processed with the Ancestry Panel and HuPi AmpliSeq Custom panel to evaluate both ancestry and skin pigmentation. Significantly different genetic distance was observed between the subgroups. Skin differentiation was also significantly different for one group compared to the other two. |
Young et al., 2021 [115] | Precision ID Ancestry Panel | Ion GeneStudio S5 Plus System | The Ancestry Panel and HIrisplex System (Ion AmpliSeq HID Phenotyping Community Panel) were used for ancestry evaluation and skin pigmentation prediction applied to touch DNA samples with direct PCR. 90% of samples generated correct ancestry assignment at the major population level. Full SNP profiles were obtained from 23% of touch samples and partial profiles (>85%) from 32%. Moreover, 42% of samples obtained high confidence ancestry assignments. Correct ancestry was assigned when >70% SNPs were detected. |
Mogensen et al., 2022 [116] | Precision ID Ancestry Panel | N/A | Data for Slovenia, Greece, Albania, and Eritrea were obtained and added to GenoGeographer as a reference population. The Admixture Module was tested on 3548 profiles; 95.5% were assigned to one or more groups (95.4% concordant), while 4.5% were not assigned. An additional 1486 profiles expected to belong to populations other than the reference were also tested; 70% of North and South America samples were rejected, while only 20% of Central, North, and Northeast Asia samples were rejected. The rejection rate was decreased by using the Admixture Module. |
Cui et al., 2023 [117] | Precision ID Ancestry Panel | Ion S5 XL System | Gannan Tibetan population samples were analyzed, and forensic parameters and ancestry were evaluated. The kit appeared useful for ancestry prediction for continental populations but less accurate for subpopulations. Individual identification appeared suitable. |
Felkl et al., 2023 [118] | HID-Ion AmpliSeq Ancestry Panel | Ion Torrent PGM | Forensic evaluation and ancestry prediction of South Brazilian heterogeneous population samples were performed. Use for individual identification and kinship appeared suitable. Ancestry analysis showed admixture and more homogeneous groups among the subtypes. |
Koksal et al., 2023 [119] | Precision ID Ancestry Panel | Ion S5 System | Ancestry and admixture investigation of Brazilians using GenoGeographer was reported. Performance was low on the heterogeneous Brazilian population; 55% of assignments failed. Likelihood Ratio (LR) < 1000 was observed as a possible indicator of admixture. Higher Asian and African genetic contributions were observed in failed samples. |
Huang et al., 2018 [120] | N/A | N/A | A panel of 117 universal SNPs with Minor Allele Frequency (MAF) > 0.39 in 37 populations was defined for identity testing. Combined Match Probability (CMP) was lower for this set rather than the HID-Ion AmpliSeq Identity Panel for the Chinese Han population. |
Ragazzo et al., 2021 [121] | N/A | N/A | Evaluation of a custom OpenArray panel for phenotype prediction and identification including 60 SNPs from HIrisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit. |
Resutik et al., 2023 [122] | N/A | N/A | Ancestry prediction performance of MAPlex, Precision ID Ancestry Panel, and VISAGE Basic Tool panels was compared using publicly available datasets. Similar results were produced from all panels when using six broad continental regions on STRUCTURE. The most consistent performance in all regions was given by the VISAGE panel. |
Continent | Country | Population | Publication/s |
---|---|---|---|
Asia | Afghanistan | Afghani | Truelsen et al., 2021 [112] |
China | Beijing Chinese | Lee et al., 2018 [105] | |
Chinese Han | Wang et al., 2017 [35], Guo et al., 2016 [57], Sun et al., 2019 [71], Wang et al., 2020 [45] | ||
Chinese Hui | He et al., 2018 [103], Liu et al., 2018 [69] | ||
Chinese Gannan Tibetan | Cui et al., 2023 [117] | ||
Chinese Tibetans | Wang et al., 2020 [45], Liu et al., 2018 [69] | ||
Chinese Tibeto-Burman | Wang et al., 2018 [100] | ||
Chinese Uyghur | He et al., 2018 [103], Tao et al., 2019 [37], Liu et al., 2018 [69] | ||
Southern Chinese | Li et al., 2018 [70], Lee et al., 2018 [105] | ||
Southern Chinese Sinitic/Tai-Kadai | He et al., 2021 [113] | ||
India | Central Indians | Dash et al., 2021 [47], Dash et al., 2022 [83] | |
Indians | Lee et al., 2018 [105] | ||
Iran | Iranians | Truelsen et al., 2017 [96], Truelsen et al., 2021 [112] | |
Iraq | Iraqi | Truelsen et al., 2021 [112] | |
Japan | Japanese | Kitayama et al., 2022 [48], Ohuchi et al., 2022 [49], Nakanishi et al., 2018 [101], Ochiai et al., 2016 [58], Lee et al., 2018 [105] | |
Korea | Koreans | Yang, Lee and Lee, 2023 [85], Lee et al., 2018 [105] | |
Malaysia | Malay | Ochiai et al., 2016 [58] | |
Myanmar | Burmese | Joo et al., 2023 [86] | |
Nepal | Nepalese | Lee et al., 2018 [105] | |
Pakistan | Pakistani | Lee et al., 2018 [105], Truelsen et al., 2021 [112] | |
Pakistani Baloch | Shan et al., 2021 [114] | ||
Pakistani Pashtun | Shan et al., 2021 [114] | ||
Pakistani Punjabi | Shan et al., 2019 [108], Shan et al., 2021 [114] | ||
Syria | Syrians | Truelsen et al., 2021 [112] | |
Turkey | Turks | Truelsen et al., 2017 [96], Truelsen et al., 2021 [112] | |
Vietnam | Vietnamese | Lee et al., 2018 [105] | |
Europe | Albania | Albanians | Truelsen et al., 2021 [112], Mogensen et al., 2022 [116] |
Denmark | Danes | Truelsen et al., 2021 [112], Buchard et al., 2016 [59], Pereira et al., 2017 [97] | |
Greece | Greeks | Truelsen et al., 2021 [112], Mogensen et al., 2022 [116] | |
Portugal | Portuguese | Truelsen et al., 2021 [112] | |
Slovenia | Slovenians | Truelsen et al., 2021 [112], Mogensen et al., 2022 [116] | |
Spain | Basques | Garcia, Soto and Yurrebaso, 2017 [64], Garcia et al., 2017 [95] | |
Spanish | Barrio et al., 2019 [43] | ||
Africa | Eritrea | Eritreans | Truelsen et al., 2021 [112], Mogensen et al., 2022 [116] |
Morocco | Moroccans | Truelsen et al., 2021 [112] | |
Somalia | Somali | Truelsen et al., 2021 [112], Pereira et al., 2017 [97], van der Heijden et al., 2017 [63] | |
South America | Brazil | Brazilians | Bottino, Silva and Moura-Neto, 2019 [74], Avila et al., 2019b [75], Koksal et al., 2023 [119] |
South Brazilians | Felkl et al., 2023 [118] | ||
Ecuador | Ecuadorians | Santangelo et al., 2017 [98] | |
North America | Greenland | Greenlanders | Themudo et al., 2016 [94] |
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Pedroza Matute, S.; Iyavoo, S. Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics. Genes 2024, 15, 1133. https://doi.org/10.3390/genes15091133
Pedroza Matute S, Iyavoo S. Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics. Genes. 2024; 15(9):1133. https://doi.org/10.3390/genes15091133
Chicago/Turabian StylePedroza Matute, Sharlize, and Sasitaran Iyavoo. 2024. "Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics" Genes 15, no. 9: 1133. https://doi.org/10.3390/genes15091133