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Infinium Assay for Large-scale SNP Genotyping Applications
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Full Sibling Testing Based on NGS-SNP Genotyping Method and IBS Strategy.

Z Y Wang1,2, D J Wang3, R Li1

  • 1Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510089, China.

Fa Yi Xue Za Zhi
|May 29, 2019
PubMed
Summary

Single nucleotide polymorphism (SNP) genotyping with identity by state (IBS) scores effectively identifies full siblings. The threshold method using 90 SNPs offers a flexible and accurate approach for relationship testing with a low false rate.

Keywords:
forensic genetics; single nucleotide polymorphism; sibling relations; identity by state; next generation sequencing

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Area of Science:

  • Forensic Genetics
  • Human Genetics
  • Population Genetics

Background:

  • Accurate determination of full sibling relationships is crucial in forensic and paternity testing.
  • Traditional methods may have limitations in accuracy and flexibility.
  • Single nucleotide polymorphisms (SNPs) offer a high-throughput genotyping approach.

Purpose of the Study:

  • To evaluate the efficacy of SNP genotyping combined with an identity by state (IBS) strategy for full sibling testing.
  • To compare the performance of Fisher discriminant function and threshold methods for relationship determination.

Main Methods:

  • Genotyped 90 autosomal SNPs from 35 individuals across four generations using the Precision ID Identity Panel.
  • Calculated and compared IBS scores for various relationships including full siblings, grandparent-grandchild, uncle/aunt-nephew/niece, first cousins, and unrelated individuals.
  • Applied Fisher discriminant function and threshold methods to determine relationships and assessed their false rates.

Main Results:

  • Identified significant distribution differences in IBS scores among most relationship pairs (P<0.05), except for grandparent-grandchild and uncle/aunt-nephew/niece.
  • Fisher discriminant function exhibited false rates ranging from 1.3% for full siblings to 38.7% for first cousins.
  • Recommended thresholds (t1=128, t2=141) for full sibling identification using the threshold method with a false rate ≤0.05%.

Conclusions:

  • The 90 SNP markers in the Precision ID Identity Panel are suitable for full sibling relationship testing.
  • The IBS-based threshold method demonstrates a lower false rate and greater flexibility compared to the Fisher discriminant function for full sibling testing.