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Investigating SNP typing using alternative reference materials with the FORCE panel and QIAseq® chemistry
Lindsay L Kotchey1, Sophie Lee2, Leah Nangeroni1
1The Center for Forensic Science Research & Education, Horsham, PA 19440, USA.
Forensic Science International. Genetics
|May 8, 2025
Summary
Forensic Genetic Genealogy (FGG) using the FORCE panel effectively analyzes alternative DNA samples like fingernails for identity, ancestry, and phenotype, even from degraded sources. This method shows high SNP concordance and reliable predictions, aiding investigations when traditional samples are unavailable.
Area of Science:
- Forensic genetics
- Molecular biology
- Genomics
Background:
- Single nucleotide polymorphism (SNP) markers are vital for forensic applications like identity, kinship, and ancestry testing.
- Forensic Genetic Genealogy (FGG) and massively parallel sequencing (MPS) enhance SNP marker utility.
- The FORensic Capture Enrichment (FORCE) panel targets 5497 SNPs for direct kinship and identification.
Purpose of the Study:
- To evaluate alternative reference materials (hair roots, shafts, fingernails) using the FORCE panel and QIAseq® chemistry for direct identification.
- To assess SNP recovery and concordance between alternative materials and buccal swabs.
- To compare phenotype, Y-haplogroup, and biogeographic ancestry predictions from these materials.
Main Methods:
- Utilized the FORCE panel (5497 SNPs) with QIAseq® chemistry on hair roots, shafts, and fingernail clippings.
- Assessed SNP recovery and concordance against buccal swabs.
- Compared phenotype, Y-haplogroup, and biogeographic ancestry predictions.
- Evaluated performance on MiSeq FGx and NextSeq 550 sequencing platforms.
Main Results:
- Achieved high SNP concordance (99.62-100%) between alternative materials and buccal swabs.
- Fingernail samples exhibited the highest SNP recovery and concordance among alternative materials.
- Phenotypic, ancestry, and Y-haplogroup predictions were 100% consistent with buccal samples.
- NextSeq 550 offered higher coverage and potential cost savings via multiplexing.
Conclusions:
- The FORCE panel and QIAseq® chemistry reliably profile SNPs from diverse alternative reference materials, including degraded samples.
- High concordance and genotype recovery support the use of alternative samples in forensic investigations.
- This approach is valuable when traditional reference samples are unavailable or unsuitable.
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