Highlights
- •Whole genome sequencing data indicate that hundreds of DIP-STRs exist.
- •Additional 23 candidates are validated here to produce a final set of 30 forensic DIP-STRs.
- •Markers are short (230 bp average), sensitive (down to 0.06 ng of DNA) and polymorphic (0.7 heterozygosity).
- •They can target a minor DNA amplification contributing only 0.1 % to the mixed trace.
Abstract
In an attempt to enhance forensic DNA mixture deconvolution several alternative DNA
typing approaches have been developed. Among these, DIP-STR compound markers can resolve
extremely unbalanced two-source DNA mixtures of same-or-opposite sex donors, up to
a 1:1000 minor:major DNA ratio. A forensic set of 10 markers was validated for casework
and a larger set of 23 DIP-STRs has proven suitable to biogeographic ancestry inference
and for prenatal paternity testing. Yet, to promote the widespread use of this original
approach, more markers and multiplex panels need to be developed.
To this end, here we describe an extended set of forensic DIP-STRs identified using
currently available whole-genome sequencing datasets. Complete lists of Indels and
STRs were obtained from reported frequencies of genetic variants of 76,156 genomes.
About 3000 identified DIP-STRs candidates were shorter than 200 bp and 500 showed
high haplotype variability estimated using the genotypes of individuals homozygous
for the DIP or the STR. Here, we present 23 additional DIP-STRs validated for sensitivity,
specificity and Swiss population variability. Finally, a set of 30 markers comprising
seven previously validated ones is proposed for the prospective development of a forensic
DIP-STR multiplex panel.
Keywords
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References
- The interpretation of single source and mixed DNA profiles.Forensic Sci. Int. Genet. 2013; 7: 516-528
- Interpretation of complex forensic DNA mixtures.Croat. Med J. 2001; 42: 244-246
- Interpreting forensic DNA profiling evidence without specifying the number of contributors.Forensic Sci. Int. Genet. 2014; 13: 269-280
- A review of probabilistic genotyping systems: EuroForMix, DNAStatistX and STRmix.Genes. 2021; 12
- Evaluating the efficacy of DNA differential extraction methods for sexual assault evidence.Forensic Sci. Int. Genet. 2017; 29: 109-117
- Isolation and genetic analysis of pure cells from forensic biological mixtures: the precision of a digital approach.Forensic Sci. Int. Genet. 2017; 29: 225-241
- 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
- Coming of age: ten years of next-generation sequencing technologies.Nat. Rev. Genet. 2016; 17: 333-351
- DIP-STR: highly sensitive markers for the analysis of unbalanced genomic mixtures.Hum. Mutat. 2013; 34: 644-654
- Forensic molecular biomarkers for mixture analysis.Forensic Sci. Int. Genet. 2019; 41: 107-119
- A novel multiplex assay of SNP-STR markers for forensic purpose.PLoS One. 2018; 13e0200700
- A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures.Biochem. Biophys. Res. Commun. 2018; 497: 591-596
- Sensitive DIP-STR markers for the analysis of unbalanced mixtures from "touch" DNA samples.Forensic Sci. Int. Genet. 2017; 28: 111-117
- A novel set of DIP-STR markers for improved analysis of challenging DNA mixtures.Forensic Sci. Int. Genet. 2015; 19: 156-164
- Application of DIP-STRs to sexual/physical assault investigations: eight case reports.Forensic Sci. Int. Genet. 2017; 30: 106-113
- Analysis of fetal DNA in maternal plasma with markers designed for forensic DNA mixture resolution.Genet. Med.: Off. J. Am. Coll. Med. Genet. 2018; 21: 613-621
- Genotyping of STR and DIP-STR Markers in Plasma Cell-Free DNA for Simple and Rapid Noninvasive Prenatal Diagnosis of Zygosity of Twin Pregnancies.Twin Res Hum. Genet. 2019; 22: 321-329
- Detection of cell-free fetal DNA in maternal plasma using two types of compound markers.Electrophoresis. 2021; 42: 1158-1167
- A human genome diversity cell line panel.Science. 2002; 296: 261-262
- Inferring biogeographic ancestry with compound markers of slow and fast evolving polymorphisms.Eur. J. Hum. Genet. 2018;
- An investigation of a set of DIP-STR markers to detect unbalanced DNA mixtures among the southwest Chinese Han population.Forensic Sci. Int. Genet. 2017; 31: 34-39
- Primer3 on the WWW for general users and for biologist programmers.Methods Mol. Biol. 2000; 132: 365-386
- An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA.Forensic Sci. Int. 2000; 112: 17-40
- Arlequin (version 3.0): an integrated software package for population genetics data analysis.Evol. Bioinform Online. 2005; 1: 47-50
- Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq system.Forensic Sci. Int. Genet. 2016; 24: 86-96
- From next generation sequencing to now generation sequencing in forensics.Forensic Sci. Int. Genet. 2019; 38: 175-180
- Current state-of-art of STR sequencing in forensic genetics.Electrophoresis. 2018; 39: 2655-2668
- Developmental validation of GlobalFiler PCR amplification kit: a 6-dye multiplex assay designed for amplification of casework samples.Int J. Leg. Med. 2018; 132: 1555-1573
- RMplex: an efficient method for analyzing 30 Y-STRs with high mutation rates.Forensic Sci. Int. Genet. 2021; 55102595
- Population genetic data of 74 microhaplotypes in four major U.S. population groups.Forensic Sci. Int. Genet. 2020; 49102398
Article info
Publication history
Published online: February 17, 2023
Accepted:
February 16,
2023
Received in revised form:
February 13,
2023
Received:
November 29,
2022
Identification
Copyright
© 2023 Elsevier B.V. All rights reserved.
