Detection and quantitative characterization of artificial extra peaks following polymerase chain reaction amplification of 14 short tandem repeat systems used in forensic investigations

Modeling the minus two base pair stutter ratio of the D1S1656 locus: A sequence-based mixture distribution model

In this study, we propose a stutter ratio for a minus two base pair stutter (-2bpSR) model of the D1S1656 locus in capillary electrophoresis (CE)-based short tandem repeat (STR) typing. DNA from a total of 108 Japanese individuals was analyzed via massively parallel sequencing to investigate the length of the longest uninterrupted stretch of two base repeat motif (2bpLUS value) within repetitive structures involving the flanking region. Additionally, -2bpSR data was collected using the GlobalFiler Kit on a 3500xL Genetic Analyzer. As a result of sequencing analysis, all alleles were classified into two types by their 2bpLUS values. The -2bpSR differed significantly between the types. Then, we modeled the -2bpSR with a mixture log-normal distribution using the classification of alleles based on the 2bpLUS values. Furthermore, probabilities of the sequence type within each repeat number in the mixture log-normal distribution model were estimated using logistic regression for each of the five major detected populations. This study is expected to enable interpretation of STR typing while considering minus two base pair stutter at the D1S1656 locus.

Development of microsatellite markers for a soricid water shrew, Chimarrogale platycephalus, and their successful use for individual identification

The soricid water shrew Chimarrogale platycephalus is a mammalian species endemic to the Japanese Islands. The animals inhabit the islands of Honshu and Kyushu, and are considered to be extinct in Shikoku. Information on this water shrew from Honshu and Kyushu is scarce, and C. platycephalus is registered on many local governments' red lists as an endangered species. There are very few studies on their ethology, ecology or phylogenetics, due to difficulties related to the shrews being both nocturnal and aquatic: to study C. platycephalus, field research must be conducted in mountain streams at night. To overcome these challenges, we previously established a genetic analysis method using the feces of C. platycephalus, as a result of which the amount of phylogenetic and phylogeographic data has increased and our understanding of the species has improved. In this study, microsatellite markers were developed, and analyses using markers for 21 loci were performed. Moreover, to confirm the ability of these 21 microsatellite markers to differentiate individuals, all markers were tested using fecal and tissue specimens from 12 individuals reared separately in an aquarium. Using as few as 12 of these loci, individual differentiation with 100% accuracy should be achievable. The development of microsatellite markers in this study and the establishment of individual identification methods should greatly contribute to future ecological, ethological, population genetics and biogeographical research on C. platycephalus.

Detection and analysis of the cause of false-tetra-allelic patterns of locus D10S1435 at the sequence level

A number of artifacts produced in forensic DNA typing make the interpretation more complicated and even lead to typing errors. Here, we reported the cause of false-tetra-allelic patterns of STR locus D10S1435 at the sequence level. To confirm the true genotyping, the sample with four allelic peaks was re-amplified and sequenced. The amplicon sequences of D10S1435, D20S482, D6S1017, and D10S1248 loci were analyzed by software BioXM and RNAstructure. We successfully reproduced the four-peak phenomenon by adding various concentration of magnesium chloride into the loading mixtures to simulate the suboptimal electrophoresis conditions. The false four allelic peaks may be caused by the specific nucleotide sequence of locus D10S1435 which tends to form secondary structures under the suboptimal electrophoresis conditions. The relatively high GC content and extremely uneven distribution give the amplicon a potency to resist complete denaturation at the phase of sample preparation and a tendency to form intra- and intermolecular secondary structures during post-injection.

Separation of Y-chromosomal haplotypes from male DNA mixtures via multiplex haplotype-specific extraction

In forensic analysis, the interpretation of DNA mixtures is the subject of ongoing debate and requires expertise knowledge. Haplotype-specific extraction (HSE) is an alternative method that enables the separation of large chromosome fragments or haplotypes by using magnetic beads in conjunction with allele-specific probes. HSE thus allows physical separation of the components of a DNA mixture. Here, we present the first multiplex HSE separation of a Y-chromosomal haplotype consisting of six Yfiler short tandem repeat markers from a mixture of male DNA.

De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) Using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers

Chinese jujube (Ziziphus jujuba Mill.) is an economically important deciduous tree that has high therapeutic value and health benefits. However, a lack of sequence data and molecular markers have constrained genetic and breeding studies for better fruit quality and other traits in Chinese jujube. In this study, two combined cDNA libraries of ‘Dongzao’ fruit representing the early and late stages of fruit development were constructed and sequenced on the 454 GS FLX Titanium platform. In total, 1,124,197 reads were generated and then de novo assembled into 97,479 unigenes. A total of 52,938 unigenes were homologous to genes in the NCBI non-redundant sequence database. A total of 33,123 unigenes were assigned to one or more Gene Ontology terms, and 16,693 unigenes were classified into 319 Kyoto Encyclopedia of Genes and Genomes pathways. The results showed that the Smirnoff-Wheeler pathway was the main pathway for the biosynthesis of ascorbic acid in Chinese jujube. The number of differentially expressed genes between the two stages of fruit development was 1,764, among which 974 and 790 genes were up-regulated and down-regulated, respectively. Furthermore, 9,893 sequences were identified containing SSRs. 93 primer pairs designed from the sequences with a tri-nucleotide repeat showed successful PCR amplification and could be validated in Chinese jujube accessions and Z. mauritiana Lam and Z. acidojujuba as well, of which 71 primer pairs were polymorphic. The obtained transcriptome provides a most comprehensive resource currently available for gene discovery and the development of functional markers in Z. jujuba. The newly developed microsatellite markers could be used in applications such as genetic linkage analysis and association studies, diversity analysis, and marker-assisted selection in Chinese jujube and related species.

Scoring microsatellite loci

Microsatellites have been utilized for decades for genotyping individuals in various types of research. Automated scoring of microsatellite loci has allowed for rapid interpretation of large datasets. Although the use of software produces an automated process to score or genotype samples, several sources of error have to be taken into account to produce accurate genotypes. A variety of problems (from extracting DNA to entering a genotype into a database) which can arise throughout this process might result in erroneous genotype assignment to one or more samples, potentially confounding the conclusions of your study. Correctly assigning a genotype to a sample requires knowledge of the chemistry you use to generate the data as well as the software you use to analyze these results. In this chapter we describe the critical and more common points that researchers experience when scoring microsatellite loci. More importantly we provide insight from an experienced perspective for these challenges.

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.

Characterising stutter in forensic STR multiplexes

Stutter is an artefact seen when amplifying short tandem repeats and typically occurs at one repeat unit shorter in length than the parent allele. In forensic analysis, stutter complicates the analysis of DNA profiles from multiple contributors, known as mixed profiles, a common profile type. Consequently it is important to both understand and predict stutter behaviour in order to improve our understanding of the resolution and interpretation of these profiles. Whilst stutter is well recognised and documented, little information is available that identifies and quantifies what influences the formation of stutter. In this work we use a novel approach to examine this. We have used synthetic oligonucleotides comprising multiple repeat units to test; the influence of repeat number, the influence of repeat sequence and the impact of interruptions to the repeat sequence length. Using multiple replicates allows detailed statistical analysis. We have confirmed a linear relationship between stutter ratio and repeat number. We have shown that increased A-T content increases stutter ratio and that interruptions in repeating sequences decreased stutter ratios to levels similar to the longest uninterrupted repeat stretch. We also found that there was no relationship between stutter ratio and repeat number for a repeat unit with an A-T content of 1/4 and that half of the interrupted repeat sequences stuttered significantly less than their longest uninterrupted repeat stretches. We have applied the knowledge gained to examine specific features of the loci present in the AmpFlSTR(®) SGM Plus(®) multiplex kit used in our laboratory.

A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping

BACKGROUND

Individual fingerprinting based on molecular markers has become a popular tool for studies of population genetics and analysis of genetic diversity in germplasm collections, including the solution of synonymy/homonymy and analysis of paternity and kinship. Genetic profiling of individuals is nowadays based on SSR (Simple Sequence Repeat) markers, which have a number of positive features that make them superior to any other molecular marker developed so far. In humans, SSRs with core repeats three to five nucleotides long are preferred because neighbour alleles are more easily separated and distinguished from each other; while in plants, SSRs with shorter repeats, namely two-nucleotides long, are still in use although they suffer lower separation of neighbour alleles and uncomfortable stuttering.

RESULTS

New microsatellite markers, containing tri-, tetra-, and penta-nucleotide repeats, were selected from a total of 26,962 perfect microsatellites in the genome sequence of nearly homozogous grapevine PN40024, assembled from reads covering 8.4 X genome equivalents. Long nucleotide repeats were selected for fingerprinting, as previously done in many species including humans. The new grape SSR markers were tested for their reproducibility and information content in a panel of 48 grape cultivars. Allelic segregation was tested in progenies derived from two controlled crosses.

CONCLUSION

A list of 38 markers with excellent quality of peaks, high power of discrimination, and uniform genome distribution (1-3 markers/chromosome), is proposed for grape genotyping. The reasons for exclusion are given for those that were discarded. The construction of marker-specific allelic ladders is also described, and their use is recommended to harmonise allelic calls and make the data obtained with different equipment and by different laboratories fully comparable.

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.

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.

A Proposal for Standardization in Forensic Canine DNA Typing: Allele Nomenclature of Six Canine-Specific STR Loci

In this study a proposal for the allele nomenclature of six polymorphic short tandem repeat (STR) loci (PEZ3, PEZ6, PEZ8, PEZ10, FHC2161, and FHC2328) for canine genotyping (Canis lupus familiaris) is presented. The nomenclature is based on the sequence data of the polymorphic region of the microsatellite markers as recommended by the DNA commission of the International Society of Forensic Haemogenetics (ISFH) in 1994 for human DNA typing. To cover commonly and rarely occurring alleles, a selection of homozygous and heterozygous animals were analyzed and subjected to sequence studies. The alleles consisted of simple tri- and tetra-nucleotide repeat patterns as well as compound and highly complex repeat patterns. Several alleles revealing the same fragment size but different repeat structures were found. The allele designation described here was adopted to the number of repeats, including all variable regions within the amplified fragment. In a second step the most commonly occurring alleles were added to an allelic ladder for each marker allowing a reliable typing of all alleles differing in size. A total number of 142 unrelated dogs from surrounding municipal animal homes, private households, and canines in police duty were analyzed. The data were added to a population database providing allele frequencies for each marker.

Effects of novel polymorphisms in the RAGE gene on transcriptional regulation and their association with diabetic retinopathy

Interactions between advanced glycation end products (AGEs) and the receptor for AGE (RAGE) are implicated in the vascular complications in diabetes. We have identified eight novel polymorphisms, of which the -1420 (GGT)n, -1393 G/T, -1390 G/T, and -1202 G/A were in the overlapping PBX2 3' untranslated region (UTR), and the -429 T/C (66.5% TT, 33.5% TC/CC), -407 to -345 deletion (99% I, 1% I/D, 0% D), -374 T/A (66.4% TT, 33.6% TA/AA), and +20 T/A were in the RAGE promoter. To evaluate the effects on transcriptional activity, we measured chloramphenicol acetyl transferase (CAT) reporter gene expression, driven by variants of the -738 to +49 RAGE gene fragment containing the four polymorphisms identified close to the transcriptional start site. The -429 C, -374 A, and 63-bp deletion alleles resulted in a mean increase of CAT expression of twofold (P < 0.0001), threefold (P < 0.001), and fourfold (P < 0.05), respectively, with the -374 T and A alleles yielding highly differential binding of nuclear protein extract from both monocyte- and hepatocyte-derived cell lines. The prevalence of the functional polymorphisms were investigated in subjects with type 2 diabetes (106 with and 109 without retinopathy), with the -429 C allele showing an increase in the retinopathy group (P < 0.05). These data suggest that the polymorphisms involved in differences in RAGE gene regulation may influence the pathogenesis of diabetic vascular complications.

Antibody repertoire development in fetal and neonatal piglets. V. VDJ gene chimeras resembling gene conversion products are generated at high frequency by PCR in vitro

The recovery of VDJ rearrangement is most often accomplished by PCR amplification of DNA extracted from mixtures of B-cells. Using this procedure in swine, VDJs containing chimeric V(H) genes that resemble gene-conversion products, are frequently encountered. To examine whether these chimeras could be the result of PCR artifacts, we used different combinations of swine VDJ templates, each having unique CDR1, CDR2 and D(H) segments, to generate >2600 clones. Using equal amounts of two templates and 30 cycles of PCR, up to 45% of the resultant clones were VDJ chimeras. The frequency of chimeras was independent of the specific VDJ template and the chimeras were generated regardless of whether Taq-, Pfu- or mixtures of Taq- and Pfu-polymerases were employed or whether PCR extension time was prolonged six-fold. The frequency of generating chimeras was dependent on the ratio of the two target DNAs although even ratios approximately 1:10 generated approximately 10% chimeric VDJs. Chimeras could be generated using only 10 cycles of PCR or using the initial template DNAs diluted as much as 1:10000. Of the 279 chimeric VDJs generated, 61% of the crossovers occurred in FR3, 21% in FR2 and 18% in both FR2 and FR3. We interpret these results to mean that in vivo gene conversion in this species can only be unambiguously proven when the VDJs from individual B-cells are bearing a single VDJ rearrangement amplified and sequenced or when VDJs are cloned without the use of PCR.

Assessing microsatellite instability with semiautomated fluorescent technology: application to the analysis of primary brain tumors

The replication error phenotype, revealed by the observation of widespread microsatellite instability (MIN), has been identified as a new mechanism of cancer susceptibility, and the comparison of the allele sizes of polymorphic microsatellite repeats between normal and tumor DNA is now frequently undertaken in colorectal and other human neoplasias. The lack of precise characterization of the electrophoretic profiles of microsatellites is one of the main sources of discord between the rate of MIN reported for the same type of tumor by different investigators. The recent introduction of fluorescent-based semiautomated microsatellite analysis allows a more accurate size comparison, but one or more artificial peaks, generated during polymerase chain reaction (PCR) and/or electrophoresis, are frequently detected along with the true allele peaks. The aim of this study was to characterize the most frequent artificial extra peaks in the short tandem repeats (STRs) used by us to assess MIN in human cancers. We analyzed eight microsatellite loci in 113 primary brain tumors. HumFibra/FGA exhibited the most frequent extra peak formation. For each microsatellite there is a characteristic pattern of artifact formation which must be recognized to avoid a false-positive diagnosis of MIN.

Detection of fetal-specific DNA after enrichment for trophoblasts using the monoclonal antibody LK26 in model systems but failure to demonstrate fetal DNA in maternal peripheral blood

Trophoblast cells can be detected in maternal blood during normal human pregnancy and DNA from these cells may be used for non-invasive prenatal diagnosis of inherited diseases. The possibility of enriching trophoblast cells from maternal blood samples using a monoclonal antibody (LK26) against a folate-binding protein, which recognizes trophoblast in normal tissues, in conjunction with immunomagnetic cell sorting was investigated. Verification of the presence of fetal DNA in the sorted samples was done by detection of fetal/paternal-specific short tandem repeat (STR) alleles using polymerase chain reaction (PCR) and automated fluorescence-based genotyping. After successful initial experiments using retroplacental blood samples with a high number of trophoblast cells or an artificial mixture of trophoblast cells and blood, several versions of the enrichment method were attempted on peripheral maternal blood samples. However, it was not possible to detect fetal DNA sequences in these samples, most probably due to the extremely low number of trophoblast cells. Positive identification and retrieval of trophoblast cells in suspension or trophoblast nuclear material prepared on microscope slides after cell sorting procedures can be a solution to this problem.

Accurate characterization of the tyrosine hydroxylase forensic allele 9.3 through development of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Accurate and precise determination of the number of repeats from a short tandem repeat (STR) sequence for a human gene locus is demonstrated for the first time by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). Specifically, the polymorphic human tyrosine hydroxylase (HUMTHO1) gene, a tetranucleotide STR forensic allele, was chosen as a model system to evaluate our approach for future characterization of both STRs and variable number of tandem repeats (VNTRs) by development of an ESI-FTICR-MS approach. The coding and noncoding strands from the HUMTHO1 9.3 allele are simultaneously resolved obtaining accurate (better than 70 ppm) average mass measurements of 25,783.23 and 24,754.55 Da for the coding and noncoding strands, respectively. The mass measurements are used to calculate the number of repeats for each strand, 'n', of 9.75169 and 9.75001 for the coding and noncoding strands, respectively. It will be shown how the value of 'n' can be used to directly determine the number of pure repeats and accurately determine the exact nature of the polymorphism within the repeat (if any). The single nucleotide deletion in the coding strand (adenine) and noncoding strand (thymine) were accurately identified using this approach. Interestingly, we observed the conversion of single-stranded to double-stranded DNA while the PCR product in the ESI buffer was being infused; the issues related to this observation will be presented. Previous results by other researchers investigating the HUMTHO1 9.3 allele using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) are directly compared with our results. Our results indicate that ESI-FTICR-MS is a powerful approach to rapidly and accurately characterize tandem repeating sequences which will ultimately lead towards the understanding of a complex class of diseases and in human identity determination.