The validation of short tandem repeat (STR) loci for use in forensic casework

Application of RapidHIT™ ID for cell authentication by fast and convenient STR profiling

BACKGROUND

As cell therapies are injected directly into the body, cell authentication is essential. Short tandem repeat (STR) profiling is used for human identification in forensics as well as for cell authentication. The standard methodology (DNA extraction, quantification, polymerase chain reaction, and capillary electrophoresis) takes at least 6 h and requires several instruments to obtain an STR profile. RapidHIT™ ID is a single automated instrument that provides an STR profile in 90 min.

OBJECTIVE

In this study, we aimed to propose a method to use RapidHIT™ ID for cell authentication.

METHODS

Four types of cells which are used for cell therapy or in the production process were used. The sensitivity of STR profiling was compared by the cell type and cell count using RapidHIT™ ID. Moreover, the effect of preservation solutions, pre-treatment with cell lysis solution, proteinase K, Flinders Technology Associates (FTA) cards, and dried or wet cotton swabs (with a single cell type or a mixture of two) were examined. The results were compared to those obtained by the standard methodology using genetic analyzer ThermoFisher SeqStudio.

RESULTS

We accomplished a high sensitivity through our proposed method that can benefit cytology laboratories. Although the pre-treatment process affected the quality of the STR profile, other variables did not significantly affect STR profiling.

CONCLUSION

As a result of the experiment, RapidHIT™ ID can be used as a faster and simpler instrument for cell authentication.

Overcoming obstacles: Analysis of blood and semen stains washed with different chemicals with ATR-FTIR

INTRODUCTION

Blood and semen stains are the most common biological stains encountered at crime scenes. The washing of biological stains is a common application that perpetrators use to spoil the crime scene. With a structured experiment approach, this study aims to investigate the effects of washing with various chemicals on the ATR-FTIR detection of blood and semen stains on cotton.

MATERIALS AND METHODS

On cotton pieces, a total of 78 blood and 78 semen stains were applied, and each group of six stains was immersed or mechanically cleaned in water, 40% methanol, 5% sodium hypochlorite solution, 5% hypochlorous acid solution, 5 g/L soap dissolved pure water, and 5 g/L dishwashing detergent dissolved water. ATR-FTIR spectra gathered from all stains and analyzed with chemometric tools.

RESULTS AND DISCUSSION

According to performance parameters of developed models, PLS-DA is a powerful tool for discrimination of washing chemical for both washed blood and semen stains. Results from this study show that FTIR is promising for use in detecting blood and semen stains that have become invisible to the naked eye due to washing of the findings.

CONCLUSION

Our approach allows blood and semen to be detected on cotton pieces using FTIR combined with chemometrics, even though it is not visible to the naked eye. Washing chemicals also can be distinguished via FTIR spectra of stains.

Analysis of five rare alleles at the STR loci D1S1656, D12S391, D13S317, Penta D, and D2S441

Short tandem repeat (STR) automatic typing technology is extensively used in forensic laboratories with commercial kits, in rare cases genotyping misinterpretations or mislabeling may occur due to unexpected rare alleles. This study refers to the investigation of several rare alleles observed from routine cases. Besides cross-kit verification with Goldeneye 25A (Beijing PeopleSpot Inc, China) and Huaxia platinum (Thermo Fisher Scientific, USA) kits, the next-generation sequencing technology by MiSeq FGx System (Illumina, USA) was applied to further validation. To solve the inconsistent outcomes reached by the above mentioned approaches at D2S441 locus, single gene amplification, gene cloning, and genetic sequencing was also performed. As a result, five rare alleles were detected. Two novel alleles of allele 3 at the D13S317 locus and allele 5 at the D2S441 locus were found; three previously reported alleles of allele 9 at D1S1656 locus, allele 19 at Penta D locus, and allele 28 at D12S391 locus in STRBase were initially supplemented with sequence information. We, therefore, propose that such uncommon observations with rare events should be carefully investigated and interpreted.

Determination of a criminal suspect using environmental plant DNA metabarcoding technology

There are criminal cases that no frequently used evidence, for example, human DNAs from the criminal, is available. Such cases usually are unresolvable. With the advent of DNA metabarcoding, evidences are mined from environmental DNA and such cases become resolvable. This study reports how a criminal suspect was determined by environmental plant DNA metabarcoding technology. A girl was killed in a rural wet area in China without a witness or video record. Pants with dried mud was found from one of her classmate's house. The mud was removed from the pants and 11 more mud or soil samples surrounding murder scene were collected. DNA was extracted from the soil. Chloroplast rbcL gene were amplified and sequenced on a next generation sequencing platform. After bioinformatics analysis, ZOTU composition of 12 samples demonstrated that the mud on the suspect's pants was from the criminal scene. The suspect finally made a clean breast of his crime. This case implies that plant DNA in the environment soil is a new source of evidence in determination of suspects using DNA metabarcoding technology and has high potentials of extensive applications in criminal cases.

Efficacy of reduced-size short tandem repeat PCR analysis for degraded DNA samples

BACKGROUND

Short tandem repeats (STR) typing is an essential analysis method for human identification in forensic field. When DNAs obtained from the field as evidences are severely degraded or in too small amounts, STR analysis often shows allele drop-out.

OBJECTIVE

To improve STR analysis for degraded DNA or trace DNA, reduced-size STR (rSTR) polymerase chain reaction (PCR) system was devised by selecting relatively large-size STR loci.

METHODS

The rSTR PCR system consisted of 8 loci (amelogenin, SE33, CSF1PO, D7S820, D13S317, D2S1338, TPOX, and FGA). The size of PCR product was reduced by designing new primers in the flanking region. The efficiency of this system was verified against existing kits through concordance study, sensitivity study, efficiency study, and casework sample study.

RESULTS

The size of PCR product in the rSTR PCR system was reduced to be less than 322 bp. The amplicon of each locus was reduced by about 100 bp on average. Results of this rSTR PCR system were confirmed using 146 Korean samples and other commercial kits. The rSTR PCR system was capable of analyzing DNA samples with a minimum amount of DNA of 16 pg and a degradation index of 4.215.

CONCLUSION

The rSTR PCR system was more effective than other PCR kits for obtaining genetic profiles from a small amount of DNA or degraded DNA. The combination of this new system and other commercial kits is more effective than existing systems. This combination is expected to be helpful for the identification of unidentified bodies and skeletal samples.

Evaluation of ten SNP Markers for Human Identification and Paternity Analysis in Persian Population

Background:

DNA markers are inevitable tools of human identification in forensic science. Single Nucleotide Polymorphisms (SNPs) are one category of these markers which is concerned to use especially in the case of degraded DNA because of their short amplicons.

Objectives:

Detection of highly informative SNPs by the criteria is the essential step to develop a useful panel of SNP markers. The purpose of this work is to get high informative SNPs for human identification in Persian ethnic of the Iranian population.

Material and Methods:

Genotype and allele frequencies of 10 SNPs from the SNPforID browser were determined by a PCR-RFLP method on 100 samples that was taken from 100 unrelated Persian people.

Results:

These ten SNPs were in Hardy-Weinberg equilibrium (P value > 0.1) except rs1355366 (P value = 0.02) and Heterozygosity of seven SNPs is greater than 0.45 but minor allele frequency of only four SNPs is more than 0.45. According to criteria only three SNPs rs1454361, rs2111980 and rs2107612 can pass all standards and are highly informative in population for forensic uses.

Conclusions:

Our data showed that the CPI (Combined probability of Identity) and CPE (Combined Power of Exclusion) for ten SNPs are 1.13 E-04 and 0.809 respectively. It was also showed based on the criteria only three SNPs (rs2107612, rs1454361 and rs2111980) are highly informative in Persian population. If we can find 39 SNPs with PE and PI close to PE and PI of these three SNPs (rs2107612, rs1454361 and rs2111980), we will be able to use of these 39 SNPs in human identification with sufficient power of discrimination.

A validation study of DNA methylation-based age prediction using semen in forensic casework samples

Previously, an age-predictive method based on DNA-methylation patterns in semen was developed, using three CpG sites (cg06304190 in the TTC7B gene, cg12837463, and cg06979108 in the NOX4 gene). Before considering the routine use of a new method in forensics, validation studies such as concordance and sensitivity tests are essential for obtaining expanded and more reliable forensic information. Here, we evaluated a previously described age-predictive method for semen for routine forensic use. Concordance testing showed a high correlation between the predicted and chronological age, with a mean absolute deviation from the chronological age of 4.8 years. Sensitivity testing suggested that age prediction with reliable accuracy and consistency was possible with >5 ng of bisulfite-converted DNA. We also confirmed the applicability of the age-predictive method in forensic casework, using forensic samples. Thus, the proposed method could serve as a very valuable forensics tool for accurate age prediction with semen samples.

Qualitative and quantitative assessment of Illumina's forensic STR and SNP kits on MiSeq FGx™

Massively parallel sequencing (MPS) is a powerful tool transforming DNA analysis in multiple fields ranging from medicine, to environmental science, to evolutionary biology. In forensic applications, MPS offers the ability to significantly increase the discriminatory power of human identification as well as aid in mixture deconvolution. However, before the benefits of any new technology can be employed, a thorough evaluation of its quality, consistency, sensitivity, and specificity must be rigorously evaluated in order to gain a detailed understanding of the technique including sources of error, error rates, and other restrictions/limitations. This extensive study assessed the performance of Illumina’s MiSeq FGx MPS system and ForenSeq™ kit in nine experimental runs including 314 reaction samples. In-depth data analysis evaluated the consequences of different assay conditions on test results. Variables included: sample numbers per run, targets per run, DNA input per sample, and replications. Results are presented as heat maps revealing patterns for each locus. Data analysis focused on read numbers (allele coverage), drop-outs, drop-ins, and sequence analysis. The study revealed that loci with high read numbers performed better and resulted in fewer drop-outs and well balanced heterozygous alleles. Several loci were prone to drop-outs which led to falsely typed homozygotes and therefore to genotype errors. Sequence analysis of allele drop-in typically revealed a single nucleotide change (deletion, insertion, or substitution). Analyses of sequences, no template controls, and spurious alleles suggest no contamination during library preparation, pooling, and sequencing, but indicate that sequencing or PCR errors may have occurred due to DNA polymerase infidelities. Finally, we found utilizing Illumina’s FGx System at recommended conditions does not guarantee 100% outcomes for all samples tested, including the positive control, and required manual editing due to low read numbers and/or allele drop-in. These findings are important for progressing towards implementation of MPS in forensic DNA testing.

Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea

Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10(-)⁵ for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.

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.

Forensic human identification in the United States and Canada: a review of the law, admissible techniques, and the legal implications of their application in forensic cases

Forensic human identification techniques are successful if they lead to positive personal identification. However, the strongest personal identification is of no use in the prosecution--or vindication--of an accused if the associated evidence and testimony is ruled inadmissible in a court of law. This review examines the U.S. and Canadian legal rulings regarding the admissibility of expert evidence and testimony, and subsequently explores four established methods of human identification (i.e., DNA profiling, forensic anthropology, forensic radiography, forensic odontology) and one complementary technique useful in determining identity, and the legal implications of their application in forensic cases.

Developmental validation of Mini-DogFiler for degraded canine DNA

Dogs (Canis lupus familiaris) are kept as pets in 39% of American households and are, therefore, a significant source of potentially probative biological evidence. As with any biological evidence, degradation can occur as a consequence of environmental exposure causing fracturing of the DNA and a resulting loss of intact template. Degraded human DNA analysis has benefited from the application of primer sets that amplify shorter nuclear sequences for core STR loci (miniSTRs), resulting in improved DNA profiles. This same approach was applied to our core canine STR loci. The 16-locus "DogFiler" panel was redesigned into three panels of miniSTRs for analysis of degraded canine DNA, with all primer pairs producing amplicons below 205 base pairs in length. These new miniSTR marker panels - known as Mini-DogFiler - were validated according to SWGDAM guidelines, and concordance with the original 16-locus multiplex was demonstrated through genotyping 1244 samples. The combination of these miniSTRs and a half-volume reaction increased the amplification success of degraded and low copy number canine biological samples resulting in a near three-fold increase in reportable alleles. This assemblage of miniSTRs along with the DogFiler panel and associated allelic ladder are the first non-human DNA profiling system to parallel the human forensic paradigm.

Human blood identification using the genome profiling method

In criminal investigations, usually it is necessary to identify whether blood spots found at crime scenes are from humans or not. Nowadays, immunohistochemical methods and DNA analysis are usually used for this purpose. However, such methods and DNA analysis are labor intensive and expensive, and require highly trained skilled technicians. Recently, the genome profiling method (GP method) was developed. However, its use as a human DNA analysis method has not been reported. In this report, an attempt was made to differentiate human blood samples from animal blood samples using the GP method for forensic purposes. DNA extracted from a rat, squirrel, cat, dog, cow, and antelope along with human blood samples were analyzed. Following cluster analysis the human samples clustered into a single group separate from the animal samples. Therefore, although the number of samples was small the results suggest that the GP method might enable us to differentiate human samples from various animal samples. It may become a powerful tool in the field of forensic science.

Capillary electrophoresis of human mtDNA control region sequences from highly degraded samples using short mtDNA amplicons

The forensic applications of mtDNA sequencing center primarily on samples that are either highly degraded or contain little or no nuclear DNA, since the testing of these sample types is often unsuccessful with more widely used nuclear STR profiling assays. In these cases, sequence data from the noncoding mtDNA control region are targeted due to its high variability. However, the ease of authentic DNA recovery and the strategy used for recovery depend strictly on the quality of the sample. In this chapter, we will cover mitochondrial DNA sequencing procedures for short mtDNA amplicons which range in size from 100 to 350 bp. Generally speaking, amplicons of this size are required only for the most degraded specimens, and the protocols described here have been specifically developed for recalcitrant human skeletal remains encountered during the course of a large-scale missing persons' identification effort. DNA templates from these types of specimens tend to exhibit various forms of intrastrand damage that, in turn, manifest as artifacts in the sequence data. Because these artifacts are not generally observed among sequence data from pristine templates, we address the particular data idiosyncrasies that warrant additional scrutiny. Although this chapter will primarily highlight this particular application, the basic experimental parameters and data considerations should easily extend to other applications and/or sample types. The protocols described here have been deliberately designed to produce raw sequence electropherograms and final mtDNA profiles that adhere to the strictest forensic guidelines in terms of overall data quality.

Molecular diagnosis of haemophilia A at Centro Hospitalar de Coimbra in Portugal: study of 103 families--15 new mutations

Haemophilia A (HA), the most commonly inherited bleeding disorder, has well known phenotype heterogeneity, influenced by the type of mutation, modulating factors and development of inhibitors. Nowadays, new technologies in association with bioinformatics tools allow a better genotype/phenotype correlation. With the main objective of identifying familial carrier women and to offer prenatal diagnosis, 141 HA patients belonging to 103 families, followed or referred to the Haemophilia Centre of CHC, E.P.E., were studied. Molecular diagnosis strategy was based on HA severity: IVS22 and IVS1 inversions, direct sequencing and MLPA technique. New missense and splicing mutations were further analyzed using molecular modelling. Genotype/phenotype correlation was assessed taking into account the known modulating factors. During this study, mutations were detected in 102/103 families, carrier status was determined in 83 women and 14 prenatal diagnoses were performed. In a total of 46 different mutations identified, 15 have not been reported previously by the HAMSTeRS and HGMD. Genotype/phenotype correlation revealed two cases with a clinical picture less severe than expected by the type of mutation identified. Six patients developed inhibitors: five severe (IVS22, IVS1, large deletion) and one mild (p. Gln2265Lys). The adopted strategy allowed the identification of 99% of the molecular alterations underlying the HA phenotype (98% detection rate for severe and 100% for moderate and mild). Evaluation of genotype-phenotype correlation was complemented with structural protein modelling of newly identified missense mutations, contributing to better understanding of the disease-causing mechanisms and to deepening knowledge on protein structure-function.

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.

Rapid typing of STRs in the human genome by HyBeacon melting

A new method based on DNA melting has been developed for the rapid analysis of STRs in the human genome. The system is based on homogeneous PCR followed by fluorescence melting analysis and utilises a HyBeacon probe combined with a PCR primer-blocker oligonucleotide. The use of blockers of different length permits identification of the full range of common D16S539 repeats enabling detection of 99.8% of known alleles. The interrogation of STRs can be carried out on standard genetic analysis platforms and could be applied to other loci to form the basis of a bespoke high-throughput system for use in forensic analysis, particularly as fluorescent genetic analysis platforms are now available for high-resolution melting. This methodology may be suitable for rapid forensic DNA analysis at the point-of-arrest or in a custody suite where it is important to identify an individual from a small group of suspects/detainees.

Developmental validation of reduced-size STR Miniplex primer sets

This paper describes a developmental validation study of three Miniplex sets covering 12 of the 13 CODIS loci. As these new sets will be used for the analysis of degraded and low level DNA, the validation studies were performed using 100-125 pg of DNA, the lowest input level at which peak balance, peak intensity, and allele consistency were stable. To demonstrate the applicability of the Miniplex sets to forensic casework, these validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM). A range of tests were performed including studies of concordance with standard multiplex kits, sensitivity and reproducibility, and PCR amplification conditions. Additionally, studies of mixtures, nonhuman and environmentally degraded DNA, and simulated forensic samples were performed. Our results demonstrate that Miniplex STR amplification procedures are a robust and sensitive tool for the analysis of degraded DNA.

Cancer and forensic microsatellites

Although not directly related, circumstances do occur in forensic investigations whereby cancer studies and forensic science cross paths. This review takes a look at the circumstances under which this may occur, and investigates some potential problems that can arise when tumor tissue is submitted for DNA profile analysis. A background to the underlying molecular biology of tumors is described, highlighting the genetic instabilities that are observed in DNA sequences of similar or identical primary structure to the short tandem repeat markers used in forensic DNA profiling kits.

Prenatal determination of the fetal RhD blood group by multiplex PCR: a 7-year Portuguese experience

OBJECTIVES

This is a retrospective study to evaluate the efficacy and accuracy of the multiplex polymerase chain reaction (PCR) amplification, for early detection of fetuses at risk for hemolytic disease, in the population living in Portugal, and to characterize the RhD-negative individuals at serologic and molecular level.

METHODS

2030 uncultured amniotic fluid samples and 2012 blood samples from the respective RhD-negative pregnant women were studied by multiplex PCR of intron 3/intron 4, exon 7 and 3'UTR. Amniocentesis was performed for a variety of medical indications. For quality control, serologic RhD blood groups were determined in the cord blood, after birth.

RESULTS

1361 fetal amniotic samples were RhD-positive (67%), 669 were RhD-negative. The average time for diagnosis was 2 days for uncultured amniocytes and the molecular versus serologic RhD typing (n = 809) had 99.5% concordance. Among the 2012 serologic RhD-negative mothers, 26 had an RhD-positive allele.

CONCLUSION

The multiplex PCR amplification used in this study was a rapid and accurate method to determine the RhD blood type in the population living in Portugal, being a great tool for management of pregnancies with fetuses at risk for alloimmune hemolytic disease. In this population, 1.3% of the serologic RhD-negative women have an RHD-positive allele.

Donor cell leukemia: a critical review

Approximately 40 cases of DCL have been reported in the literature; cases have been reported after allografts from bone marrow, peripheral blood and cord blood. The study of these cases may provide new insights into the mechanisms of leukemogenesis. Some data suggest that the prevalence of this complication has been under-estimated. Most cases of DCL have occurred following transplantation for leukemia, but there have also been cases reported after transplantation for non-malignant conditions. Various mechanisms have been proposed to explain how DCL arise and are briefly discussed. Additional studies are needed to define with more detail both the true prevalence of this complication and its precise pathogenetic mechanism.

Low volume amplification and sequencing of mitochondrial DNA on a chemically structured chip

Low volume (LV) amplification (1 microL) of nuclear DNA (nucDNA) on a chemically structured chip is an appropriate and highly sensitive method to simultaneously amplify amelogenin and 15 forensically relevant short tandem repeats (STR). In this study, a combined method using on-chip LV amplification of mitochondrial DNA (mtDNA) and subsequent on-chip LV cycle sequencing was established to obtain a method, which is sensitive and robust enough to allow reliable analysis of DNA amounts representing the single cell level. All the necessary steps of the procedure--except for the purification of the sequencing products--were accomplished within the same final 2-microL reaction volume.

Validation of sensitive human leukocyte antigen-sequence-specific primer and probe typing in forensic DNA examination

Validation studies were carried out with the commercially available HLA typing kit using a PCR-SPP (sequence-specific primer and probe) technique. This technique has made it possible to type class I (HLA-A and -B) and class II (HLA-DRB1 and -DQB1) alleles at low-resolution level with total 10 ng of template DNA, in addition to amplify directly from various forms of blood samples without DNA isolation procedure. Experimental examinations with bloodstains smeared on cotton cloth that were a week to 3 months old, bloodstains on gauze stored for 18 years, and buccal cells revealed that this HLA-SPP typing kit is a sensitive and reliable method for forensic investigations.

The dbMHC microsatellite portal: a public resource for the storage and display of MHC microsatellite information

Major histocompatibility complex (MHC) region Microsatellites (Msat) have been extensively used in various applications, such as disease mapping, forensics, and population genetics. A comprehensive review of HLA Msat primers has been previously published based on literature and sequence analysis, but electronic tools are lacking to make it easily accessible and actually used by the community. We have integrated data from this review, with an overlapping set of 31 Msat markers used in the 13th International Histocompatibility and Immunogenetics Workshop (IHIWS) to create a public archive that will synchronize published descriptions to a common framework. http://www.ncbi.nlm.nih.gov/projects/mhc. Currently, the dbMHC contains 389 primer pairs across the extended MHC targeting 281 distinct repeat regions (approximately 1/45 kb). Literature review and analysis of the primers reveal that over 200 synonymous names have been published for these markers. Users may view or download specific Msat data sets using the portal. Query options include name or partial name, primer sequence, neighboring genes, and/or position. Query results include locus name(s), a graphic showing of the relative location of the marker in relation to the classical HLA genes, a listing of the constituent primer pairs and name, a link to UniSTS, aliases, allele range (bp), overlapping single nucleotide polymorphisms, a link to e-polymerase chain reaction, and physical mapping information. To increase the utility of this resource, researchers using Msat markers in the HLA region are encouraged by the authors to submit new primers to the dbMHC. The minimal Msat submission consists of primers sequences, a submitter's name and contact information. Additional information recommended but not required is the laboratory protocol(s), known allele size range (bp), known aliases, and an exemplar sequence. Assigned UniSTS numbers can be used for primer pair standard identification.

Incestuous Paternity Detected by STR-typing of Chorionic Villi Isolated from Archival Formalin-fixed Paraffin-embedded Abortion Material Using Laser Microdissection

Microscopic examination of a blood clot expelled by a physically and mentally disabled woman taken to the emergency room because of genital bleeding revealed the presence of chorionic villi encircled by decidua, hemorrhage, and necrosis. In order to identify the father of the product of conception, sections of formalin-fixed, paraffin-embedded abortion material were subjected to laser microdissection: DNA extraction from chorionic villi selectively isolated from the surrounding tissues allowed successful STR-typing of fetal cells, which was otherwise prevented by excess maternal DNA. The large number of homozygous genotypes in the fetal profile suggested incestuous paternity. Analysis of reference DNA samples from male relatives excluded the woman's father, paternal grandfather, and maternal grandfather, whereas the obligate paternal alleles of the fetus were constantly present in the genotypes of the woman's brother, clearly demonstrating brother-sister incest (probability of paternity > 99.99999%).

Low-volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit

In forensic DNA analysis, improvement of DNA typing technologies has always been an issue. It has been shown that DNA amplification in low volumes is a suitable way to enhance the sensitivity and efficiency of amplification. In this study, DNA amplification was performed on a flat, chemically structured glass slide in 1-microl reaction volumes from cell line DNA contents between 1,000 and 4 pg. On-chip DNA amplification reproducibly yielded full allelic profiles from as little as 32 pg of template DNA. Applicability on the simultaneous amplification of 15 short tandem repeats and of a segment of the Amelogenin gene, which are routinely used in forensic DNA analysis, is shown. The results are compared to conventional in-tube amplification carried out in 25-microl reaction volumes.

Species and sex identification of western lowland gorillas (Gorilla gorilla gorilla), eastern lowland gorillas (Gorilla beringei graueri) and humans

Methods for the identification of the sex and species of individuals from samples non-invasively taken from humans and gorillas were established. Amplification of a segment of amelogenin (AMG), which is an X-Y homologous gene, using two pairs of primers from human AMG, revealed both X- and Y-specific bands. The possibility of sex identification was examined by typing the AMG gene using hair and fecal samples from captive western lowland gorillas (Gorilla gorilla gorilla) in Japan and hair samples from wild eastern lowland gorillas (Gorilla beringei graueri) in the Kahuzi-Biega National Park, Democratic Republic of Congo, which were sexed by direct observation. Species-specific bands of AMG in gorillas and humans were identified by restriction fragment length polymorphisms analysis. These tests could be used for sexing unidentified individuals of wild western and eastern lowland gorillas, and screening contamination of human DNA from non-invasively acquired samples.

Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.)

Mutation rates are often elevated in plants regenerated from in vitro culture, giving rise to so-called 'somaclonal variation'. Detailed characterisation of mutation profiles that arise during culture should improve our understanding of processes influencing mutation and allow the selection of protocols yielding the fewest/least severe changes. Somatic mutations will usually produce genetic chimeras where unchanged alleles are retained by some cells. Such chimeras are difficult to detect but likely to form a significant proportion of any regenerant population. We present a simple protocol that enables the provisional diagnosis of both homogenous and chimeric mutants among large regenerant populations, together with a semi-quantitative means of estimating the proportion of mutant cells. The assay exploits consistent differential amplification of alternate simple sequence repeat alleles at heterozygous loci. Calibration of the relative amplification of alleles from two genotypes-and the synthetic chimeras created from them-revealed a strong linear relationship between 'peak heights' representing alternate alleles following capillary electrophoresis. The assay predicts chimeric composition to a reasonable level of confidence (+/-5%) so long as the infrequent allele exceeds 15% of the template. The system was applied to 233 regenerants of cocoa somatic embryogenesis and identified 72 (31%) putative chimeric mutants for slippage mutation or allele loss across two loci.

Forensic DNA-typing of dog hair: DNA-extraction and PCR amplification

The forensic application of DNA-typing for the identification of dog hair provides objective evidence in the characterisation of traces found at crime scenes. During the past few years forensic dog identity testing has been improved considerably using multiplex PCR systems. However, DNA-typing from samples of one up to 10 dog hairs is often problematic in forensic science. A single dog hair contains very small quantities of DNA or the hair sample consists of hairs with roots of bad quality or even of broken hairshafts without roots. Here we describe an experimental study about dog hairs by means of a Ca(2+) improved DNA-extraction method, quantification and amplification.

DNA mixtures in forensic casework: a 4-year retrospective study

Occasionally interpretation guidelines from validation studies are difficult to apply to real forensic casework, especially in the case of mixed samples. Exogenous contamination, an unknown number of contributors or unbalanced proportion of each one in the sample and a varied degree of degradation of the biological materials, contribute to the difficulties in the interpretation of sample profiles. In this paper we have reviewed all the mixed genetic STR profiles encountered in our laboratory over 4 years (1997-2000) and evaluated the problems in the interpretation of the results. From 1547 criminal cases with 2424 samples typed, 163 showed a mixed profile (6.7%). We have observed that occasionally, a mixture appeared in the same sample with one multiplex amplification kit (e.g. Blue) and not with another (e.g. Green). From our results, it can be suggested that technical characteristics of the different fluorochrome groups in the multiplexes override the molecular characteristics of each STR in their capacity to detect mixtures.

Identification of two fire victims by comparative nuclear DNA typing of skeletal remains and stored umbilical tissues

We describe here our collaborative efforts in identifying 2 fatalities of a fire disaster by using a variety of identification techniques. Postmortem findings in both cases were reinforced using Short Tandem Repeat (STR) DNA technology to establish with a high degree of certainty the identities of 2 child victims. STR markers used in the present study include HUMAMEL, HUMCSFIPO, HUMTHO1, HUMvWA, HUMFES/FPS, HUMF13A01, HUMFOLP23, D8S3O6, HUMFGA, and HUMTPOX. Unambiguous identification was made possible through matching DNA profiles generated from skeletal remains with those from umbilical tissues. These tissues were kept by their mothers in accordance with a Philippine tradition and were submitted for DNA analysis. Of the DNA profiles generated from exhumed bone samples of 21 child victims, comparison with the genetic profiles of children A and B obtained from umbilical tissues showed consistent DNA matches with remains 1756 and 1758, respectively.

Ancient DNA in anthropology: methods, applications, and ethics

Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken.

Variation at 16 STR loci in Rwandans (Hutu) and implications on profile frequency estimation in Bantu-speakers

A data set of 16 autosomal STRs (the 13 CODIS loci plus HumCD4, HumFES, HumF13A1) was obtained in a sample of 52 unrelated Hutus from Rwanda. Genotypes at all loci met Hardy-Weinberg expectations with the exception of HumCSF1PO. No significant evidence of association across alleles at independent loci was obtained. Statistical parameters demonstrated the forensic usefulness of the analysed systems (combined PE=0.9999996, combined PD=1:2.27 x 10(18)). Pairwise comparisons showed that the Hutu gene pool differs substantially from that of other Bantu-speaking populations suggesting the use of ethnic-specific population databases in forensic casework analysis. The introduction of a non-negligible bias was confirmed by calculating the differences between multiple-locus profile frequencies of western and eastern Bantoids using local and non-local reference databases.

Allogeneic bone marrow transplantation (BMT) for adults with acute lymphoblastic leukemia (ALL): predictive role of minimal residual disease monitoring on relapse

We developed a PCR-based method to monitor clonogenic IgH VDJ rearrangement as a possible predictor of relapse in patients with acute B-ALL after allogeneic bone marrow transplantation (BMT). We studied 23 patients at diagnosis, before and after BMT. At the time of BMT, 13 patients were in first complete remission, eight in second complete remission and two in relapse. Four patients were PCR negative before BMT and remained PCR negative also after BMT (-/- pattern). They are still in remission after a median follow-up of 41 months. Nineteen patients were MRD-positive before BMT: three were PCR negative at first determination after BMT (+/- pattern) and maintain remission. Sixteen patients were PCR-positive at first determination after BMT (+/+ pattern): five became PCR negative (+/+/- pattern) (four with chronic graft-versus-host disease (GVHD) and two after donor lymphocyte infusions (DLI)). Nine patients remained PCR-positive (+/+/+ pattern) (four remain in remission, and six relapsed); two patients died before transplant. In conclusion, PCR negative patients before BMT remained negative post-BMT; many pre-BMT positive patients had initial MRD positivity after BMT: 37% of them achieved a molecular remission with cGVHD or DLI.

Allelic alterations at the STR markers in the buccal tissue cells of oral cancer patients and the oral epithelial cells of healthy betel quid-chewers: an evaluation of forensic applicability

Although cancerous specimens are usually not used in forensic DNA typing, they might be forcibly employed under certain instances. On the other hand, though the oral epithelial samples have been applied to forensic identification, the great popularity of betel quid (BQ)-chewing in Taiwan, which is known to be a risk factor leading to an oral cancer, makes this application questionable. The DNA stability of nine short tandem repeat (STR) markers (the AmpFlSTR kit) was first investigated and then used to evaluate the forensic appropriateness of the oral samples of both healthy BQ-chewers and the archived clinical specimens from oral cancer patients. The analyses were performed on buccal samples from 100 BQ-chewers and 100 oral cancer patients, as well as their paired peripheral blood samples, and a group of 100 non-BQ-chewers were used for the control. In the group of 100 oral cancer patients, two types of DNA instability were found. They were major allelic imbalance, and allelic alterations including the expansion, the contraction and the un-classified type (i.e. can not be confirmed as the expansion or the contraction). The overall percentage of the cancerous subjects demonstrating DNA instability was 33% (five patients possessing both types of DNA instability). Both types of DNA instability showed a tendency of increasing with the severity of the pathological stage of oral cancer. Forty-four occurrences of major allelic imbalance were found from 21 cancer patients. The statistical result revealed that there was no significant difference in the allelic imbalanced occurrence among the nine STR loci. Allelic alterations were found in 17 patients, within which 12 individuals had the expansion, five had the contraction, and three were the un-classified type. Further, among these 17 patients, three were found to acquire multiple allelic alterations at multiple loci. In the group of 100 unrelated healthy BQ-chewers, two loci with major allelic imbalance were detected. However, the two imbalanced alleles were virtually half lost, and could still be recognized as heterozygous alleles. The statistical results of ANOVA, chi(2), and Scheffe tests indicated that the means of allelic imbalance at the nine STR loci of the oral cancerous group revealed a significant difference from those in the control group. Our results suggest that oral cancer tissues cannot be used as references for forensic purposes using the PCR-based STR systems, whereas the oral swabs from healthy BQ-chewers can be employed, but should be done with caution.

A "de novo" mutation of the LDL-receptor gene as the cause of familial hypercholesterolemia

Familial hypercholesterolemia (FH) is a common genetic disorder caused by mutations of the LDL-receptor gene and transmitted as a co-dominant trait. However, there are some forms of hypercholesterolemia which have a recessive type of transmission. We have identified a subject with the clinical phenotype of heterozygous FH whose parents had normal plasma lipid values, suggesting a recessive type of transmission. The analysis of the LDL-receptor gene revealed that the patient was heterozygous for a G>C transversion in exon 4, which results in a serine for cysteine substitution at position 88 (C88S) of the receptor protein. Since this novel mutation was not found in the proband's parents and non-paternity was excluded, we concluded that the patient was a carrier of a "de novo" mutation. Haplotype analysis of LDL-receptor locus indicated that this "de novo" mutation occurred in the paternal germ line. The C88S mutation is the likely cause of LDL-receptor defect as it was present in the proband's hypercholesterolemic son and was not found in 200 chromosomes of control subjects.

Increased frequency of combined methylenetetrahydrofolate reductase C677T and A1298C mutated alleles in spontaneously aborted embryos

The pathogenesis of spontaneous abortion is complex, presumably involving the interaction of several genetic and environmental factors. The methylenetetrahydrofolate reductase (MTHFR) gene C677T and A1298C polymorphisms are commonly associated with defects in folate dependent homocysteine metabolism and have been implicated as risk factors for recurrent embryo loss in early pregnancy. In the present study we have determined the prevalence of combined MTHFR C677T and A1298C polymorphisms in DNA samples from spontaneously aborted embryos (foetal death between sixth and twentieth week after conception) and adult controls using solid-phase minisequencing technique. There was a significant odds ratio of 14.2 (95% CI 1.78-113) in spontaneously aborted embryos comparing the prevalence of one or more 677T and 1298C alleles vs the wild type combined genotype (677CC/1298AA), indicating that the MTHFR polymorphisms may have a major impact on foetal survival. Combined 677CT/1298CC, 677TT/1298AC or 677TT/1298CC genotypes, which contain three or four mutant alleles, were not detected in any of the groups, suggesting complete linkage disequilibrium between the two polymorphisms. The present finding of high prevalence of mutated MTHFR genotypes in spontaneously aborted embryos emphasises the potential protective role of periconceptional folic acid supplementation.