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Pilli E, Tarallo R, Riccia PL, Berti A, Novelletto A. Kinship assignment with the ForenSeq™ DNA Signature Prep Kit: Sources of error in simulated and real cases. Sci Justice 2022; 62:1-9. [PMID: 35033321 DOI: 10.1016/j.scijus.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 08/31/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
Abstract
Kinship recognition between anonymous DNA samples is becoming a relevant issue in forensics, more so with the increasing number of DNA profiles in databanks. Also, NGS-based genotyping is being increasingly used in routine personal identification, to simultaneously type large numbers of markers of different kind. In the present work, we explored computationally and experimentally the performance of the ForenSeq™ DNA Signature Prep Kit in identifying the true relationship between two anonymous samples, distinguishing it from other possible relationships. We analyzed with Familias R series of 10,000 pairs with 9 different simulated relationships, corresponding to different degrees of autosomal sharing. For each pair we obtained likelihood ratios for five kinship hypotheses vs. unrelatedness, and used their ranking to identify the preferred relationship. We also typed 21 subjects from two pedigrees, representing from parent-child to 4th cousins relationships. As expected, the power for identifying the true relationship decays in the order of autosomal sharing. Parent-child and full siblings can be robustly identified against other relationships. For half-siblings the chance of reaching a significant conclusion is already small. For more distant relationships the proportion of cases correctly and significantly identified is 10% or less. Bidirectional errors in kinship attribution include the suggestion of relatedness when this does not exist (10-50%), and the suggestion of independence in pairs of individuals more than 4 generations apart (25-60%). The real cases revealed a relevant effect of genotype miscalling at some loci, which could only be partly avoided by modulating the analysis parameters. In conclusion, with the exception of first degree relatives, the kit can be useful to inform additional investigations, but does not usually provide probatory results.
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Affiliation(s)
- Elena Pilli
- Department of Biology, University of Florence, Florence, Italy.
| | - Roberta Tarallo
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Pietro La Riccia
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche, Sezione di Biologia, Roma, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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Confirmation of Paternity despite Three Genetic Incompatibilities at Chromosome 2. Genes (Basel) 2021; 12:genes12010062. [PMID: 33406744 PMCID: PMC7824413 DOI: 10.3390/genes12010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 11/21/2022] Open
Abstract
DNA testing in cases of disputed paternity is a routine analysis carried out in genetic laboratories. The purpose of the test is to demonstrate similarities and differences in analyzed genetic markers between the alleged father, mother, and a child. The existence of differences in the examined loci between the child and the presumed father may indicate the exclusion of biological parenthood. However, another reason for such differences is genetic mutations, including chromosome aberrations and genome mutations. The presented results relate to genetic analyses carried out on three persons for the purposes of disputed paternity testing. A deviation from inheritance based on Mendel’s Law was found in 7 out of 53 STR-type loci examined. All polymorphic loci that ruled out the paternity of the alleged father were located on chromosome 2. Additional analysis of 32 insertion–deletion markers (DIPplex, Qiagen) and sequencing of 94 polymorphic positions of the single nucleotide polymorphism (SNP) type (Illumina, ForenSeq) did not exclude the defendant’s biological paternity. A sequence analysis of STR alleles and their flanking regions confirmed the hypothesis that the alleles on chromosome 2 of the child may originate only from the mother. The results of the tests did not allow exclusion of the paternity of the alleged father, but are an example of uniparental maternal disomy, which is briefly described in the literature.
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Pilli E, Boccone S, Agostino A, Virgili A, D'Errico G, Lari M, Rapone C, Barni F, Moggi Cecchi J, Berti A, Caramelli D. From unknown to known: Identification of the remains at the mausoleum of fosse Ardeatine. Sci Justice 2018; 58:469-478. [DOI: 10.1016/j.scijus.2018.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/08/2018] [Accepted: 05/20/2018] [Indexed: 11/26/2022]
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Mo SK, Ren ZL, Yang YR, Liu YC, Zhang JJ, Wu HJ, Li Z, Bo XC, Wang SQ, Yan JW, Ni M. A 472-SNP panel for pairwise kinship testing of second-degree relatives. Forensic Sci Int Genet 2018; 34:178-185. [PMID: 29510334 DOI: 10.1016/j.fsigen.2018.02.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 10/17/2022]
Abstract
Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105-106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use. With rapid growth of human genome data sets, it is worthwhile to explore additional markers, especially SNPs, for kinship analysis. Here, we reported an autosomal SNP panel consisted of 342 SNP selected from >84 million SNPs and 131 SNPs from previous systems. We genotyped these SNPs in 136 Chinese individuals by multiplex amplicon Massively Parallel Sequencing, and performed pairwise gender-independent kinship testing. The specificity and sensitivity of these SNPs to distinguish second-degree relatives and the unrelated was 99.9% and 100%, respectively, compared with 53.7% and 99.9% of 19 commonly-used forensic STRs. Moreover, the specificity increased to 100% by the combined use of these STRs and SNPs. The 472-SNP panel could also greatly facilitate the discrimination among different relationships. We estimated that the power of ∼6.45 SNPs were equivalent to one forensic STR in the scenario of 2nd-degree relative pedigree. Altogether, we proposed a panel of 472 SNP markers for kinship analysis, which could be important supplementary of current forensic STRs to solve the problem of second-degree relative testing.
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Affiliation(s)
- Shao-Kang Mo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China; Department of Reproductive Center, General Hospital of Lanzhou Military Region, Lanzhou 730050, China.
| | - Zi-Lin Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ya-Cheng Liu
- Department of Genetics, Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100192, China.
| | - Jing-Jing Zhang
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Hui-Juan Wu
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Xiao-Chen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
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Multiplex assay development and mutation rate analysis for 13 RM Y-STRs in Chinese Han population. Int J Legal Med 2016; 131:345-350. [DOI: 10.1007/s00414-016-1489-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022]
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Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 2015; 18:140-51. [DOI: 10.1016/j.fsigen.2015.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/22/2015] [Accepted: 03/24/2015] [Indexed: 11/17/2022]
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Lindner I, von Wurmb-Schwark N, Meier P, Fimmers R, Büttner A. Usefulness of SNPs as Supplementary Markers in a Paternity Case with 3 Genetic Incompatibilities at Autosomal and Y Chromosomal Loci. Transfus Med Hemother 2014; 41:117-21. [PMID: 24847187 PMCID: PMC4025154 DOI: 10.1159/000357989] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In kinship testing, investigation of 15 short tandem repeats (STRs) usually provides decisive genetic information for resolving relationship cases. However, in complex deficiency cases, in cases with more than 2 mutations at different STR loci or when close (untested) relatives of the alleged father are suggested to be the biological father of the child, STR typing alone may not be sufficient. In these cases, the application of supplementary markers such as single nucleotide polymorphisms (SNPs) is recommended. METHODS We describe a paternity case with 3 genetic incompatibilities (Penta D, VWA, and DYS385) between the alleged father and the child after analyzing 23 autosomal and 16 Y chromosomal STR loci. The question arose as to whether the alleged father could be excluded and a related person could be the biological father of the child, or whether the observed genetic incompatibilities were mutations. Interestingly, the 2 excluded full brothers of the alleged father possessed identical genetic incompatibilities at locus VWA and DYS385 as the alleged father. RESULTS AND CONCLUSIONS Additional performance of a 50-plex SNP assay demonstrated that the observed mismatches were indeed mutations and the alleged father was the biological father of the child. The results show the usefulness of SNPs as supplementary markers in relationship testing when STR analyses show ambiguous results.
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Affiliation(s)
- Iris Lindner
- Institute of Legal Medicine, University of Rostock, Kiel, Germany
| | | | - Patrick Meier
- Institute of Legal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Rolf Fimmers
- Institute for Medical Biometry, Informatics and Epidemiology, Rheinische Friedrich Wilhelms University Bonn, Germany
| | - Andreas Büttner
- Institute of Legal Medicine, University of Rostock, Kiel, Germany
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Tsutsumi H, Komuro T, Mukoyama R, Izawa H, Tie J, Uchigasaki S. A case of personal identification due to detection of rare DNA types from seminal stain. J Oral Sci 2009; 51:645-50. [PMID: 20032621 DOI: 10.2334/josnusd.51.645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Following a rape incident in an apartment in Japan, we were requested to perform a DNA analysis on a body fluid stain left on a bath towel to determine whether it could be attributed to the suspect. The acid phosphatase and prostatic-specific antigen tests confirmed it to be a seminal stain. Based on the DNA analysis by autosomal and Y-chromosome short tandem repeat (STR) systems, no inconsistency was found with the profile of the suspect with African ancestry. In this case, allele 21 of DYS390 at the Y-STR locus was examined, as it is reported to have a distinctly lower frequency in the Japanese population. Furthermore, the haplotype combinations of Y-STR at the DYS389I, DYS389II and DYS390 loci are powerful for personal identification, as these have not yet been found in the Japanese population.
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Affiliation(s)
- Hirofumi Tsutsumi
- Department of Legal Medicine, Nihon University School of Dentistry, Chiyoda-ku, Tokyo, Japan.
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