Robust detection of individual forensic profiles in DNA mixtures

Isaacson, Joe; Schwoebel, Eric; Shcherbina, Anna; Ricke, Darrell O.; Harper, James D.; Petrovick, Martha; Bobrow, Johanna; Boettcher, Tara; Helfer, Brian S.; Zook, Christina; Wack, Edward C.

doi:10.1016/j.fsigen.2014.09.003

Cited by 44 publications

(42 citation statements)

References 8 publications

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“…Multiple individuals can be identified in HTS sequenced SNP DNA mixtures with high confidence 2,3 . The confidence of such identifications can be quantified by the probability that a random man not excluded, or P(RMNE) 2,5 .…”

Section: Methodsmentioning

confidence: 99%

“…The confidence of such identifications can be quantified by the probability that a random man not excluded, or P(RMNE) 2,5 . Since saturated mixtures contain a lower number of major allele loci, it is less likely to identify individuals in saturated mixtures with low P(RMNE) using standard mixture analysis techniques.…”

Section: Methodsmentioning

confidence: 99%

“…Panels of SNPs can be specifically designed to identify multiple individuals in complex DNA samples [1][2][3][4] . Isaacson et al 2 introduced SNP panel mixture analysis with drop-in and drop-out alleles present with confidence calculations for detecting individuals in mixtures.…”

Section: Introductionmentioning

confidence: 99%

“…Isaacson et al 2 introduced SNP panel mixture analysis with drop-in and drop-out alleles present with confidence calculations for detecting individuals in mixtures. The confidence with which an individual can be identified in a DNA mixture using a given SNP panel is dependent upon the number of SNP loci in the panel and the average population ratio of minor to major SNP alleles 1,2 . Ricke and Schwartz 5 refined the calculations for larger HTS SNP panels.…”

Section: Introductionmentioning

confidence: 99%

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TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

Ricke

Watkins

Fremont-Smith

et al. 2018

Preprint

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High throughput sequencing (HTS) of complex DNA mixtures with single nucleotide polymorphisms (SNPs) panels can identify multiple individuals in forensic DNA mixture samples. SNP mixture analysis relies upon the exclusion of non-contributing individuals with the subset of SNP loci with no detected minor alleles in the mixture. Few, if any, individuals are anticipated to be detectable in saturated mixtures by this mixture analysis approach because of the increased probability of matching random individuals. Being able to identify a subset of the contributors in saturated HTS SNP mixtures is valuable for forensic investigations. A desaturated mixture can be created by treating a set of SNPs with the lowest minor allele ratios as having no minor alleles. Leveraging differences in DNA contributor concentrations in saturated mixtures, we introduce TranslucentID for the identification of a subset of individuals with high confidence who contributed DNA to saturated mixtures by desaturating the mixtures.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

Ricke

Watkins

Fremont-Smith

et al. 2018

Preprint

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“…One possible solution to the limitation imposed by the stutter problem is to replace or augment STRs with thousands of SNPs for the purpose of mixture analysis and deconvolution 23,24 . However, since there are no current analysis methods for mixture deconvolution using SNPs, we introduce the Plateau method for those mixtures with modest numbers of contributors and imbalanced contributor DNA concentrations.…”

Section: Introductionmentioning

confidence: 99%

The Plateau Method for Forensic DNA SNP Mixture Deconvolution

Ricke¹,

Isaacson²,

Watkins³

et al. 2017

Preprint

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Identification of individuals in complex DNA mixtures remains a challenge for forensic analysts. Recent advances in high throughput sequencing (HTS) are enabling analysis of DNA mixtures with expanded panels of Short Tandem Repeats (STRs) and/or Single Nucleotide Polymorphisms (SNPs). We present the plateau method for direct SNP DNA mixture deconvolution into sub-profiles based on differences in contributors' DNA concentrations in the mixtures in the absence of matching reference profiles. The Plateau method can detect profiles of individuals whose contribution is as low as 1/200 in a DNA mixture (patent pending) 1 .

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Application of SNPs with low minor allele frequencies in missing person identification (MPI) through kinship analysis of DNA mixtures

et al. 2023

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The need to identify a missing person (MP) through kinship analysis of DNA samples found at a crime scene has become increasingly prevalent. DNA samples from MPs can be severely degraded, contain little DNA and mixed with other contributors, which often makes it difficult to apply conventional methods in practice. This study developed a massively parallel sequencing–based panel that contains 1661 single‐nucleotide polymorphisms (SNPs) with low minor allele frequencies (MAFs) (averaged at 0.0613) in the Chinese Han population, and the strategy for relationship inference from DNA mixtures comprising different numbers of contributors (NOCs) and of varying allele dropout probabilities. Based on the simulated dataset and genotyping results of 42 artificial DNA mixtures (NOC = 2–4), it was observed that the present SNP panel was sufficient for balanced mixtures when referenced to the closest relatives (parents/offspring and full siblings). When the mixture profiles suffered from dropout, incorrect assignments were markedly associated with relatedness, NOC and the dropout level. We, therefore, indicate that SNPs with low MAFs could be reliably interpreted for MP identification through the kinship analysis of complex DNA mixtures. Further studies should be extended to more possible scenarios to test the feasibility of this present approach.

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Robust detection of individual forensic profiles in DNA mixtures

Cited by 44 publications

References 8 publications

TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

The Plateau Method for Forensic DNA SNP Mixture Deconvolution

Application of SNPs with low minor allele frequencies in missing person identification (MPI) through kinship analysis of DNA mixtures

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