51
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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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52
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Turchi C, Melchionda F, Pesaresi M, Tagliabracci A. Evaluation of a microhaplotypes panel for forensic genetics using massive parallel sequencing technology. Forensic Sci Int Genet 2019; 41:120-127. [DOI: 10.1016/j.fsigen.2019.04.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 11/29/2022]
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53
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Non-invasive prenatal paternity testing using a standard forensic genetic massively parallel sequencing assay for amplification of human identification SNPs. Int J Legal Med 2019; 133:1361-1368. [PMID: 31243529 DOI: 10.1007/s00414-019-02106-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023]
Abstract
Prenatal paternity testing often relies on invasive procedures that cause risk to both the mother and the foetus. Non-invasive, prenatal paternity testing by investigating paternally inherited single nucleotide polymorphisms (SNPs) in cell-free foetal DNA (cffDNA) in maternal plasma was performed at consecutive time points during early gestation. Plasma from 15 pregnant women was investigated at consecutive time points from gestational weeks (GWs) 4-20. The Precision ID Identity Panel and an Ion S5 Sequencer was used to analyse the cffDNA. Paternally inherited foetal SNP alleles were detected from GW7. The median foetal fractions were 0%, 3.9%, 5.1%, 5.2%, and 4.7% at GWs 4, 7, 12, 16, and 20, respectively. The corresponding median numbers of detected paternally inherited foetal autosomal SNP alleles were 0, 3, 9, 10, and 12, respectively. The typical (i.e. geometric mean) paternity indices at GW12 and GW20 were 24 (range 0.0035-8389) and 199 (range 5.1-30,137), respectively. The method is very promising. However, the method can be improved by shortening the lengths of the PCR amplicons and increasing the number of SNPs. To our knowledge, this is the first study to successfully identify paternally inherited foetal SNP alleles at consecutive time points in early gestation independently of the foetal gender.
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54
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England R, Harbison S. A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ryan England
- Forensic Science Program, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Sallyann Harbison
- Institute of Environmental Science and Research Ltd Auckland New Zealand
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55
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Pfeifer JD. Identity determination in diagnostic surgical pathology. Semin Diagn Pathol 2019; 36:355-365. [PMID: 31196743 DOI: 10.1053/j.semdp.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
From a technical perspective, specimen identity determination in surgical pathology over the last several decades has primarily focused on analysis of repetitive DNA sequences, specifically microsatellite repeats. However, a number of techniques have recently been developed that have similar, if not greater, utility in surgical pathology, most notably analysis of single nucleotide polymorphism (SNPs) and gene panels by next generation sequencing (NGS). For cases with an extremely limited sample or a degraded sample, sequence analysis of mitochondrial DNA continues to be the method of choice. From a diagnostic perspective, interest in identity determination in surgical pathology is usually centered on resolving issues of specimen provenance due to specimen labeling/accessioning deficiencies and possible contamination, but is also frequently performed in cases for which the patient's clinical course following definitive therapy is remarkably atypical, in cases of an unexpected diagnosis, and by patient request for "peace of mind". However, the methods used for identity determination have a much broader range of applications in surgical pathology beyond tissue provenance analysis. The methods can be used to provide ancillary information for cases in which the histomorphology is not definitively diagnostic, as for example for tumors that have a virtually identical microscopic appearance but for which the differential diagnosis includes synchronous/metachronous tumors versus a metastasis, and for the diagnosis of hydropic early gestations versus hydatidiform molar pregnancies. The methods also have utility in several other clinical settings, for example to rule out a donor-transmitted malignancy in a transplant recipient, to monitor bone marrow transplant engraftment, and to evaluate natural chimerism.
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Affiliation(s)
- John D Pfeifer
- Department of Pathology, Washington University School of Medicine, Campus Box 8118, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
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56
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Chu F, Mason KE, Anex DS, Jones AD, Hart BR. Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification. Sci Rep 2019; 9:7641. [PMID: 31113963 PMCID: PMC6529471 DOI: 10.1038/s41598-019-44007-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/16/2019] [Indexed: 11/10/2022] Open
Abstract
Human hair contains minimal intact nuclear DNA for human identification in forensic and archaeological applications. In contrast, proteins offer a pathway to exploit hair evidence for human identification owing to their persistence, abundance, and derivation from DNA. Individualizing single nucleotide polymorphisms (SNPs) are often conserved as single amino acid polymorphisms in genetically variant peptides (GVPs). Detection of GVP markers in the hair proteome via high-resolution tandem mass spectrometry permits inference of SNPs with known statistical probabilities. To adopt this approach for forensic investigations, hair proteomic variation and its effects on GVP identification must first be characterized. This research aimed to assess variation in single-inch head, arm, and pubic hair, and discover body location-invariant GVP markers to distinguish individuals. Comparison of protein profiles revealed greater body location-specific variation in keratin-associated proteins and intracellular proteins, allowing body location differentiation. However, robust GVP markers derive primarily from keratins that do not exhibit body location-specific differential expression, supporting GVP identification independence from hair proteomic variation at the various body locations. Further, pairwise comparisons of GVP profiles with 8 SNPs demonstrated greatest interindividual variation and high intraindividual consistency, enabling similar differentiative potential of individuals using single hairs irrespective of body location origin.
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Affiliation(s)
- Fanny Chu
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA.,Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Katelyn E Mason
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA
| | - Deon S Anex
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA.
| | - A Daniel Jones
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI, 48824, USA
| | - Bradley R Hart
- Forensic Science Center, Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA, 94550, USA
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57
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Tao R, Zhang J, Sheng X, Zhang J, Yang Z, Chen C, Bian Y, Liu X, Zhang S, Li C. Development and validation of a multiplex insertion/deletion marker panel, SifaInDel 45plex system. Forensic Sci Int Genet 2019; 41:128-136. [PMID: 31079022 DOI: 10.1016/j.fsigen.2019.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/22/2019] [Accepted: 04/29/2019] [Indexed: 01/08/2023]
Abstract
In addition to commonly used short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because they combine desirable characteristics of both STRs and SNPs. In the present study, the SifaInDel 45plex system was designed to amplify 45 InDel markers, including 27 autosomal InDels (A-InDels), 16 X chromosome InDels (X-InDels) and two Y chromosome InDels (Y-InDels), simultaneously in a single PCR procedure and then detect products by capillary electrophoresis (CE). We also optimized the PCR conditions for the novel panel and performed several validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics. The results confirmed that full profiles could be obtained from ≥62.5 pg of input DNA and from a series of challenging samples encountered in routine casework. The SifaInDel 45plex panel could tolerate different concentrations of inhibitors, such as ≤50 μM hematin, ≤20 ng/μL nigrosine and ≤8000 ng/μL urea. In a population investigation, for the 27 A-InDels, the combined power of discrimination (CPD) exceeded 0.999999, and the combined power of exclusion in duos (CPED) and trios (CPET) was 0.955118 and 0.997754, respectively. For the 16 X-InDels, the combined PDMale and PDFemale was computed as 0.999845 and 0.999998, respectively, and the combined mean exclusion chance in father/daughter or mother/son duos (MECDuo) and mean exclusion chance in standard trios involving daughters (MECTrio) was 0.976220 and 0.998163, respectively. In addition, the two Y-InDels could play a role in correctly determining gender. Overall, the established SifaInDel 45plex panel is a well-performing, reliable and robust multiplex system that stands out for combining a considerable number of A-indels, X-indels and Y-indels based on a CE platform. The population study results also demonstrated that the SifaInDel 45plex panel could be a valid complementary approach for human identification and complex kinship analysis.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China
| | | | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, PR China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Chong Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, PR China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China.
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58
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Chen R, Zhao X, Ma K, Li H, Cao Y, Cao Y, Liu W. Separation of SNP profiles from DNA mixtures with two contributors via massively parallel sequencing technology. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1586997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ronghua Chen
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Xueying Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yandong Cao
- Technical department, Analyses Technology Co. Ltd, Beijing, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
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59
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Ricke DO, Fremont‐Smith P, Watkins J, Stankiewicz S, Boettcher T, Schwoebel E. Estimating Individual Contributions to Complex DNA SNP Mixtures.,. J Forensic Sci 2019; 64:1468-1474. [DOI: 10.1111/1556-4029.14030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Darrell O. Ricke
- Bioengineering Systems & Technologies Massachusetts Institute of Technology Lincoln Laboratory 244 Wood Street Lexington MA
| | - Philip Fremont‐Smith
- Bioengineering Systems & Technologies Massachusetts Institute of Technology Lincoln Laboratory 244 Wood Street Lexington MA
| | - James Watkins
- Bioengineering Systems & Technologies Massachusetts Institute of Technology Lincoln Laboratory 244 Wood Street Lexington MA
| | - Sara Stankiewicz
- Bioengineering Systems & Technologies Massachusetts Institute of Technology Lincoln Laboratory 244 Wood Street Lexington MA
| | - Tara Boettcher
- Bioengineering Systems & Technologies Massachusetts Institute of Technology Lincoln Laboratory 244 Wood Street Lexington MA
| | - Eric Schwoebel
- Bioengineering Systems & Technologies Massachusetts Institute of Technology Lincoln Laboratory 244 Wood Street Lexington MA
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60
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Schweizer MT, Wang H, Bivalacqua TJ, Partin AW, Lim SJ, Chapman C, Abdallah R, Levy O, Bhowmick NA, Karp JM, De Marzo A, Isaacs JT, Brennen WN, Denmeade SR. A Phase I Study to Assess the Safety and Cancer-Homing Ability of Allogeneic Bone Marrow-Derived Mesenchymal Stem Cells in Men with Localized Prostate Cancer. Stem Cells Transl Med 2019; 8:441-449. [PMID: 30735000 PMCID: PMC6477003 DOI: 10.1002/sctm.18-0230] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/07/2019] [Indexed: 12/12/2022] Open
Abstract
Animal models show that systemically administered bone marrow‐derived mesenchymal stem cells (MSCs) home to sites of primary and metastatic prostate cancer (PC)—making them candidates to selectively deliver cytotoxic agents. To further assess this potential as a cell‐based therapeutic vehicle, a phase I study testing homing of systemically infused allogeneic MSCs preprostatectomy was conducted. The primary objective was to assess safety and feasibility and to determine if MSCs accumulate within primary PC tissue. MSCs were quantified using beads, emulsion, amplification, magnetics digital polymerase chain reaction (limit of detection: ≥0.01% MSCs) to measure allogeneic MSC DNA relative to recipient DNA. MSCs were harvested from healthy donors and expanded ex vivo using standard protocols by the Johns Hopkins Cell Therapy Laboratory. PC patients planning to undergo prostatectomy were eligible for MSC infusion. Enrolled subjects received a single intravenous infusion 4–6 days prior to prostatectomy. The first three subjects received 1 x 106 cells per kilogram (maximum 1 x 108 cells), and subsequent four patients received 2 x 106 cells per kilogram (maximum 2 x 108 cells). No dose‐limiting toxicities were observed and all patients underwent prostatectomy without delay. Pathologic assessment of prostate cores revealed ≥70% tumor involvement in cores from four subjects, with benign tissue in the others. MSCs were undetectable in all subjects, and the study was stopped early for futility. MSC infusions appear safe in PC patients. Although intended for eventual use in metastatic PC patients, in this study, MSCs did not home primary tumors in sufficient levels to warrant further development as a cell‐based therapeutic delivery strategy using standard ex vivo expansion protocols. stem cells translational medicine2019;8:441–449
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Affiliation(s)
- Michael T Schweizer
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hao Wang
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Trinity J Bivalacqua
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alan W Partin
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Su Jin Lim
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carolyn Chapman
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rehab Abdallah
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Oren Levy
- Center for Nanomedicine and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Neil A Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jeffrey M Karp
- Center for Nanomedicine and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Division of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Angelo De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John T Isaacs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - W Nathaniel Brennen
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Samuel R Denmeade
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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61
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Bourgeois S, Kaden J, Senn H, Bunnefeld N, Jeffery KJ, Akomo-Okoue EF, Ogden R, McEwing R. Improving cost-efficiency of faecal genotyping: New tools for elephant species. PLoS One 2019; 14:e0210811. [PMID: 30699177 PMCID: PMC6353156 DOI: 10.1371/journal.pone.0210811] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 01/02/2019] [Indexed: 11/18/2022] Open
Abstract
Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and preparation methods in order to improve sample set quality and provide cost-efficient tools that can effectively support wildlife management. In this study, we collected an extensive set of forest elephant (Loxodonta cyclotis) faecal samples throughout Gabon, Central Africa, and prepared them for genotyping using 107 single-nucleotide polymorphism assays. We developed a new quantitative polymerase chain reaction (PCR) assay targeting a 130-bp nuclear DNA fragment and demonstrated its suitability for degraded samples in all three elephant species. Using this assay to compare the efficacy of two sampling methods for faecal DNA recovery, we found that sampling the whole surface of a dung pile with a swab stored in a small tube of lysis buffer was a convenient method producing high extraction success and DNA yield. We modelled the influence of faecal quality and storage time on DNA concentration in order to provide recommendations for optimized collection and storage. The maximum storage time to ensure 75% success was two months for samples collected within 24 hours after defecation and extended to four months for samples collected within one hour. Lastly, the real-time quantitative PCR assay allowed us to predict genotyping success and pre-screen DNA samples, thus further increasing the cost-efficiency of our approach. We recommend combining the validation of an efficient sampling method, the build of in-country DNA extraction capacity for reduced storage time and the development of species-specific quantitative PCR assays in order to increase the cost-efficiency of routine non-invasive DNA analyses and expand the use of next-generation markers to non-invasive samples.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- * E-mail:
| | - Jenny Kaden
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Helen Senn
- WildGenes Laboratory, The Royal Zoological Society of Scotland, RZSS Edinburgh Zoo, Edinburgh, United Kingdom
| | - Nils Bunnefeld
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Institut de Recherche en Écologie Tropicale, Libreville, Gabon
| | | | - Rob Ogden
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, United Kingdom
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62
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Hwa HL, Wu MY, Lin CP, Hsieh WH, Yin HI, Lee TT, Lee JCI. A single nucleotide polymorphism panel for individual identification and ancestry assignment in Caucasians and four East and Southeast Asian populations using a machine learning classifier. Forensic Sci Med Pathol 2019; 15:67-74. [PMID: 30649693 DOI: 10.1007/s12024-018-0071-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2018] [Indexed: 11/26/2022]
Abstract
Single nucleotide polymorphism (SNP) profiling is an effective means of individual identification and ancestry inferences in forensic genetics. This study established a SNP panel for the simultaneous individual identification and ancestry assignment of Caucasian and four East and Southeast Asian populations. We analyzed 220 SNPs (125 autosomal, 17 X-chromosomal, 30 Y-chromosomal, and 48 mitochondrial SNPs) of the DNA samples from 563 unrelated individuals of five populations (89 Caucasian, 234 Taiwanese Han, 90 Filipino, 79 Indonesian and 71 Vietnamese) and 18 degraded DNA samples. Informativeness for assignment (In) was used to select ancestry informative SNPs (AISNPs). A machine learning classifier, support vector machine (SVM), was used for ancestry assignment. Of the 220 SNPs, 62 were individual identification SNPs (IISNPs) (51 autosomal and 11 X-chromosomal SNPs) and 191 were AISNPs (100 autosomal, 13 X-chromosomal, 30 Y-chromosomal, and 48 mitochondrial SNPs). The 51 autosomal IISNPs offered cumulative random match probabilities (cRMPs) ranging from 1.56 × 10-21 to 3.16 × 10-22 among these five populations. Using AISNPs with the SVM, the overall accuracy rate of ancestry inference achieved in the testing dataset between Caucasian, Taiwanese Han, and Filipino populations was 88.9%, whereas it was 70.0% between Caucasians and each of the four East and Southeast Asian populations. For the 18 degraded DNA samples with incomplete profiling, the accuracy rate of ancestry assignment was 94.4%. We have developed a 220-SNP panel for simultaneous individual identification and ethnic origin differentiation between Caucasian and the four East and Southeast Asian populations. This SNP panel may assist with DNA analysis of forensic casework.
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Affiliation(s)
- Hsiao-Lin Hwa
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Ming-Yih Wu
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, No. 7 Chung Shan S. Rd, Taipei, 100, Taiwan
| | - Chih-Peng Lin
- Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan
| | - Wei Hsin Hsieh
- Yourgene Bioscience, No.376-5 Fuxing Rd., Shulin Dist, New Taipei City, 238, Taiwan
| | - Hsiang-I Yin
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - Tsui-Ting Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan
| | - James Chun-I Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen Ai Rd, Taipei, 100, Taiwan.
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63
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The QIAGEN 140-locus single-nucleotide polymorphism (SNP) panel for forensic identification using massively parallel sequencing (MPS): an evaluation and a direct-to-PCR trial. Int J Legal Med 2018; 133:677-688. [DOI: 10.1007/s00414-018-1975-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/23/2018] [Indexed: 02/04/2023]
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64
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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65
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Tillmar A, Grandell I, Montelius K. DNA identification of compromised samples with massive parallel sequencing. Forensic Sci Res 2018; 4:331-336. [PMID: 32002491 PMCID: PMC6968675 DOI: 10.1080/20961790.2018.1509186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 11/04/2022] Open
Abstract
Genetic profiling is a standard procedure for human identification, i.e. in criminal cases and mass disasters, and has been proven to be an important part in the process in the repatriation of victims to their relatives. In the event of a catastrophe whether it be a natural disaster, terror attack or accident, fatalities of many nationalities may be a consequence and international collaboration becomes necessary. Current DNA techniques used on a routine basis at forensic laboratories world-wide are very useful, and results reported from different labs are compared, making it possible to be matched in order to declare the identification of a victim. Statistical calculations of possibilities of a random match are achievable since population data from many parts of the world are available. However, decomposition and degradation of the remains are not uncommon in the aftermath of a catastrophe and hence it may be difficult to retrieve detailed DNA profiles from such samples. Massive parallel sequencing (MPS) is a technique capable of producing a vast amount of DNA sequence data in a high-through put manner, and panels of single nucleotide polymorphism (SNP) markers allow the amplification of small DNA fragments, often seen in compromised samples. Here, we report the results from a set of 10 samples from missing person identification cases, analyzed with an MPS based method comprising 131 SNP markers and compared with direct reference material or buccal swab samples collected from relatives of the deceased. We assess the weight of evidence of a match by statistical calculation. Furthermore, we compare results reported on different platforms using different SNP panels, and conclude that more work has to be done if results from missing person identification cases analyzed on MPS with SNP panels at different laboratories are to be fully reliable and thus comparable.
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Affiliation(s)
- Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Ida Grandell
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Kerstin Montelius
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
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66
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Hwa HL, Wu MY, Chung WC, Ko TM, Lin CP, Yin HI, Lee TT, Lee JCI. Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq™ system in combination with EuroForMix software. Int J Legal Med 2018; 133:25-37. [DOI: 10.1007/s00414-018-1961-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
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67
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Oldoni F, Kidd KK, Podini D. Microhaplotypes in forensic genetics. Forensic Sci Int Genet 2018; 38:54-69. [PMID: 30347322 DOI: 10.1016/j.fsigen.2018.09.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/28/2023]
Abstract
Microhaplotype loci (microhaps, MHs) are a novel type of molecular marker of less than 300 nucleotides, defined by two or more closely linked SNPs associated in multiple allelic combinations. The value of these markers is enhanced by massively parallel sequencing (MPS), which allows the sequencing of both parental haplotypes at each of the many multiplexed loci. This review describes the features of these multi-SNP markers and documents their value in forensic genetics, focusing on individualization, biogeographic ancestry inference, and mixture deconvolution. Foreseeable applications also include missing person identification, relationship testing, and medical diagnostic applications. The technique is not restricted to humans.
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Affiliation(s)
- Fabio Oldoni
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States
| | - Kenneth K Kidd
- Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Daniele Podini
- Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States.
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68
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Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.07.188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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69
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Kidd KK, Pakstis AJ, Speed WC, Lagace R, Wootton S, Chang J. Selecting microhaplotypes optimized for different purposes. Electrophoresis 2018; 39:2815-2823. [PMID: 29931757 DOI: 10.1002/elps.201800092] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is transforming forensic work by allowing various useful forensic markers, such as STRPs and SNPs, to be multiplexed providing information on ancestry, individual and familial identification, phenotypes for eye/hair/skin pigmentation, and the deconvolution of mixtures. Microhaplotypes also become feasible with massively parallel sequencing, these are DNA segments (smaller than 300 nucleotides) that are selected to contain multiple SNPs unambiguously defining three or more haplotype alleles occurring at common frequencies. The physical extent of a microhaplotype can thus be covered by a single sequence read making these loci phase-known codominant genetic systems. Such microhaplotypes supply significantly more information than a single SNP can. Our efforts to develop useful sets of microhaplotypes have already identified 182 such loci that we have studied on a large number of human populations from around the world. We present various analyses on 83 populations in our ongoing study for a subset of the best microhaplotypes currently available illustrating their characteristics and potential utility for ancestry, identification, and mixture deconvolution.
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Affiliation(s)
- Kenneth K Kidd
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew J Pakstis
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - William C Speed
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Lagace
- Human Identification Group, ThermoFisher Scientific, South San Francisco, CA, USA
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, South San Francisco, CA, USA
| | - Joseph Chang
- Human Identification Group, ThermoFisher Scientific, South San Francisco, CA, USA
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70
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Liu J, Wang Z, He G, Zhao X, Wang M, Luo T, Li C, Hou Y. Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three East Asian minority ethnicities. Forensic Sci Int Genet 2018; 35:141-148. [DOI: 10.1016/j.fsigen.2018.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022]
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71
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Bose N, Carlberg K, Sensabaugh G, Erlich H, Calloway C. Target capture enrichment of nuclear SNP markers for massively parallel sequencing of degraded and mixed samples. Forensic Sci Int Genet 2018. [DOI: 10.1016/j.fsigen.2018.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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72
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Decouchant J, Fernandes M, Völp M, Couto FM, Esteves-Veríssimo P. Accurate filtering of privacy-sensitive information in raw genomic data. J Biomed Inform 2018; 82:1-12. [PMID: 29660494 DOI: 10.1016/j.jbi.2018.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/07/2018] [Indexed: 10/17/2022]
Abstract
Sequencing thousands of human genomes has enabled breakthroughs in many areas, among them precision medicine, the study of rare diseases, and forensics. However, mass collection of such sensitive data entails enormous risks if not protected to the highest standards. In this article, we follow the position and argue that post-alignment privacy is not enough and that data should be automatically protected as early as possible in the genomics workflow, ideally immediately after the data is produced. We show that a previous approach for filtering short reads cannot extend to long reads and present a novel filtering approach that classifies raw genomic data (i.e., whose location and content is not yet determined) into privacy-sensitive (i.e., more affected by a successful privacy attack) and non-privacy-sensitive information. Such a classification allows the fine-grained and automated adjustment of protective measures to mitigate the possible consequences of exposure, in particular when relying on public clouds. We present the first filter that can be indistinctly applied to reads of any length, i.e., making it usable with any recent or future sequencing technologies. The filter is accurate, in the sense that it detects all known sensitive nucleotides except those located in highly variable regions (less than 10 nucleotides remain undetected per genome instead of 100,000 in previous works). It has far less false positives than previously known methods (10% instead of 60%) and can detect sensitive nucleotides despite sequencing errors (86% detected instead of 56% with 2% of mutations). Finally, practical experiments demonstrate high performance, both in terms of throughput and memory consumption.
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Affiliation(s)
- Jérémie Decouchant
- SnT - Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, Luxembourg.
| | - Maria Fernandes
- SnT - Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, Luxembourg.
| | - Marcus Völp
- SnT - Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, Luxembourg.
| | - Francisco M Couto
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Portugal.
| | - Paulo Esteves-Veríssimo
- SnT - Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg, Luxembourg.
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73
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Farris MH, Scott AR, Texter PA, Bartlett M, Coleman P, Masters D. TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing. BMC Bioinformatics 2018; 19:126. [PMID: 29642839 PMCID: PMC5896139 DOI: 10.1186/s12859-018-2133-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 03/26/2018] [Indexed: 01/26/2023] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA sequencing (MPS) technologies and human genome SNP databases allow for the design of suites of identity-linked target regions, amenable to sequencing in a multiplexed and massively parallel manner. Therefore, tools are needed for leveraging the genotypic information found within SNP databases for the discovery of genomic targets that can be evaluated on MPS platforms. Results The SNP island target identification algorithm (TIA) was developed as a user-tunable system to leverage SNP information within databases. Using data within the 1000 Genomes Project SNP database, human genome regions were identified that contain globally ubiquitous identity-linked SNPs and that were responsive to targeted resequencing on MPS platforms. Algorithmic filters were used to exclude target regions that did not conform to user-tunable SNP island target characteristics. To validate the accuracy of TIA for discovering these identity-linked SNP islands within the human genome, SNP island target regions were amplified from 70 contributor genomic DNA samples using the polymerase chain reaction. Multiplexed amplicons were sequenced using the Illumina MiSeq platform, and the resulting sequences were analyzed for SNP variations. 166 putative identity-linked SNPs were targeted in the identified genomic regions. Of the 309 SNPs that provided discerning power across individual SNP profiles, 74 previously undefined SNPs were identified during evaluation of targets from individual genomes. Overall, DNA samples of 70 individuals were uniquely identified using a subset of the suite of identity-linked SNP islands. Conclusions TIA offers a tunable genome search tool for the discovery of targeted genomic regions that are scalable in the population frequency and numbers of SNPs contained within the SNP island regions. It also allows the definition of sequence length and sequence variability of the target region as well as the less variable flanking regions for tailoring to MPS platforms. As shown in this study, TIA can be used to discover identity-linked SNP islands within the human genome, useful for differentiating individuals by targeted resequencing on MPS technologies. Electronic supplementary material The online version of this article (10.1186/s12859-018-2133-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Heath Farris
- The Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA. .,Department of Advanced Technology, The MITRE Corporation, 7515 Colshire Drive, McLean, Virginia, 22102, USA.
| | - Andrew R Scott
- The Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA
| | - Pamela A Texter
- The Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA
| | - Marta Bartlett
- The Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA
| | - Patricia Coleman
- The Department of Homeland Security, U.S. Customs and Border Protection, Washington, DC, USA
| | - David Masters
- The Department of Homeland Security, Science and Technology Directorate, Washington, DC, USA
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74
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Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases. Sci Rep 2018; 8:5553. [PMID: 29615764 PMCID: PMC5882920 DOI: 10.1038/s41598-018-23888-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/15/2018] [Indexed: 11/09/2022] Open
Abstract
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population. For 116 of the 117 SNPs, cumulative match probability (CMP) ranged from 2.01 × 10-48 to 1.93 × 10-50 and cumulative exclusion probability (CEP) ranged from 0.9999999996653 to 0.9999999999945. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 × 10-47 and CEP = 0.999999999862. By analyzing the same number of autosomal SNPs as in the HID-Ion AmpliSeq Identity Panel, i.e. 90 randomized out of the 110 SNPs, our panel yielded preferable CMP and CEP. Taken together, the 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels.
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75
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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: 31] [Impact Index Per Article: 5.2] [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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76
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Loreille O, Ratnayake S, Bazinet AL, Stockwell TB, Sommer DD, Rohland N, Mallick S, Johnson PLF, Skoglund P, Onorato AJ, Bergman NH, Reich D, Irwin JA. Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens. Genes (Basel) 2018; 9:genes9030135. [PMID: 29494531 PMCID: PMC5867856 DOI: 10.3390/genes9030135] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
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Affiliation(s)
- Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Shashikala Ratnayake
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Timothy B Stockwell
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Daniel D Sommer
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Nadin Rohland
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Swapan Mallick
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Philip L F Johnson
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, 4094 Campus Drive, College Park, MD 20742, USA.
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.
| | - Anthony J Onorato
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - David Reich
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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77
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Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, 't Hoen PAC. A SNP panel for identification of DNA and RNA specimens. BMC Genomics 2018; 19:90. [PMID: 29370748 PMCID: PMC5785835 DOI: 10.1186/s12864-018-4482-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping. RESULTS To determine a small set of SNPs with maximally discriminative power, genotype calls were obtained from DNA and blood-derived RNA sequencing data belonging to healthy, geographically dispersed, Dutch individuals. SNPs were selected based on different criteria like genotype call rate, minor allele frequency, Hardy-Weinberg equilibrium and linkage disequilibrium. A panel of 50 SNPs was sufficient to identify an individual uniquely: the probability of identity was 6.9 × 10- 20 when assuming no family relations and 1.2 × 10- 10 when accounting for the presence of full sibs. The ability of the SNP panel to uniquely identify individuals on DNA and RNA level was validated in an independent population dataset. The panel is applicable to individuals from European descent, with slightly lower power in non-Europeans. Whereas most of the genes containing the 50 SNPs are expressed in various tissues, our SNP panel needs optimization for other tissues than blood. CONCLUSIONS This first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.
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Affiliation(s)
- Soheil Yousefi
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Tooba Abbassi-Daloii
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter van 't Hof
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Daria V Zhernakova
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Leen M 't Hart
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands.,Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.,Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Amber van der Heijden
- Department of Epidemiology and Biostatistics, VU Medical Center, Amsterdam, The Netherlands.,Department of General Practice and Elderly Care Medicine, VU Medical Center, Amsterdam, The Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | | | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC, Leiden, The Netherlands. .,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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78
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Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples. Genes (Basel) 2018; 9:genes9010049. [PMID: 29361782 PMCID: PMC5793200 DOI: 10.3390/genes9010049] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/14/2018] [Accepted: 01/17/2018] [Indexed: 12/15/2022] Open
Abstract
The application of next generation sequencing (NGS) for the analysis of mitochondrial (mt) DNA, short tandem repeats (STRs), and single nucleotide polymorphism (SNPs) has demonstrated great promise for challenging forensic specimens, such as degraded, limited, and mixed samples. Target enrichment using probe capture rather than PCR amplification offers advantages for analysis of degraded DNA since two intact PCR primer sites in the template DNA molecule are not required. Furthermore, NGS software programs can help remove PCR duplicates to determine initial template copy numbers of a shotgun library. Moreover, the same shotgun library prepared from a limited DNA source can be enriched for mtDNA as well as nuclear markers by hybrid capture with the relevant probe panels. Here, we demonstrate the use of this strategy in the analysis of limited and mock degraded samples using our custom probe capture panels for massively parallel sequencing of the whole mtgenome and 426 SNP markers. We also applied the mtgenome capture panel in a mixed sample and analyzed using both phylogenetic and variant frequency based bioinformatics tools to resolve the minor and major contributors. Finally, the results obtained on individual telogen hairs demonstrate the potential of probe capture NGS analysis for both mtDNA and nuclear SNPs for challenging forensic specimens.
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79
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A 1204-single nucleotide polymorphism and insertion–deletion polymorphism panel for massively parallel sequencing analysis of DNA mixtures. Forensic Sci Int Genet 2018; 32:94-101. [DOI: 10.1016/j.fsigen.2017.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 11/19/2022]
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80
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Viscardi LH, Paixão-Côrtes VR, Comas D, Salzano FM, Rovaris D, Bau CD, Amorim CEG, Bortolini MC. Searching for ancient balanced polymorphisms shared between Neanderthals and Modern Humans. Genet Mol Biol 2018; 41:67-81. [PMID: 29658973 PMCID: PMC5901502 DOI: 10.1590/1678-4685-gmb-2017-0308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/26/2017] [Indexed: 01/06/2023] Open
Abstract
Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS). We identified a significant excess of trans-SNPs in IMMS (N=547), of which six of these located within genes previously associated with schizophrenia. No excess of trans-SNPs was found in BEHS, but five genes in this system harbor potential signals for balancing selection and are associated with psychiatric or neurodevelopmental disorders. Our approach evidenced recent Homo trans-SNPs that have been previously implicated in psychiatric diseases such as schizophrenia, suggesting that a genetic repertoire common to the immune and behavioral systems could have been maintained by balancing selection starting before the split between archaic and modern humans.
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Affiliation(s)
- Lucas Henriques Viscardi
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de LaSalut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Diego Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Claiton Dotto Bau
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Carlos Eduardo G. Amorim
- Department of Biological Sciences, Columbia University, New York, NY, U.S.A
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, U.S.A
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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81
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Koopman JJE, Pijpe J, Böhringer S, van Bodegom D, Eriksson UK, Sanchez-Faddeev H, Ziem JB, Zwaan B, Slagboom PE, de Knijff P, Westendorp RGJ. Genetic variants determining survival and fertility in an adverse African environment: a population-based large-scale candidate gene association study. Aging (Albany NY) 2017; 8:1364-83. [PMID: 27356285 PMCID: PMC4993336 DOI: 10.18632/aging.100986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/10/2016] [Indexed: 12/15/2022]
Abstract
Human survival probability and fertility decline strongly with age. These life history traits have been shaped by evolution. However, research has failed to uncover a consistent genetic determination of variation in survival and fertility. As an explanation, such genetic determinants have been selected in adverse environments, in which humans have lived during most of their history, but are almost exclusively studied in populations in modern affluent environments. Here, we present a large-scale candidate gene association study in a rural African population living in an adverse environment. In 4387 individuals, we studied 4052 SNPs in 148 genes that have previously been identified as possible determinants of survival or fertility in animals or humans. We studied their associations with survival comparing newborns, middle-age adults, and old individuals. In women, we assessed their associations with reported and observed numbers of children. We found no statistically significant associations of these SNPs with survival between the three age groups nor with women's reported and observed fertility. Population stratification was unlikely to explain these results. Apart from a lack of power, we hypothesise that genetic heterogeneity of complex phenotypes and gene-environment interactions prevent the identification of genetic variants explaining variation in survival and fertility in humans.
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Affiliation(s)
- Jacob J E Koopman
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen Pijpe
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.,University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Stefan Böhringer
- Section of Medical Statistics, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - David van Bodegom
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands.,Leyden Academy on Vitality and Ageing, Leiden, the Netherlands
| | - Ulrika K Eriksson
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Juventus B Ziem
- Department of Clinical Laboratory Sciences, School of Medicine and Health Sciences, University for Development Studies, Tamale, Ghana
| | - Bas Zwaan
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Rudi G J Westendorp
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands.,Department of Public Health and Center of Healthy Aging, University of Copenhagen, Copenhagen, Denmark
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82
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Comparison of manual and automated AmpliSeq™ workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Sci Int Genet 2017; 31:118-125. [DOI: 10.1016/j.fsigen.2017.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 01/15/2023]
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83
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Meiklejohn KA, Robertson JM. Evaluation of the Precision ID Identity Panel for the Ion Torrent™ PGM™ sequencer. Forensic Sci Int Genet 2017; 31:48-56. [DOI: 10.1016/j.fsigen.2017.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/14/2017] [Accepted: 08/06/2017] [Indexed: 01/02/2023]
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84
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Li R, Zhang C, Li H, Wu R, Li H, Tang Z, Zhen C, Ge J, Peng D, Wang Y, Chen H, Sun H. SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population. Int J Legal Med 2017; 132:997-1006. [DOI: 10.1007/s00414-017-1706-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 10/11/2017] [Indexed: 01/04/2023]
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85
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Du Y, Martin JS, McGee J, Yang Y, Liu EY, Sun Y, Geihs M, Kong X, Zhou EL, Li Y, Huang J. A SNP panel and online tool for checking genotype concordance through comparing QR codes. PLoS One 2017; 12:e0182438. [PMID: 28926565 PMCID: PMC5604942 DOI: 10.1371/journal.pone.0182438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/18/2017] [Indexed: 01/02/2023] Open
Abstract
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade. Here, we first describe a method to identify a small set of Single nucleotide polymorphisms (SNPs) that can uniquely identify a personal genome, which utilizes allele frequencies of five major continental populations reported in the 1000 genomes project and the ExAC Consortium. To make this panel more informative, we added four SNPs that are commonly used to predict ABO blood type, and another two SNPs that are capable of predicting sex. We then implement a web interface (http://qrcme.tech), nicknamed QRC (forQR code based Concordance check), which is capable of extracting the relevant ID SNPs from a raw genetic data, coding its genotype as a quick response (QR) code, and comparing QR codes to report the concordance of underlying genetic datasets. The resulting 80 fingerprinting SNPs represent a significant decrease in complexity and the number of markers used for genetic data labelling and tracking. Our method and web tool is easily accessible to both researchers and the general public who consider the accuracy of complex genetic data as a prerequisite towards precision medicine.
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Affiliation(s)
- Yonghong Du
- School of Statistics, Beijing Normal University, Beijing, China
| | - Joshua S. Martin
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - John McGee
- NC Translational and Clinical Sciences Institute, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yuchen Yang
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Eric Yi Liu
- Department of Computer Science, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yingrui Sun
- Department of Mathematics & Statistics, Boston University, Boston, Massachusetts, United States of America
| | - Matthias Geihs
- Department of Computer Science, Technische Universität Darmstadt, Darmstadt, Germany
| | - Xuejun Kong
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Eric Lingfeng Zhou
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (YL); (JH)
| | - Jie Huang
- Boston VA Research Institute, Boston, Massachusetts, United States of America
- Brigham Women’s Hospital Division of Aging, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (YL); (JH)
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86
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Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing. Forensic Sci Int Genet 2017; 28:35-43. [DOI: 10.1016/j.fsigen.2017.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 01/21/2023]
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87
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Goodwin W, Alimat S. Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNP forID markers. Electrophoresis 2017; 38:1007-1015. [DOI: 10.1002/elps.201600383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 11/10/2022]
Affiliation(s)
- William Goodwin
- School of Forensic and Applied Sciences; University of Central Lancashire; Preston United Kingdom of Great Britain and Northern Ireland
| | - Sharizah Alimat
- School of Forensic and Applied Sciences; University of Central Lancashire; Preston United Kingdom of Great Britain and Northern Ireland
- Biotechnology Section; Department of Chemistry Malaysia (MOSTI); Jalan Sultan, Petaling Jaya Selangor Malaysia
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88
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Comparison of Two Massively Parallel Sequencing Platforms using 83 Single Nucleotide Polymorphisms for Human Identification. Sci Rep 2017; 7:398. [PMID: 28341840 PMCID: PMC5428557 DOI: 10.1038/s41598-017-00510-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/28/2017] [Indexed: 02/06/2023] Open
Abstract
The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq® FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively. In this study, we compared the genotyping performance of the two MPS systems based on 83 SNP markers that are present in both MPS marker panels. Results show that MiSeq® FGx™ has greater sample-to-sample variation than the HID-Ion PGM™ in terms of read counts for all the 83 SNP markers. Allele coverage ratio (ACR) values show generally balanced heterozygous reads for both platforms. Two and four SNP markers from the MiSeq® FGx™ and HID-Ion PGM™, respectively, have average ACR values lower than the recommended value of 0.67. Comparison of genotype calls showed 99.7% concordance between the two platforms.
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89
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García O, Soto A, Yurrebaso I. Allele frequencies and other forensic parameters of the HID-Ion AmpliSeq™ Identity Panel markers in Basques using the Ion Torrent PGM™ platform. Forensic Sci Int Genet 2017; 28:e8-e10. [PMID: 28342798 DOI: 10.1016/j.fsigen.2017.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/23/2017] [Accepted: 03/07/2017] [Indexed: 11/28/2022]
Abstract
The HID-Ion AmpliSeq™ Identity Panel amplifies 90 autosomal SNPs and 34 Y- SNPs with massively parallel sequencing (MPS) using the Ion Torrent PGM™ platform. In the present study, 105 Basques were analyzed to assess this panel. All loci were in Hardy-Weinberg equilibrium and no association between them was detected. Forensic parameters were calculated as 5.74×10-36 for combined match probability and 99.99998% for combined power of exclusion. In conclusion, the HID Identity panel and the use of this new MPS technology are very promising tools for paternity testing and human identification in routine casework in the forensic field.
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Affiliation(s)
- O García
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain.
| | - A Soto
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
| | - I Yurrebaso
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police, Erandio, Bizkaia, Spain
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90
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Zhang S, Bian Y, Chen A, Zheng H, Gao Y, Hou Y, Li C. Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM. Forensic Sci Int Genet 2017; 27:50-57. [DOI: 10.1016/j.fsigen.2016.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 01/18/2023]
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91
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Li L, Wang Y, Yang S, Xia M, Yang Y, Wang J, Lu D, Pan X, Ma T, Jiang P, Yu G, Zhao Z, Ping Y, Zhou H, Zhao X, Sun H, Liu B, Jia D, Li C, Hu R, Lu H, Liu X, Chen W, Mi Q, Xue F, Su Y, Jin L, Li S. Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations. Forensic Sci Int Genet 2017; 28:118-127. [PMID: 28249201 DOI: 10.1016/j.fsigen.2017.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/07/2017] [Accepted: 02/10/2017] [Indexed: 10/20/2022]
Abstract
The applications of DNA profiling aim to identify perpetrators, missing family members and disaster victims in forensic investigations. Single nucleotide polymorphisms (SNPs) based forensic applications are emerging rapidly with a potential to replace short tandem repeats (STRs) based panels which are now being used widely, and there is a need for a well-designed SNP panel to meet such challenge for this transition. Here we present a panel of 175 SNP markers (referred to as Fudan ID Panel or FID), selected from ∼3.6 million SNPs, for the application of personal identification. We optimized and validated FID panel using 729 Chinese individuals using a next generation sequencing (NGS) technology. We showed that the SNPs in the panel possess very high heterozygosity as well as low within- and among-continent differentiations, enabling FID panel exhibit discrimination power in both regional and worldwide populations, with the average match probabilities ranging from 4.77×10-71 to 1.06×10-64 across 54 world populations. With the advent of biomedical research, the SNPs connecting physical anthropological, physiological, behavioral and phenotypic traits will be eventually added to the forensic panels that will revolutionize criminal investigation.
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Affiliation(s)
- Liming Li
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Wang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shuping Yang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Mingying Xia
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yajun Yang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China
| | - Jiucun Wang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China
| | - Daru Lu
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China
| | - Xingwei Pan
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Teng Ma
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Pei Jiang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ge Yu
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ziqin Zhao
- Department of Forensic Medicine, Shanghai Medicine College, Fudan University, Shanghai, 200000, China
| | - Yuan Ping
- Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China
| | - Huaigu Zhou
- Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China
| | - Xueying Zhao
- Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China
| | - Hui Sun
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Bing Liu
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Dongtao Jia
- Nantong Bureau of Public Safety, Jiangsu, 226000, China
| | - Chengtao Li
- National Institute of Forensics, Ministry of Justice, Shanghai, 200000, China
| | - Rile Hu
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Medical College of Inner Mongolia, Ulaanbaatar, Autonomous Region of Inner Mongolia, 010000, China
| | - Hongzhou Lu
- Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200000, China
| | - Xiaoyang Liu
- China-Japan Friendship Hospital, Jilin University, Changchun, Jilin, 130000, China
| | - Wenqing Chen
- Cancer Hospital, Changchun, Jilin, 130000, China
| | - Qin Mi
- Department of Biology and Geography, Qinghai Normal University, Xining, Qinghai, 810000, China
| | - Fuzhong Xue
- School of Public Health, Shandong University, Jinan, Shandong, 250000, China
| | - Yongdong Su
- Bureau of Public Safety, Lhasa, Autonomous Region of Tibet, 850000, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China.
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China.
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92
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Zhang S, Bian Y, Chen A, Zheng H, Gao Y, Hou Y, Li C. Massively parallel sequencing of 231 autosomal SNPs with a custom panel: a SNP typing assay developed for human identification with Ion Torrent PGM. Forensic Sci Res 2017; 2:26-33. [PMID: 30483616 PMCID: PMC6197105 DOI: 10.1080/20961790.2017.1281011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 11/26/2022] Open
Abstract
The custom-designed single nucleotide polymorphism (SNP) panel amplified 231 autosomal SNPs in one PCR reaction and subsequently sequenced with massively parallel sequencing (MPS) technology and Ion Torrent personal genome machine (PGM). SNPs were chosen from SNPforID, IISNP, HapMap, dbSNP, and related published literatures. Full concordance was obtained between available MPS calling and Sanger sequencing with 9947A and 9948 controls. Ten SNPs (rs4606077, rs334355, rs430046, rs2920816, rs4530059, rs1478829, rs1498553, rs7141285, rs12714757 and rs2189011) with low coverage or heterozygote imbalance should be optimized or excluded from the panel. Sequence data had sufficiently high coverage and gave reliable SNP calling for the remaining 221 loci with the custom MPS–SNP panel. A default DNA input amount of 10 ng per reaction was recommended by Ampliseq technology but sensitivity testing revealed positive results from as little as 1 ng input DNA. Mixture testing with this panel is possible through analysis of the FMAR (frequency of major allele reads) values at most loci with enough high coverage depth and low level of sequencing noise. These results indicate the potential advantage of the custom MPS–SNP assays and Ion Torrent PGM platform for forensic study.
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Affiliation(s)
- Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
| | - Anqi Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hancheng Zheng
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yuzhen Gao
- Department of Forensic Medicine, Medical College of Soochow University, Suzhou, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, PRC, Shanghai, China
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93
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Jäger AC, Alvarez ML, Davis CP, Guzmán E, Han Y, Way L, Walichiewicz P, Silva D, Pham N, Caves G, Bruand J, Schlesinger F, Pond SJK, Varlaro J, Stephens KM, Holt CL. Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories. Forensic Sci Int Genet 2017; 28:52-70. [PMID: 28171784 DOI: 10.1016/j.fsigen.2017.01.011] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 12/08/2016] [Accepted: 01/23/2017] [Indexed: 01/01/2023]
Abstract
Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction. Targeted loci include Amelogenin, 27 common, forensic autosomal STRs, 24 Y-STRs, 7 X-STRs and three classes of single nucleotide polymorphisms (SNPs). The ForenSeq™ kit includes two primer sets: Amelogenin, 58 STRs and 94 identity informative SNPs (iiSNPs) are amplified using DNA Primer Set A (DPMA; 153 loci); if a laboratory chooses to generate investigative leads using DNA Primer Set B, amplification is targeted to the 153 loci in DPMA plus 22 phenotypic informative (piSNPs) and 56 biogeographical ancestry SNPs (aiSNPs). High-resolution genotypes, including detection of intra-STR sequence variants, are semi-automatically generated with the ForenSeq™ software. This system was subjected to developmental validation studies according to the 2012 Revised SWGDAM Validation Guidelines. A two-step PCR first amplifies the target forensic STR and SNP loci (PCR1); unique, sample-specific indexed adapters or "barcodes" are attached in PCR2. Approximately 1736 ForenSeq™ reactions were analyzed. Studies include DNA substrate testing (cotton swabs, FTA cards, filter paper), species studies from a range of nonhuman organisms, DNA input sensitivity studies from 1ng down to 7.8pg, two-person human DNA mixture testing with three genotype combinations, stability analysis of partially degraded DNA, and effects of five commonly encountered PCR inhibitors. Calculations from ForenSeq™ STR and SNP repeatability and reproducibility studies (1ng template) indicate 100.0% accuracy of the MiSeq FGx™ System in allele calling relative to CE for STRs (1260 samples), and >99.1% accuracy relative to bead array typing for SNPs (1260 samples for iiSNPs, 310 samples for aiSNPs and piSNPs), with >99.0% and >97.8% precision, respectively. Call rates of >99.0% were observed for all STRs and SNPs amplified with both ForenSeq™ primer mixes. Limitations of the MiSeq FGx™ System are discussed. Results described here demonstrate that the MiSeq FGx™ System meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities.
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Affiliation(s)
- Anne C Jäger
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | - Carey P Davis
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Ernesto Guzmán
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Yonmee Han
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Lisa Way
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | - David Silva
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Nguyen Pham
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Glorianna Caves
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Jocelyne Bruand
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | | | - Joe Varlaro
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | - Cydne L Holt
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
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94
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Chen P, Zhu J, Pu Y, Jiang Y, Chen D, Wang H, Mao J, Zhou B, Gao L, Bai P, Liang W, Zhang L. Microhaplotype identified and performed in genetic investigation using PCR-SSCP. Forensic Sci Int Genet 2017; 28:e1-e7. [PMID: 28174015 DOI: 10.1016/j.fsigen.2017.01.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 12/02/2016] [Accepted: 01/17/2017] [Indexed: 01/04/2023]
Abstract
The recently introduced concept of microhaplotype loci has attracted attention in forensics. Previous studies estimated the allele frequencies generally through obtaining genotypic data on the individual SNPs from a larger set of unrelated individuals then phasing microhaplotypes by statistical and computational techniques. Determining phase for a single new individual requires the larger set of individuals to have been genotyped previously. Rare microhaplotypes possessed only by the target individual or microhaplotypes private to a specific population not previously studied are unlikely to be accurately phased using data sets of SNPs. Thus, there is a demand for an approach that could directly determine a gain single individual's precise microhaplotype information. In the present study, we introduced potential approaches of single chain sequencing based Massively Parallel Sequencing Technology (MiSeq) and PCR based Single Strand Conformational Polymorphism (SSCP) technology which was simple, accurate, and cost-effective. The results indicated that microhaplotypes contain much more polymorphic information than divided SNPs per locus (average heterozygosity of microhaplotype 0.61 VS SNPs 0.41). When microhaplotype allele frequencies were compared among five Chinese ethnic populations, significantly different distributions were found between the Han and Uyghur populations. Further analysis of pairwise Fst values and analysis of molecular variance (AMOVA), showed significant population differentiation between the Uyghur and other populations.
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Affiliation(s)
- Peng Chen
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Jing Zhu
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Yan Pu
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Youjing Jiang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Dan Chen
- Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, PR China
| | - Hui Wang
- Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, PR China
| | - Jiong Mao
- Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081, Sichuan, PR China
| | - Bin Zhou
- Laboratory of Molecular Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China
| | - Linbo Gao
- Laboratory of Molecular Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China
| | - Peng Bai
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Weibo Liang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China.
| | - Lin Zhang
- Department of Forensic Biology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Laboratory of Molecular Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, PR China.
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95
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Development of a SNP-based panel for human identification for Indian populations. Forensic Sci Int Genet 2016; 27:58-66. [PMID: 27992827 DOI: 10.1016/j.fsigen.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/27/2016] [Accepted: 12/03/2016] [Indexed: 12/31/2022]
Abstract
The widely employed short tandem repeat (STR)-based panels for forensic human identification (HID) have limitations while dealing with challenging forensic samples involving DNA degradation, resulting in dropping-out of higher molecular weight alleles/loci. To address this issue, bialleic markers like single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), which can be scored even when the template DNA is heavily degraded (<100bp), have been suggested as alternative markers for HID testing. Recent studies have highlighted their utility in forensic HID and several panels based on biallelic markers have been described for worldwide populations. However, there has been very little information about the behavior of such DNA markers in Indian populations, which is known to possess great genetic diversity. This study describes a two-step approach for designing a SNP-based panel consisting of 70 SNPs for HID testing in Indian populations. In the first step, candidate SNPs were shortlisted from public databases by screening them for several criteria including allelic distribution, genomic location, potential phenotypic expression or functionality and species specificity. The second step involved genotyping the shortlisted SNPs in various Indian populations followed by shortlisting of the best performers for identity-testing. Starting with 592,652 SNPs listed in Human660W-Quad Beadchip (Illumina Inc.), we shortlisted 275 candidate SNPs for identity-testing and genotyped them in 462 unrelated individuals from different population groups in India. Post genotyping and statistical analyses based on biogeographic regions, 206 SNPs demonstrated desired allelic distribution (Heterozygosity≥0.4 and FST≤0.02), from which 2-4 widely separated (>20 Mb apart) SNPs from each chromosome were finally selected to construct a panel of 70 SNPs. This panel on average possessed match probability 10e-29 and probability of paternity of 0.99999997, which was orders of magnitude higher than most of the currently employed STR-based chemistries and SNP-based panels that were proposed previously for HID testing. For comparison purpose, genotyping previously reported SNPs for HID in our samples led us to conclude that the panel developed in this study is much more efficient and robust and better suited for the Indian populations.
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96
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Grskovic M, Hiller DJ, Eubank LA, Sninsky JJ, Christopherson C, Collins JP, Thompson K, Song M, Wang YS, Ross D, Nelles MJ, Yee JP, Wilber JC, Crespo-Leiro MG, Scott SL, Woodward RN. Validation of a Clinical-Grade Assay to Measure Donor-Derived Cell-Free DNA in Solid Organ Transplant Recipients. J Mol Diagn 2016; 18:890-902. [DOI: 10.1016/j.jmoldx.2016.07.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/28/2016] [Accepted: 07/08/2016] [Indexed: 12/13/2022] Open
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97
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Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform. Forensic Sci Int Genet 2016; 25:73-84. [DOI: 10.1016/j.fsigen.2016.07.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/10/2016] [Accepted: 07/28/2016] [Indexed: 11/24/2022]
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98
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Tillmar AO, Phillips C. Evaluation of the impact of genetic linkage in forensic identity and relationship testing for expanded DNA marker sets. Forensic Sci Int Genet 2016; 26:58-65. [PMID: 27792893 DOI: 10.1016/j.fsigen.2016.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 12/21/2022]
Abstract
Advances in massively parallel sequencing technology have enabled the combination of a much-expanded number of DNA markers (notably STRs and SNPs in one or combined multiplexes), with the aim of increasing the weight of evidence in forensic casework. However, when data from multiple loci on the same chromosome are used, genetic linkage can affect the final likelihood calculation. In order to study the effect of linkage for different sets of markers we developed the biostatistical tool ILIR, (Impact of Linkage on forensic markers for Identity and Relationship tests). The ILIR tool can be used to study the overall impact of genetic linkage for an arbitrary set of markers used in forensic testing. Application of ILIR can be useful during marker selection and design of new marker panels, as well as being highly relevant for existing marker sets as a way to properly evaluate the effects of linkage on a case-by-case basis. ILIR, implemented via the open source platform R, includes variation and genomic position reference data for over 40 STRs and 140 SNPs, combined with the ability to include additional forensic markers of interest. The use of the software is demonstrated with examples from several different established marker sets (such as the expanded CODIS core loci) including a review of the interpretation of linked genetic data.
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Affiliation(s)
- Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden.
| | - Chris Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
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99
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Buchard A, Kampmann ML, Poulsen L, Børsting C, Morling N. ISO 17025 validation of a next-generation sequencing assay for relationship testing. Electrophoresis 2016; 37:2822-2831. [DOI: 10.1002/elps.201600269] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 06/10/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Anders Buchard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Lena Poulsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
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100
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Gordon PMK, Khan A, Sajid U, Chang N, Suresh V, Dimnik L, Lamont RE, Parboosingh JS, Martin SR, Pon RT, Weatherhead J, Wegener S, Isaac D, Greenway SC. An Algorithm Measuring Donor Cell-Free DNA in Plasma of Cellular and Solid Organ Transplant Recipients That Does Not Require Donor or Recipient Genotyping. Front Cardiovasc Med 2016; 3:33. [PMID: 27713880 PMCID: PMC5031701 DOI: 10.3389/fcvm.2016.00033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/09/2016] [Indexed: 11/22/2022] Open
Abstract
Cell-free DNA (cfDNA) has significant potential in the diagnosis and monitoring of clinical conditions. However, accurately and easily distinguishing the relative proportion of DNA molecules in a mixture derived from two different sources (i.e., donor and recipient tissues after transplantation) is challenging. In human cellular transplantation, there is currently no useable method to detect in vivo engraftment, and blood-based non-invasive tests for allograft rejection in solid organ transplantation are either non-specific or absent. Elevated levels of donor cfDNA have been shown to correlate with solid organ rejection, but complex methodology limits implementation of this promising biomarker. We describe a cost-effective method to quantify donor cfDNA in recipient plasma using a panel of high-frequency single nucleotide polymorphisms, next-generation (semiconductor) sequencing, and a novel mixture model algorithm. In vitro, our method accurately and rapidly determined donor:recipient DNA admixture. For in vivo testing, donor cfDNA was serially quantified in an infant with a urea cycle disorder after receiving six daily infusions of donor liver cells. Donor cfDNA isolated from 1 to 2 ml of recipient plasma was detected as late as 24 weeks after infusion suggesting engraftment. The percentage of circulating donor cfDNA was also assessed in pediatric and adult heart transplant recipients undergoing routine endomyocardial biopsy with levels observed to be stable over time and generally measuring <1% in cases without moderate or severe cellular rejection. Unlike existing non-invasive methods used to define the proportion of donor cfDNA in solid organ transplant patients, our assay does not require sex mismatch, donor genotyping, or whole-genome sequencing and potentially has broad application to detect cellular engraftment or allograft injury after transplantation.
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Affiliation(s)
- Paul M K Gordon
- Alberta Children's Hospital Research Institute, University of Calgary , Calgary, AB , Canada
| | - Aneal Khan
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Paediatrics, University of Calgary, Calgary, AB, Canada; Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Umair Sajid
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Paediatrics, University of Calgary, Calgary, AB, Canada
| | - Nicholas Chang
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Paediatrics, University of Calgary, Calgary, AB, Canada
| | - Varun Suresh
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Paediatrics, University of Calgary, Calgary, AB, Canada
| | - Leo Dimnik
- Molecular Diagnostic Laboratory, Genetic Laboratory Services-South, Alberta Health Services , Calgary, AB , Canada
| | - Ryan E Lamont
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Medical Genetics, University of Calgary, Calgary, AB, Canada; Molecular Diagnostic Laboratory, Genetic Laboratory Services-South, Alberta Health Services, Calgary, AB, Canada
| | - Jillian S Parboosingh
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Medical Genetics, University of Calgary, Calgary, AB, Canada; Molecular Diagnostic Laboratory, Genetic Laboratory Services-South, Alberta Health Services, Calgary, AB, Canada
| | - Steven R Martin
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Paediatrics, University of Calgary, Calgary, AB, Canada
| | - Richard T Pon
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Jene Weatherhead
- Alberta Children's Hospital Research Institute, University of Calgary , Calgary, AB , Canada
| | - Shelly Wegener
- Alberta Children's Hospital Research Institute, University of Calgary , Calgary, AB , Canada
| | - Debra Isaac
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary , Calgary, AB , Canada
| | - Steven C Greenway
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Department of Paediatrics, University of Calgary, Calgary, AB, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
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