Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo Ward, Tokyo 113-0033, Japan; Forensic Science Laboratory, Tokyo Metropolitan Police Department, 3-35-21, Shakujiidai, Nerima Ward, Tokyo 177-0045, Japan.
Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo Ward, Tokyo 113-0033, Japan.
Forensic Sci Int Genet. 2022 Nov;61:102752. doi: 10.1016/j.fsigen.2022.102752. Epub 2022 Jul 29.
Instead of traditional short tandem repeat (STR) profiling, the genetic genealogy method, which uses hundreds of thousands of single nucleotide polymorphisms (SNPs) spread across genome-wide, has emerged as a powerful kinship determination tool and recently attracted great attention in forensic genetics. In this study, we explored the tolerance and viability of kinship discrimination based on a high-density SNP profile for forensic DNA, especially focusing on low-quantity DNA. Using the Affymetrix Genome-Wide Human SNP Array 6.0 platform (Thermo Fisher Scientific), the influence of low-quantity DNA on SNP genotype determination was evaluated. The low-quantity DNA samples failed once every few samples, the generated SNP profile had low data quality. Our investigation revealed that the SNP profile with low data quality contained many genotyping errors in which the SNP genotype changed from homozygote to heterozygote. The kinship discrimination analysis using KING software was directly influenced by these genotyping errors, which was confirmed that some unrelated pairs were mis-specified as 4th-degree relatives. We confirmed that the false heterozygous SNPs resulted in an inflation of kinship coefficient and a decrease of non-shared allele between a tested pair. To eliminate the influence of these genotyping errors and acquire an accurate kinship discrimination result, we developed a novel method to select only the robust SNPs, which stably give the genotype determination with high accuracy even in SNP profiles with low data quality. The application of our novel method led to the improved results of kinship discrimination up to the same level as in the SNP profile with high data quality. In addition, this study demonstrated the advantage of kinship analysis using a high-density SNP profile in the forensic field. It is well known that likelihood ratio calculation based on autosomal STR profile, which is the most commonly applied approach, has difficulty in gaining true kinship analysis results, especially when the relationship between the tested two individuals is more biologically distant. We showed the kinship discrimination analysis with a high-density SNP profile is more suitable for the case without close relatives, using the real case data. Although further study with larger samples will be necessary, this study indicated that practical forensic use of kinship determination with a high-density SNP profile would bring benefits to the forensic field.
本研究旨在探索基于高通量 SNP 图谱的亲缘关系判别在法医 DNA 中的可行性和适用范围，特别是针对低浓度 DNA。本研究使用 Affymetrix Genome-Wide Human SNP Array 6.0 平台（Thermo Fisher Scientific），评估了低浓度 DNA 对 SNP 基因型判读的影响。当每几个样本中就有一个样本无法获得时，会导致 SNP 图谱数据质量降低。我们的研究表明，低质量 SNP 图谱中包含许多基因分型错误，这些错误导致 SNP 基因型由纯合子变为杂合子。KING 软件的亲缘关系判别分析受到这些基因分型错误的直接影响，有些无亲缘关系的个体被错误地判定为 4 度亲属。我们确认，这些假杂合 SNP 导致亲缘系数膨胀，并且降低了测试个体之间的非共享等位基因。为了消除这些基因分型错误的影响并获得准确的亲缘关系判别结果，我们开发了一种新的方法，仅选择稳健的 SNP，即使在 SNP 图谱数据质量较低的情况下，也能稳定地提供高准确性的基因分型结果。该方法可以筛选出 SNP 图谱中稳定的 SNP，从而提高亲缘关系判别结果，使其与高质量 SNP 图谱的结果相当。此外，本研究还展示了高通量 SNP 图谱在法医领域进行亲缘关系分析的优势。众所周知，基于常染色体 STR 图谱的似然比计算是最常用的方法，但在测试个体间的生物学关系较疏远时，该方法很难获得准确的亲缘关系分析结果。本研究通过真实案例数据，展示了高通量 SNP 图谱在无近亲关系的案例中进行亲缘关系分析的适用性。虽然需要进一步的大样本研究，但本研究表明，高通量 SNP 图谱在亲缘关系判别的实际法医应用中可能会给法医领域带来益处。
