Extraction of DNA from decomposed human tissue. An evaluation of five extraction methods for short tandem repeat typing

Hyperpolymorphic short tandem repetitive DNA sequences, STRs or microsatellites, have become widely used in human identification, particularly in criminal cases and in mass disasters. In such cases the substrates for the analyses may be decomposed biological material, a fact that has to be taken into account when choosing the appropriate casework methods. In this paper we report the evaluation of five different DNA extraction methods, namely the phenol-chloroform, the silica based, the InstaGene Matrix (BioTest), the glass fiber filter, and the Chelex based methods. The substrates for the analyses are decomposed human liver tissue specimens from forensic autopsy cases. Extracted DNA was quantified and DNA profiled by a set of seven STRs. We have compared laboratory time consumption and costs of the five methods, showing that the Chelex method is the more rapid and less expensive of the methods, the phenol-chlorophorm and silica extractions being the most time consuming and resource demanding ones. A full profile was obtained by the silica method in nine out of ten cases and this method failed to give a reliable type in four out of 70 STR analyses. The phenol-chlorophorm and the glass fiber filter methods failed in 16 analyses, the InstaGene Matrix (BioTest) in 25 and the Chelex extracts in 56 of the 70 STR analyses. By multiple logistic regression we show that the difference between the silica procedure and the other methods are statistically significant. In our hands, the silica gel extraction procedure is an obvious choice when the biological material available is decomposed human tissue--even if this procedure is one of the more laborious ones.     

The Achilles tendon as a DNA source for STR typing of highly decayed corpses

Forensic criminal casework often involves DNA profiling of human postmortem tissues, whereas degradational processes can affect PCR-based Short Tandem Repeat (STR) analysis. Degradation of DNA is observed to vary among different tissues and with time. Therefore, the stability of DNA in Achilles tendon samples is compared to that in muscle and kidney specimens with a variety of postmortem histories. Tissue samples from 28 autopsy cases, including 15 decomposed corpses and a control group of 13 nondecayed corpses were analysed. DNA was isolated using the All-tissue DNA Kit (GEN-IAL, Troisdorf, Germany), quantified by spectrophotometric measurement, amplified by the multiplex PCR genRES MPX-2 (Serac, Bad Homburg, Germany), and analysed on the ABI PRISM 310 Genetic Analyzer (Applied Biosystems, Darmstadt, Germany). Quantitative analysis of nondecomposed tissues revealed that the recovery of DNA was highest in kidney followed by muscle, whereas Achilles tendon tissue was the poorest source of isolated DNA. Only small amounts of DNA were present in both kidney and muscle samples from decomposed corpses. However, from decayed Achilles tendon samples twice as much DNA as from nondecayed samples could be isolated on average. These results suggest DNA to be better protected in Achilles tendons. Moreover, postmortem changes in Achilles tendons may even improve DNA isolation.     

Mutations at 17 STR loci in Chinese population

Knowledge about mutation rates and the mutational process of short-tandem-repeat (STR) or microsatellite loci used in forensic analysis is crucial for the correct interpretation of resulting genetic profiles. We analysed a total of 19,754 samples from 6532 paternity testing cases at 17 STR loci which are commonly applied to forensics. The parenthood in each of these cases was highly validated (probability>99.99%). We identified 178 mutations. Locus-specific mutation rate estimates varied between 7.0 x 10(-5) and 2.2 x 10(-3), and the overall average mutation rate estimate was 8.4 x 10(-4). The observed mutational features for STRs have important consequences for forensic application such as the definition of criterions for exclusion in paternity testing and the interpretation of DNA profiles in identification analysis. In order to enrich the reference data of STRs mutations which are valuable for forensic application, we suggest the establishment of such database and ask the whole forensic community for data contribution including China.     

Evaluation of gastrointestinal cancer tissues as a source of genetic information for forensic investigations by using STRs

Malignant tissue samples may sometimes be the only source of biological material for forensic investigations, including identification of individuals or paternity testing. However, in use of such samples, uncertainties due to microsatellite instability (MSI) and loss of heterozygosity (LOH) often associated with neoplasias may be encountered. In this study, we have analysed the applicability of autosomal tetranucleotide short tandem repeat (STR) markers, which are routinely used in forensic analysis, to gain genetic information. MSI and LOH were analysed in 41 surgically removed gastrointestinal cancer specimens and the adjascent non-cancerous tissue marginals. The cancer specimens showed great variability in their genetic phenotypes due to MSI or LOH, with only 32% being microsatellite-stable. Of the 15 autosomal STR loci analysed, only TH01 had no MSI-type alteration in these samples. The loci most frequently affected by MSI were D8S1179, D21S11, D18S51 and D19S433 (MSI in 15-17% of cases). LOH-type alterations were observed at all of the loci, including the amelogenin locus used for sex determination. The highest LOH frequency was found at locus D18S51 (27%). The genetic alterations at the marker loci may indicate false homozygosity or heterozygosity, and false gender may result from erroneous deduction of DNA profiles. Therefore, typing of autosomal STRs from malignant tissues in forensic settings warrants careful interpretation of MSI and LOH results together with microscopic analysis of a tissue specimen. Results by two commercially available and widely used forensic DNA profiling kits used here were comparable.     

应用自动化工作站提取常见生物样本DNA

目的建立使用自动化工作站提取法医案件生物样本DNA的方法。方法选用Biomek 3000自动化工作站,采用DNA IQTM系统及Chelex法对法医案件中常见生物样本进行DNA提取,荧光定量技术进行定量,PCR扩增16个STR基因座并与手工提取方法比较。结果与手工提取方法进行比较,选用自动化工作站结合使用DNAIQTM系统及Chelex法提取DNA可获得满意的STR检验结果。结论自动化工作站可用于法医案件中常见生物样本的DNA提取。     

妇科肿瘤和乳腺癌组织常染色体和X染色体STR的突变分析

目的探讨妇科肿瘤组织和乳腺癌组织的法医学常用STR基因座突变类型和规律,以及显微切割技术在肿瘤组织法医学鉴定中的应用。方法应用Power Plex 21 System和Argus X-12试剂盒对62例乳腺癌患者,62例妇科恶性肿瘤患者,10例良性妇科肿瘤患者外周血、肿瘤组织和癌旁组织DNA样本进行复合扩增,获得STR分型,并选取存在突变的部分肿瘤组织进行显微切割。结果妇科恶性肿瘤患者外周血的STR分型与癌旁组织一致;46.77%的妇科恶性肿瘤组织中观察到4种STR突变类型,显著高于良性肿瘤的STR突变率(P0.01)和乳腺癌的STR突变率(P=0.009)。显微切割获得的间质细胞的STR分型与癌旁组织一致。结论本研究所检测的STR基因座在妇科恶性肿瘤组织中的稳定性较差,不适用于该系统肿瘤组织的法医学鉴定;显微切割技术可准确分离间质细胞,能够代表肿瘤来源个体的正常DNA分型,是解决此类案件法医学鉴定的一种有效方法。     

荧光标记STR分型技术检验腐败组织基因型

探讨腐败组织荧光标记STR分型检测技术的应用价值。应用含12个STR基因座及一个性别基因座的2个荧光标记的复合扩增系统,对40例1～6周的腐败肌肉提取的DNA进行扩增,用变性聚丙烯酰胺凝胶电泳,PE377测序仪分析基因型。所检测样本在12个STR基因座均扩增出特异性谱带,并可判定其基因型。荧光标记STR检测技术对腐败组织分型可靠,在实际检案中具有较高的应用价值。     

ABO基因分型与多重STR联合检测在法医学中的应用

目的建立ABO基因型和Goldeneye16A试剂盒联合检测的方法,并评价其在法医学实践中的应用价值。方法将6种ABO基因型(A/A,A/O,B/B,B/O,A/B,O/O)的序列特异性引物(PCR-SSP)检测方法与Goldeneye16A试剂盒相整合进行同步分型。通过对460份男性个体血痕样本、9947A DNA及90份案件样本进行检测,考察方法的一致性、灵敏度及对法庭科学检材的适用性。结果应用本文方法可同时检出6种ABO基因型和15个常染色体STR基因座及性别决定基因座,检测灵敏度为125pg,其中ABO基因检测灵敏度达63pg。460份男性血痕和90份案件检材证实该联合分型方法用于各类检材结果准确、稳定。结论本文ABO基因分型与多重STR联合检测方法,适用于各类含有核细胞的生物检材,在法庭科学DNA鉴定中有较好的应用前景。     

STR基因座荧光标记复合扩增检测及其法医学应用

目的建立荧光标记复合扩增检测4个STR基因座的方法,应用于法医学亲权鉴定与个人识别。方法用6-FAM标记D3S1754引物,HEX标记D4S2366和D12S375引物,TMR标记D1S549引物,PCR复合扩增,310基因分析仪电泳自动收集电泳结果数据,GeneScanAnalysisSoftware3.7NT计算扩增产物片段相对大小,Genotyper誖3.7NT软件进行样本基因型分型。将该方法应用于法医学亲权鉴定与个人识别。结果建立了荧光标记复合扩增检测4个STR基因座基因型的方法,具有良好的稳定性和较好的灵敏度,分型结果准确。结论研究建立的方法操作简便,分型结果稳定可靠,可用于遗传多态性研究和法医学亲权鉴定与个人识别。     

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。     

RNA/DNA co-analysis from blood stains—Results of a second collaborative EDNAP exercise

A second collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling was organized by the European DNA Profiling Group (EDNAP). Six human blood stains, two blood dilution series (5-0.001 μl blood) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by the participating laboratories using a RNA/DNA co-extraction or solely RNA extraction method. Two novel mRNA multiplexes were used for the identification of blood: a highly sensitive duplex (HBA, HBB) and a moderately sensitive pentaplex (ALAS2, CD3G, ANK1, SPTB and PBGD). The laboratories used different chemistries and instrumentation. All of the 18 participating laboratories were able to successfully isolate and detect mRNA in dried blood stains. Thirteen laboratories simultaneously extracted RNA and DNA from individual stains and were able to utilize mRNA profiling to confirm the presence of blood and to obtain autosomal STR profiles from the blood stain donors. The positive identification of blood and good quality DNA profiles were also obtained from old and compromised casework samples. The method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise involving a RNA/DNA co-extraction strategy support the potential use of an mRNA based system for the identification of blood in forensic casework that is compatible with current DNA analysis methodology.     

HE染色切片组织的STR检测及法医学应用

目的建立并优化HE染色切片组织STR分型方法,评估HE染色切片组织的STR分型有效性。方法用QIAgen法提取2例尸检人体的心、肝、肺、肠等8种组织的HE染色切片DNA,用TaqMan荧光探针法通过荧光域值循环数(Ct值)测定获得各提取液中的DNA质量浓度,以阳性内对照(internal posi-tive control,IPC)监测PCR过程中的抑制水平。再用Identifiler试剂盒扩增,在3100-Avant上进行STR片段分析。结果在本研究建立优化的STR分型技术条件下,8种人体组织的HE染色切片DNA提取液质量浓度均可达到1ng/μL以上,其IPC的Ct值提示无PCR抑制剂。HE染色切片组织的STR分型有效性与石蜡包埋组织相当,其DNA随时间延续而缓慢降解。结论在一定保存时限内,HE染色切片的DNA质和量可以满足STR分型检测需要,但受残余甲醛固定剂的影响,HE染色切片的分型成功率随保存时间延长而降低。     

磁珠法自动化纯化现场检材DNA方法研究

目的利用TE-MAGS在TECAN工作站上结合磁珠试剂盒,建立自动化工作站批量纯化现场检材DNA的方法,并探讨其在法医物证检案中的应用。方法灵敏度测试:标准品使用0.1ng/μL 9947A,用200μL TES稀释制备DNA总量0.1ng~1ng共10种的标准样品,采用本文方法提取纯化,使用IdentifilerTM试剂盒扩增,用3130XL型测序仪检测,Gene Mapper ID-X分析,分析STR图谱质量;纯化能力测试:在1ng总量的标准样品中加入腐殖酸、血红素,采用本文方法提取纯化、扩增检测,分析STR图谱质量;实际案件应用对比:收集304份现场检材,分别采用本方法和硅珠法进行提取纯化,经扩增检测,统计对比两种提取纯化方法 STR分型成功率。结果灵敏度测试:0.1ng~0.2ng总量标准样品提取的DNA模板,扩增后可检测到部分基因座STR图谱,0.3ng~1ng总量标准样品提取的DNA模板,扩增后可以得到完整的STR图谱;纯化能力测试:对混合有一定浓度的腐殖酸、血红素的标准样品的提取产物检测图谱未见明显抑制;实际案件应用对比测试:304份现场检材工作站磁珠法检出成功率(50%)高于硅珠法(40.8%)。结论本文所建立的方法缓冲范围较大,回收率高,纯化能力强,提取产物STR分型成功率高,适合现场检材批量化DNA检验。     

Genetic profiling of a central Venezuelan population using 15 STR markers that may be of forensic importance

The AmpFlSTR Identifiler kit has recently been accepted for use in DNA databasing of forensic samples in the FBI's National DNA Index System. In the present study, we used this kit to analyze the allele distribution of 15 short tandem repeat markers (STR) in individuals living in Caracas city, Venezuela. The allele frequencies of two of these STR, D2S1338 and D19S433, have not previously been reported for this or any other Latin American population. The results indicate that for the population here studied, the 15 STR tested are useful markers for paternity testing and forensic casework.     

Polymorphism analysis of D19S253 locus in Guangzhou area population

Frequency data for STR system D19S253 were obtained from 105 unrelated individuals of Guangzhong population. PCR products were detected by horizontal native polyacrylamide gel electrophoresis and a total of 9 alleles were identified by side-by-side comparison with a sequenced allelic ladder prepared by ourselves. The observed genotype distribution conformed with Hardy-Weinberg equilibrium. The high information content found in this system(heterozygosity rate was 0.8353, the mean exclusion chance was 0.7499, the discrimination power was 0.9211, the polymorphism information content was 0.8203) indicated it is a useful means in forensic routine casework both in criminal and paternity cases.     

STR analysis of degraded DNA using a miniplex

Analysis of short tandem repeat (STR) markers currently represents the most useful instrument in the field of forensic genetics. The problem with forensic material is the degradation of the sample material. In recent years, several papers have demonstrated that short amplicon STR (miniSTR) represents one of the most useful tools for analyzing degraded DNA samples.In the present study, we attempted to develop a short amplicon STR multiplex system (autosomal and y-chromosomal) for analyzing degraded DNA using some newly designed primer sets for a multiplex polymerase chain reaction (PCR) systems for typing.An assay of degraded DNA samples using the designed multiplex systems, including artificially degraded samples and degraded forensic casework samples, proved remarkably effective. Comparing the multiplex with commercial kits, first results show a well success rate.     

Rapid quantification and sex determination of forensic evidence materials

DNA quantification of forensic evidence is very valuable for an optimal use of the available biological material. Moreover, sex determination is of great importance as additional information in criminal investigations as well as in identification of missing persons, no suspect cases, and ancient DNA studies. While routine forensic DNA analysis based on short tandem repeat markers includes a marker for sex determination, analysis of samples containing scarce amounts of DNA is often based on mitochondrial DNA, and sex determination is not performed. In order to allow quantification and simultaneous sex determination on minute amounts of DNA, an assay based on real-time PCR analysis of a marker within the human amelogenin gene has been developed. The sex determination is based on melting curve analysis, while an externally standardized kinetic analysis allows quantification of the nuclear DNA copy number in the sample. This real-time DNA quantification assay has proven to be highly sensitive, enabling quantification of single DNA copies. Although certain limitations were apparent, the system is a rapid, cost-effective, and flexible assay for analysis of forensic casework samples.     

清代遗骸Y-STR检验1例

法医学实践中经常遇到对骨骼DNA检验的案例,但对保存超过100年的骨骼样本的检验报道较少。本文成功提取到150年前土埋遗骸的骨骼DNA,采用Y—filer试剂盒在9700型扩增仪上进行扩增,3130XL型遗传分析仪进行检测,得到遗骸Y—STR分型,并与对照样本比对,确认了遗骸身份。     

Validation of the PowerPlex 1.1 loci for use in human identification

STR typing is now the favored method of DNA analysis for the purposes of human identification in the forensic community. The Forensic Services Division of the Detroit Police Department has completed its validation of the PowerPlex 1.1 loci (CSF1PO, TPOX, THO1, vWA, D16S539, D7S820, D13S317, and D5S818) for use in forensic casework. Detroit Metro Area Red Cross samples were typed from each of five racial/ethnic groups--the Hispanic, Caucasian, African American, Asian, and American Indian populations--and allele and genotype frequencies were calculated. A rare off-ladder variant (9.1 allele at D7S820) was identified among the database samples. A number of validation studies were performed. DNA was extracted from different substrates and typed as expected, except for the DNA extracted from leather (signal absent from the D16S539, D7S820, D13S317, CSF1PO, and TPOX loci) and from dirt (no PCR product generated). The minor contributor in the mixture study (250 pg input DNA) was facile to discern. The Concordance study, the variety of fluids from the same individual, and NIST standards studies all produced the expected results. Finally, STR data confirmed previous DNA typing results from adjudicated casework samples.     

wizard clean up在混合斑DNA检验中的应用

目的建立一种快速、简单、有效的混合斑DNA检验方法。方法在100例检案中,利用wizardcleanup直接对精子消化液进行纯化浓缩。采用profilerplus试剂盒进行复合扩增,产物经ABI310基因分析仪检测。结果从混合斑中成功获得精斑10个STR位点的DNA分型。结论wizardcleanup处理混合斑,能有效去除女性成份,得到精斑DNA进行分型。