Trisomy 21 disclosure using STR and SNP markers typed by MiSeq FGx™ Forensic Genomics System

The presence of a tri-allelic pattern at a single locus in a multiplex short tandem repeat (STR) profile is a rarely observable event. Generally, based on peak height measured by the capillary electrophoresis (CE) method and combination of alleles, the tri-allelic pattern is distinguishable into two predominant types: type 1 and 2, which are caused, respectively, by somatic mutations and chromosomal rearrangements. When tri-allelic patterns at more than one STR located on the same chromosome are detected, there is a reasonable suspicion of a trisomy due to an extra copy of a chromosome. Therefore, information on the type of three-band pattern is usually limited to STRs localized on the same chromosome included in the forensic kit in use and sometimes in insufficient numbers to classify this event correctly. The opportunity to extend this evaluation to additional markers, such as SNPs detectable using NGS, has not yet been explored. In this study, using the ForenSeq™ DNA Signature Prep kit, two cases of autosomal aneuploidy were revealed on chromosome 21, relying not only on STRs assessment but also extending the analysis to the five identity-informative single nucleotide polymorphisms (iiSNPs) localized on chromosome 21.     

Combined analysis of two different ancestry informative assays using SNPs and Indels in Eurasian populations

In the absence of a suspect or DNA database match, small multiplex assays with ancestry informative markers (AIMs) provide an alternative to comparative DNA analysis as the knowledge of an unknown stain donor's biogeographic ancestry can be helpful in guiding criminal investigations. AIMs can provide valuable information in such cases. The research focus for AIMs has been on multiplex assays of single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (Indels). This work presents a combined analysis of two different AIM assays to increase differentiation between Eurasian populations.     

单核苷酸多态性与法医学DNA分型技术

单核苷酸多态性(single nucleotide polymorphism,SNP)分型技术越来越成为法医学领域关注的热点,它在研究Y染色体或线粒体单倍型以及DNA表型的分析中具有重要应用价值。本文着重比较分析了SNP技术与片段长度多态性技术之间的优劣,同时就当前STR位点识别概率与所需选择的SNP位点数进行探讨。此外,本文还就各类SNP分型方法的优缺点及其法医学应用进行了论述。     

A New Method for Human ABO Genotyping Using a Universal Reporter Primer System

Abstract: We developed a new method for forensic ABO genotyping based on a universal reporter primer (URP) system. This allows for the simultaneous detection of six single nucleotide polymorphism (SNP) sites in the ABO gene (nucleotide positions 261, 297, 526, 703, 796, and 803). This URP system provides obvious peaks, ranging from 82 to 151 bp in length. ABO genotypes were classified and successfully genotyped by our method, including minor alleles that may cause a discrepancy between the genetic data and serological phenotypes. Full profiles were identified using as little as 0.1 ng (0.05 ng/reaction) of standard K562 and 9947A DNA. Moreover, the success rate of genotyping from a URP system was much higher than that from a conventional primer extension method in degraded DNA. This method enables simple and rapid detection of multiple SNP sites on human ABO genes and is highly specific and sensitive when using limited and degraded DNA.     

辽宁汉族TAP2基因SNPs遗传多态性

抗原处理相关转运体（transporter associated with antigenprocessing,TAP）蛋白是一种分布于内质网膜上的转运蛋白,TAP基因于1990年分别由Trowsdale和Spies等发现,位于6p21．3,在MHCII区的DQB1和DPB1之间,包括TAP1和TAP2两个基因。     

血小板同种抗原基因中9个单核苷酸多态性在广西地区壮族和汉族人群中的差异分析

目的检测血小板同种抗原基因中9个单核苷酸多态性在广西地区壮族和汉族人群中的差异。方法利用基于单碱基延伸的单核苷酸多态性（SNP）分型芯片,对广西壮族地区99例壮族个体和107例汉族个体的染色体基因组上10个SNP位点进行了分型,其中9个位于6个血小板同种抗原基因中,1个位于基因间区。此外,结合Hapmap计划第二期公布的四个人群的SNP分型数据,分析这六个人群的遗传结构。结果广西原住汉族人在等位基因频率上未检测到与当地壮族有显著性的差异位点,但在基因型频率上,rs630014和rs9441951两位点是显著差异的。广西壮族人与广西汉族、北京汉族人及日本东京人的遗传结构相近,但与祖先来自欧洲西部和北部的犹他州居民以及尼日利亚伊巴丹的约鲁巴人有显著差异的遗传成分存在。结论壮汉两族由于历史上的多次基因交流可能导致其遗传信息在很大程度上是相近的。     

Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples

For the analysis of degraded DNA in disaster victim identification (DVI) and criminal investigations, single nucleotide polymorphisms (SNPs) have been recognized as promising markers mainly because they can be analyzed in short sized amplicons. Most SNPs are bi-allelic and are thereby ineffective to detect mixtures, which may lead to incorrect genotyping. We developed an algorithm to find non-binary (i.e. tri-allelic or tetra-allelic) SNPs in the NCBI dbSNP database. We selected 31 potential tri-allelic SNPs with a minor allele frequency of at least 10%. The tri-allelic nature was confirmed for 15 SNPs residing on 14 different chromosomes. Multiplex SNaPshot™ assays were developed, and the allele frequencies of 16 SNPs were determined among 153 Dutch and 111 Netherlands Antilles reference samples. Using these multiplex SNP assays, the presence of a mixture of two DNA samples in a ratio up to 1:8 could be recognized reliably. Furthermore, we compared the genotyping efficiency of the tri-allelic SNP markers and short tandem repeat (STR) markers by analyzing artificially degraded DNA and DNA from 30 approximately 500-year-old bone and molar samples. In both types of degraded DNA samples, the larger sized STR amplicons failed to amplify whereas the tri-allelic SNP markers still provided valuable information. In conclusion, tri-allelic SNP markers are suited for the analysis of degraded DNA and enable the detection of a second DNA source in a sample.     

What makes your “eyes” look different?

Facial morphology is the most distinguishable appearance and represents a promising subfield of Forensic DNA phenotyping. Located in the center of the face, eyes are important for facial recognition. In this study, epicanthal fold and palpebral fissure were selected for a preliminary genotype-phenotype analysis. Two SNPs were genotyped with SNaPshot method in 156 Chinese Han adults. A significant increased incidence of high ratio of palpebral fissure width to height was observed in the populations with AG genotype for SNP rs2074612 on gene HBEGF: AG versus GG, OR = 2.36, 95%CI = 1.08–5.18, p <0.05; AG versus GG/AA, OR = 2.07, 95%CI = 1.03–4.16, p < 0.05. No significant genotype difference was detected between epicanthal fold positive/negative populations for both SNPs (p > 0.05). Further study including more samples should be conducted to discover SNPs associated with epicanthal fold and palpebral fissure traits.     

Microhaplotype loci are a powerful new type of forensic marker

Modern sequencing technology makes it possible to genotype polymorphisms with high throughput and high multiplexing. We have searched for and identified many loci with 2 or more SNPs within the expanse of a 200 bp single sequence run and show that when linkage disequilibrium is not complete these loci have multiple alleles detected as phase-known haplotypes. These microhaplotype loci (microhaps) are a powerful tool for individual identification, ancestry inference, and determining family/clan relationships.     

Introduction of the python script MHinNGS for analysis of microhaplotypes

MHinNGS is a Python application developed for analysis of microhaplotypes (MHs) in single-end sequencing data. MHinNGS analyses reads in standard formats and store each sequence into bins, one bin for each MH as defined by the two flanking sequences. MHinNGS requires a reference genome and a configuration file with information about each locus. Four mandatory and 15 optional criteria defined in the configuration file allow detailed locus-specific analyses of the MH loci. The program 1) removes noise, 2) identify and name alleles, 3) test the genotypes, and 4) test unique sequences not identified as noise or alleles. MHinNGS produces a result file, where every unique sequence that passed the noise filter is presented with MH allele, read depth, warning flags based on the genotyping criteria, sequence, heterozygote balance, and MH name. Furthermore, variation in other parts of the fragment that is not defined as SNPs in the MH, linked variants, or rare SNPs are listed in a separate column of the result file.