Towards developing forensically relevant single-cell pipelines by incorporating direct-to-PCR extraction: compatibility, signal quality, and allele detection

Abstract

Current analysis of forensic DNA stains relies on the probabilistic interpretation of bulk-processed samples that represent mixed profiles consisting of an unknown number of potentially partial representations of each contributor. Single-cell methods, in contrast, offer a solution to the forensic DNA mixture problem by incorporating a step that separates cells before extraction. A forensically relevant single-cell pipeline relies on efficient direct-to-PCR extractions that are compatible with standard downstream forensic reagents. Here we demonstrate the feasibility of implementing single-cell pipelines into the forensic process by exploring four metrics of electropherogram (EPG) signal quality—i.e., allele detection rates, peak heights, peak height ratios, and peak height balance across low- to high-molecular-weight short tandem repeat (STR) markers—obtained with four direct-to-PCR extraction treatments and a common post-PCR laboratory procedure. Each treatment was used to extract DNA from 102 single buccal cells, whereupon the amplification reagents were immediately added to the tube and the DNA was amplified/injected using post-PCR conditions known to elicit a limit of detection (LoD) of one DNA molecule. The results show that most cells, regardless of extraction treatment, rendered EPGs with at least a 50% true positive allele detection rate and that allele drop-out was not cell independent. Statistical tests demonstrated that extraction treatments significantly impacted all metrics of EPG quality, where the Arcturus® PicoPure™ extraction method resulted in the lowest median allele drop-out rate, highest median average peak height, highest median average peak height ratio, and least negative median values of EPG sloping for GlobalFiler™ STR loci amplified at half volume. We, therefore, conclude the feasibility of implementing single-cell pipelines for casework purposes and demonstrate that inferential systems assuming cell independence will not be appropriate in the probabilistic interpretation of a collection of single-cell EPGs.

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Abbreviations

STR:

Short tandem repeat

CE:

Capillary electrophoresis

EPG:

Electropherogram

PCR:

Polymerase chain reaction

RFU:

Relative fluorescence unit

b.p.:

Base pairs

ILS:

Internal lane standard

LoD:

Limit of detection

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Funding

This work was partially supported by NIJ2018-DU-BX-K0185 and NIJ2014-DN-BX-K026 awarded by the National Institute of Justice, Office of Justice Programs, US Department of Justice.

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Correspondence to Catherine M. Grgicak.

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Sheth, N., Swaminathan, H., Gonzalez, A.J. et al. Towards developing forensically relevant single-cell pipelines by incorporating direct-to-PCR extraction: compatibility, signal quality, and allele detection. Int J Legal Med (2021). https://doi.org/10.1007/s00414-021-02503-4

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Keywords

  • Forensic DNA
  • Human identification
  • Single-cell forensic DNA
  • Direct-to-PCR
  • Forensic DNA Mixtures