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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Related Experiment Video

Updated: Jul 1, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
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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
PubMed
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.

Keywords:
Alternative reference materialsFingernailsHair rootHair shaftMassively parallel sequencingSingle nucleotide polymorphism

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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.