1
|
Bredemeyer S, Roewer L, Willuweit S. Next generation sequencing of Y-STRs in father-son pairs and comparison with traditional capillary electrophoresis. Forensic Sci Res 2021; 7:484-489. [PMID: 36353309 PMCID: PMC9639519 DOI: 10.1080/20961790.2021.1898078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To evaluate the promising advantages of massively parallel sequencing (MPS) in our casework, we analysed a total of 33 Y-chromosomal short tandem repeats (Y-STRs) with traditional capillary electrophoresis (CE) and 25 Y-STRs using the newer MPS technology. We studied the outcome of both technologies in 64 father-son pairs using stock and custom-designed kits. Current MPS technology confirmed the 13 mutational events observed with CE and improved our understanding of the complex nature of STR mutations. By detecting isometric sequence variants between unrelated males, we show that sequencing Y-STRs using MPS can boost discrimination power.
Collapse
Affiliation(s)
- Steffi Bredemeyer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
2
|
Buckleton JS, Lohmueller KE, Inman K, Cheng K, Curran JM, Pugh SN, Bright JA, Taylor DA. Testing whether stutter and low-level DNA peaks are additive. Forensic Sci Int Genet 2019; 43:102166. [DOI: 10.1016/j.fsigen.2019.102166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 10/26/2022]
|
3
|
Buckleton JS, Bright JA, Gittelson S, Moretti TR, Onorato AJ, Bieber FR, Budowle B, Taylor DA. The Probabilistic Genotyping Software STRmix: Utility and Evidence for its Validity. J Forensic Sci 2018; 64:393-405. [PMID: 30132900 DOI: 10.1111/1556-4029.13898] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 01/08/2023]
Abstract
Forensic DNA interpretation is transitioning from manual interpretation based usually on binary decision-making toward computer-based systems that model the probability of the profile given different explanations for it, termed probabilistic genotyping (PG). Decision-making by laboratories to implement probability-based interpretation should be based on scientific principles for validity and information that supports its utility, such as criteria to support admissibility. The principles behind STRmix™ are outlined in this study and include standard mathematics and modeling of peak heights and variability in those heights. All PG methods generate a likelihood ratio (LR) and require the formulation of propositions. Principles underpinning formulations of propositions include the identification of reasonably assumed contributors. Substantial data have been produced that support precision, error rate, and reliability of PG, and in particular, STRmix™. A current issue is access to the code and quality processes used while coding. There are substantial data that describe the performance, strengths, and limitations of STRmix™, one of the available PG software.
Collapse
Affiliation(s)
- John S Buckleton
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142, New Zealand.,Department of Statistics, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland, 1142, New Zealand
| | - Simone Gittelson
- Centre for Forensic Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Tamyra R Moretti
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Anthony J Onorato
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Frederick R Bieber
- Center for Advanced Molecular Diagnostics, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA, 02115
| | - Bruce Budowle
- Center for Human Identification, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107
| | - Duncan A Taylor
- Forensic Science South Australia, 21 Divett Place, Adelaide, SA, Australia.,Flinders University - School of Biology, Stuart Road, Bedford Park, Adelaide, SA, Australia
| |
Collapse
|
4
|
Flanking Variation Influences Rates of Stutter in Simple Repeats. Genes (Basel) 2017; 8:genes8110329. [PMID: 29149052 PMCID: PMC5704242 DOI: 10.3390/genes8110329] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/03/2022] Open
Abstract
It has been posited that the longest uninterrupted stretch (LUS) of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL). While there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well. For example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the PAL, examples to the contrary are apparent in commonly assayed forensic markers. Further, flanking variation that is 7 bp from the repeat region can impact rates of stutter. These findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers.
Collapse
|
5
|
YfilerⓇ Plus population samples and dilution series: stutters, analytic thresholds, and drop-out probabilities. Int J Legal Med 2017; 131:1503-1511. [DOI: 10.1007/s00414-017-1568-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/20/2017] [Indexed: 11/25/2022]
|
6
|
Taylor D, Bright JA, Buckleton J. Using probabilistic theory to develop interpretation guidelines for Y-STR profiles. Forensic Sci Int Genet 2016; 21:22-34. [DOI: 10.1016/j.fsigen.2015.11.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/06/2015] [Accepted: 11/25/2015] [Indexed: 01/28/2023]
|
7
|
England R, Harbison S. Massively parallel sequencing for the forensic scientist – sequencing archived amplified products of AmpFlSTR Identifiler and PowerPlex Y multiplex kits to capture additional information. AUST J FORENSIC SCI 2016. [DOI: 10.1080/00450618.2015.1134658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ryan England
- Forensic Business Group, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
| | - SallyAnn Harbison
- Forensic Business Group, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
| |
Collapse
|