Development of an Okinawa panel for biogeographic inference of Okinawans

The Precision ID Ancestry Panel with 165 SNP markers was unable to differentiate between mainland Japanese and Okinawa Japanese or to distinguish either of them from other East Asian populations. An Okinawa panel was developed with the aim of further separating Okinawa Japanese individuals from mainland Japanese and other Asian groups. Seventy-five SNPs were selected using the most informative markers from the literature. Further, 22 SNPs were selected to separate Okinawa Japanese at minimum SNPs. Samples were collected from 48 unrelated individuals from mainland Japan and 46 unrelated residents of the Okinawa prefecture. Data were evaluated by STRUCTURE, principal component, and GenoGeographer analyses. The 22 SNP set had similar levels of differentiation in STRUCTURE and PCA analyses as the 75 SNP set. GenoGeographer analysis showed that, out of the 46 Okinawa Japanese individuals, the 75 SNP and 22 SNP sets correctly assigned the Okinawan population as the most likely population of origin for 32 and 31 individuals, respectively. Neither SNP set could completely differentiate between Okinawa Japanese and other Asian groups, however, these sets should be useful for crime investigation, when the sample, cost and time are limited.

含165个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记的Precision ID祖源分析面板（Precision ID Ancestry Panel）无法区分日本本土人群与冲绳日本人群，亦无法将二者与其他东亚人群区分开来。为此研发了冲绳专属祖源分析面板，旨在进一步将冲绳日本人群与日本本土人群及其他亚洲人群区分开来。该面板从已发表文献中筛选出75个信息量最优的SNP标记；此外，还筛选出22个SNP标记，以在标记数量最少的前提下实现冲绳日本人群的区分。本次研究共采集了来自日本本土的48名无亲缘关系个体，以及冲绳县的46名无亲缘关系居民的样本。通过STRUCTURE软件、主成分分析（Principal Component Analysis, PCA）及GenoGeographer工具对测序数据进行了评估。在STRUCTURE与PCA分析中，22个SNP组成的标记集与75个SNP组成的标记集展现出相近的群体区分效能。GenoGeographer分析结果显示，在46名冲绳日本个体中，75个SNP标记集与22个SNP标记集分别可将32名、31名个体正确归类为以冲绳人群为最可能起源群体的个体。不过，两类SNP标记集均无法完全区分冲绳日本人群与其他亚洲人群，但在样本量、检测成本与时间均受限的刑侦场景中，这两类标记集仍具备实际应用价值。