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Sidstedt M, Gynnå AH, Kiesler KM, Jansson L, Steffen CR, Håkansson J, Johansson G, Österlund T, Bogestål Y, Tillmar A, Rådström P, Ståhlberg A, Vallone PM, Hedman J. Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method. Forensic Sci Int Genet 2024; 71:103047. [PMID: 38598919 DOI: 10.1016/j.fsigen.2024.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
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Affiliation(s)
- Maja Sidstedt
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden
| | - Arvid H Gynnå
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden
| | - Kevin M Kiesler
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Linda Jansson
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden
| | - Carolyn R Steffen
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Joakim Håkansson
- RISE Unit of Biological Function, Division Materials and Production, Box 857, Borås SE-501 15, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg SE-405 30, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Gustav Johansson
- SIMSEN Diagnostics, Sahlgrenska Science Park, Gothenburg, Sweden
| | - Tobias Österlund
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, Gothenburg 41390, Sweden; Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland 41390, Sweden
| | - Yalda Bogestål
- RISE Unit of Biological Function, Division Materials and Production, Box 857, Borås SE-501 15, Sweden
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping SE-587 58, Sweden
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden
| | - Anders Ståhlberg
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, Gothenburg 41390, Sweden; Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Gothenburg 41390, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Region Västra Götaland 41390, Sweden
| | - Peter M Vallone
- National Institute of Standards and Technology, 100 Bureau Drive, M/S 8314, Gaithersburg, MD 20899, USA
| | - Johannes Hedman
- National Forensic Centre, Swedish Police Authority, Linköping SE-581 94, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund SE-221 00, Sweden.
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Kiesler KM, Borsuk LA, Steffen CR, Vallone PM, Gettings KB. US Population Data for 94 Identity-Informative SNP Loci. Genes (Basel) 2023; 14:genes14051071. [PMID: 37239431 DOI: 10.3390/genes14051071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of iiSNP amplicons compared to short tandem repeat (STR) markers increases the likelihood of successful amplification with degraded DNA samples. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data in the regions flanking the targeted SNPs identified additional variants, which can be combined with the target SNPs to form microhaplotypes (multiple phased SNPs within a short-read sequence). Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15% over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 × 10-38 for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes.
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Affiliation(s)
- Kevin M Kiesler
- National Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USA
| | - Lisa A Borsuk
- National Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USA
| | - Carolyn R Steffen
- National Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USA
| | - Peter M Vallone
- National Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USA
| | - Katherine B Gettings
- National Institute of Standards and Technology, 100 Bureau Drive, Mailstop 8314, Gaithersburg, MD 20899, USA
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Cleveland MH, Romsos EL, Steffen CR, Olson ND, Servetas SL, Valiant WG, Vallone PM. Rapid production and free distribution of a synthetic RNA material to support SARS-CoV-2 molecular diagnostic testing. Biologicals 2023; 82:101680. [PMID: 37178559 PMCID: PMC10154543 DOI: 10.1016/j.biologicals.2023.101680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
In response to the COVID-19 pandemic, the National Institute of Standards and Technology released a synthetic RNA material for SARS-CoV-2 in June 2020. The goal was to rapidly produce a material to support molecular diagnostic testing applications. This material, referred to as Research Grade Test Material 10169, was shipped free of charge to laboratories across the globe to provide a non-hazardous material for assay development and assay calibration. The material consisted of two unique regions of the SARS-CoV-2 genome approximately 4 kb nucleotides in length. The concentration of each synthetic fragment was measured using RT-dPCR methods and confirmed to be compatible with RT-qPCR methods. In this report, the preparation, stability, and limitations of this material are described.
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Affiliation(s)
- Megan H Cleveland
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA.
| | - Erica L Romsos
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
| | - Carolyn R Steffen
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
| | - Nathan D Olson
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
| | - Stephanie L Servetas
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
| | - William G Valiant
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
| | - Peter M Vallone
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
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Lenz KA, Rabbach DR, Liu C, Xu Q, Zeng Y, Steffen CR, Storts DR. Retraction notice to Developmental Validation of the VersaPlex™ 27PY System [Forensic Science International: Reports 2 C (2020) 100156]. Forensic Science International: Reports 2023. [DOI: 10.1016/j.fsir.2023.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Steffen CR, Romsos EL, Kiesler KM, Borsuk LA, Gettings KB, Vallone PM. Make it "SNPPY" - Updates to SRM 2391d: PCR-Based DNA Profiling Standard. Forensic Science International: Genetics Supplement Series 2022. [DOI: 10.1016/j.fsigss.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Borsuk LA, Steffen CR, Kiesler KM, Vallone PM, Gettings KB. Sequence-based U.S. population data for 7 X-STR loci. Forensic Science International: Reports 2020. [DOI: 10.1016/j.fsir.2020.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Lenz KA, Rabbach DR, Liu C, Xu Q, Zeng Y, Steffen CR, Storts DR. Developmental validation of the VersaPlex™ 27PY system. Forensic Science International: Reports 2020. [DOI: 10.1016/j.fsir.2020.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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He HJ, Das B, Cleveland MH, Chen L, Camalier CE, Liu LC, Norman KL, Fellowes AP, McEvoy CR, Lund SP, Almeida J, Steffen CR, Karlovich C, Williams PM, Cole KD. Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements. Clin Chem Lab Med 2020; 57:1142-1152. [PMID: 31112502 PMCID: PMC6875440 DOI: 10.1515/cclm-2018-1306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/21/2019] [Indexed: 01/04/2023]
Abstract
Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.
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Affiliation(s)
- Hua-Jun He
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899, USA, Phone: +301-975-2169, Fax: +301-330-3447
| | - Biswajit Das
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Megan H Cleveland
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Li Chen
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Corinne E Camalier
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | | | | | - Steve P Lund
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jamie Almeida
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Carolyn R Steffen
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Chris Karlovich
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - P Mickey Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kenneth D Cole
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899, USA, Phone: +301-975-2169, Fax: +301-330-3447
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Steffen CR, Gettings KB, Kiesler KM, Borsuk LA, Vallone PM. Sequence variation observed in 27 Y-STR markers with U.S. population samples. Forensic Science International: Genetics Supplement Series 2019. [DOI: 10.1016/j.fsigss.2019.10.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Almeida JL, Dakic A, Kindig K, Kone M, Letham DLD, Langdon S, Peat R, Holding-Pillai J, Hall EM, Ladd M, Shaffer MD, Berg H, Li J, Wigger G, Lund S, Steffen CR, Fransway BB, Geraghty B, Natoli M, Bauer B, Gollin SM, Lewis DW, Reid Y. Interlaboratory study to validate a STR profiling method for intraspecies identification of mouse cell lines. PLoS One 2019; 14:e0218412. [PMID: 31220119 PMCID: PMC6586308 DOI: 10.1371/journal.pone.0218412] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
The Consortium for Mouse Cell Line Authentication was formed to validate Short Tandem Repeat (STR) markers for intraspecies identification of mouse cell lines. The STR profiling method is a multiplex polymerase chain reaction (PCR) assay comprised of primers targeting 19 mouse STR markers and two human STR markers (for interspecies contamination screening). The goals of the Consortium were to perform an interlaboratory study to–(1) validate the mouse STR markers to uniquely identify mouse cell lines (intraspecies identification), (2) to provide a public database of mouse cell lines with the National Institute of Standards and Technology (NIST)-validated mouse STR profiles, and (3) to publish the results of the interlaboratory study. The interlaboratory study was an international effort that consisted of 12 participating laboratories representing institutions from academia, industry, biological resource centers, and government. The study was based on 50 of the most commonly used mouse cell lines obtained from the American Type Culture Collection (ATCC). Of the 50 mouse cell lines, 18 had unique STR profiles that were 100% concordant (match) among all Consortium laboratory members, and the remaining 32 cell lines had discordance that was resolved readily and led to improvement of the assay. The discordance was due to low signal and interpretation issues involving artifacts and genotyping errors. Although the total number of discordant STR profiles was relatively high in this study, the percent of labs agreeing on allele calls among the discordant samples was above 92%. The STR profiles, including electropherogram images, for NIST-validated mouse cell lines will be published on the NCBI BioSample Database (https://www.ncbi.nlm.nih.gov/biosample/). Overall, the interlaboratory study showed that the multiplex PCR method using 18 of the 19 mouse STR markers is capable of discriminating at the intraspecies level between mouse cell lines. Further studies are ongoing to refine the assay including (1) development of an allelic ladder for improving the accuracy of allele calling and (2) integration of stutter filters to identify true stutter.
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Affiliation(s)
- Jamie L. Almeida
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Gaithersburg, Maryland, United States of America
- * E-mail:
| | - Aleksandra Dakic
- ATCC, Standards Resource Center, Manassas, Virginia, United States of America
| | - Karin Kindig
- ATCC, Standards Resource Center, Manassas, Virginia, United States of America
| | - Maikan Kone
- ATCC, Standards Resource Center, Manassas, Virginia, United States of America
| | | | - Scott Langdon
- Duke University, Durham, North Carolina, United States of America
| | - Ruth Peat
- The Francis Crick Institute, Cell Services, London, United Kingdom
| | | | - Erin M. Hall
- Genetica Cell Line Testing –a LabCorp brand, Burlington, North Carolina, United States of America
| | - Mark Ladd
- Genetica Cell Line Testing –a LabCorp brand, Burlington, North Carolina, United States of America
| | - Megan D. Shaffer
- Genetica Cell Line Testing –a LabCorp brand, Burlington, North Carolina, United States of America
| | - Heath Berg
- IDEXX BioAnalytics, Columbia, Missouri, United States of America
| | - Jinliang Li
- Laragen Inc., Culver City, California, United States of America
| | | | - Steve Lund
- National Institute of Standards and Technology, Statistical Engineering Division, Gaithersburg, Maryland, United States of America
| | - Carolyn R. Steffen
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, Maryland, United States of America
| | - Barbara B. Fransway
- University of Arizona, Genetics Core Lab, University of Arizona Genetics Core, Tucson, Arizona, United States of America
| | - Bob Geraghty
- University of Cambridge, Cancer Research UK, Cambridge Institute, Cambridge, United Kingdom
| | - Manuela Natoli
- University of Cambridge, Cancer Research UK, Cambridge Institute, Cambridge, United Kingdom
| | - Beth Bauer
- University of Maryland, College Park, Maryland
| | - Susanne M. Gollin
- University of Pittsburgh, Department of Human Genetics, Pittsburgh, Pennsylvania, United States of America
| | - Dale W. Lewis
- University of Pittsburgh, Department of Human Genetics, Pittsburgh, Pennsylvania, United States of America
| | - Yvonne Reid
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Gaithersburg, Maryland, United States of America
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Gettings KB, Borsuk LA, Steffen CR, Kiesler KM, Vallone PM. Sequence-based U.S. population data for 27 autosomal STR loci. Forensic Sci Int Genet 2018; 37:106-115. [PMID: 30144646 DOI: 10.1016/j.fsigen.2018.07.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Abstract
This manuscript reports Short Tandem Repeat (STR) sequence-based allele frequencies for 1036 samples across 27 autosomal STR loci: D1S1656, TPOX, D2S441, D2S1338, D3S1358, D4S2408, FGA, D5S818, CSF1PO, D6S1043, D7S820, D8S1179, D9S1122, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D17S1301, D18S51, D19S433, D20S482, D21S11, Penta D, and D22S1045. Sequence data were analyzed by two bioinformatic pipelines and all samples have been evaluated for concordance with alleles derived from CE-based analysis at all loci. Each reported sequence includes high-quality flanking sequence and is properly formatted according to the most recent guidance of the International Society for Forensic Genetics. In addition, GenBank accession numbers are reported for each sequence, and associated records are available in the STRSeq BioProject (https://www.ncbi.nlm.nih.gov/bioproject/380127). The D3S1358 locus demonstrates the greatest average increase in heterozygosity across populations (approximately 10 percentage points). Loci demonstrating average increase in heterozygosity from 10 to 5 percentage points include (in descending order) D9S1122, D13S317, D8S1179, D21S11, D5S818, D12S391, and D2S441. The remaining 19 loci each demonstrate less than 5 percentage point increase in average heterozygosity. Discussion includes the utility of this data in understanding traditional CE results, such as informing stutter models and understanding migration challenges, and considerations for population sampling strategies in light of the marked increase in rare alleles for several of the sequence-based STR loci. This NIST 1036 data set is expected to support the implementation of STR sequencing forensic casework by providing high-confidence sequence-based allele frequencies for the same sample set which are already the basis for population statistics in many U.S. forensic laboratories.
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Affiliation(s)
- Katherine Butler Gettings
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Lisa A Borsuk
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Carolyn R Steffen
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Kevin M Kiesler
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
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12
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Borsuk LA, Gettings KB, Steffen CR, Kiesler KM, Vallone PM. Sequence-based US population data for the SE33 locus. Electrophoresis 2018; 39:2694-2701. [PMID: 29736954 DOI: 10.1002/elps.201800091] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 01/10/2023]
Abstract
A set of 1036 U.S. Population Samples were sequenced using the Illumina ForenSeq DNA Signature Prep Kit. This sample set has been highly characterized using a variety of marker systems for human identification. The FASTQ files obtained from a ForenSeq DNA Signature Prep Kit experiment include several STR loci that are not reported in the associated software. These include SE33, DXS8377, DXS10148, DYS456, and DYS461. The sequence variation within the autosomal STR marker SE33 was evaluated using a customized bioinformatic approach to identify and characterize the locus in the 1036 data set. The analysis identified 53 unique alleles by length and 264 by sequence. An additional 10 alleles were detected when selected extended flanking regions were examined to resolve discordances. Allele frequencies and SE33 sequence motif patterns are reported for the 1036 data set. The comparison of numerical allele calls derived from sequence data to the allele calls obtained from commercial capillary electrophoresis-based STR typing kits resulted in 100% concordance, after manual data review and confirmation sequencing of three flanking region deletions. The analysis of this data set involved significant manual sequence curation and information support from length-based genotypes to ensure high confidence in the sequence-based allele calls. The challenges of interpreting the sequence data for SE33 consisted of high sequence noise, allele-size dependent variance in coverage, and heterozygote imbalance. As allele length increased, sequence depth of coverage and quality decreased at the terminal end. Accordingly, heterozygous genotype imbalance increased in proportion to increased distance between alleles.
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Affiliation(s)
- Lisa A Borsuk
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Carolyn R Steffen
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Kevin M Kiesler
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Peter M Vallone
- National Institute of Standards and Technology, Gaithersburg, MD, USA
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13
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Sidstedt M, Hedman J, Romsos EL, Waitara L, Wadsö L, Steffen CR, Vallone PM, Rådström P. Inhibition mechanisms of hemoglobin, immunoglobulin G, and whole blood in digital and real-time PCR. Anal Bioanal Chem 2018; 410:2569-2583. [PMID: 29504082 PMCID: PMC5857286 DOI: 10.1007/s00216-018-0931-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/18/2018] [Accepted: 01/30/2018] [Indexed: 11/25/2022]
Abstract
Blood samples are widely used for PCR-based DNA analysis in fields such as diagnosis of infectious diseases, cancer diagnostics, and forensic genetics. In this study, the mechanisms behind blood-induced PCR inhibition were evaluated by use of whole blood as well as known PCR-inhibitory molecules in both digital PCR and real-time PCR. Also, electrophoretic mobility shift assay was applied to investigate interactions between inhibitory proteins and DNA, and isothermal titration calorimetry was used to directly measure effects on DNA polymerase activity. Whole blood caused a decrease in the number of positive digital PCR reactions, lowered amplification efficiency, and caused severe quenching of the fluorescence of the passive reference dye 6-carboxy-X-rhodamine as well as the double-stranded DNA binding dye EvaGreen. Immunoglobulin G was found to bind to single-stranded genomic DNA, leading to increased quantification cycle values. Hemoglobin affected the DNA polymerase activity and thus lowered the amplification efficiency. Hemoglobin and hematin were shown to be the molecules in blood responsible for the fluorescence quenching. In conclusion, hemoglobin and immunoglobulin G are the two major PCR inhibitors in blood, where the first affects amplification through a direct effect on the DNA polymerase activity and quenches the fluorescence of free dye molecules, and the latter binds to single-stranded genomic DNA, hindering DNA polymerization in the first few PCR cycles. Graphical abstract PCR inhibition mechanisms of hemoglobin and immunoglobulin G (IgG). Cq quantification cycle, dsDNA double-stranded DNA, ssDNA single-stranded DNA.
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Affiliation(s)
- Maja Sidstedt
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
- Swedish National Forensic Centre, 581 94, Linköping, Sweden
| | - Johannes Hedman
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden.
- Swedish National Forensic Centre, 581 94, Linköping, Sweden.
| | - Erica L Romsos
- Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8314, USA
| | - Leticia Waitara
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
- Government Chemist Laboratory Authority, P.O. Box 164, Dar es Salaam, Tanzania
| | - Lars Wadsö
- Division of Building Materials, Lund University, 221 00, Lund, Sweden
| | - Carolyn R Steffen
- Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8314, USA
| | - Peter M Vallone
- Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8314, USA
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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Kiesler KM, Steffen CR, Coble MD, Vallone PM. Initial assessment of the Precision ID Globalfiler Mixture ID panel on the Ion Torrent S5XL DNA sequencer and Converge v2.0 software. Forensic Science International: Genetics Supplement Series 2017. [DOI: 10.1016/j.fsigss.2017.09.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Steffen CR, Coble MD, Gettings KB, Vallone PM. Corrigendum to 'U.S. Population Data for 29 Autosomal STR Loci' [Forensic Sci. Int. Genet. 7 (2013) e82-e83]. Forensic Sci Int Genet 2017; 31:e36-e40. [PMID: 28867528 DOI: 10.1016/j.fsigen.2017.08.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/15/2022]
Affiliation(s)
- Carolyn R Steffen
- National Institute of Standards and Technology, Material Measurement Laboratory, Gaithersburg, MD 20899-8314, United States
| | - Michael D Coble
- National Institute of Standards and Technology, Material Measurement Laboratory, Gaithersburg, MD 20899-8314, United States
| | - Katherine B Gettings
- National Institute of Standards and Technology, Material Measurement Laboratory, Gaithersburg, MD 20899-8314, United States
| | - Peter M Vallone
- National Institute of Standards and Technology, Material Measurement Laboratory, Gaithersburg, MD 20899-8314, United States.
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16
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Sidstedt M, Romsos EL, Hedell R, Ansell R, Steffen CR, Vallone PM, Rådström P, Hedman J. Accurate Digital Polymerase Chain Reaction Quantification of Challenging Samples Applying Inhibitor-Tolerant DNA Polymerases. Anal Chem 2017; 89:1642-1649. [PMID: 28118703 DOI: 10.1021/acs.analchem.6b03746] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning of the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentration is determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrixes such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. In this study, we evaluated the impact of varying the DNA polymerase in chamber-based dPCR for both pure and impure samples using the common PCR inhibitor humic acid (HA) as a model. We compared the TaqMan Universal PCR Master Mix with two alternative DNA polymerases: ExTaq HS and Immolase. By using Bayesian modeling, we show that there is no difference among the tested DNA polymerases in terms of accuracy of absolute quantification for pure template samples, i.e., without HA present. For samples containing HA, there were great differences in performance: the TaqMan Universal PCR Master Mix failed to correctly quantify DNA with more than 13 pg/nL HA, whereas Immolase (1 U) could handle up to 375 pg/nL HA. Furthermore, we found that BSA had a moderate positive effect for the TaqMan Universal PCR Master Mix, enabling accurate quantification for 25 pg/nL HA. Increasing the amount of DNA polymerase from 1 to 5 U had a strong effect for ExTaq HS, elevating HA-tolerance four times. We also show that the average Cq values of positive reactions may be used as a measure of inhibition effects, e.g., to determine whether or not a dPCR quantification result is reliable. The statistical models developed to objectively analyze the data may also be applied in quality control. We conclude that the choice of DNA polymerase in dPCR is crucial for the accuracy of quantification when analyzing challenging samples.
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Affiliation(s)
- Maja Sidstedt
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Swedish National Forensic Centre , SE-581 94 Linköping, Sweden
| | - Erica L Romsos
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Ronny Hedell
- Swedish National Forensic Centre , SE-581 94 Linköping, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ricky Ansell
- Swedish National Forensic Centre , SE-581 94 Linköping, Sweden.,Department of Physics, Chemistry and Biology, IFM, Linköping University , SE-581 83 Linköping, Sweden
| | - Carolyn R Steffen
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Peter M Vallone
- Materials Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8314, United States
| | - Peter Rådström
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden
| | - Johannes Hedman
- Applied Microbiology, Department of Chemistry, Lund University , SE-221 00 Lund, Sweden.,Swedish National Forensic Centre , SE-581 94 Linköping, Sweden
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17
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Gittelson S, Steffen CR, Coble MD. Low-template DNA: A single DNA analysis or two replicates? Forensic Sci Int 2016; 264:139-45. [PMID: 27131143 DOI: 10.1016/j.forsciint.2016.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 03/12/2016] [Accepted: 04/05/2016] [Indexed: 11/28/2022]
Abstract
This study investigates the following two questions: (1) Should the DNA analyst concentrate the DNA extract into a single amplification or should he/she split it up to do two replicates? (2) Given the electropherogram obtained from a first analysis, is it worthwhile for the DNA analyst to invest in obtaining a second replicate? A decision-theoretic approach addresses these questions by quantitatively expressing the expected net gain (ENG) of each DNA analysis of interest. The results indicate that two replicates generally have a greater ENG than a single DNA analysis for DNA quantities capable of producing two replicates having an average allelic peak height as low as 43rfu. This supports the position that two replicates increase the information content with regard to a single analysis.
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Affiliation(s)
- Simone Gittelson
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, United States.
| | - Carolyn R Steffen
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, United States
| | - Michael D Coble
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, United States
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18
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Phillips C, Parson W, Amigo J, King JL, Coble MD, Steffen CR, Vallone PM, Gettings KB, Butler JM, Budowle B. D5S2500 is an ambiguously characterized STR: Identification and description of forensic microsatellites in the genomics age. Forensic Sci Int Genet 2016; 23:19-24. [PMID: 26974236 DOI: 10.1016/j.fsigen.2016.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 12/18/2022]
Abstract
In the process of establishing short tandem repeat (STR) sequence variant nomenclature guidelines in anticipation of expanded forensic multiplexes for massively parallel sequencing (MPS), it was discovered that the STR D5S2500 has multiple positions and genomic characteristics reported. This ambiguity is because the marker named D5S2500 consists of two different microsatellites forming separate components in the capillary electrophoresis multiplexes of Qiagen's HDplex (Hilden, Germany) and AGCU ScienTech's non-CODIS STR 21plex (Wuxi, Jiangsu, China). This study outlines the genomic details used to identify each microsatellite and reveals the D5S2500 marker in HDplex has the correctly assigned STR name, while the D5S2500 marker in the AGCU 21plex, closely positioned a further 1643 nucleotides in the human reference sequence, is an unnamed microsatellite. The fact that the D5S2500 marker has existed as two distinct STR loci undetected for almost ten years, even with reported discordant genotypes for the standard control DNA, underlines the need for careful scrutiny of the genomic properties of forensic STRs, as they become adapted for sequence analysis with MPS systems. We make the recommendation that precise chromosome location data must be reported for any forensic marker under development but not in common use, so that the genomic characteristics of the locus are validated to the same level of accuracy as its allelic variation and forensic performance. To clearly differentiate each microsatellite, we propose the name D5S2800 be used to identify the Chromosome-5 STR in the AGCU 21plex.
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Affiliation(s)
- C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - J Amigo
- Galician Public Foundation in Genomics Medicine (FPGMX), Santiago de Compostela, Spain
| | - J L King
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - M D Coble
- U.S. National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - C R Steffen
- U.S. National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - P M Vallone
- U.S. National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - K B Gettings
- U.S. National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - J M Butler
- U.S. National Institute of Standards and Technology, Applied Genetics Group, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA; U.S. National Institute of Standards and Technology, Special Programs Office, 100 Bureau Drive, Mail Stop 4701, Gaithersburg, MD 20899, USA
| | - B Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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He HJ, Almeida JL, Lund SP, Steffen CR, Choquette S, Cole KD. Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements. Biomol Detect Quantif 2016; 8:1-8. [PMID: 27335805 PMCID: PMC4906140 DOI: 10.1016/j.bdq.2016.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 11/29/2022]
Abstract
NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratios of the HER2 gene copy numbers to the copy numbers of selected reference genes DCK, EIF5B, RPS27A, and PMM1. The ratios were measured using quantitative polymerase chain reaction and digital PCR, methods that gave similar ratios. The five components of SRM 2373 have certified HER2 amplification ratios that range from 1.3 to 17.7. The stability and homogeneity of the reference materials were shown by repeated measurements over a period of several years. SRM 2373 is a well characterized genomic DNA reference material that can be used to improve the confidence of the measurements of HER2 gene copy number.
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Affiliation(s)
- Hua-Jun He
- Bioassay Methods Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Jamie L Almeida
- Bioassay Methods Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Steve P Lund
- Statistical Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Carolyn R Steffen
- Applied Genetics Group, Biomolecular Measurements Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Steve Choquette
- Bioassay Methods Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Kenneth D Cole
- Bioassay Methods Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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Steffen CR, Kline MC, Duewer DL, Vallone PM. Establishing traceability to NIST SRM 2391c: PCR-Based DNA Profiling Standard. Forensic Science International: Genetics Supplement Series 2015. [DOI: 10.1016/j.fsigss.2015.09.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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