Using STR,MiniSTR and SNP markers to solve complex cases of kinship analysis

In complex kinship investigation, miniSTRs and SNPs have been frequently used in order to increase the likelihood ratio (LR), when the results obtained for the most commonly used STR multiplexes were not informative enough. In this work, we describe the results obtained when using a battery of 23 STRs, 3 miniSTRs and 52 SNPs to investigate three complex paternity cases where the father was not available, and one paternity case with bone samples, from which no results could be obtained for STRs (including the 3 miniSTRs, D10S1248, D14S1434 and D22S1045). In all cases, the additional information provided by the SNPforID 52plex identification panel was enough to achieve conclusive results.     

Implementation of a semi-automated processing system for DNA profiling of forensic casework samples

The concept for a semi-automated processing system for DNA analysis of crime scene samples was developed at the Landeskriminalamt Baden-Württemberg (LKA BW) and comprises the extraction of genomic DNA from human cells by ChargeSwitch^® magnetic bead technology (CST), quantification of purified DNA by real-time PCR, amplification of short tandem repeats (STRs) by PCR and DNA fragment length analysis of STRs by capillary electrophoresis. Three liquid handling workstations from Tecan, a real-time PCR device and a 16-channel capillary electrophoresis (CE) system, both from Applied Biosystems (AB), are linked via laboratory data network. Transmission and management of sample and analysis data is enabled by a Laboratory Information and Management System (LIMS). Suitability for a wide range of stain types, early exclusion of DNA-free samples, barcode sample identification and prevention of cross-contaminations guarantee efficiency and high quality standards.     

Challenging DNA: Assessment of a range of genotyping approaches for highly degraded forensic samples

It is common in forensic casework to encounter highly degraded DNA samples from a variety of sources. In this category bone and teeth samples are often the principal source of evidential material for criminal investigations or identification of long-deceased individuals. In these circumstances standard STRs are prone to fail due to their long amplicon sizes (since DNA becomes progressively more fragmented as it degrades). To successfully resolve such cases alternative markers can be used and until recently the only other tool available was mitochondrial DNA, which despite being more resistant to degradation, is much less informative. A rapidly developing approach to analyzing degraded DNA is the typing of loci from short-amplicon PCR products based on markers such as mini-STRs and autosomal SNPs. We have performed an analysis of several cases with naturally degraded DNA using established STRs plus mini-STRs and autosomal SNPs in order to make an objective comparison of the performance of each method using challenging DNA. The main aim was to establish the benefits and drawbacks of each marker set to help the practitioner choose the DNA analysis method most suited to the circumstances of each case.     

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.     

Frequency assessment of SNPs for forensic identification in different populations

Allele frequencies for 16 previously described autosomal SNPs were tested in 1020 unrelated individuals originating from three different continents (Africa, Asia and Europe). The populations analyzed included Africans from Benin Gulf (180), Asians from Mongolia (160) and Europeans from Italy (680).     

Application of mtDNA SNP analysis in forensic casework

In this study six forensic cases are presented where the routine analysis of samples for short tandem repeats (STRs) failed. The sequencing of the mitochondrial hypervariable region I (HVR I) also failed. Nevertheless, it was possible to analyse the samples with mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) via SNaPshot technique. The age of the analysed samples ranged from 2 months to 1400 years. Saliva-, blood-, sperm-, hair-, tooth- and bone-samples were investigated. Furthermore the mtDNA SNP analysis of a forensic case sample showing a mixed stain profile is presented. It was possible to discriminate two different haplogroups in this mixed-person stain. If compared to another mtDNA SNP profile that was found in a hair, the discriminating SNPs of the hair were as well found in the mixed-person stain.To disburden the SNP analysis in forensic casework, haplogroup assignment criteria and quality criteria for mtDNA SNaPshot analysis are announced.     

Use of subpopulation data in Australian forensic DNA casework

DNA profiling evidence presented in court should be accompanied by a reliable estimate of its evidential weight. In calculating such statistics, allele frequencies from commonly employed autosomal microsatellite loci are required. These allele frequencies should be collected at a level that appropriately represents the genetic diversity that exists in the population. Typically this occurs at broadly defined bio-geographic categories, such as Caucasian or Asian. Datasets are commonly administered at the jurisdictional level. This paper focuses on Australian jurisdictions and assesses whether this current practice is appropriate for Aboriginal Australian and Caucasian populations alike. In keeping with other studies we observe negligible differences between Caucasian populations within Australia when segregated geographically. However segregation of Aboriginal Australian population data along contemporary State and Territory lines appears to mask the diversity that exists within this subpopulation. For this reason datasets collated along more traditional lines may be more appropriate, particularly to distinguish the most genetically differentiated populations residing in the north of the continent.     

焦磷酸测序技术分析单核苷酸多态性在法医学中的应用

单核苷酸多态性（SNP）是新一代的法医学遗传标记,有望成为法医实践中解决高度降解检材及特殊案件DNA鉴定的重要工具。近年来涌现出许多高通量的SNP分析方法,如引物延伸结合时间飞行质谱分析法、微测序法、SNP lex以及焦磷酸测序法等。本文重点对焦磷酸测序技术的原理、步骤及其在法医学中的应用进展进行简要的综述。     

Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples

The analysis of LCN or highly degraded DNA samples presents a challenge for forensic science. Improving the quantity and/or quality of samples would greatly increase the profiling success rate from LCN and degraded samples. Whole genome amplification (WGA) is one method that has such potential. Two commercially available WGA kits, GenomePlex and GenomiPhi, were investigated for use on LCN and degraded DNA samples. Both kits amplified genomic DNA, producing microgram quantities from sub-nanogram templates. Profiling success of LCN DNA samples was increased, with improvements of over 700% from 10pg template DNA compared to non-WGA-amplified control samples. The amplification success with degraded DNA was also improved by WGA. Degraded DNA was simulated using restriction enzymes to demonstrate that the application of WGA can result in the typing of STR loci that could not previously be amplified. An increase in artefacts, such as stutter alleles and amplification biases, were observed in many samples. Results show that WGA is capable of increasing both the quality and quantity of DNA, and has the potential to improve profiling success from difficult samples in forensic casework.     

用熔解曲线法分析插入/缺失多态性和Y染色体SNPs多态性

随着单核苷酸多态性SNPs (SingleNucleotidePolymorphisms)及插入 /缺失多态性Indels (Insertion/Dele tion)的分型技术研究的深入 ,SNPs和Indels在法医学上的应用将受到深刻的影响。本文研究和探讨Indels的分型方法 ,通过测定扩增DNA片段在溶液中的溶解曲线图确定每个样品的基因型 ,称为溶解曲线Indels基因分型方法(McI/D)。溶解曲线图由被测样品DNA片段的特殊溶解温度组成 ,扩增结果直接由仪器分析不需要繁杂的PCR后期操作。     

Quantifiler observations of relevance to forensic casework

The Quantifiler (QF) kit is regularly used by forensic scientists for DNA quantitation. We performed in-house validation studies which revealed some interesting observations. The QF standard displayed a two-fold difference between two different lot numbers which suggests that every standard should be tested prior to use. The Promega K562 DNA standard works well with the QF kit. c. 41% of samples that inhibited the internal PCR control (IPC) system within the QF kit still produced good Profiler Plus reactions. QIAquick was effective at removing inhibitors. The presence of dyes within casework samples were observed not to inhibit QF amplifications. Template DNA greater than 100 ng/muL appeared to inhibit the IPC. Close to identical concentration results were obtained when alternative analysis settings were used. These validation findings will assist DNA processes involved in forensic casework.     

A novel method for ABO genotyping using a DNA chip

ABO genotyping is often performed to identify the blood type of decomposed samples, which is difficult to be determined by a serological test. In this study, we developed a simple method for ABO genotyping using a DNA chip. In this method, polymerase chain reaction-amplified and fluorescent-labeled fragments in the ABO gene and primate-specific D17Z1 were hybridized with DNA probes on a chip designed to detect single nucleotide polymorphisms (SNPs) in the ABO gene and part of the D17Z1 sequence. Using blood samples from 42 volunteers and 10 animal species, we investigated whether the chip could be used to detect SNPs in the ABO gene and the D17Z1 sequence. This method was then applied to various forensic samples, and it was confirmed that this method was suitable for the simultaneous analyses of ABO genotyping and species identification. This method fulfills the recent need for the development of rapid and convenient methods for criminal investigations.     

Automated processing of forensic casework samples using robotic workstations equipped with nondisposable tips: contamination prevention

An automated process has been developed for the analysis of forensic casework samples using TECAN Genesis RSP 150/8 or Freedom EVO liquid handling workstations equipped exclusively with nondisposable tips. Robot tip cleaning routines have been incorporated strategically within the DNA extraction process as well as at the end of each session. Alternative options were examined for cleaning the tips and different strategies were employed to verify cross-contamination. A 2% sodium hypochlorite wash (1/5th dilution of the 10.8% commercial bleach stock) proved to be the best overall approach for preventing cross-contamination of samples processed using our automated protocol. The bleach wash steps do not adversely impact the short tandem repeat (STR) profiles developed from DNA extracted robotically and allow for major cost savings through the implementation of fixed tips. We have demonstrated that robotic workstations equipped with fixed pipette tips can be used with confidence with properly designed tip washing routines to process casework samples using an adapted magnetic bead extraction protocol.     

DNA芯片分析单核苷酸多态性及其法医学应用

DNA芯片技术作为一门新兴的高科技生物技术,显示了它旺盛的生命力和迅猛的发展势头。单核苷酸多态性(SingleNucleotidePolymorphisms,SNPs)是最常见的人类基因组变异类型。它作为一种有效的人类遗传标记,在疾病相关性研究、药物基因组学、法医学、人类进化和迁移等研究中发挥了重要作用。它同DNA芯片技术结合运用也将在法医检验,尤其是亲子鉴定和个人识别中发挥重要作用。本文主要讨论了DNA芯片和SNPs的特点,以及二者联合运用于法医学的价值。     

Developmental validation of a multiplex qPCR assay for assessing the quantity and quality of nuclear DNA in forensic samples

Forensic scientists are constantly searching for better, faster, and less expensive ways to increase the first-pass success rate of forensic sample analysis. Technological advances continue to increase the sensitivity of analysis methods to enable genotyping of samples containing minimal amounts of DNA, yet few tools are available that can simultaneously alert the analyst to both the presence of inhibition and level of degradation in samples prior to genotyping to allow analysts the opportunity to make appropriate modifications to their protocols and, consequently, to use less sample. Our laboratory developed a multiplex quantitative PCR assay that amplifies two human nuclear DNA target sequences of different length to assess DNA degradation and a third amplification target, a synthetic oligonucleotide internal PCR control (IPC), to allow for the assessment of PCR inhibition. We chose the two nuclear targets to provide quantity and fragment-length information relevant to the STR amplification targets commonly used for forensic genotyping. The long target (nuTH01, 170-190 bp) spans the TH01 STR locus and uses a FAM-labeled TaqMan probe for detection. The short nuclear target (nuCSF, 67 bp) is directed at the upstream flanking region of the CSF1PO STR locus and is detected using a VIC-labeled TaqManMGB probe. The IPC target sequence is detected using a NED-labeled TaqManMGB probe. The assay was validated on the Applied Biosystems 7500 Real-Time PCR system, which is optimized for NED detection. We report the results of a developmental validation in which the assay was rigorously tested, in accordance with the current SWGDAM guidelines, for precision, sensitivity, accuracy, reproducibility, species specificity, and stability.     

用dHPLC技术检测线粒体DNA编码区单核苷酸多态性

目的研究线粒体DNA(m tDNA)编码区单核苷酸多态性,建立检测m tDNA编码区单核苷酸多态性(SNP)的变性高效液相色谱(dHPLC)方法。方法设计针对线粒体DNA编码区nt10287-10679及nt8507-8805引物,应用dHPLC技术检测其序列多态性。结果100例中国汉族无关个体中,m tDNA nt10287-10679检出13个SNP位点,13种单倍型,基因多样性(H)为70.79%,偶合概率(P)为29.92%;m tDNA nt8507-8805检出10个SNP位点,12种单倍型,H为70.42%,P为30.28%;两段序列联合起来共检出23个SNP位点,23种单倍型,H为84.14%,P为16.70%。结论所建立的dHPLC方法可用于快速、准确地检测m tDNA编码区序列多态性;m tDNA编码区多态性位点作为m tDNA控制区多态性位点的补充,联合应用可以提高m tDNA的个体识别能力。     

Genetic identification of biological samples buried in clay soil during summer and winter seasons

The analysis of a biological samples found in crime scenes can be a challenging task. Minute amount of DNA, degraded DNA and the presence of inhibitors in biological samples, can interfere with the achievement of a complete genetic profile.Chelating resin, silica membranes and silica-coated with paramagnetic resin were the techniques used in this study for the isolation and purification of DNA. Our aim was to find out the best DNA extraction method for application in the presence of biological samples buried in clay soil.     

Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods

Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the software methods.     

Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers

When using a standard battery of STRs for relationship testing a small proportion of analyses can give ambiguous results – where the claimed relationship cannot be confirmed by a high enough paternity index or excluded with fully incompatible genotypes. The majority of such cases arise from unknowingly testing a brother of the true father and observing only a small number of exclusions that can each be interpreted as one- or two-step mutations. Although adding extra STRs might resolve a proportion of cases, there are few properly validated extra STRs available, while the commonly added hypervariable SE33 locus is four times more mutable than average, increasing the risk of ambiguous results. We have found SNPs in large multiplexes are much more informative for both low initial probabilities or ambiguous exclusions and at the same time provide a more reliable genotyping approach for the highly degraded DNA encountered in many identification cases. Eight relationship cases are outlined where the addition of SNP data resolved analyses that had remained ambiguous even with extended STR typing. In addition we have made simulations to ascertain the frequency of failing to obtain exclusions or conclusive probabilities of paternity with different marker sets when a brother of the true father is tested. Results indicate that SNPs are statistically more efficient than STRs in resolving cases that distinguish first-degree relatives in deficient pedigrees.     

Applicability of DNA analysis on adhesive tape in forensic casework

Adhesive tape is commonly used in crimes and is often the subject of forensic evaluation. DNA analysis of adhesive tape can provide DNA profiles of suspects. The object of this study was to evaluate the applicability of DNA analysis on adhesive tape samples in forensic casework. We retrospectively reviewed all cases involving adhesive tape or similar items received by our institute for DNA analysis during the past 11 years. From 100 forensic cases reviewed, 150 adhesive tape samples were examined. A total of 98 DNA profiles were obtained from these samples. Sixty-two of the profiles provided feasible case-relevant information. In conclusion, DNA profiling of adhesive tape samples can be useful in a variety of forensic cases.