Abstract：
Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the \'Rita\' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel\'s performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel\'s performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel\'s reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.
摘要：
单核苷酸多态性（SNPs），作为人类基因组中最普遍的变异类型，在影响人类特质方面起着举足轻重的作用。它们被广泛用于不同的领域，如人口遗传学，法医学,和遗传医学。这项研究的重点是\'Rita\'BeadChip，使用IlluminaInfiniumHTS技术开发的自定义SNP微阵列面板。设计用于高通量基因分型，该小组促进了4000多个标记的有效和成本效益的分析。在对一组1000个样本进行仔细聚类后，对丽塔小组进行了评估，评估其敏感性，重复性,再现性，精度,准确度,和耐污染。在各种情况下评估了面板的性能，包括性别估计和父母关系评估，使用GenomeStudio数据分析软件。研究结果表明，超过95%的定制BeadChip检测标记是成功的，具有比其他突变更好的转换性能，Y染色体位点的成功率要低得多。对照样品的异常调用率超过99%，即使DNA输入低至0.781ng。在DNA数量低于0.1ng的情况下，仍可获得超过80％的呼叫率，表明DNA数量通常有限的法医应用的高灵敏度和适用性。重复性,再现性，精度研究揭示了不同批次和操作员之间面板性能的一致性，呼叫率或基因分型结果没有显著偏差。准确性评估,涉及与多个可用的遗传数据库进行比较，包括1000基因组计划和HapMap,表示超过99%的一致性，建立Rita小组在基因分型中的可靠性。污染研究揭示了对背景噪声的见解，并允许定义样品质量评估的阈值。突出显示了区分阴性对照和真实样品的多个指标，提高所获得结果的可靠性。GenomeStudio中的性别估计工具被证明非常有效，在所有常染色体位点调用率高于97%的样本中正确分配性别。家庭三重奏的父母关系评估强调了GenomeStudio在识别基因分型错误或潜在的孟德尔不一致方面的效用，促进Rita等阵列在亲属关系测试中的应用。总的来说,这个评估证实了Rita微阵列是一个强大的，高通量基因分型工具，强调其在遗传研究和法医应用中的潜力。凭借其自定义内容和适应性设计，它不仅满足了当前的基因分型要求，而且为遗传分析领域的进一步研究和应用扩展开辟了途径。
