Forensic Science International: Genetics - SNP Analysis in Human Identification

Introduction to SNPs in Forensics

  • Single Nucleotide Polymorphisms (SNPs) are important genetic markers that complement traditional forensic techniques such as short tandem repeat (STR) markers.

  • SNPs offer potential advantages in forensic analyses, especially in difficult cases involving degraded samples.

Case Study Overview

  • Disaster Incident: A massive disaster occurred in Jeju Province, Korea, between 1948 and 1954, leading to the recovery of 402 human bone remains.

  • Initial identification from 2010 utilized conventional DNA typing (autosomal and Y-chromosomal STR typing, mitochondrial DNA sequencing), successfully identifying 74 remains (18.4%).

  • Further identification involved applying SNP typing to aid in the identification of 327 unidentified remains.

Identification Process

  • SNP Typing Methodology:

    • Used an Affymetrix resequencing array to conduct SNP typing on bone remains and reference samples from 782 family members.

    • 51 additional remains were identified using SNP data, which proved useful for kinship testing and clarifying ambiguous relationships.

Technical Aspects

  • Advantages of SNPs:

    • Smaller-sized amplicons allow better recovery from degraded DNA.

    • Lower mutation rates facilitate distant kinship analysis.

    • High-throughput SNP analysis can be conducted via microarrays and massively parallel sequencing.

  • General Methodology:

    • DNA Extraction: Employed phenol/chloroform extraction for the bone samples and standard protocols for blood samples from family members.

    • SNP Genotyping: Conducted using custom SNP markers and the GeneChip® CustomSeq Resequencing Array.

    • Kinship Probability Calculation: Used likelihood ratio (LR) for evaluating kinship based on SNP data.

Results

  • From 327 tested bone samples, 305 (93.3%) yielded successful SNP data.

  • Average number of successfully genotyped SNPs was 90.0 ± 25.1 per sample.

  • SNPs significantly enhanced kinship analysis for 51 identified bone remains and clarified various relationships (parent-child, full-sibling, uncle-nephew).

Case Specifics

  • Example Case Outcomes:

    • One bone with partial autosomal STR data showed a >99.9998% probability of paternity via SNP analysis.

    • Another sample linked paternally to a potential relative with >99.9999% probability using SNP data.

Importance of Software in Analysis

  • The AccuID® Console software enabled efficient kinship analysis, computing LR for all potential relatives, confirming the effectiveness of large-scale SNP analysis.

Discussion

  • The utility of SNPs in forensic work is evidenced by the identification of previously ambiguous relationships.

  • SNP typing improved identification rates from 18.4% to 31.1% when used in conjunction with conventional methods.

  • Challenges: Quality of DNA samples impacted SNP typing success, particularly in degraded bone samples, highlighting the need for continual technological improvements.

  • Future Directions: Plans to enhance the SNP typing system with more markers to facilitate distant kinship testing based on continued advancements.

Conclusion

  • SNP typing is a promising supplement to traditional forensic genetic methods, offering enhanced identification and kinship analysis in complex and degraded samples.