Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX, 76107, USA.
Int J Legal Med. 2013 Nov;127(6):1079-86. doi: 10.1007/s00414-013-0879-7. Epub 2013 Jun 5.
The Ion AmpliSeq™ HID single nucleotide polymorphism (SNP) panel, a primer pool of 103 autosomal SNPs and 33 Y-SNPs, was evaluated using the Ion 314™ Chip on the Ion PGM™ Sequencer with four DNA samples. The study focused on the sequencing of DNA at three different initial target quantities, related interpretation issues, and concordance of results with another sequencing platform, i.e., Genome Analyzer IIx. With 10 ng of template DNA, all genotypes at the 136 SNPs were detected. With 1 ng of DNA, all SNPs were detected and one SNP locus in one sample showed extreme heterozygote imbalance on allele coverage. With 100 pg of DNA, an average of 1.6 SNP loci were not detected, and an average of 4.3 SNPs showed heterozygote imbalance. The average sequence coverage was 945-600× at autosomal SNPs and 465-209× at Y-SNPs for 10 ng-100 pg of DNA. The average heterozygote allele coverage ratio was 89.6-61.8 % for 10 ng-100 pg of DNA. At 10 ng of DNA, all genotypes of the 95 SNPs shared between the two different sequencing platforms were concordant except for one SNP, rs1029047. The error was due to the misalignment of a flanking homopolymer. Overall, the data support that genotyping a large battery of SNPs is feasible with massively parallel sequencing. With barcode systems, better allele balance, and specifically designed alignment software, a more comprehensive rapid genotyping and more cost-effective results may be obtained from multiple samples in one analysis than are possible with current typing and capillary electrophoresis systems.
Ion AmpliSeq™ HID 单核苷酸多态性（SNP）面板是一个包含 103 个常染色体 SNP 和 33 个 Y-SNP 的引物池，使用 Ion 314™ Chip 在 Ion PGM™ 测序仪上对 4 个 DNA 样本进行了评估。该研究集中于三个不同初始靶标量的 DNA 测序、相关解释问题以及与另一个测序平台（即 Genome Analyzer IIx）的结果一致性。使用 10ng 的模板 DNA，可检测到 136 个 SNP 中的所有基因型。使用 1ng 的 DNA，可检测到所有 SNP，并且一个样本中的一个 SNP 位点在等位基因覆盖度上显示出极端杂合子不平衡。使用 100pg 的 DNA，平均有 1.6 个 SNP 位点未被检测到，平均有 4.3 个 SNP 显示杂合子不平衡。对于 10ng-100pg 的 DNA，常染色体 SNP 的平均序列覆盖度为 945-600×，Y-SNP 的平均序列覆盖度为 465-209×。对于 10ng-100pg 的 DNA，平均杂合子等位基因覆盖比为 89.6-61.8%。在 10ng 的 DNA 中，两种不同测序平台之间共享的 95 个 SNP 的所有基因型都是一致的，除了一个 SNP，rs1029047。错误是由于侧翼同源多聚体的不对齐。总体而言，数据支持使用大规模平行测序对大量 SNP 进行基因分型是可行的。使用条码系统、更好的等位基因平衡以及专门设计的对齐软件，与当前的分型和毛细管电泳系统相比，在一次分析中从多个样本中可能获得更全面的快速基因分型和更具成本效益的结果。
