Jaiprakash G. Shewale

Quantitative intra-short interspersed element PCR for species-specific DNA identification

We have designed and evaluated four assays based upon PCR amplification of short interspersed elements (SINEs) for species-specific detection and quantitation of bovine, porcine, chicken, and ruminant DNA. The need for these types of approaches has increased drastically in response to the bovine spongiform encephalopathy epidemic. Using SYBR Green-based detection, the minimum effective quantitation levels were 0.1, 0.01, 5, and 1 pg of starting DNA template using our bovine, porcine, chicken, and ruminant species-specific SINE-based PCR assays, respectively. Background cross-amplification with DNA templates derived from 14 other species was negligible. Species specificity of the PCR amplicons was further demonstrated by the ability of the assays to accurately detect trace quantities of species-specific DNA from mixed (complex) sources. Bovine DNA was detected at 0.005% (0.5 pg), porcine DNA was detected at 0.0005% (0.05 pg), and chicken DNA was detected at 0.05% (5 pg) in a 10-ng mixture of bovine, porcine, and chicken DNA templates. We also tested six commercially purchased meat products using these assays. The SINE-based PCR methods we report here are species-specific, are highly sensitive, and will improve the detection limits for DNA sequences derived from these species.

Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues

Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using short tandem repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues.

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 Boards (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.

Development and Validation of a Multiplexed Y-Chromosome STR Genotyping System, Y-PLEX ™ 6, for Forensic Casework

A Y-chromosome multiplex polymerase chain reaction (PCR) amplification kit, known as Y-PLEX 6, has been developed for use in human identification. The Y-PLEX 6 kit enables simultaneous amplification of six polymorphic short tandem repeat (STR) loci located on the non-recombinant region of the human Y-chromosome. These loci are: DYS393, DYS19, DYS38911, DYS390, DYS391, and DYS385. Our studies show that as little as 0.2 ng of template DNA can be used for analysis. The specificity of the amplification reaction enabled analysis of male DNA in a male:female DNA mixture at a ratio of 1:125. Among the six Y-STR loci, the maximum mean stutter percentage was 11.9 for allele at DYS38911 locus. Attempts at amplification of DNA from various animal sources revealed that the Y-PLEX 6 primers are human specific. Details of the development of the kit, generation and description of the allelic ladders, and validation of the multiplex PCR are presented. In addition, Y-STR allele and haplotype frequencies in three populations have been investigated. The data indicate that results obtained using the Y-PLEX 6 kit are robust, sensitive, and reliable and can be used in human forensic and male lineage identification cases.

DNA profiling of azoospermic semen samples from vasectomized males by using Y-PLEX 6 amplification kit.

Post-vasectomized azoospermic semen samples (N = 6) were analyzed for short tandem repeats (STR) on the Y-chromosome by using Y-PLEX 6 and the 310 Genetic Analyzer. We have observed a wide variation in the yield of extracted DNA from 12.5-1,000 ng. This variation was attributed to the number of epithelial and/or white blood cells that are present in these azoospermic samples. DNA profiles of these vasectomized males were obtained for all six Y-STR loci, namely DYS393, DYS 19, DYS389II, DYS390, DYS391, and DYS385 amplified by using the Y-PLEX 6.

Automated Extraction of DNA from Forensic Sample Types Using the PrepFiler Automated Forensic DNA Extraction Kit

The HID EVOlution—Extraction System (Tecan Group Ltd., Mannedorf, Switzerland) was developed to automate DNA extraction from biological samples using the PrepFiler Automated Forensic DNA Extraction Kit (Applied Biosystems, Foster City, CA). The system consists of a Tecan Freedom EVO 150 robot (Tecan Group Ltd., Mannedorf, Switzerland), a graphical user interface designed for use with Freedom EVOware software v 2.1 SPI (Tecan Group Ltd., Mannedorf, Switerland) as well as instrument hardware and plastic to support the PrepFiler reagents and protocol. The DNA quality and quantity obtained were comparable to that observed with the corresponding manual extraction protocol. Purified DNA was free of inhibitors and ready for downstream applications, such as real-time quantitative PCR and PCR for short tandem repeat (STR) analysis. The DNA quantity and quality obtained were consistent as demonstrated by the quantification and STR results. Our studies indicate that the HID EVOlution—Extraction System can easily be adopted in forensic laboratories to alleviate some of the bottlenecks of sample preparation in forensic laboratories.

AutoMate Express™ Forensic DNA Extraction System for the Extraction of Genomic DNA from Biological Samples*

Abstract:  The AutoMate Express™ Forensic DNA Extraction System was developed for automatic isolation of DNA from a variety of forensic biological samples. The performance of the system was investigated using a wide range of biological samples. Depending on the sample type, either PrepFiler™ lysis buffer or PrepFiler BTA™ lysis buffer was used to lyse the samples. After lysis and removal of the substrate using LySep™ column, the lysate in the sample tubes were loaded onto AutoMate Express™ instrument and DNA was extracted using one of the two instrument extraction protocols. Our study showed that DNA was recovered from as little as 0.025 μL of blood. DNA extracted from casework‐type samples was free of detectable PCR inhibitors and the short tandem repeat profiles were complete, conclusive, and devoid of any PCR artifacts. The system also showed consistent performance from day‐to‐day operation.

Quantifiler ® Duo DNA Quantification Kit: A Guiding Tool for Short Tandem Repeat Genotyping of Forensic Samples

Forensic analysts routinely encounter samples containing mixtures of DNA from male and female contributors and PCR inhibitors due to exposure to environmental insults. In order to select the appropriate STR analysis methodology for such samples and obtain optimal results at first pass, it is desirable to determine the relative quantities of male and female DNA and to detect the presence of PCR inhibitors at an early stage in the sample processing workflow. Here we describe a multiplex real-time PCR assay that can provide the desired information in a single reaction. Briefly, the simultaneous quantification of human and human male DNA is achieved by measuring the RPPH1 human target and the SRY male-specific target. At the same time a synthetic sequence is co-amplified as an Internal PCR Control (IPC) to detect the presence of PCR inhibitors. The assay has a good dynamic range (0.023–50 ng/μL) and can detect 25 pg/μL of human male DNA in the presence of ten thousand-fold excess of human female DNA. In addition, the ability of the assay to predict PCR inhibition was demonstrated by shifted IPC C T values in the presence of increasing quantities of hematin. All the real-time PCR results showed a good correlation with the downstream STR profiles obtained from a large set of various sample types therefore demonstrating that this assay can be considered a guiding tool to predict the performance of the STR genotyping kits with forensic samples.

The HID EVOlution System for Automation of DNA Quantification and Short Tandem Repeat Analysis

The HID EVOlution—qPCR/STR Setup System enables automation of DNA quantitative real-time polymerase chain reaction (PCR) setup, normalization of DNA sample, and PCR setup for short tandem repeat (STR) analysis. The HID EVOlution System tracks sample and reagent information and facilitates data transfer of DNA quantification, normalization, and PCR setup for STR analysis steps, eliminating the need for manual processing and repetitive data entry. Instruments for the automated system include a Tecan Freedom EVO 150 robot for liquid handling, the 7500 Real-Time PCR System for DNA quantification, the GeneAmp PCR System 9700 for STR amplification, and the 3130xl Genetic Analyzer for the detection of amplified STR fragments. Validation studies including reproducibility, accuracy, correlation, and contamination studies were performed. Results demonstrated clean liquid-handling capabilities and maintenance of sample integrity. Variation in average allele peak height obtained using automated protocol was similar to that obtained using the manual protocol.

Detection and correction of a migration anomaly on a 310 genetic analyzer.

During STR analysis on the 310 Genetic Analyzer, retarded migration of GS500ROX size standards and alleles in some samples was observed. The contribution of reagents, capillary and performance optimized polymer POP 4 to the observed anomaly was experimentally eliminated. Variation in electrophoresis temperature between 55 degrees C and 65 degrees C did not alter the rate of migration of GX500ROX size standard and sample alleles. An eroded connector for the cathode mounted on the heat plate assembly caused the abnormal migration. Hence, it is important to verify the mobility of all fragments in the size standard for each sample to avoid any erroneous allele calls by the automated data analysis software.