Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing
Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing
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DOI：
10.1016/j.fsigen.2014.06.004
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发表时间：
2014-09-01
影响因子：
3.1
通讯作者：
Morling, Niels
中科院分区：
文献类型：
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作者：
Borsting, Claus;Fordyce, Sarah L.;Morling, Niels
Ion Torrent（TM）HID SNP检测在一次PCR中扩增了136个常染色体SNP和33个Y染色体标记，随后使用Ion PGM（TM）第二代测序平台对标记进行分型。从我们ISO 17025认证实验室常规使用的SNPforID面板中选择了总共51个常染色体SNP。通过用Ion Torrent（TM）HID SNP分析对44名伊拉克人进行两次分型来测试Ion Torrent（TM）HID SNP分析和SNPforID分析之间的一致性。相同的样品先前用SNPforID测定进行分型，并且先前通过分型45个Y染色体SNP来鉴定个体的Y染色体单倍型群。除了两个SNP的SNP基因型外，获得了测定之间的完全一致性。这些SNPs是样本间等位基因平衡不一致的8个SNPs（rs2399332、rs1029047、rs10776839、rs4530059、rs8037429、rs430046、rs1031825和rs1523537）之一。这些SNP应排除在小组之外。PCR中DNA的最佳量似乎>= 0.5 ng。等位基因脱落是罕见的，只在实验中看到，
The Ion Torrent (TM) HID SNP assay amplified 136 autosomal SNPs and 33 Y-chromosome markers in one PCR and the markers were subsequently typed using the Ion PGM (TM) second generation sequencing platform. A total of 51 of the autosomal SNPs were selected from the SNPforID panel that is routinely used in our ISO 17025 accredited laboratory. Concordance between the Ion Torrent (TM) HID SNP assay and the SNPforID assay was tested by typing 44 Iraqis twice with the Ion Torrent (TM) HID SNP assay. The same samples were previously typed with the SNPforID assay and the Y-chromosome haplogroups of the individuals were previously identified by typing 45 Y-chromosome SNPs. Full concordance between the assays were obtained except for the SNP genotypes of two SNPs. These SNPs were among the eight SNPs (rs2399332, rs1029047, rs10776839, rs4530059, rs8037429, rs430046, rs1031825 and rs1523537) with inconsistent allele balance among samples. These SNPs should be excluded from the panel.The optimal amount of DNA in the PCR seemed to be >= 0.5 ng. Allele drop-outs were rare and only seen in experiments with