High-throughput Kidd blood group genotyping based on molecular inversion probe and next generation sequencing technology
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摘要: 目的 开发一种基于分子倒置探针(molecular inversion probe，MIP)捕获技术的靶向二代测序(next generation sequencing，NGS)血型分型方法，以允许在一次运行中同时鉴定大量患者的Kidd血型。方法 提取基因组DNA后，使用MIP探针捕获靶标。然后，使用带有样品条形码和Illumina衔接子的引物通过聚合酶链式反应(PCR)扩增产物，之后使用Illumina MiSeq对样品进行测序。用序列特异引物引导的聚合酶链反应(PCR-SSP)和新建方法同时检测10例献血者样品的Kidd血型以确定新建立的方法是否能够有效检测JKA、JKB等位基因。然后用基于MIP的NGS方法和血清学方法检测100例样本并比较结果的一致性。结果 基于MIP的NGS血型分型方法检测10例样本的结果均与PCR-SSP所得结果相同，表明新建方法能够有效检测JKA、JKB等位基因。建立的基于MIP的NGS分型方法检测100例样本的基因分型结果与血清学方法检测结果一致率为100%。在100例随机样本中，Jka和Jkb的频率分别为0.39和0.61，抗原频率符合其在东方人群中的分布规律。结论 基于MIP的NGS方法是一种可行的血型分析策略，允许进行大规模的Kidd血型检测。此外，将这种MIP方法扩展到新的血型系统只需要加入新的捕获探针。Abstract: Objective To develop a molecular inversion probe(MIP) capture for targeted next generation sequencing(NGS) based to allow simultaneous identification of the Kidd blood group in multiple patients in a single run.Methods After DNA extraction, MIP probes were used to capture the targets. Primers with sample barcodes and Illumina adaptors were used to amplified the products by polymerase chain reaction(PCR). Samples were sequenced using an Illumina MiSeq. Three samples from blood donors previously test by PCR-SSP assay were used for comparison testing to determine if the established method could distinguish JKA and JKB alleles effectively. Then, MIP based NGS results were compared to serologic for 100 samples.Results The results of the MIP-based NGS blood typing method were the same as those of the PCR-SSP method, indicating that the new method could distinguish JKA and JKB alleles effectively. MIP based NGS red blood cell antigen typing was 100% concordant with serologic and SNP based typing. The frequencies of Jka and Jkb were 0.39 and 0.61 in the 100 individuals, and the antigen frequency was consistent with its distribution in the Eastern population.Conclusion The MIP-based NGS test may be a viable blood typing strategy that allows for large-scale Kidd blood group testing. Furthermore, extending this overall MIP approach to new blood group systems will only require the incorporation of new capture probes.
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表 1 基于MIP的NGS方法所用的MIP和通用引物
名称 序列 长度/bp MIP-Kidd-1 TGAGGCAATGCATGGGATGGANNNN
AGATCGGAAGAGCACACGTGACTCGCCAAGCTGAAG
NNNNNNNNNNCCCAGAGTCCAAAGTAGATGT92 MIP-Kidd-2 GAGGAATGTTCATGGCGCTCACNNNN
AGATCGGAAGAGCACACGTGACTCGCCAAGCTGAAG
NNNNNNNNNNGAGATCTTGGCTTCCTAGGGA93 通用正向引物 CGTGTGCTCTTCCGATCT 18 通用反向引物 TGACTCGCCAAGCTGAAG 18 注：加粗表示与基因组DNA互补的同源序列；斜体表示分子标志符；下划线表示引物互补序列。 
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表 2 所选引物
引物名称 序列(5’-3’) 扩增产物长度/bp JKA F：GAGTTCTGACCCCTCCTGTCTTA
R：TGAGCGCCATGAACATTCC301 JKB F：AGTCTTCAGCCCCATTTGAGA
R：GAGCCAGGAGGTGGGTTTGC121 HGH F：GCCTTCCCAACCATTCCCTTA
R：TCACGGATTTCTGTTGTGTTT429
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表 4 100名献血者Kidd血型表型和基因频率分布情况
表型 观察值 期望值 基因频率 χ2 P Jk(a+b-) 16 14.82 Jka=0.39 0.134 >0.05 Jk(a+b+) 46 47.36 Jkb=0.61 Jk(a-b+) 38 37.82 Jk(a-b-) 0 0
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