移植时间和检测方法与allo-HSCT受者的DNA嵌合率及法医学意义

影响allo-HSCT受者DNA嵌合率的因素有很多:如受者的疾病类型、移植前预处理方案、移植时病情的严重程度、造血干细胞来源、局部的GVHD、HLA是否相合等。本文主要讨论与法医学关系最为密切的2个影响因素,即移植后时间和检测方法的灵敏度。法医物证学工作者在检案实践中,对allo-HSCT受者进行亲权鉴定或个体识别时,需注意移植后时间和检测方法的灵敏度对嵌合率的影响。女性受者接受男性供者HSCT的情况下,受者毛囊中可以检出供者Y染色体DNA,检案实践中来源于犯罪现场的生物检材不能仅仅检测Y染色体特异遗传标记,以免导致错误判断。     

Simultaneous Identification of Four “Legal High” Plant Species in a Multiplex PCR High‐Resolution Melt Assay,

The international prevalence of “legal high” drugs necessitates the development of a method for their detection and identification. Herein, we describe the development and validation of a tetraplex multiplex real‐time polymerase chain reaction (PCR) assay used to simultaneously identify morning glory, jimson weed, Hawaiian woodrose, and marijuana detected by high‐resolution melt using LCGreen Plus^®. The PCR assay was evaluated based on the following: (i) specificity and selectivity—primers were tested on DNA extracted from 30 species and simulated forensic samples, (ii) sensitivity—serial dilutions of the target DNA were prepared, and (iii) reproducibility and reliability—sample replicates were tested and remelted on different days. The assay is ideal for cases in which inexpensive assays are needed to quickly detect and identify trace biological material present on drug paraphernalia that is too compromised for botanical microscopic identification and for which analysts are unfamiliar with the morphology of the emerging “legal high” species.     

Molecular Assay for Screening and Quantifying DNA in Biological Evidence: The Modified Q‐TAT Assay*

Abstract: A method is described for the quantitation of total human and male DNA. Q‐TAT utilizes end‐point, multiplex polymerase chain reaction (PCR) amplification of the amelogenin and SRY loci to quantify DNA and incorporates a cloned nonhuman template to detect PCR inhibition. Standard curves of fluorescence from amelogenin or SRY amplicons were generated from amplification of known amounts of NIST traceable SRM‐female or SRM‐male DNA. Curves showed good linearity up to 500 pg of SRM‐template (R² > 0.99) and reliably estimated total and male DNA content in casework samples. The nonhuman pRL_null template included in each PCR was a sensitive indicator of known PCR inhibitors including EDTA, hemin, blue denim dye, and humic acid. Finally, the SRY amplicon was a sensitive indicator of male DNA and, in mixtures, could reliably estimate male DNA present in an excess of female DNA. The Q‐TAT multiplex is a reliable quantitation method for forensic DNA typing.     

用双色荧光原位杂交技术鉴定血痕性别

目的 探讨荧光原位杂交技术在血痕性别鉴定中应用及其价值。方法对20例新鲜人血及20例1-2年人血痕的X、Y染色体采用双色荧光探针进行原位杂交分析。结果 人新鲜血,男性X、Y信号检出的完整率为98.8％,其中Y信号的检出率为100％,女性X、X信号检出的完整率为96.5％;1-2年人血痕,男性X、Y信号检出的完整率为88％,其中Y信号的检出率为90％,女性X、X信号检出的完整率为80％;40例血液(痕)性别检测的符合率为100％。结论双色荧光原位杂交技术可以鉴定血痕性别。     

Standard 28-cycle amplification of X/Y-FISH labelled epithelial cells for DNA profiling

The examination of sexual assault evidence frequently involves the analysis of samples that comprise mixtures of male and female cells. Separating male and female cells benefits analysis as the results are more likely to be simplified into profiles from single contributors. Some separation methods have focussed on separation of sperm from epithelial cells, but samples without sperm also require separation (vasectomised males, licked skin, etc.). X/Y chromosome FISH labelling when combined with laser micro-dissection (LMD) is a reliable method to separate male and female epithelial cells, but has mostly been combined with increased cycle PCR to create DNA profiles, limiting its use in many forensic laboratories. This study aimed to determine the limits of cell numbers collected by LMD for standard 28-cycle DNA profiling, and to test the effects, if any, on stochastic variation normally caused by sampling effects. Male and female epithelial cells were stained using the Vysis CEP X/Y DNA Probe kits, and collected using a Leica LMD6000. DNA was extracted and amplified by the ESR in-house one-tube method, using standard 28-cycle PCR with the AmpFISTR Identifiler™ (Applied Biosystems) multiplex kit. Full IdentifilerTM DNA profiles were produced using standard 28-cycle PCR, and partial profiles suitable for submission were produced from even relatively low numbers of cells collected. Profiling results were compared with low-copy number PCR on low numbers of cells stained and collected in the same manner, and the observed effects on heterozygote balance are discussed.     

Validation and casework application of a Y chromosome specific STR multiplex

A series of validation experiments was performed for a Y chromosome specific STR multiplex system following the suggestions made by the Technical Working Group DNA Analysis Methods (TWGDAM). The multiplex PCR products were detected on Perkin-Elmer 373 and 377 automated sequencers using two labeling colors. No problems regarding the stability, robustness and sensitivity of the Y STR multiplex were observed. Mixture studies revealed a cut off rate similar to autosomal STRs for mixtures of male DNAs and no interference of any female admixture. The comparison of the Y STR results to the autosomal typing results for 56 nonprobative semen stains and swabs, showed a slightly higher success rate in detecting the semen donor's alleles for the Y STR multiplex. Two examples are shown to illustrate the usefulness of Y STR typing for DNA mixtures. In one case the Y STR results confirmed an isolated exclusion; in the other case, the interpretation of a mixture was clarified since the Y STR results proved the presence of DNA from at least two semen donors. Y STR typing is a valuable addition to the forensic DNA testing panel.     

A 21‐Locus Autosomal SNP Multiplex and its Application in Forensic Science

To develop a cost‐effective technique for single‐nucleotide polymorphism (SNP) genotyping and improve the efficiency to analyze degraded DNA, we have established a novel multiplex system including 21‐locus autosomal SNPs and amelogenin locus, which was based on allele‐specific amplification (ASA) and universal reporter primers (URP). The target amplicons for each of the 21 SNPs arranged from 63 base pair (bp) to 192 bp. The system was tested in 539 samples from three ethnic groups (Han, Mongolian, and Zhuang population) in China, and the total power of discrimination (TPD) and cumulative probability of exclusion (CPE) were more than 0.99999999 and 0.98, respectively. The system was further validated with forensic samples and full profiles could be achieved from degraded DNA and 63 case‐type samples. In summary, the multiplex system offers an effective technique for individual identification of forensic samples and is much more efficient in the analysis of degraded DNA compared with standard STR typing.     

Validation and casework application of a Y chromosome specific STR multiplex

A series of validation experiments was performed for a Y chromosome specific STR multiplex system following the suggestions made by the Technical Working Group DNA Analysis Methods (TWGDAM). The multiplex PCR products were detected on Perkin-Elmer 373 and 377 automated sequencers using two labeling colors. No problems regarding the stability, robustness and sensitivity of the Y STR multiplex were observed. Mixture studies revealed a cut off rate similar to autosomal STRs for mixtures of male DNAs and no interference of any female admixture. The comparison of the Y STR results to the autosomal typing results for 56 nonprobative semen stains and swabs, showed a slightly higher success rate in detecting the semen donor’s alleles for the Y STR multiplex. Two examples are shown to illustrate the usefulness of Y STR typing for DNA mixtures. In one case the Y STR results confirmed an isolated exclusion; in the other case, the interpretation of a mixture was clarified since the Y STR results proved the presence of DNA from at least two semen donors. Y STR typing is a valuable addition to the forensic DNA testing panel.     

Applicability of the ParaDNA® Screening System to Seminal Samples

Seminal fluid represents a common biological material recovered from sexual assault crime scenes. Such samples can be prescreened using different techniques to determine cell type and relative amount before submitting for full STR profiling. The ParaDNA^® Screening System is a novel forensic test which identifies the presence of DNA through amplification and detection of two common STR loci (D16S539 and TH01) and the Amelogenin marker. The detection of the Y allele in samples could provide a useful tool in the triage and submission of sexual assault samples by enforcement authorities. Male template material was detected on a range of common sexual assault evidence items including cotton pillow cases, condoms, swab heads and glass surfaces and shows a detection limit of 1 in 1000 dilution of neat semen. These data indicate this technology has the potential to be a useful tool for the detection of male donor DNA in sexual assault casework.     

Y-chromosome STR system, Y-PLEX 12, for forensic casework: development and validation

The Y-PLEX 12 system, developed for use in human identification, enables simultaneous amplification of eleven polymorphic short tandem repeat (STR) loci, namely DYS392, DYS390, DYS385 a/b, DYS393, DYS389I, DYS391, DYS389II, DYS 19, DYS439 and DYS438, residing on the Y chromosome and Amelogenin. Amelogenin provides results for gender identification and serves as internal control for PCR. The validation studies were performed according to the DNA Advisory Board's (DAB) Quality Assurance Standards. The minimal sensitivity of the Y-PLEX 12 system was 0.1 ng of male DNA. The mean stutter values ranged between 3.76-15.72%. A full male profile was observed in mixture samples containing 0.5 ng of male DNA and up to 400 ng of female DNA. Amelogenin did not adversely affect the amplification of Y-STRs in mixture samples containing male and female DNA. The primers for the Y-STR loci present in Y-PLEX 12 are specific for human DNA and some higher primates. None of the primate samples tested provided a complete profile at all 11 Y-STR loci amplified with the Y-PLEX 12 system. Y-PLEX 12 is a sensitive, valid, reliable, and robust multiplex system for forensic analysis, and it can be used in human forensic and male lineage identification cases.     

Haplotype analysis for Irish ancestry

Forensic haplotype analysis of the male Y chromosome is currently used to establish the number of male donors in sexual assaults, the number of male bleeders in blood pattern analysis, and for ancestry correlation to genetic founder populations in biogeographic studies. In forensic laboratory applications, its primary use is for DNA profile generation with trace amounts of male DNA in the presence of excess female DNA (e.g. spermatozoa identification, male component of fingernail scrapings). Our study supports the potential use of the Y chromosome in a “dragnet” approach (most haplotypes are unique) similar to that described by Kayser in 2017 for solving a cold case sex assault and homicide in The Netherlands. Our study also researched the potential for the identification of an ancestral Irish genetic “footprint” linked to surname O’Brien and identified multiple founder group origins in Ireland and England as well as three samples with the Dal Riata (a Gaelic overkingdom) ancestral haplotype. This study indicates correlation to ancestral Irish ancestry by haplotype but not conclusively to the O’Brien surname.     

What is she doing here? Klinefelter syndrome in forensic casework

In this case report, we describe a sexual assault incident in which the male victim’s seminal fluid contained no sperm cells, as indicated by sperm cell staining and microscopic screening, and DNA profiling results from the non-sperm cell fraction showed a major/minor DNA mixture that could be interpreted as female and male. DNA profiling of a sample from a disposable drinking cup used by the victim at the crime scene provided a single source profile, and showed a 2:1 imbalance between the heights of the X and Y chromosomes, respectively. The victim’s DNA reference sample showed a similar imbalance of the X and Y chromosomes. These observations suggested that the victim might suffer from Klinefelter syndrome, a genetic disorder related to the sex chromosomes.Here, we describe the first reported use of the QIAGEN Investigator® Argus X-12 kit for characterization of X-chromosomal STR loci to potentially identify a case of Klinefelter syndrome. This commercially available kit is primarily used in forensic laboratories to investigate kinship relations and for paternity testing in alleged father/daughter cases. Results of the X chromosome DNA profiling from the victim’s disposable drinking cup and reference samples revealed two alleles at various X-chromosomal STR loci. Moreover, this kit can also amplify a Y chromosome specific sequence (AMEL-Y), and the results indicated that this sample actually originated from a male. Evidence of two X chromosomes in the victim's DNA suggested that he was likely to have Klinefelter syndrome. In this case report, we propose the use of the QIAGEN Investigator® Argus X-12 kit as a practical forensic tool for the detection of potential genetic syndromes related to the sex chromosomes, which can affect test results and, at times, make them difficult to interpret. We also aim to increase awareness within the forensic science community regarding the existence of genetic anomalies, which should be considered when analyzing DNA profiles.     

Validation of SRY Marker for Forensic Casework Analysis

Abstract:  Determining the gender of the source of forensic DNA evidence is based on the amelogenin test. However, at times the assay may not be indicative of gender assignment, because of deletions at the amelogenin site. Previously, we described successful coamplification of a marker residing within the SRY gene with the short tandem repeat markers from two commercially available human identification kits. The study herein addresses the validation of primers for the target SRY gene regarding specificity, sensitivity, and robustness. Among 115 unrelated male Slovenians no null allele was observed. Repeatable and reliable results were obtained from as little as 25 pg of template DNA, indicating a high sensitivity of detection for the assay. No polymerase chain reaction product was observed even at a concentration of 10 ng/μL of template female DNA. Additionally, the male specific marker could be detected in mixed male and female samples down to a ratio of 1:16.     

Developmental validation of the quantifiler real-time PCR kits for the quantification of human nuclear DNA samples

The Quantifiler Human DNA Quantification Kit and the Quantifiler Y Human Male DNA Quantification Kit were designed for the quantification of human genomic DNA in forensic samples. The kits use a real-time PCR-based process to quantify, respectively, total human DNA or human male DNA only. We report the results of a developmental validation study that we performed with the Quantifiler Kits, following the official SWGDAM guidelines. The Quantifiler Kits were tested for performance criteria such as species specificity, sensitivity, stability, precision and accuracy, and in addition, were tested with forensic case-type samples and mixed (male:female) DNA samples. The Quantifiler Kit methods were highly specific for human DNA, and could detect as little as 32 picograms of DNA using 2 microL of sample per assay. The accuracy and precision of the Quantifiler Kit methods was comparable or superior to that of other quantification methods.     

Use of a Y chromosome probe as an aid in the forensic proof of sexual assault

Currently, the most common procedures for the forensic identification of semen that may be present due to a sexual assault include the microscopic identification of spermatozoa, acid phosphatase activity, or the detection of PSA. However, not all cases of sexual assault result in the deposit of semen. Fluorescent In Situ Hybridization (FISH) has been found to be a very sensitive and specific method for detection of the Y chromosome from male cells. This study was undertaken to demonstrate the presence of epithelial cells of male origin in the postcoital vaginal tract using a commercially available probe. Results identified Y chromosome in intact epithelial cells on postcoital Days 1 through 4, and on Day 7. Additionally, Y chromosome positive epithelial cells were identified in vaginal swabs obtained following intercourse with no ejaculation. The method developed in this study demonstrates that FISH is a sensitive method for the identification of the presence of male epithelial cells in the postcoital vagina.     

A LDR‐PCR Approach for Multiplex Polymorphisms Genotyping of Severely Degraded DNA with Fragment Sizes <100 bp*

Abstract: Reducing amplicon sizes has become a major strategy for analyzing degraded DNA typical of forensic samples. However, amplicon sizes in current mini‐short tandem repeat‐polymerase chain reaction (PCR) and mini‐sequencing assays are still not suitable for analysis of severely degraded DNA. In this study, we present a multiplex typing method that couples ligase detection reaction with PCR that can be used to identify single nucleotide polymorphisms and small‐scale insertion/deletions in a sample of severely fragmented DNA. This method adopts thermostable ligation for allele discrimination and subsequent PCR for signal enhancement. In this study, four polymorphic loci were used to assess the ability of this technique to discriminate alleles in an artificially degraded sample of DNA with fragment sizes <100 bp. Our results showed clear allelic discrimination of single or multiple loci, suggesting that this method might aid in the analysis of extremely degraded samples in which allelic drop out of larger fragments is observed.     

Evaluation of prostate-specific antigen (PSA) membrane test assays for the forensic identification of seminal fluid.

Prostate specific antigen (PSA, also known as p30), a glycoprotein produced by the prostatic gland and secreted into seminal plasma, is a marker used for demonstrating the presence of seminal fluid. Methods for the detection of PSA include Ouchterlony double diffusion, crossover electrophoresis, rocket immuno-electrophoresis, radial immunodiffusion, and ELISA. The extremely sensitive ELISA technique can detect PSA in concentrations as low as approximately 4 ng/mL. However, all these techniques are cumbersome and time consuming to perform in forensic laboratories, especially when only a few samples per week are processed. Various membrane tests are currently used in clinical settings to screen a patient's serum for the presence of PSA at levels greater than 4 ng/mL. In this study we evaluated three immunochromatographic PSA membrane tests by analyzing semen stains stored at room temperature for up to 30 years, post-coital vaginal swabs taken at different time after intercourse, semen-free vaginal swabs, and various female and male body fluids, including urine. The data demonstrate that PSA membrane test assays offer the same sensitivity as ELISA-based tests and provide a rapid approach for the forensic identification of seminal fluid. Furthermore, when the supernatant from a DNA extraction is used for the assay, there is essentially no DNA consumption for determining the presence of PSA in a forensic sample.     

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。     

Internal Validation of the AmpFlSTR Yfiler™ Amplification Kit for Use in Forensic Casework

Abstract:  Y-chromosomal short-tandem repeat (Y-STR) amplification has been used in forensic casework at the Bureau of Criminal Apprehension (BCA) Forensic Science Laboratory since 2003. At that time, two separate amplifications were required to type the SWGDAM recommended loci (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439). The Yfiler™ kit coamplifies these loci as well as DYS437, DYS448, DYS456, DYS458, DYS635, and Y GATA H4. The Yfiler™ kit was validated following the internal validations outlined in the SWGDAM revised validation guidelines. Our studies show that 0.125 ng of male DNA will generate a complete 17 locus profile and that as little as 0.06 ng of male DNA yields an average of nine loci. In the male–male mixtures, a complete profile from the minor component was detected up to 1:5 ratio; most of the alleles of the minor component were detected at a 1:10 ratio and more than half the alleles of the minor component were detected at a 1:20 ratio. Complete YSTR profiles were obtained when 500 pg male DNA was mixed with female DNA at ratios up to 1:1000. At ratios of 1:5000 and 1:10,000 (male DNA to female DNA) inhibition of the YSTR amplification was evident. The YSTR results obtained for the adjudicated case samples gave significantly more probative information than the autosomal results. Our studies demonstrate that the Yfiler™ kit is extremely sensitive, does not exhibit cross-reactivity with female DNA, successfully types male DNA in the presence of overwhelming amounts of female DNA and is successful in typing actual forensic samples from adjudicated cases.     

High-performance LAMP-based method for human sex identification using Y chromosome-specific genetic markers

Finding fast and cheap strategies for DNA typing and human sample identification is of interest in forensic science. We report a new versatile alternative for molecular sex determination using Y-specific targets (TSPY, TTTY, alphoid regions, and Y-Amelogenin). This system uses an isothermal loop-mediated DNA amplification (LAMP) with a set of 6 primers for each target, designed to improve sensibility and specificity, and reducing detection time to only 45 min. Furthermore, detecting the different targets on the Y chromosome either individually or in combination revealed accurate results. Assay sensitivity was determined with a mixture of human female and male DNA at different concentrations to mimic forensic samples. Single primer sets showed high sensitivity at DNA concentrations ranging from 58.6 to 3.7 pg/µL. When a combined primers set was used, sensitivity yielded a detection as low as 0.1 pg/µL of male DNA, making it 10 times more sensitive than qPCR-DNA quantification kits. Finally, high specificity was observed when tested against 6 domestic species.