GrigoraSNPs: Optimized HTS DNA Forensic SNP Analysis

Ricke, Darrell O.; Shcherbina, Anna; Michaleas, Adam; Fremont-Smith, Philip

doi:10.1101/173716

Cited by 4 publications

(5 citation statements)

References 16 publications

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“…Ion Torrent BAM files were converted to FASTQ format using Samtools fastq . The GrigoraSNPs program was used to call SNP alleles from multiplexed HTS FASTQ sequences. Mixture analysis was performed using the IDPrism HTS DNA Forensics system.…”

Section: Methodsmentioning

confidence: 99%

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Estimating Individual Contributions to Complex DNA SNP Mixtures.,

Ricke

Fremont-Smith

Watkins

et al. 2019

Journal of Forensic Sciences

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High‐throughput sequencing (HTS) of large panels of single nucleotide polymorphisms (SNPs) provides an alternative or complimentary approach to short tandem repeats (STRs) panels for the analysis of complex DNA mixture forensic samples. For STRs, methods to estimate individual contribution concentrations compare capillary electrophoresis peak heights, peak areas, or HTS allele read counts within a mixture. This article introduces three approaches (mean, median, and slope methods) for estimating individual DNA contributions to forensic mixtures for HTS/massively parallel sequencing (MPS) SNP panels. For SNPs, the major:minor allele ratios or counts, unique to each contributor, were compared to estimate contributor proportion within the mixture using the mean, median, and slope intercept for these alleles. The estimates for these three methods were typically within 5% of planned experimental contributions for defined mixtures.

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Section: Methodsmentioning

confidence: 99%

“…Forensic HTS SNP panels enable mixture deconvolution capabilities, expanded kinship identification (due to the larger number of loci characterized), biogeographic ancestry prediction , and phenotype predictions . GrigoraSNPs , ForenSeq , ExactID , and STRaitRazor are programs capable of characterizing MPS forensic SNP panels.…”

mentioning

confidence: 99%

Estimating Individual Contributions to Complex DNA SNP Mixtures.,

Ricke

Fremont-Smith

Watkins

et al. 2019

Journal of Forensic Sciences

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“…Ion Torrent BAM files were converted to FASTQ format using Samtools fastq [30]. The GrigoraSNPs [25] program was used to call SNP alleles from multiplexed HTS FASTQ sequences. Mixture analysis was performed using the MIT Lincoln Laboratory IdPrism HTS DNA Forensics system.…”

Section: Mps Snp Data Analysismentioning

confidence: 99%

“…Additional benefits that forensic SNP panels enable are enhanced mixture deconvolution capabilities [19], expanded kinship identification [20,21] due to the larger number of loci characterized, biogeographic ancestry prediction [22,23], and phenotype predictions [24]. GrigoraSNPs [25], ForenSeq [26], ExactID [27], and STRaitRazor [28] are programs capable of characterizing MPS forensic SNP panels.…”

Section: Introductionmentioning

confidence: 99%

Estimating Individual Contributions to Complex DNA SNP Mixtures

Ricke

Fremont-Smith

Watkins

et al. 2018

Preprint

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A B S T R A C T Mixture analysis and deconvolution methods can identify both known and unknown individuals contributing to DNA mixtures. These methods may not identify all DNA contributors with the remaining fraction of the mixture being contributed by one or more unknown individuals. The proportion of DNA contributed by individuals to a forensic sample can be estimated using their quantified mixture alleles. For short tandem repeats (STRs), methods to estimate individual contribution concentrations compare capillary electrophoresis peak heights and or peak areas within a mixture. For single nucleotide polymorphisms (SNPs), the major:minor allele ratios or counts, unique to each contributor, can be compared to estimate contributor proportion within the mixture. This article introduces three approaches (mean, median, and slope methods) for estimating individual DNA contributions to forensic mixtures for high throughput sequencing (HTS)/massively parallel sequencing (MPS) SNP panels.

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“…The GrigoraSNPs 25 program was used to call SNP alleles from multiplexed HTS FASTQ sequences. Mixture analysis was performed using the MIT Lincoln Laboratory IdPrism HTS DNA Forensics system.…”

Section: Hts Snp Data Analysismentioning

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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GrigoraSNPs: Optimized HTS DNA Forensic SNP Analysis

Cited by 4 publications

References 16 publications

Estimating Individual Contributions to Complex DNA SNP Mixtures.,

Estimating Individual Contributions to Complex DNA SNP Mixtures.,

Estimating Individual Contributions to Complex DNA SNP Mixtures

The Plateau Method for Forensic DNA SNP Mixture Deconvolution

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