Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan.
BMC Med Genomics. 2013 Sep 12;6:31. doi: 10.1186/1755-8794-6-31.
Neutrophil antigens are involved in a variety of clinical conditions including transfusion-related acute lung injury (TRALI) and other transfusion-related diseases. Recently, there are five characterized groups of human neutrophil antigen (HNA) systems, the HNA1 to 5. Characterization of all neutrophil antigens from whole genome sequencing (WGS) data may be accomplished for revealing complete genotyping formats of neutrophil antigens collectively at genome level with molecular variations which may respectively be revealed with available genotyping techniques for neutrophil antigens conventionally.
We developed a computing method for the genotyping of human neutrophil antigens. Six samples from two families, available from the 1000 Genomes projects, were used for a HNA typing test. There are 500 ~ 3000 reads per sample filtered from the adopted human WGS datasets in order for identifying single nucleotide polymorphisms (SNPs) of neutrophil antigens. The visualization of read alignment shows that the yield reads from WGS dataset are enough to cover all of the SNP loci for the antigen system: HNA1, HNA3, HNA4 and HNA5. Consequently, our implemented Bioinformatics tool successfully revealed HNA types on all of the six samples including sequence-based typing (SBT) as well as PCR sequence-specific oligonucleotide probes (SSOP), PCR sequence-specific primers (SSP) and PCR restriction fragment length polymorphism (RFLP) along with parentage possibility.
The next-generation sequencing technology strives to deliver affordable and non-biased sequencing results, hence the complete genotyping formats of HNA may be reported collectively from mining the output data of WGS. The study shows the feasibility of HNA genotyping through new WGS technologies. Our proposed algorithmic methodology is implemented in a HNATyping software package with user's guide available to the public at http://sourceforge.net/projects/hnatyping/.
中性粒细胞抗原参与多种临床情况，包括输血相关急性肺损伤（TRALI）和其他输血相关疾病。最近，已经确定了五个特征性的人类中性粒细胞抗原（HNA）系统，即 HNA1 至 HNA5。通过全基因组测序（WGS）数据对所有中性粒细胞抗原进行特征描述，可能揭示出在基因组水平上中性粒细胞抗原的完整基因分型格式，其中的分子变化可能分别通过现有的中性粒细胞抗原基因分型技术来揭示。
我们开发了一种用于人类中性粒细胞抗原基因分型的计算方法。来自两个家庭的六个样本，可从 1000 基因组项目中获得，用于 HNA 分型测试。从采用的人类 WGS 数据集中过滤出每个样本中约有 500 到 3000 个读数，以识别中性粒细胞抗原的单核苷酸多态性（SNP）。读取比对的可视化显示，来自 WGS 数据集的产量读数足以覆盖抗原系统的所有 SNP 位置：HNA1、HNA3、HNA4 和 HNA5。因此，我们实施的生物信息学工具成功地揭示了所有六个样本中的 HNA 类型，包括基于序列的分型（SBT）以及聚合酶链反应序列特异性寡核苷酸探针（SSOP）、聚合酶链反应序列特异性引物（SSP）和聚合酶链反应限制性片段长度多态性（RFLP），以及亲子关系的可能性。
下一代测序技术致力于提供经济实惠且无偏的测序结果，因此可以通过挖掘 WGS 的输出数据来报告 HNA 的完整基因分型格式。该研究展示了通过新的 WGS 技术进行 HNA 基因分型的可行性。我们提出的算法方法已在 HNATyping 软件包中实现，用户指南可在 http://sourceforge.net/projects/hnatyping/ 上获取。
