A fast analysis system for forensic DNA reference samples

On January 1st, 2006, the Swedish legislation on obtaining DNA reference samples from suspects and the recording of DNA profiles in databases was changed. As a result the number of samples analysed at the Swedish National Laboratory of Forensic Science (SKL) increased from about 4500 in 2005 to more than 25,000 in 2006. To meet this challenge, SKL launched a new analysis system to create an unbroken chain, from sampling to incorporation of a profile in the national DNA database and subsequent automatic generation of digitally signed hit reports. The system integrates logistics, digital data transfer, new functions in LIMS (ForumDNA Version 4, Ida Infront AB) and laboratory automation. Buccal swab samples are secured on a FTA^® card attached to an identity form, which is barcoded with a unique sample ID. After sampling, the police officer sends a digital request to SKL. The sample is automatically registered in LIMS and processed on delivery. The resulting DNA profiles are automatically classified according to quality using a custom-made expert system. Building the evaluation around mathematical rules makes it reproducible, standardised and minimises manual work and clerk errors. All samples are run in duplicate and the two profiles are compared within LIMS before incorporation in the database. In the first year of operation, the median time for completion of an analysis was 3 days, measured from delivery of the sample to incorporation of the profile in the national DNA database. In spite of the dramatic increase in the number of reference samples there was no backlog.     

IGNA's original LIMS: A complete traceability of administrative and analytic processes for forensic cases

IGNA is the first French laboratory for forensic DNA analysis. IGNA LIMS was developed from the software Microsoft Dynamics NAV which is an ERP (Enterprise Resource Planning) with a real opened solution for specific development and compatible with a lot of Microsoft applications.Thanks to the LIMS, we assure the traceability of analysis and also administrative process (traceability of letters, quotes or phone calls for each case and registration of actions to be done in a case (call for results …)).For one penal case, we can associate one or more sealed items. The DNA expert indicates the analysis to do on each piece (biological fluid detection, type of extraction, nuclear or mitochondrial DNA analysis …).During the technical process, samples automatically pass from a step to the next. Technicians indicate all the information needed for traceability (consumables lot number, used robots …).At the end of the process, the DNA expert validates his results, which are then directly transferred to the final report.Development of the IGNA LIMS from Microsoft Dynamics NAV allows us to use all specific applications of an ERP such as purchases, marketing, sales, etc. and to assure computerization of all our process, from quote to analysis report.     

法医物证DNA自动化检验技术体系的研究

目的建立自动化工作站同步提取不同种类涉案法医生物检材DNA的新方法。方法选用TECAN Freedom EVO100．4、75—2型自动化提取、加样工作站,采用磁珠法及Chelex-100法对各类涉案生物检材进行DNA提取、PCR扩增、毛细管电泳检测其STR分型,进行比较测试。在“全国公安机关DNA数据库应用系统”中建立并应用实验室信息管理系统（LIMS）模拟实施规范化DNA检案。结果1552份各类检材,采用工作站-磁珠法提取DNA效果最佳,STR检测成功率为95％,工作站-Chelex法为88％;二者分别与其手工提取法比较,成功率无明显差异。92个样本同期检测,自动化工作站较手工操作DNA检案时间可缩减1．25倍。结论工作站域珠法提取涉案检材DNA,可获得满意的STR分型结果。应用LIMS管控,可有效防控污染,明显提高检案效率及鉴定质量。     

Customizing a commercial laboratory information management system for a forensic genetic laboratory

The need for high-throughput laboratories to comply with regulatory requirements makes data management an important aspect of forensic genetics. A Laboratory Information Management System (LIMS) enables efficient workflows and ensures traceability if designed and implemented properly. We customized a commercial LIMS to support STR typing of reference samples according to in-house defined requirements. The customization focused on data validity, traceability and automated solutions.     

Multiple interchanging of tissue samples in cases of breast cancer

Due to the suspicion of a gynaecologist, a pathologist was suspected of incorrect diagnoses in cases of breast cancer and the interchanging of tissue samples. Many women applied to the attorney's bureau to clarify the reproaches. The privately owned laboratory for pathology was searched and 926 histological slides, roughly the same number of paraffin blocks and about 20 formalin fixed tissue samples were confiscated. Together with other confiscated material, at least 1236 histological slides and additional 249 paraffin blocks had to be sorted. Histological slides and paraffin blocks were matched with patients as far as possible following the laboratory book. Many of the warranted samples which were diagnosed as containing the carcinoma by the pathologist were missing. A total of 160 samples were chosen and rediagnosed by two independent pathologists. The formalin fixed tissue was negative for DNA most likely due to storage in formalin for years. Most of the histological slides were positive for DNA. On the whole, 18 expertises about histological findings and the DNA results were given. In some cases only DNA results could be presented, as previous experts had only performed DNA examinations without controlling the histological diagnosis. In six cases a carcinoma could be confirmed and the DNA profile matched with patient's DNA; in seven cases a carcinoma was confirmed without match with the patient; in two cases the carcinoma could not be confirmed in the presented samples. A jurisdictional solution was impossible because the accused pathologist died during the investigation. In conclusion, it must be stated that a DNA examination of histological slides should never be performed without a rediagnosis of an independent pathologist and photographic documentation of the findings. Whenever possible, material should be left on the slide.     

GoldeneyeTM 20A-M试剂盒在数据库建设中的应用

目的 研究GoldeneyeTM 20A-M试剂盒在DNA数据库建设中的应用.方法 针对血滤纸特性,优化不同条件血痕样品的取样量、扩增循环次数,缩短PCR扩增时间,以建立适合批量样品直接快速扩增检验的方法,并将其应用于1 200份数据库样品的检验中.结果 确定了批量样本检验的最适取样量和扩增循环次数,建立了快速扩增反应程序,1 200份样品的直接快速扩增检验成功率为98.4％,批量检验92份样品(1板)从取样到电泳完成只需6h.结论 GoldeneyeTM 20A-M试剂盒的应用,免去DNA提取过程,方法简单、快速、获得信息量大,适用于DNA数据库建设的需要.     

96孔过滤板在接触性DNA自动化检验中的应用

目的将96孔过滤板用于自动化工作站,对接触性DNA进行检验。方法收集553份现场提取的附着在烟蒂、饮料瓶、门窗把手、电源网线头、作案工具、手套上的微量接触性生物检材,在96孔过滤板上进行裂解后整体离心,分离载体与裂解液;应用自动化核酸提取纯化仪结合M48磁珠纯化试剂盒提取纯化DNA,采用IdentifilerPlus试剂盒进行扩增,3500XL测序仪电泳分型,ID-X专家系统分析结果。结果在553份检材中,成功获得STR分型的有271份,检验成功率在31.6%~97.3%之间,烟蒂、饮料瓶检材的成功率均在90%以上,提取纯化过程约90min。结论将96孔过滤板用于自动化工作站,可在实现批量接触性DNA的快速、自动化提取的同时,有效提高接触性DNA检出率。     

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.     

The BodeChecks solution: A high throughput analysis software combining GeneMapper ID, FSS-i, LIMS, and artificial intelligence

Combining key attributes of GeneMapper^® ID and FSS-i³ software packages with our internally created LIMS and some additional analytical programming has permitted us to increase quality checks on DNA profile data review while eliminating analysis time.     

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.     

Establishing an integrated pipeline for automatic and efficient detection of trace DNA encountered in forensic applications

The analysis of trace DNA is a crucial component in forensic applications. Biological materials containing low-level DNA collected at crime scenes, such as fingerprints, can be valuable as evidence. Automatic detection of biological samples has been largely embraced in forensic applications to meet the increasing throughput requirements. However, the amount of DNA automatically retrieved from trace evidence often tends to be small and unstable, ultimately resulting in poor detection of DNA profiles. Thus, in this work, we introduced a robust DNA extraction and purification platform named Bionewtech® BN3200 (Bionewtech®, Shanghai, China) with the goal of constructing a rapid automatic detection system for trace DNA. The establishment of automatic detection system for trace DNA mainly encompassed two parts: assessing the sensitivity of automatic extraction platform and screening the optimal short tandem repeat (STR) typing kit. The sensitivity of Bionewtech® BN3200 platform based on Ultra-sensitive DNA Extraction kit was initially estimated, demonstrating that this extraction platform might contain large potential in the trace DNA extraction. For the amplification part, three sets of commercial multiplex STR typing kits were selected as candidates, and the amplified products were further genotyped on the Applied Biosystems 3500xl Genetic Analyzer. After comparation, SiFa™ 23 Plex Kit was determined as the most suitable amplification system for trace DNA. Eventually, the newly exploited trace DNA detection system was successfully implemented in the detection of fingerprints derived from glass surfaces with the five-seconds contact time. As a result, the DNA recovered from the fingerprints fluctuated approximately from 57.60 pg to 18.05 ng, in addition, over 70% of the total STR loci were detected in 75% of the fingerprint samples.     

The use of crossover immunoelectrophoresis to detect human blood protein in soil from an ambush scene in Kosovo

This study examines the survivability of human blood proteins in soils from a year and a half old ambush scene in Kosovo. A total of 72 soil samples were collected, a number of which were directly associated with bone fragments or bullet projectiles. The samples were examined using crossover immunoelectrophoresis (CIEP) to determine the presence of blood protein and species affiliation. Human blood proteins were identified in 44 of the 72 samples (61%) with the majority of the positive observations (29 of 44) found 0.0-4.5 cm below ground surface (65%). Chi-squared and two-sample difference of proportions tests confirmed significant differences between samples with and without associated physical evidence and the presence and depth of human blood proteins. While DNA has largely replaced immunological analysis in forensic analyses, our results suggest that in particular situations, CIEP may still be a valuable tool in criminology.     

生物检材中DNA损伤及修复研究进展

从犯罪现场遗留的生物斑迹中提取到的DNA样本可能因为长时间暴露于恶劣的环境中而遭受到各种类型的损伤,导致扩增失败不能获得分型结果。对这些受损伤的DNA样本进行修复并提高其检测成功率,是近年来法庭遗传学领域新的研究热点。本文通过对DNA损伤的原因和类型、DNA损伤修复机制、生物检材中DNA损伤修复研究和应用进行综述,希望能对相关研究和应用提供帮助。     

Internal Validation of RapidHIT®ID ACE Sample Cartridge and Assessment of the EXT Sample Cartridge*†

A new rapid DNA solution, the RapidHIT^®ID, can accommodate two different sample cartridges, ACE, for the analysis of a single swab and EXT, for the analysis of DNA extracts. An efficient internal validation designed for low‐throughput rapid DNA is described. An evaluation of the EXT sample cartridge is also described. Each cartridge generated profiles with sufficient data quality to meet CODIS eligibility in fewer than 120 min. The results exhibited 100% correlation when compared to conventional DNA typing methods. Precision, reproducibility, stochastic, mixture, and contamination experiments produced expected results. Sensitivity of the ACE sample cartridge was acceptable for buccal swab analysis. The sensitivity of the EXT sample cartridge is discussed. The ACE validation and the EXT evaluation utilized a minimalist, cost‐saving, efficient design to generate a validated RapidHIT^®ID instrument capable of producing genetic profiles from both extracted forensic DNA samples and buccal swab samples within 120 min.     

实验室信息管理系统在毒品检测实验室的应用

介绍了一种基于计算机数据库平台的实验室信息管理系统（Laboratory Information Management System,简称LIMS）为平台的毒品检测工作的质量保证体系,将毒品检测工作的一般流程和LIMS的基本功能结合,制作建立在LIMS体系架构下的每个流程的交互界面和监控程序.实现了毒品实验室的样品管理、样品状态监控、数据的录入和采集、样品分析、工作流程管理、报告的审核和发布等信息管理功能.通过在毒品检测实验室建立LIMS,充分辅助了实验室的质量管理工作,有效减少了管理工作量,使实验室工作更高效、准确和规范.     

Direct STR amplification from whole blood and blood- or saliva-spotted FTA without DNA purification

The DNA purification step has been thought to be essential for typing of STR DNA. However, this process is time-consuming, and there is a risk of unexpected cross-contamination during purification. We report a new method for direct short tandem repeat (STR) amplification using a newly developed direct PCR buffer, AnyDirect, which can amplify STR loci from whole blood and blood- or saliva-spotted FTA cards without DNA purification. The autosomal and Y chromosomal STR loci were analyzed for whole blood and blood or saliva spots of random individuals, followed by comparison of the results with those of corresponding purified DNA. The results from whole blood and blood spots showed perfect concordance with those from purified DNA without allele or locus drop-out. However, in the case of saliva spots, no amplification or locus drop-out was observed in some of the samples, which offers a topic for further study. Additionally, some commercial hot-start DNA polymerases other than AmpliTaq Gold DNA polymerase were also found to be compatible with this buffer system. Therefore, this direct PCR buffer was demonstrated to be useful for fast forensic DNA analysis or criminal DNA databases for which there is no need to store DNA samples.     

Analyzing degraded DNA and challenging samples using the ForenSeq™ DNA Signature Prep kit

Typing short tandem repeats (STRs) is the basis for human identification in current forensic testing. The standard method uses capillary electrophoresis (CE) to separate amplicons by length and fluorescent labeling. In recent years new methods, including massively parallel sequencing (MPS), have been developed which increased the discriminative power of STRs through sequencing. MPS also offers the opportunity to test more genetic markers in a run than is possible with standard CE technology. Verogen’s ForenSeq™ DNA Signature Prep kit includes over 150 genetic markers [STRs and single nucleotide polymorphisms (SNPs)]. Further, MPS separation depends on sequences rather than lengths; therefore, amplicons can be small or even of the same lengths. These improvements are advantageous when testing challenging forensic samples that could be severely degraded.This study tested the ForenSeq™ DNA Signature Prep kit in repeated experimental runs on series of degraded DNA samples, ranging from mild to severe degradation, as well as 24 mock case-type samples, derived from bones, blood cards, and teeth. Despite passing the quality metrics, positive controls (2800 M) showed drop-outs at some loci, mostly SNPs. Sequencing DNA samples repeatedly in two experimental runs as well as sequencing one pooled library in triplicate led to the assumption that spurious alleles of the Y-STRs in this study were not a result of sequencing artifacts but could be due to sequence structures (e.g. duplications, palindromes) of the Y-chromosome and/or might be accumulated during library preparation.Two sets of serially degraded DNA samples revealed that dropped-out loci were primarily loci with long amplicons as well as low read numbers (coverage), e.g. PentaE, DXS8378, and rs1736442. STRs started to drop out at degradation indices (DIs) > 4. However, severely degraded DNA (DI: 44) still resulted in 90% of the 20 CODIS loci, while only 35% were obtained using Promega’s PowerPlex® Fusion kit, a current standard CE kit. Mock case-type samples confirmed these results. ForenSeq™ DNA Signature Prep kit demonstrated that it can be successfully used on degraded DNA samples. This study may be helpful for other laboratories assessing and validating MPS technologies.     

Recovery of human DNA profiles from poached deer remains part 2: Improved recovery protocol without the need for LCN analysis

Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was successfully isolated and amplified from simulated poaching incidents, however a low template protocol was required which made this method unsuitable for use in many laboratories. We now report on an optimised recovery and amplification protocol which removes the need for low template analysis.Samples from 10 deer (40 samples total — one from each leg) analysed in the original study were re-analysed in the current study with an additional 11 deer samples. Four samples analysed using Chelex did not show any results and a new method was devised whereby the available DNA was concentrated. By combining the DNA extracts from all tapings of the same deer remains followed by concentration, the recovered quantity of human DNA was found to be 29.5 pg ± 43.2 pg, 31 × greater than the previous study. The use of the Investigator Decaplex SE (QIAGEN) STR kit provided better results in the form of more complete profiles than did the AmpF?STR® SGM Plus® kit at 30 cycles (Applied Biosystems). Re-analysis of the samples from the initial study using the new, optimised protocol resulted in an average increase of 18% of recovered alleles. Over 17 samples, 71% of the samples analysed using the optimised protocol showed sufficient amplification for comparison to a reference profile and gave match probabilities ranging from 7.7690 × 10^? 05 to 2.2706 × 10^? 14.The removal of low template analysis means this optimised method provides evidence of high probative value and is suitable for immediate use in forensic laboratories. All methods and techniques used are standard and are compatible with current SOPs. As no high cost non-human DNA analysis is required the overall process is no more expensive than the investigation of other volume crime samples. The technique is suitable for immediate use in poaching incidents.     

Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study

An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable.