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Fattorini P, Previderè C, Livieri T, Zupanc T, Pajnič IZ. SNP analysis of challenging bone DNA samples using the HID-Ion AmpliSeq™ Identity Panel: facts and artefacts. Int J Legal Med 2023:10.1007/s00414-023-03019-9. [PMID: 37212920 PMCID: PMC10247551 DOI: 10.1007/s00414-023-03019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
PCR-MPS is an emerging tool for the analysis of low-quality DNA samples. In this study, we used PCR-MPS to analyse 32 challenging bone DNA samples from three Second World War victims, which previously yielded no results in conventional STR PCR-CE typing. The Identity Panel was used with 27 cycles of PCR. Despite that we only had an average of 6.8 pg of degraded DNA as template, 30 out of 32 libraries (93.8%) produced sequencing data for about 63/90 autosomal markers per sample. Out of the 30 libraries, 14 (46.7%) yielded single source genetic profiles in agreement with the biological identity of the donor, whereas 12 cases (40.0%) resulted in SNP profiles that did not match or were mixed. The misleading outcomes for those 12 cases were likely due to hidden exogenous human contamination, as shown by the higher frequencies of allelic imbalance, unusual high frequencies of allelic drop-ins, high heterozygosity levels in the consensus profiles generated from challenging samples, and traces of amplified molecular products in four out of eight extraction negative controls. Even if the source and the time of the contamination were not identified, it is likely that it occurred along the multi-step bone processing workflow. Our results suggest that only positive identification by statistical tools (e.g. likelihood ratio) should be accepted as reliable; oppositely, the results leading to exclusion should be treated as inconclusive because of potential contamination issues. Finally, strategies are discussed for monitoring the workflow of extremely challenging bone samples in PCR-MPS experiments with an increased number of PCR cycles.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Tommaso Livieri
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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2
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Zupanič Pajnič I, Zupanc T, Leskovar T, Črešnar M, Fattorini P. Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach. Genes (Basel) 2022; 13:genes13081432. [PMID: 36011343 PMCID: PMC9407562 DOI: 10.3390/genes13081432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tamara Leskovar
- Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia
| | - Matija Črešnar
- Department of Archaeology, Faculty of Arts, University of Ljubljana, Zavetiška 5, 1000 Ljubljana, Slovenia
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Strada per Fiume 447, 34149 Trieste, Italy
- Correspondence: ; Tel.: +39-040-399-3265
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3
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Ennaifer E, Salhi F, Laassili T, Fehri E, Ben Alaya N, Guizani I, Boubaker S. Type-Specific Human Papillomavirus Distribution in Invasive Squamous Cervical Carcinomas in Tunisia and Vaccine Impact. Asian Pac J Cancer Prev 2016; 16:6769-72. [PMID: 26434909 DOI: 10.7314/apjcp.2015.16.15.6769] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High risk human papillomaviruses (HPVs) are the leading cause of cervical cancer (CC) and Pap smear screening has not been successful in preventing CC in Tunisia. HPV vaccination that targets HPV16 and 18 offers a new efficient prevention tool. Identification of HPV types in CC is thus essential to determine the impact of HPV vaccine implementation. The aim of this study is to provide specific data from Tunisia. MATERIALS AND METHODS A total of 89 histological confirmed paraffin embedded samples isolated from patients with CC diagnosed between 2001 and 2011 were collected from five medical centres from Northern and Southern Tunisia. HPV DNA was detected using a nested PCR (MY09/MY11-GP5+/GP6+) and genotyping was assessed using a reverse blot line hybridisation assay that enables the detection of 32 HPV types. RESULTS HPV DNA was detected in all samples. Twelve high risk types were detected; HPV16 and/or 18 were predominant, accounting together for 92.1% of all the CC cases (HPV16: 83.1%). Single infections accounted for 48.8% of the cases and were mostly linked to HPV 16 (32.6%) and less frequently to HPV 18 (2.4%). The other high risk HPV single infections were linked to HPV 35 (4.6%), 45 (4.6%), 58 (2.3%) and 59 (2.3%). Multiple infections with mixing of 2 to 4 genotypes predominately featrued HPV16 and/or 18 with HPV 35 and 45 (96.6 %) and less frequently with HPV 59, 40, 66, 73 and 58. There was no statistically significant variation in the relative distribution of HPV types with age. CONCLUSIONS These results strongly indicate that prophylactic HPV vaccines can have a major impact in preventing CC in Tunisia.
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Affiliation(s)
- Emna Ennaifer
- HPV Research Unit, Laboratory of Molecular Epidemiology and Experimental Pathology Applied to Infectious Diseases, Pasteur Institute of Tunis, Tunis, Tunisia *E-mail : ,
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Fattorini P, Previderè C, Sorçaburu-Cigliero S, Marrubini G, Alù M, Barbaro AM, Carnevali E, Carracedo A, Casarino L, Consoloni L, Corato S, Domenici R, Fabbri M, Giardina E, Grignani P, Baldassarra SL, Moratti M, Nicolin V, Pelotti S, Piccinini A, Pitacco P, Plizza L, Resta N, Ricci U, Robino C, Salvaderi L, Scarnicci F, Schneider PM, Seidita G, Trizzino L, Turchi C, Turrina S, Vatta P, Vecchiotti C, Verzeletti A, De Stefano F. The molecular characterization of a depurinated trial DNA sample can be a model to understand the reliability of the results in forensic genetics. Electrophoresis 2014; 35:3134-44. [PMID: 25176610 DOI: 10.1002/elps.201400141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 07/31/2014] [Accepted: 08/12/2014] [Indexed: 11/09/2022]
Abstract
The role of DNA damage in PCR processivity/fidelity is a relevant topic in molecular investigation of aged/forensic samples. In order to reproduce one of the most common lesions occurring in postmortem tissues, a new protocol based on aqueous hydrolysis of the DNA was developed in vitro. Twenty-five forensic laboratories were then provided with 3.0 μg of a trial sample (TS) exhibiting, in mean, the loss of 1 base of 20, and a molecular weight below 300 bp. Each participating laboratory could freely choose any combination of methods, leading to the quantification and to the definition of the STR profile of the TS, through the documentation of each step of the analytical approaches selected. The results of the TS quantification by qPCR showed significant differences in the amount of DNA recorded by the participating laboratories using different commercial kits. These data show that only DNA quantification "relative" to the used kit (probe) is possible, being the "absolute" amount of DNA inversely related to the length of the target region (r(2) = 0.891). In addition, our results indicate that the absence of a shared stable and certified reference quantitative standard is also likely involved. STR profiling was carried out selecting five different commercial kits and amplifying the TS for a total number of 212 multiplex PCRs, thus representing an interesting overview of the different analytical protocols used by the participating laboratories. Nine laboratories decided to characterize the TS using a single kit, with a number of amplifications varying from 2 to 12, obtaining only partial STR profiles. Most of the participants determined partial or full profiles using a combination of two or more kits, and a number of amplifications varying from 2 to 27. The performance of each laboratory was described in terms of number of correctly characterized loci, dropped-out markers, unreliable genotypes, and incorrect results. The incidence of unreliable and incorrect genotypes was found to be higher for participants carrying out a limited number of amplifications, insufficient to define the correct genotypes from damaged DNA samples such as the TS. Finally, from a dataset containing about 4500 amplicons, the frequency of PCR artifacts (allele dropout, allele drop-in, and allelic imbalance) was calculated for each kit showing that the new chemistry of the kits is not able to overcome the concern of template-related factors. The results of this collaborative exercise emphasize the advantages of using a standardized degraded DNA sample in the definition of which analytical parameters are critical for the outcome of the STR profiles.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy*
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Fattorini P, Marrubini G, Grignani P, Sorçaburu-Cigliero S, Previderé C. Assessment of DNA damage by micellar electrokinetic chromatography. Methods Mol Biol 2013; 984:341-51. [PMID: 23386356 DOI: 10.1007/978-1-62703-296-4_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
A simple and inexpensive MEKC method, which is able to assess base damage within DNA samples, is illustrated. After heat-acid hydrolysis of the DNA samples, both the percentage of each canonical DNA base and the relative amount of uncanonical DNA bases can be measured. This method is useful for an evaluation of the integrity of PCR templates used in several fields of investigation.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, surgery and Health, University of Trieste, Trieste, Italy.
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Marrubini G, Fattorini P, Previderé C, Goi S, Sorçaburu Cigliero S, Grignani P, Serra M, Biesuz R, Massolini G. Experimental design applied to the optimization of microwave-assisted DNA hydrolysis. J Chromatogr A 2012; 1249:8-16. [PMID: 22749458 DOI: 10.1016/j.chroma.2012.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 06/05/2012] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
Abstract
The assessment of the integrity of the DNA primary structure and the identification of canonical and modified bases are useful tools in medical, pharmaceutical, and forensic applications. In this article we report on the first microwave-assisted hydrolyses of deoxyribonucleoside-triphosphates (dNTPs) and human DNA using "Design of Experiments" methodology. We use hydrophilic interaction chromatography (HILIC) and UV detection at 260 nm for the determination of purinic and pyrimidinic bases at levels of 0.5 μM. We use a ZIC-HILIC 150mm × 2.1 mm i.d., 5 μm particle size column and ammonium formate buffers in acetonitrile for gradient separation of the analytes. We then compare the final concentrations of Thymine, Adenine, Cytosine, and Guanine with the nominal amounts of such bases in the dNTPs and DNA submitted to hydrolysis. After optimization of the hydrolysis (11.5 min, 0.15 M aqueous HCl, 150 °C), the method turns out to be suitable for the determination of products released from quantities of human DNA as low as 500 ng with precision (RSD<10%) and accuracy (REC 97-104%). These results confirm that the kinetics of the release of the bases depends on their molecular structure and show that the concentration of the substrate plays a relevant role. We conclude with a discussion of the method and a comparison to the methods described in previous studies.
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Affiliation(s)
- Giorgio Marrubini
- Department of Drug Sciences, University of Pavia, viale Taramelli 12, 27100 Pavia, Italy.
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Falck E, Groenhagen A, Mühlisch J, Hempel G, Wünsch B. Genome-wide DNA methylation level analysis by micellar electrokinetic chromatography and laser-induced fluorescence detection after treatment of cell lines with azacytidine and antifolates. Anal Biochem 2012; 421:439-45. [DOI: 10.1016/j.ab.2011.09.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/28/2022]
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Previderè C, Marrubini G, Sorçaburu-Cigliero S, Grignani P, Fattorini P. Capillary electrophoresis analysis of DNA primary structure: Toward a quality control test for the reliability of the STR-typing from forensic specimens. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.09.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fattorini P, Marrubini G, Sorçaburu-Cigliero S, Pitacco P, Grignani P, Previderè C. CE analysis and molecular characterisation of depurinated DNA samples. Electrophoresis 2011; 32:3042-52. [PMID: 22002769 DOI: 10.1002/elps.201100130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 05/06/2011] [Accepted: 05/31/2011] [Indexed: 11/08/2022]
Abstract
A DNA sample was partially degraded by scalar heat-acid treatments to study the extent of apurinic-apyrimidinic (A-P) lesions produced along the molecule. A CE-UV method allowed us to measure the rate of depurination at pH 5.0 and 70°C which was calculated to be 5.41×10(-6) s(-1) for adenine and 6.27×10(-6) s(-1) for guanine. CE identified depurination on treated samples when it occurred with a loss of >4% of the basic moieties. The molecular features of the A-P enriched samples were investigated by using molecular assays (agarose gel electrophoresis, UV spectrophotometry and quantitative PCR) and the consistency of the results of the STR typing were compared with the degree of depurination of the PCR template. The treated DNA samples showed molecular features such as fragmentation, altered OD(260) /OD(280) ratios and decreased ability of the quantitative PCR to synthesise the human target, related to the severity of depurination. A satisfactory correlation between the degree of damage and the amount of residual PCR-sensitive target sequences was also demonstrated (r(2) =0.9717). The conventional and mini-STR typing of the samples showed that the genetic outcome was influenced by a depurination damage that exceeded 4% when locus drop-outs and artefactual PCR results were evident. As the success of STR typing depends on the integrity of the DNA recovered from the samples, the CE-UV, physical and molecular assays described here are proposed as a set of useful methods in the analysis of certain forensic and clinical samples, for a critical evaluation of the outcome of the genetic testing.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Italy.
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Marrubini G, Mendoza BEC, Massolini G. Separation of purine and pyrimidine bases and nucleosides by hydrophilic interaction chromatography. J Sep Sci 2010; 33:803-16. [PMID: 20222071 DOI: 10.1002/jssc.200900672] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The separation of 12 model compounds chosen among purine and pyrimidine bases and nucleosides was studied by using hydrophilic interaction chromatography (HILIC). The compounds investigated were small molecules with relevant properties for biomedical and pharmaceutical studies. The mixture of pyrimidines and purines was applied on a ZIC-HILIC 150 x 2.1 mm, 5 microm, and two TSKgel Amide-80 150 x 2.0 mm, 5 microm and 3 microm particle size columns. The retention of the analytes was studied by varying ACN%, ammonium formate concentration, pH, and column temperature. The results obtained confirmed the elution order of nucleobases, nucleosides, and nucleotides based on their hydrophobicity. The retention mechanism of the columns was studied considering the models used for describing partitioning and surface adsorption. The influence on retention of chromatographic conditions (ACN%, salt concentration, pH, and temperature) was described and discussed for both columns. The optimization of the conditions studied allowed to assess a gradient method for the separation of the 12 analytes. The developed method is a valuable alternative to existing methods for the separation of the compounds concerned.
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Affiliation(s)
- Giorgio Marrubini
- Department of Pharmaceutical Chemistry, University of Pavia, Pavia, Italy.
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Nikcevic I, Piruska A, Wehmeyer KR, Seliskar CJ, Limbach PA, Heineman WR. Parallel separations using capillary electrophoresis on a multilane microchip with multiplexed laser-induced fluorescence detection. Electrophoresis 2010; 31:2796-803. [PMID: 20737446 PMCID: PMC3031587 DOI: 10.1002/elps.201000030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Parallel separations using CE on a multilane microchip with multiplexed LIF detection is demonstrated. The detection system was developed to simultaneously record data on all channels using an expanded laser beam for excitation, a camera lens to capture emission, and a CCD camera for detection. The detection system enables monitoring of each channel continuously and distinguishing individual lanes without significant crosstalk between adjacent lanes. Multiple analytes can be determined in parallel lanes within a single microchip in a single run, leading to increased sample throughput. The pK(a) determination of small molecule analytes is demonstrated with the multilane microchip.
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Affiliation(s)
| | | | | | | | | | - William R. Heineman
- To whom correspondence should be addressed. . Tel: (513) 556-9210. Fax: (513) 556-9239
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