Haplotype diversity in mitochondrial DNA hypervariable region I, II and III in northeast China Han

Sequence polymorphism of the mitochondrial DNA (mtDNA) control region, hypervariable regions HVR I, HVR II and HVR III, from 51 unrelated China Han (Yan Bian area) were determined by PCR amplification and cycle sequencing.     

Haplotype diversity in mitochondrial DNA hypervariable region I, II and III in a Korean ethnic group from northeast China

Sequence polymorphism of the mitochondrial DNA (mtDNA) control region, hypervariable regions HVR I, II and III, from 55 unrelated Korean ethnic group individuals from northeast China (YanBian area) were determined by PCR amplification and cycle sequencing.     

Successful DNA typing of a urine sample in a doping control case using human mitochondrial DNA analysis

In a doping control case, a urine sample was tested positive for nandrolon. We were asked by the athlete to perform DNA investigations on the questioned urine sample and compare these to a fresh blood sample taken from the athlete in order to detect or rule out manipulation and/or switching of the samples. The urine sample had been collected nine months prior to the investigation and had been stored at 4 degrees C. In a first approach, nuclear DNA systems were investigated that failed with the exception of the Amelogenin system. Due to the high copy number of mitochondrial DNA molecules and the robustness of the mitochondrial genome, we investigated the HVR I and HVR II regions of mitochondrial DNA and obtained reproducible and clear sequencing results for both the blood and the urine samples. Due to the identical sequences, it could not be excluded that the blood sample and the urine sample were from the same individual or an individual having the same maternal lineage.     

Single-strand conformation polymorphism of hyper-variable regions HV1 and HV2 of human mitochondrial DNA: detection by silver staining

Human mitochondrial DNA from 50 trios consisting of mother (M), child (C) and father (F) was PCR amplified with primers flanking the hyper-variable regions, HVR1 and HVR2. The amplified products were then fractionated under non-denaturing conditions, silver-stained and compared by single-stranded conformational polymorphism (SSCP). In all but one case, mother and child displayed identical patterns, which could be promptly distinguished from that of the father. For the remaining cases, either set of primers was sufficient to resolve the familial ties. In no instance, M displayed alleles different from those of C within each trio, demonstrating that no false exclusions occurred. The SSCP approach proved to be a robust technique suitable as a preliminary screening in cases requiring identification of multiple samples.     

Hypervariable regions of DNA for parentage testing and individual identification

Four kinds of DNA probes that recognize hypervariable regions (HVR) were studied for parentage testing and individual identification. Allele frequencies and their confidence intervals among unrelated Japanese individuals were obtained. Codominant segregation of the polymorphism was confirmed in family studies. Two a priori probabilities were calculated for each HVR locus: the exclusion probabilities for an alleged father/mother/child trio and for an alleged parent/child duo, and the probabilities of matching of genotypes of two unrelated individuals or two siblings. The ease of availability of the probes and their highly discriminating polymorphic patterns mean they could be very useful for forensic purposes.     

染色毛干mtDNA不同提取方法的研究

目的为染色毛发线粒体DNA选择最佳的提取方法。方法在5个染发个体中各取5根头发,采用Chelex-100法、有机法、磁珠法、H2O2结合Chelex-100法及Chelex-100结合M icrocon100法等5种不同的提取方法提取染色毛发m tDNA,利用2%琼脂糖凝胶电泳检测扩增产物。结果Chelex-100结合M icrocon100方法提取染色毛发扩增m tDNA效果较好,其余方法无扩增产物。毛发的不同部位对扩增结果无影响。结论染色毛发采用恰当的提取方法可以提取到m tDNA模板,为法医日常检案提供帮助。     

应用DNA Typer15TM Direct试剂盒对河南地区汉族人群14个基因座遗传多态性的调查

目的调查河南地区汉族人群14个STR基因座的遗传多态性。同时简要介绍本实验室建库流程。方法应用DNA Typer15TM Direct试剂盒检测359名河南地区汉族无关个体14个STR基因座的等位基因频率,并应用统计软件计算群体遗传学参数。结果 14个STR基因座的基因型分布均符合Hardy-Weinberg平衡(P>0.05),14个基因座的杂合度(H)在0.694～0.922之间,匹配概率(Pm)在0.017～0.131之间,个人识别率(PD)在0.869～0.983之间,多态信息含量(PIC)在0.670～0.910之间,非父排除概率(PE)在0.418～0.841之间。结论 14个STR基因座在河南汉族人群中有较高的多态性,所得的群体遗传学数据可为法医学个人识别和亲子鉴定提供结果评估的依据。应用DNA Typer 15TM Direct试剂盒构建DNA数据库简单经济实用。     

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.     

STR typing of human DNA from fly larvae fed on decomposing bodies

In homicides with entomological evidence, it may be important to prove the presumed association of fly larvae to a corpse, especially if it is in doubt whether all maggots used for entomological expertise developed and fed on it. The present study demonstrates for the first time the possibility of analyzing human microsatellite DNA present in the digestive tract of necrophagous larvae that fed on decomposed bodies with a postmortem interval up to four months. The obtained human STR profiles support the association of a maggot to a specific corpse. In addition, the identification of the host species (e.g., animal source like pig) can be achieved by analysis of the cytochrome b gene. Maggots were collected from 13 corpses after various postmortem intervals and STR typing and HVR amplifications were performed using their crop contents. In seven cases, a complete STR profile was established, in two cases, an incomplete set of alleles was obtained, and in four cases, STR typing was not successful. HVR analysis was successful in all cases except one. The time of storage of the maggots and the length of the postmortem interval up to 16 weeks appeared to have no particular influence on the quality of the results.     

Species identification using sequences of the trnL intron and the trnL-trnF IGS of chloroplast genome among popular plants in Taiwan

Forensic botanical comparison can be hampered by the lack of appropriate DNA databases. While DNA sequence databases for many mitochondrial loci have been established for the identification of animal species, less is known regarding the genomes of plants. We report on the use of the trnL intron and the trnL-trnF intergenic spacer (IGS) in the chloroplast genome and establish a DNA sequence database for plant species identification. The DNA sequences at these two loci from commonly encountered plants, including monocots and dicots, were aligned to establish a DNA database of local plants. The database comprises 373 individual sequences representing 80 families, 206 genera and 269 species. These plant species can be grouped to species level using both sequence and length polymorphisms at these loci. To validate the database for future forensic purposes, we sequenced 20 blind samples and searched the local database and the databases of GenBank and EMBL. Fifteen of these 20 samples used in blind trial testing matched their respective species from our local DNA database but only 6 matched species registered in the GenBank and EMBL databases. The sequences of two species used in the blind trial did not match any sequence registered in any of these databases. Cluster analysis was performed to demonstrate the family and genus distribution of samples. Neighbor-joining trees of the two DNA regions from 70 samples of the local database and 10 of the species used in the blind trials were constructed and clustered to both family and genus. The bootstrap values of the trnL intron were higher than most of those of the trnL-trnF IGS. The sequence database described in this study can be used to identify plant species using DNA sequences of the trnL intron and trnL-trnF IGS of chloroplast genome and illustrates its value in plant species identification.     

Modeling Forensic DNA Database Performance*

Abstract: Over the past decade or more, DNA databases have been a focal point of development for the forensic field. Using this approach, forensic and law enforcement agencies have aided millions of investigations, many of which would remain unsolved but for the intelligence links provided from DNA database comparison. However, despite their widespread use and increasingly broad legislative and operational reach, there has been limited overarching performance modeling or reflection on drivers of operational or financial efficiency. This study derives an inferential model for DNA database performance using data from major national DNA database programs. Parameters that optimize desirable database outputs (matches) are isolated and discussed, as is an approach for maximizing financial efficiency and minimizing ethical impact. This research takes important steps toward identifying measures of performance for forensic DNA database operations.     

DNA in the Criminal Justice System: The DNA Success Story in Perspective,

Current figures on the efficiency of DNA as an investigative tool in criminal investigations only tell part of the story. To get the DNA success story in the right perspective, we examined all forensic reports from serious (N = 116) and high‐volume crime cases (N = 2791) over the year 2011 from one police region in the Netherlands. These data show that 38% of analyzed serious crime traces (N = 384) and 17% of analyzed high‐volume crime traces (N = 386) did not result in a DNA profile. Turnaround times (from crime scene to DNA report) were 66 days for traces from serious crimes and 44 days for traces from high‐volume crimes. Suspects were truly identified through a match with the Offender DNA database of the Netherlands in 3% of the serious crime cases and in 1% of the high‐volume crime cases. These data are important for both the forensic laboratory and the professionals in the criminal justice system to further optimize forensic DNA testing as an investigative tool.     

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were calculated. The robustness of this combined European database was tested by estimating parameter d for every DNA profile, where d=log(10)(Pm(c)/Pm(E)) Pm(c) is the match probability of the profile calculated from its cognate database and Pm(E) is the match probability of the combined European database. Overall there was a small tendency for Pm(c)>Pm(E) primarily because of sampling bias. This bias was removed by the simple expediency of applying an adjustment factor to the calculation of Pm(E). These were selected from the Balding size bias correction, the Balding and Nichols Fst correction, a minimum allele proportion (between 0.01 and 0.02), an upper bound of a 95% confidence interval (CI) and a lower bound on the genotype match probability. It was demonstrated that a single European database is a feasible proposition. A combination of different adjustment methods can be used to ensure that the result is conservative relative to the cognate database, and their effect measured by parameter d.     

Species identification of Kachuga tecta using the cytochrome b gene

A DNA technique has been established for the identification to species level of tortoises. The test on the shell of the animal was used to identify samples from the species Kachuga tecta. A total of 100 tortoise shell specimens collected from the National Council of Agriculture (COA), Taiwan, were used in this study. Primer pairs were designed to amplify partial DNA fragments of cytochrome b within the mitochondrial genome. The DNA data showed that among the 100 samples, there were four distinct haplotype DNA sequences, within which there were a total of 90 variable sites. Between haplotypes I and II, there was only 1 nucleotide difference at position 228. Between haplotypes I and III, 65 nucleotide differences were observed; haplotypes I and IV, 62 nucleotide differences; and haplotypes III and IV, 56 nucleotide differences were observed. There were 66 and 63 nucleotide differences between haplotypes II and III and haplotypes II and IV respectively. All four haplotypes were compared with the DNA sequences held at the GenBank and EMBL databases. The most similar species were K. tecta (haplotype I and II), Morenia ocellata (haplotype III) and Geoclemys hamiltonii (haplotype IV), and their respective mtDNA similarities were 99.5%, 99.3%, 89.9% and 99.5%. However, as haplotype III was only 89.9% homologous with M. ocellata, it would seem that this haplotype shows only a limited relationship with a similar species registered currently in these databases. The method established by this study is an additional method for the identification of samples protected under Convention International Trade in Endangered Species (CITES) and will improve the work for the preservation of the endangered species.     

Average Probability that a "Cold Hit" in a DNA Database Search Results in an Erroneous Attribution

Abstract:  We consider a hypothetical series of cases in which the DNA profile of a crime-scene sample is found to match a known profile in a DNA database (i.e., a "cold hit"), resulting in the identification of a suspect based only on genetic evidence. We show that the average probability that there is another person in the population whose profile matches the crime-scene sample but who is not in the database is approximately 2( N  −  d ) p _A , where N is the number of individuals in the population, d is the number of profiles in the database, and p _A is the average match probability (AMP) for the population. The AMP is estimated by computing the average of the probabilities that two individuals in the population have the same profile. We show further that if a priori each individual in the population is equally likely to have left the crime-scene sample, then the average probability that the database search attributes the crime-scene sample to a wrong person is ( N  −  d ) p _A .     

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.     

中国DNA数据库建设应用技术现状及发展趋势

中国的法庭科学DNA数据库建设历经10年,在应用中取得了显著成果.随着DNA分析技术的进步,DNA数据库更加完善,DNA信息作用更加突显.本文综述了中国DNA数据库的规划与建设,DNA数据库建设中的应用技术,以及DNA数据库建设应用技术发展趋势,为完善DNA数据库建设提供借鉴.     

DNA‐Based Identification of Forensically Important Lucilia (Diptera: Calliphoridae) in the Continental United States*

Abstract: Correct species identification is critical when dipteran larvae are used for inference of the postmortem interval. To facilitate DNA‐based identification of forensically important flies of the genus Lucilia in the continental United States, we develop a vouchered reference collection and DNA sequence database. A total of 122 specimens were collected for nine of the 10 species of Lucilia reported to occur in the continental United States. Using the polymerase chain reaction and DNA sequencing, data were obtained for an 1100‐bp region of the mitochondrial gene encoding cytochrome oxidase I (COI). We consider a species suitable for DNA‐based identification if it is exclusively monophyletic in >95% of bootstrap pseudoreplicate phylogenetic analyses. Seven of the nine species meet that criterion. Two species (Lucilia coeruleiviridis and Lucilia mexicana) share COI sequence and cannot be distinguished using our reference database. We conclude that DNA‐based identification is likely to be successful for the other seven species.