Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software

Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGx^TM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.

Identification of a common single nucleotide polymorphism at the primer binding site of D2S1360 that causes heterozygote peak imbalance when using the Investigator HDplex Kit

Phenomena known as null alleles and peak imbalance can occur because of mutations in the primer binding sites used for DNA typing. In these cases, an accurate statistical evaluation of DNA typing is difficult. The estimated likelihood ratio is incorrectly calculated because of the null allele and allele dropout caused by mutation-induced peak imbalance. Although a number of studies have attempted to uncover examples of these phenomena, few reports are available on the human identification kit manufactured by Qiagen. In this study, 196 Japanese individuals who were heterozygous at D2S1360 were genotyped using an Investigator HDplex Kit with optimal amounts of DNA. A peak imbalance was frequently observed at the D2S1360 locus. We performed a sequencing analysis of the area surrounding the D2S1360 repeat motif to identify the cause for peak imbalance. A point mutation (G>A transition) 136 nucleotides upstream from the D2S1360 repeat motif was discovered in a number of samples. The allele frequency of the mutation was 0.0566 in the Japanese population. Therefore, human identification or kinship testing using the Investigator HDplex Kit requires caution because of the higher frequency of single nucleotide polymorphisms at the primer binding site of D2S1360 locus in the Japanese population.

Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories

Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction. Targeted loci include Amelogenin, 27 common, forensic autosomal STRs, 24 Y-STRs, 7 X-STRs and three classes of single nucleotide polymorphisms (SNPs). The ForenSeq™ kit includes two primer sets: Amelogenin, 58 STRs and 94 identity informative SNPs (iiSNPs) are amplified using DNA Primer Set A (DPMA; 153 loci); if a laboratory chooses to generate investigative leads using DNA Primer Set B, amplification is targeted to the 153 loci in DPMA plus 22 phenotypic informative (piSNPs) and 56 biogeographical ancestry SNPs (aiSNPs). High-resolution genotypes, including detection of intra-STR sequence variants, are semi-automatically generated with the ForenSeq™ software. This system was subjected to developmental validation studies according to the 2012 Revised SWGDAM Validation Guidelines. A two-step PCR first amplifies the target forensic STR and SNP loci (PCR1); unique, sample-specific indexed adapters or "barcodes" are attached in PCR2. Approximately 1736 ForenSeq™ reactions were analyzed. Studies include DNA substrate testing (cotton swabs, FTA cards, filter paper), species studies from a range of nonhuman organisms, DNA input sensitivity studies from 1ng down to 7.8pg, two-person human DNA mixture testing with three genotype combinations, stability analysis of partially degraded DNA, and effects of five commonly encountered PCR inhibitors. Calculations from ForenSeq™ STR and SNP repeatability and reproducibility studies (1ng template) indicate 100.0% accuracy of the MiSeq FGx™ System in allele calling relative to CE for STRs (1260 samples), and >99.1% accuracy relative to bead array typing for SNPs (1260 samples for iiSNPs, 310 samples for aiSNPs and piSNPs), with >99.0% and >97.8% precision, respectively. Call rates of >99.0% were observed for all STRs and SNPs amplified with both ForenSeq™ primer mixes. Limitations of the MiSeq FGx™ System are discussed. Results described here demonstrate that the MiSeq FGx™ System meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities.

Current trends in microsatellite genotyping

Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.

Development and characterization of two mini-X chromosomal short tandem repeat multiplexes

This study presents the development and characterization of two X chromosomal short tandem repeat (STR) multiplexes utilizing reduced-size amplicons (less than 200 base pairs) for identity and kinship testing with degraded DNA. Approximately 1360 samples across 4 U.S. population groups were typed for 15 X chromosomal STR markers: DXS6789, DXS7130, DXS9902, GATA31E08, DXS7424, GATA165B12, DXS101, DXS6795, GATA172D05, DXS10147, DXS8378, DXS7132, DXS6803, HPRTB, and DXS7423. A high degree of polymorphism was observed for each marker and both multiplexes were sensitive down to 200pg of pristine DNA. The two proposed multiplexes are suitable for forensic use, and show potential for improved analysis of compromised bone samples.

Quality standards in Biobanking: authentication by genetic profiling of blood spots from donor's original sample

The field of Biobanking requires extensive work to maintain traceability of samples. However, sometimes the necessity to authenticate a sample may arise. To address these circumstances, we herein present a method for authenticating derivatives by using a blood spot from each donor, attached to a sample authentication form, by means of genetic profiling. Blood spots are collected at the time a blood sample is donated at a health centre and before processing the blood sample at the biobank. To test the validity of our approach over time, we analyzed 26 blood spots stored at room temperature in our facilities for more than 15 years. DNA was successfully extracted from the three storage materials tested in this study and 15 STR markers plus amelogenin were subsequently analyzed. The storage of a small blood spot attached to a sample authentication form proved to be efficient for genetic profiling and, therefore, may constitute a long-lasting (at least 15 years), cost-effective and effortless approach for genetic authentication of samples in biobanks.

Increased efficiency of genetic profiling through quantity and quality assessment of fluorescently labeled oligonucleotide primers

Optimizing the amount of primer to use in PCR amplification is one of the most important steps when developing protocols for genetic profiling, where subtle changes in primer concentration result in major impacts on the amount of desired product that is amplified. However; there are frequently discrepancies between the reported and actual quantity of primers delivered by suppliers, resulting in a need for re-optimization of conditions between primer orders and limiting the ability to standardize conditions between laboratories. To increase the consistency of genetic profiling protocols, we have developed a simple method to assess the quantity and quality of fluorescently labeled primers and therefore standardize reaction conditions through time and across laboratories. The method is based on analysis by electrophoresis with an automated fluorescent DNA analyzer.

Genotyping of simple sequence repeats--factors implicated in shadow band generation revisited

PCR amplification of microsatellite sequences generates, besides the main product corresponding to allele size, also additional, undesired products usually shorter by multiples of the repeated unit. These extra products known as shadow bands or stutter products may complicate genotyping. The mechanism by which these artifacts are formed is not well understood and so no effective remedy has been found to cope with these spurious products. In this study, using the DNA templates containing the CAG/CTG repeats flanked by gene-specific sequences and universal priming sites, we analyzed the effects of many PCR variables on the shadow band generation. The most important result was that at the decreased temperature of the denaturation step during PCR cycling the shadow bands were either not formed or were strongly suppressed. Several possible sources of this effect are discussed.

An investigation of sequence deletions of amelogenin (AMELY), a Y-chromosome locus commonly used for gender determination

BACKGROUND

Accurate gender determination is crucial in many scientific disciplines, but especially so in prenatal diagnosis of X-linked diseases and forensic investigations. Today, molecular techniques, especially typing for a length variation in the X-Y homologous amelogenin gene (AMELX and AMELY), are used for gender assignation. This amelogenin test is an integral part of most PCR multiplex kits that are used for DNA profiling, but in 1998 there was a report of two normal males being typed as female with this test. Subsequently, a small number of amelogenin negative (or AMELY null) males have been reported in various populations but little data are available characterising these deletions.

AIMS

The study aims to determine the size of the deletion in five AMELY null males by typing DNA samples for markers surrounding this gender-determining locus. The possible relationships among the AMELY null samples are examined through analysis of their deletion size and associated Y-chromosome microsatellite haplotypes. We also attempt to determine the frequency of AMELY negative males in Australia.

SUBJECTS AND METHODS

DNA samples from five AMELY null males, from different geographical regions, were made available for this study. The samples were typed for eight sites, all located on the short arm of the Y chromosome, using PCR and gel electrophoresis. Eleven Y-chromosome specific microsatellites were also typed on each sample in order to generate haplotypes for phylogenetic analysis. A questionnaire was sent to all Australian forensic centres requesting information on the frequency of AMELY negative males observed in their laboratories.

RESULTS

Two different sized deletions were seen in the five AMELY null samples. One deletion (in two samples) has a size of between 304 and 731 kbp, whereas the other (in three samples) ranges between 712 and 1001 kbp. Y-microsatellite haplotypes indicate that the smaller deletion is probably identical in the two samples, but this is not the case with the larger deletion. The frequency of AMELY negative is rare in Australia, with an overall frequency of 0.02%.

CONCLUSION

Comparisons of both deletion size and haplotypes with published data suggest that most AMELY nulls are the result of independent evolutionary events, even in those populations where the frequency is relatively high. Although AMELY null males are extremely rare in most populations, typing an additional gender-determining locus should be considered in forensic investigations where the reference sample is of unknown gender.

Multiplex_QA: an exploratory quality assessment tool for multiplexed electrophoretic assays

Multiplex_QA is a data analysis tool for visualizing short- and long-term changes in the performance of multiplexed electrophoretic assays, particularly the commercial short tandem repeat (STR) kits used by the human forensic identity community. A number of quality metrics are calculated from the signal collected for the internal size standard included in nearly all multiplex assays. These quality metrics are related to the signal intensity, symmetry, retention, resolution, and noise of data collected by capillary electrophoresis systems. Interlocking graphical displays enable the identification of changes in the quality metrics with time, evaluation of relationships among the metrics, and detailed examination of electropherographic features of particularly interesting analyses. While primarily intended for exploring which metrics are most useful for documenting data quality, the current version of the tool is sufficiently robust for use by forensic scientists with an interest in data analysis and access to a fast desktop computer.

NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes

Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.

Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing

Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

Ultrafast diagnosis of the genetic-related disorders using the combined technologies of multiplex PCR and multichannel microchip electrophoresis

For the diagnosis of unexplained male infertility a multiplex PCR for 6 markers, which are well-known as candidate genes for studying male infertility and located on the human Y-chromosome, has been designed. The multiplex PCR products have been separated on a 12 channel microchip electrophoresis system, which can analyze different samples simultaneously. By combining the technologies of multiplex PCR with multichannel microchip electrophoresis, the number of the DNA markers that can be screened simultaneously is increased to be 72 marker (12 x 6) in a single run while the electrophoresis analysis time is reduced to be only 180 s.

Separation of Sperm and Epithelial Cells in a Microfabricated Device: Potential Application to Forensic Analysis of Sexual Assault Evidence

Forensic DNA analysis of sexual assault evidence requires separation of DNA from epithelial (victim) and sperm (perpetrator) cells. The conventional method used by crime laboratories, which is termed "differential extraction", is a time-consuming process. To supplant the conventional process, separation of sperm from a biological mixture containing epithelial cells has been demonstrated on a microfluidic device. This separation utilizes the differential physical properties of the cells that result in settling of the epithelial cells to the bottom of the inlet reservoir and subsequent adherence to the glass substrate. As a result, low flow rates can be used to separate the sperm cells from the epithelial cell-containing biological mixture. Following cell separation on the microdevice, DNA extraction, amplification, and separation were performed using conventional laboratory methods, showing that the cell separation product in the outlet reservoir was of male origin. The reported cell separation has the potential to impact the forensic DNA analysis backlog of sexual assault cases by circumventing the time-consuming conventional differential extraction procedure.

NIST Mixed Stain Study 3: DNA quantitation accuracy and its influence on short tandem repeat multiplex signal intensity

The Mixed Stain Study 3 (MSS3) interlaboratory challenge exercise evaluated the 2001 performance of STR multiplex DNA typing systems using a set of seven DNA extracts of designed concentration and composition. This initial report focuses on the linkages connecting the measurement of the concentration of DNA ([DNA]) to the observed STR multiplex signal intensities. There is a causal relationship between [DNA] measurement accuracy and the efficiency of STR multiplex analysis. There are no intrinsic measurement performance differences among the [DNA] measurement technologies reported. However, there are large differences in the efficiencies of amplification, separation, and detection among participants using the same nominal measurement systems.

Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles

A population study of Chamorros and Filipinos using short tandem repeat (STR) loci amplified with the AmpFlSTR Profiler Plus PCR amplification kit demonstrated an excess of observed homozygosity at the D8S1179 locus. Use of a different set of D8S1179 primers to type the same samples did not demonstrate an excess of homozygosity and showed discordant genotypes at the D8S1179 locus. A single point mutation, G-to-A transition, 16 nucleotides from the 3' end of the reverse primer, was identified to cause allele dropout when using the AmpFlSTR Profiler Plus primer set. An additional D8S1179 reverse primer specific for the variant was constructed resulting in the recovery of the null allele. The primer was included in the newly developed AmpFlSTR Identifiler PCR amplification kit. No deleterious effects or non-specific peaks were observed in validation experiments evaluating primer concentration, Mg2+ concentration, annealing temperature and population samples.