Developmental validation of the ForenSeq® Kintelligence kit, MiSeq FGx® sequencing system and ForenSeq Universal Analysis Software

Forensic Investigative Genetic Genealogy, a recent sub discipline of forensic genomics, leverages the high throughput and sensitivity of detection of next generation sequencing and established genetic and genealogical approaches to support the identification of human remains from missing persons investigations and investigative lead generation in violent crimes. To facilitate forensic DNA evidence analysis, the ForenSeq® Kintelligence multiplex, consisting of 10,230 SNPs, was developed. Design of the ForenSeq Kintelligence Kit, the MiSeq FGx® Sequencing System and the ForenSeq Universal Analysis Software is described. Developmental validation in accordance with SWGDAM guidelines and forensic quality assurance standards, using single source samples, is reported for the end-to-end workflow from library preparation to data interpretation. Performance metrics support the conclusion that more genetic information can be obtained from challenging samples compared to other commercially available forensic targeted DNA assays developed for capillary electrophoresis (CE) or other current next generation sequencing (NGS) kits due to the higher number of markers, the overall shorter amplicon sizes (97.8% <150 bp), and kit design. Data indicate that the multiplex is robust and fit for purpose for a wide range of quantity and quality samples. The ForenSeq Kintelligence Kit and the Universal Analysis Software allow transfer of the genetic component of forensic investigative genetic genealogy to the operational forensic laboratory.

On the Forensic Use of Y-Chromosome Polymorphisms

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies.

Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion

Background

The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quantity or degraded evidence leading to allele and locus dropout; allele sharing of contributors leading to allele stacking; and differentiation of PCR stutter artifacts from true alleles. There is variation in statistical approaches used to evaluate the strength of the evidence when inclusion of a specific known individual(s) is determined, and the approaches used must be supportable. There are concerns that methods utilized for interpretation of complex forensic DNA mixtures may not be implemented properly in some casework. Similar questions are being raised in a number of U.S. jurisdictions, leading to some confusion about mixture interpretation for current and previous casework.

Results

Key elements necessary for the interpretation and statistical evaluation of forensic DNA mixtures are described. Given the most common method for statistical evaluation of DNA mixtures in many parts of the world, including the USA, is the Combined Probability of Inclusion/Exclusion (CPI/CPE). Exposition and elucidation of this method and a protocol for use is the focus of this article. Formulae and other supporting materials are provided.

Conclusions

Guidance and details of a DNA mixture interpretation protocol is provided for application of the CPI/CPE method in the analysis of more complex forensic DNA mixtures. This description, in turn, should help reduce the variability of interpretation with application of this methodology and thereby improve the quality of DNA mixture interpretation throughout the forensic community.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0429-7) contains supplementary material, which is available to authorized users.

SNP Miniplexes for Individual Identification of Random-Bred Domestic Cats

Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random‐bred domestic cats, focusing on individual and phenotypic identification. Seventy‐eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot^®). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10⁻¹⁹ across all Western cat populations and the likelihood ratio was 1.52 × 10¹⁸. These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications.

Species specificities among primates probed with commercially available fluorescence-based multiplex PCR typing kits

To assess species specificities among primates of signals from short tandem repeat (STR) loci included in two commercially available kits, mainly the AmpFlSTR Identifiler kit and additionally the GenePrint PowerPlex 16 system, we analyzed 69 DNA samples from 22 nonhuman primate species representing apes, Old World Monkeys (OWMs), New World Monkeys (NWMs), and prosimians. Each prosimian species and the NWM cotton-top tamarin apparently lacked all STR loci probed. Only one peak, the amelogenin-X peak, was evident in samples from all other NWMs, except the owl monkey. In contrast, several loci, including the amelogenin-X peak, was evident in samples from each OWM species. Notably, for each ape sample, the amelogenin peaks were concordant with morphological gender of the individual. Among the primates, especially in apes, the numbers of alleles for STR loci were increasing according to their phylogenetic order: prosimians<NWMs<OWNs<apes, and so among apes: agile gibbons<white handed gibbons<orangutans<gorillas/common chimpanzees/bonobos. The species specificities among primates for a few commercially released multiplex STR kits examined in this study would contribute to forensic examinations.

I-DNASE21 system: development and SWGDAM validation of a new STR 21-plex reaction

I-DNASE21 is a new STR multiplex system that amplifies 21 STR autosomal loci, plus the amelogenin locus in one reaction. This system has been designed to analyze all the STR loci included in the Combined DNA Index System (CODIS), Interpol Standard Set of Loci (ISSL), Extended European Standard Set (ESS-Extended), UK National Criminal Intelligence DNA Database (NDNAD) and German Core loci (GCL). This manuscript presents the validation of the I-DNASE21 system according to the revised guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). The results of this validation, added to the extremely high discriminatory power showed, suggest that I-DNASE21 could be a potentially helpful tool for identification and kinship determination even in complex paternity cases.

Past, present and future of forensic DNA typing

Recent advances in our ability to dissect the human genome and the availability of platforms for genome-wide analysis and whole-genome sequencing are expected to develop new tools for both biomedical and forensic DNA analyses. Nowadays, we can individualize single cells left at the crime scene or analyze ancient human remains. Here, we provide a general view on the past, current and likely future directions of forensic DNA analysis.

Development and validation of I-DNA1: a 15-Loci multiplex system for identity testing

This paper presents a system for the multiplex amplification of 15 loci, known as I-DNA1, which combines mini and midiSTR technology, with amplicon sizes ranging from 49 to 297 bp. I-DNA1 analyses all the STR loci included in the CODIS and the Interpol Standard Set of loci, nine of the ten European core loci and seven of the eight German core loci, making it suitable for use in identifying humans. Moreover, its high sensitivity and the small size of its amplicons mean that I-DNA1 is potentially highly useful for analysing highly degraded and/or very small DNA samples.

Normalization of red cell enolase level following allogeneic bone marrow transplantation in a child with Diamond-Blackfan anemia

We describe a girl with Diamond-Blackfan anemia with accompanying red cell enolase deficiency. At the age of 9 yr old, the patient received allogeneic bone marrow transplantation from her HLA-identical sister who had normal red cell enolase activity. While the post transplant DNA analysis with short tandem repeat has continuously demonstrated a stable mixed chimerism on follow-up, the patient remains transfusion independent and continues to show a steady increase in red cell enolase activity for over two and a half years following bone marrow transplantation.

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.

A multiplex assay with 52 single nucleotide polymorphisms for human identification

A total of 52 SNPs reported to be polymorphic in European, Asian and African populations were selected. Of these, 42 were from the distal regions of each autosome (except chromosome 19). Nearly all selected SNPs were located at least 100 kb distant from known genes and commonly used STRs. We established a highly sensitive and reproducible SNP-typing method with amplification of all 52 DNA fragments in one PCR reaction followed by detection of the SNPs with two single base extension reactions analysed using CE. The amplicons ranged from 59 to 115 bp in length. Complete SNP profiles were obtained from 500 pg DNA. The 52 loci were efficiently amplified from degraded samples where previously only partial STR profiles had been obtained. A total of 700 individuals from Denmark, Greenland, Somalia, Turkey, China, Germany, Taiwan, Thailand and Japan were typed, and the allele frequencies estimated. All 52 SNPs were polymorphic in the three major population groups. The mean match probability was at least 5.0 x 10(-19) in the populations studied. Typical paternity indices ranged from 336 000 in Asians to 549 000 in Europeans. Details of the 52 SNP loci and population data generated in this work are freely available at http://www.snpforid.org.

A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA

Analysis of short tandem repeat makers has become the most powerful tool for DNA typing in forensic casework analysis. Unfortunately, typing of DNA extracted from telogen shed hairs, bones buried in the soil or from paraffin-embedded, formalin-fixed tissue often reveals no results due to the degradation of DNA. The reduction in size of the target fragments by development of new primers and their combination in multiplex approaches open a new field of DNA analysis. Here we present a new sensitive short pentaplex PCR including the loci amelogenin, TH01, VWA, D3S1358 and D8S1179. Validation tests of our new method included sensitivity, mixtures, human specificity, artificial degradation of DNA by DNase I and case work analysis on a panel of different forensic samples. The detection limit was 12.5 pg of human DNA, and mixtures of 50 pg in a total of 1000 pg were clearly detectable and revealed complete profiles. Only DNA extracts of human primates displayed a few signals, whereas other animal, fungal or bacterial DNA showed no signals. Our method proved extremely valuable in the analysis of artificially degraded DNA and in forensic cases, where only poorly preserved DNA was available. This approach and other similar methods can aid in the analysis of samples where allelic drop out of larger fragments is observed. It is highly recommended to develop more of these multiplexes to improve poor quality DNA typing.

The application of miniplex primer sets in the analysis of degraded DNA from human skeletal remains

A new set of multiplexed PCR primers has been applied to the analysis of human skeletal remains to determine their efficacy in analyzing degraded DNA. These primer sets, known as Miniplexes, produce shorter amplicons (50-280 base pairs (bp)) than standard short tandem repeat (STR) kits, but still utilize the 13 CODIS STR loci, providing results that are searchable on national DNA databases. In this study, a set of 31 different human remains were exposed to a variety of environmental conditions, extracted, and amplified with commercial and Miniplex DNA typing kits. The amplification efficiency of the Miniplex sets was then compared with the Promega PowerPlex 16 system. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only 16% of the samples generated full profiles with the Powerplex 16 kit. Complete profiles were obtained for 11 of the 12 Miniplex loci with amplicon sizes less than 200 bp. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for anthropological and forensic analysis of degraded DNA from human skeletal remains.

Short amplicon STR multiplex for stain typing

We developed a short tandem repeat (STR) typing kit based on DNA database systems that are included in, for example, the Interpol Standard Set of Loci recommendations (i.e., TH01, VWA, D3S1358, FGA) and the gender typing system Amelogenin. Two different multiplex sets were tested using the fluorescent dyes FAM, JOE, and VIC. The PCR results were compared to the commercially available AmpFISTR Blue kit, which contains the STRs D3S1358, VWA, and FGA. The advantage of our multiplex compared with the Blue kit was the generation of shorter amplicons (<200 bp) and the higher combined power of discrimination.

Co-amplification of ENFSI-loci D3S1358, D8S1179 and D18S51: validation of new primer sequences and allelic distribution among 2874 individuals

The present communication presents a new triplex PCR co-amplifying three loci (D3S1358, D8S1179 and D18S51) recommended for STR typing by the European Network of Forensic Science Institutes (ENFSI). Twenty-two different primers were tested to optimise the PCR. Four of the six primer sequences finally chosen were self selected, the fifth was a published one and the sixth derived from a commercially available multiplex kit. Using this PCR-setup, even minimum amounts of genomic DNA are sufficient to analyse the STR loci D3S1358, D8S1179 and D18S51 in parallel. Especially in forensic casework, where DNA is mostly limited and often contaminated with enzyme inhibitors, this new PCR proved to be very advantageous. To demonstrate the reliability, buccal swabs from 2874 persons were typed not only with the new triplex PCR but also with a commercially available multiplex kit.

Nine short tandem repeat loci analysis in aged semen stains using the AmpFLSTR Profiler Kit and description of a new vWA variant allele

Nine short tandem repeat (STR) loci, D3S1358, D5S818, vWA, TH01, D13S317, TPOX, FGA, D7S820 and CSF1PO, were investigated in semen stains of various ages using the AmpFLSTR Profiler Kit. The nine STR loci were typed from semen stains stored for up to 25 years with the application of 1-10 ng DNA. This system provides a useful tool in medicolegal individualization of aged semen stains. During this investigation we found a new variant allele 18.1 at the vWA locus.

Multiplex short tandem repeat typing in degraded samples using newly designed primers for the TH01, TPOX, CSF1PO, and vWA loci

We performed multiplex polymerase chain reaction (PCR) for the TH01, TPOX, CSF1PO, and vWA loci using a newly designed pair of primers that yield smaller fragments than reported previously [Fujii et al., J Hum Genet 45 (2000) 303; Lederer et al., Int J Legal Med 114 (2000) 87]. These loci can be detected in the range of 74-143 bp amplifying products. This system required genomic DNA in a range of 80 pg to 2 ng, and proved to be a sensitive typing method. We compared our system against the GenePrint Fluorescent STR Multiplex Systems CTTv (Promega, Madison, WI, USA), using DNA extracted from old bloodstains left to stand for 17-26 years at room temperature. With our designed system, all allele-typing efforts were successful in the range of 1-5 ng DNA, while no signal peaks were detected, even with when using 10 ng of DNA GenePrint Fluorescent STR Multiplex Systems CTTv.

Comparison of short tandem repeat and variable number tandem repeat genetic markers for quantitative determination of allogeneic bone marrow transplant engraftment

Variable number tandem repeats (VNTRs) were among the first genetic markers used to quantitate bone marrow transplant engraftment. The limitations of PCR-based VNTR markers in distinguishing some donor/recipient pairs has shown the need for additional genetic markers to analyze engraftment. Short tandem repeats (STRs) provide an excellent tool for this purpose because of their high degree of polymorphism and relatively short length. We compared STR analysis results with previous VNTR results for 16 post-transplantation samples from four allogeneic bone marrow transplant patients. Previously analyzed patient samples were chosen to cover the full range of engraftment. DNA samples from each patient were analyzed in a blinded fashion. Good quantitative correlation was found between STR and VNTR results in samples from all four patients. STR markers were informative in one patient for whom PCR-based VNTR markers were not available. Correlation of VNTR and STR methods helps to validate the use of STRs for the quantitative analysis of bone marrow transplant engraftment. This study demonstrates that STR-based human identity testing kits are well suited for engraftment analysis.

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.

Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing

A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testing were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA, vWA, TH01) is an extension of published work, whereas no extensive sequence information is available with respect to the D3S1358, CSF1PO, and TPOX loci. Sequencing of alleles at each locus has provided quantitative data with respect to the true nucleotide length of common alleles, and of alleles that vary in length from the common alleles. All alleles that were identified as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CSF1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tandem repeat is demonstrated at the FGA locus. Alleles in which the core tandem repeat is interrupted by a repeat unit of different sequence have a reduced percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particular locus, and methods used to interpret amplification imbalance of heterozygous alleles at a locus is also addressed.

Practical applications of genotypic surveys for forensic STR testing

Legitimate genotype frequency estimation for multiallelic loci relies on component allele frequencies, as population surveys represent only a fraction of possible DNA profiles. Multilocus genotypes from two ethnic human populations, African American (n=195) and U.S. Caucasian (n=200), were compiled at 13 STR loci that are used worldwide in forensic investigation (D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820). Sex-specific AmpFlSTR multiplexes provided stringent PCR-based STR typing specifically optimized for multicolor fluorescence detection. Heterozygosity at each STR locus ranged from 0.57 to 0.89 and encompassed from seven (TH01) to twenty-one (D21S11) alleles. Homozygosity tests, tests based on the distinct numbers of observed homozygous and heterozygous classes, log likelihood ratio tests, and exact tests assessed that the degree of divergence from theoretical Hardy-Weinberg proportions for all 13 STRs does not have practical consequence in genotype frequency estimation. Departures from linkage equilibrium, between loci, that imposed significance to forensic calculations were not indicated by observed variance of the number of heterozygous loci or Karlin interclass correlation tests. For forensic casework, reliable multilocus profile estimates may be obtained from the product of component genotype frequencies, each calculated through application of the Hardy-Weinberg equation to population database allele frequency estimates reported here. The average probability that two randomly selected, unrelated individuals possess an identical thirteen-locus DNA profile was one in 1.8x10(15) African Americans and one in 3.8x10(14) U.S. Caucasians.

Short tandem repeat methodology for genotypic identification of single-person versus multi-person use of syringes

OBJECTIVE

To develop laboratory methods to differentiate between single- versus multi-person use of syringes by injection drug users.

METHODS

Forensic short tandem repeat (STR) genetic analysis was undertaken to cross-validate a test panel of trace blood contents from syringes representing single- versus multi-person syringe use. Laboratory-simulated scenarios of needle sharing generated 34 syringe washes that were blinded for evaluation. Polymerase chain reaction was used to amplify the polymorphic STR locus D6S502 from blood trace contents in used syringes. Alleles were sized and quantified using a commercial gene sequencer. A statistical algorithm was developed to determine the number of alleles present in the amplified DNA fragments. Syringes with more than two expected alleles were considered to represent multi-person syringe use. Sensitivity, specificity and the kappa coefficient were calculated.

RESULTS

Allelic matrix-based analysis of alleles from the single STR successfully characterized single-use (n = 12) and multiple-use (n = 22) syringes with 68% sensitivity and 100% specificity upon re-analysis. The extent of agreement over and above chance (kappa = 0.6; P < 0.0001) indicated good agreement for differentiating single- versus multi-person syringe use.

CONCLUSIONS

These findings suggest that improved genotypic STR analysis of syringe material could be an adjunct to methods for validating self-reported needle sharing, conducting behavioral surveillance of needle-sharing behaviors, and evaluating interventions such as needle-exchange programs. Assays based on multiple STR loci will undoubtedly improve upon the promising results obtained from laboratory simulations of needle sharing.

DNA microsatellite analysis using ion-pair reversed-phase high-performance liquid chromatography

Genotyping based on short tandem repeat (STR) regions is used in human identification and parentage testing, gene mapping studies, cancer diagnostics, and diagnosis of hereditary diseases. Analysis of STR systems using slab gel electrophoresis requires lengthy and labor-intensive procedures. Therefore, alternative methods such as capillary electrophoresis or ion-pair reversed-phase high-performance liquid chromatography (IPRP HPLC) have been used to analyze DNA. IPRP HPLC offers an attractive substitute to gel electrophoresis for STR analysis because of the reduced analysis time, and there is no need for the waste disposal associated with radioisotopic, enzyme-linked, or fluorescence detection systems. We evaluated the use of IPRP HPLC for the sizing and typing of STR alleles from the HUMTHO1 locus. The IPRP HPLC conditions (column temperature, flow rate, percent organic modifier per minute) were optimized for the separation of PCR products. Using the optimized separation conditions, the alleles of the HUMTHO1 system were sized in their native state (double standard) with the use of internal markers. The typing results correlated 100% to accepted methods of DNA typing. The analysis time for the HUMTHO1 locus was less than 14 min, and the alleles could be peak captured for further examination following such as sequencing.

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.