STR primer concordance study

Gestational trophoblastic disease: STR genotyping for precision diagnosis

INTRODUCTION

Gestational trophoblastic disease (GTD) encompasses a constellation of rare to common gynecologic conditions stemming from aberrant gestations with distinct genetic backgrounds and variable degrees of trophoblast proliferation of either neoplastic or non-neoplastic nature. GTD is categorized into hydatidiform moles and gestational trophoblastic neoplasms, and their clinical outcomes vary widely across different subtypes. Prompt and accurate diagnosis plays a pivotal role in the effective management and prognostication of patients. Short tandem repeats (STRs) are repetitive DNA sequences dispersed throughout the human genome and inherit a tremendous genetic polymorphism among individuals. Widely recognized for its applications in forensic identity and paternity testing, the relevance of STR genotyping in the diagnosis of GTD has emerged as an essential ancillary test in the classification and management of GTD of both non-neoplastic hydatidiform moles and gestational trophoblastic tumors.

AREA COVERED

This review discusses fundamental principles, laboratory operation, and diagnostic interpretations of STR genotyping in the context of diagnosis and differential diagnosis of GTD. PubMed was searched for all references up to 2024.

EXPERT OPINION

STR genotyping is the gold standard in the diagnosis and subclassification of hydatidiform moles and has an important application in diagnostic workup and risk stratifications of gestational trophoblastic tumors as well.

Evaluating the effects of silent genes on pairwise kinship testing

Short tandem repeat (STR) loci are frequently utilized in kinship testing, and mutations of a single base occurring in the primer-binding region of the STR locus can result in the failure of allelic amplification and the emergence of silent genes. Silent genes are not observable and, therefore, are excluded from the genotypes assessed. Pedigree likelihood ratios (LRs) are often employed in kinship testing to determine the likelihood of different kinship scenarios. LR values are derived from various types of genotypes. LRexact values are based on the exact or actual genotypes, which may include silent genes. Conversely, LRobserve values are based on observed genotypes that exclude silent genes, while LRadjust values incorporate all potential genotypes, including both observed and those with silent genes. Initially, the formulae for LRs in 1st degree, 2nd degree, and 3rd degree kinship testing are presented according to different genotype forms of pairwise individuals. The correctness of these formulae is then verified using the Familias software, and the results are compared with those from the GeneVisa software (www.genevisa.net). Lastly, the simulation modules of GeneVisa are used to assess the impact of silent genes on pairwise kinship testing. The findings indicate that the overall impact of silent genes is minimal, although in some cases, the effects can be relatively significant. The influence of silent genes generally decreases as the kinship relationship becomes more distant. In specific kinship tests, the effect of silent genes is reduced when the individuals are unrelated compared to when there is a kinship relationship. Utilizing the LRadjust value for 1st degree and 2nd degree kinship testing can substantially mitigate the effects of silent genes.

Concordance testing between Powerplex ESI 16 Fast System and VeriFiler Express

DNA profiles generated by different STR kits may show different alleles for identical amplified loci. This well-known phenomenon affects the smooth transition of data generated by new STR kits to a database or casework laboratory or cross-laboratory comparison of STR profiles. As in other DNA databases throughout the world, it has become clear that the number of the analyzed loci should be expanded for a variety of reasons, such as partial profiles resulting from low copy-number DNA template or degraded samples, working with mixtures or when prevalence of familial inbreeding. In the course of introducing a new STR kit, VeriFiler™ Express (Applied Biosystems, Foster City, CA, USA), we compared genotyping data of 1568 samples amplified by the VeriFiler™ Express with the data generated on the same samples by the Powerplex™ ESI FAST (Promega, Madison WI, USA) kit. Discordance was noted in 20 samples (1.27%), 14 (0.89%) of them showing allele dropout mismatch and six (0.38%) showing an additional fixed-size third allele. These rates are well above the reported rates of 0.4% for this kit. Since correct genotyping and accurate consistent allele assignment is of paramount importance, it seems timely to recommend for DNA laboratories and genetic-match search systems to take these possible inconsistencies into account.

Forensic investigation approaches of searching relatives in DNA databases

There are several indirect database searching approaches to identify the potential source of a forensic biological sample. These DNA-based approaches are familial searching, Y-STR database searching, and investigative genetic genealogy (IGG). The first two strategies use forensic DNA databases managed by the government, and the latter uses databases managed by private citizens or companies. Each of these search strategies relies on DNA testing to identify relatives of the donor of the crime scene sample, provided such profiles reside in the DNA database(s). All three approaches have been successfully used to identify the donor of biological evidence, which assisted in solving criminal cases or identifying unknown human remains. This paper describes and compares these approaches in terms of genotyping technologies, searching methods, database structures, searching efficiency, data quality, data security, and costs, and raises some potential privacy and legal considerations for further discussion by stakeholders and scientists. Y-STR database searching and IGG are advantageous since they are able to assist in more cases than familial searching readily identifying distant relatives. In contrast, familial searching can be performed more readily with existing laboratory systems. Every country or state may have its own unique economic, technical, cultural, and legal considerations and should decide the best approach(es) to fit those circumstances. Regardless of the approach, the ultimate goal should be the same: generate investigative leads and solve active and cold criminal cases to public safety, under stringent policies and security practices designed to protect the privacy of its citizenry.

Population genetics data for 22 autosomal STR loci in European, South Asian and African populations using SureID® 23comp Human DNA Identification Kit

Allele frequency data for 22 short tandem repeat loci; D18S1364, D1S1656, D13S325, D5S2800, D9S1122, D4S2366, D3S1744, D12S391, D11S2368, D21S2055, D20S482, D8S1132, D7S3048, D2S441, D19S253, D10S1248, D17S1301, D22-GATA198B05, D16S539, D6S474, D14S1434 and D15S659 from the SureID^® 23comp Human DNA Identification Kit have been determined for unrelated individuals in European, South Asian and African populations. Deviations from Hardy-Weinberg equilibrium were observed in loci D1S1656 and D19S253 in European; D18S1364, D6S474 and D14S1434 in South Asian; and D9S1122 and D8S1132 in African populations (p-value <0.05). However, after Bonferroni correction no significant deviations were observed (p-value <0.002). The most discriminating loci were D1S1656 and D12S391 for European (PD=0.977), D21S2055 for South Asian (PD=0.980), and D21S2055 and D7S3048 for African (PD=0.972) populations. The match probabilities were 1 in 6.7×10²⁵ for European, 1 in 1.4×10²⁶ for South Asian and 1 in 1.6×10²⁶ for African populations. These findings established the high discriminatory capacity and robustness of the tested STR loci for forensic identification and kinship testing.

Practical applications of DNA genotyping in diagnostic pathology

INTRODUCTION

Among various human tissue identity testing platforms, short tandem repeat (STR) genotyping has emerged as the most powerful and cost-effective method. Beyond forensic applications, tissue identity testing has become increasingly important in modern medical practice, in areas such as diagnostic pathology. Areas covered: A brief overview of various molecular/genetic techniques for identity testing is provided. This includes restriction fragment length polymorphism, single nucleotide polymorphism array and STR genotyping by multiplex PCR. Diagnostic applications of STR genotyping are covered in greater details: genotyping diagnosis of gestational trophoblastic disease, resolving tissue specimen mislabeling or histologic contaminant or 'floaters', bone marrow engraftment/chimerism analysis and interrogation of the primary source of malignancy in patients receiving organ donation. Four clinical cases are then presented to further illustrate these important clinical applications along with discussion of the interpretation, limitations, and pitfalls of STR genotyping. Expert commentary: STR genotyping is currently the most applicable method of identity testing and has extended its role well into the practice of diagnostic pathology with novel and powerful applications beyond forensics.

Next generation sequencing: an application in forensic sciences?

CONTEXT

Over the last few decades, advances in sequencing have improved greatly. One of the most important achievements of Next Generation Sequencing (NGS) is to produce millions of sequence reads in a short period of time, and to produce large sequences of DNA in fragments of any size. Libraries can be generated from whole genomes or any DNA or RNA region of interest without the need to know its sequence beforehand. This allows for looking for variations and facilitating genetic identification.

OBJECTIVES

A deep analysis of current NGS technologies and their application, especially in forensics, including a discussion about the pros and cons of these technologies in genetic identification.

METHODS

A systematic literature search in PubMed, Science Direct and Scopus electronic databases was performed for the period of December 2012 to June 2015.

RESULTS

In the forensic field, one of the main problems is the limited amount of sample available, as well as its degraded state. If the amount of DNA input required for preparing NGS libraries continues to decrease, nearly any sample could be sequenced; therefore, the maximum information from any biological remains could be obtained. Additionally, microbiome typification could be an interesting application to study for crime scene characterisation.

CONCLUSIONS

NGS technologies are going to be crucial for DNA human typing in cases like mass disasters or other events where forensic specimens and samples are compromised and degraded. With the use of NGS it will be possible to achieve the simultaneous analysis of the standard autosomal DNA (STRs and SNPs), mitochondrial DNA, and X and Y chromosomal markers.

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

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

D5S818 Typing Discrepancy Between PowerPlex(®) Fusion and Other STR Kits Including GlobalFiler(®) Caused by a One-base Deletion in 31 Nucleotides Upstream of the Repeat Region

Short tandem repeat (STR) typing is widely used in forensic investigation. When the same DNA sample is analyzed with different STR typing kits, a typing discrepancy is occasionally observed. In this study, we examined the cause of a typing discrepancy in a sample at D5S818 locus. This sample was designated as 10, 12 using Identifiler(®) , Identifiler(®) Plus, GlobalFiler(®) , PowerPlex(®) 16HS, and PowerPlex(®) 18D, but as 9.3, 12 using PowerPlex(®) Fusion. Sequencing results indicated that the shorter allele in the sample had a deletion (U31Tdel) at 31 nucleotides upstream of the repeat region (AGAT)10 . This deletion was located in the binding site of the published D5S818 forward primer in PowerPlex(®) 16 and was only 9 and 11 nucleotides downstream of our estimated 5' end position of D5S818 forward primer in GlobalFiler(®) and PowerPlex(®) 18D, respectively. We also examined the effect of primer length on the heterozygous peak balance in this sample.

Development of a 20-locus fluorescent multiplex system as a valuable tool for national DNA database

The multiplex system allows the detection of 19 autosomal short tandem repeat (STR) loci [including all Combined DNA Index System (CODIS) STR loci as well as D2S1338, D6S1043, D12S391, D19S433, Penta D and Penta E] plus the sex-determining locus Amelogenin in a single reaction, comprising all STR loci in various commercial kits used in the China national DNA database (NDNAD). Primers are designed so that the amplicons are distributed ranging from 90 base pairs (bp) to 450 bp within a five-dye fluorescent design with the fifth dye reserved for the internal size standard. With 30 cycles, 125 pg to 2 ng DNA template showed optimal profiling result, while robust profiles could also be achieved by adjusting the cycle numbers for the DNA template beyond that optimal DNA input range. Mixture studies showed that 83% and 87% of minor alleles were detected at 9:1 and 1:9 ratios, respectively. When 4 ng of degraded DNA was digested by 2-min DNase and 1 ng undegraded DNA was added to 400 μM haematin, the complete profiles were still observed. Polymerase chain reaction (PCR)-based procedures were examined and optimized including the concentrations of primer set, magnesium and the Taq polymerase as well as volume, cycle number and annealing temperature. In addition, the system has been validated by 3000 bloodstain samples and 35 common case samples in line with the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The total probability of identity (TPI) can reach to 8×10(-24), where DNA database can be improved at the level of 10 million DNA profiles or more because the number of expected match is far from one person (4×10(-10)) and can be negligible. Further, our system also demonstrates its good performance in case samples and it will be an ideal tool for forensic DNA typing and databasing with potential application.

Screening of cerebral infarction-related genetic markers using a Cox regression analysis between onset age and heterozygosity at randomly selected short tandem repeat loci

The aim of this paper is to explore whether the heterozygosity at the 9 CODIS short tandem repeats (STR) loci including D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 is associated with the risk of atherosclerotic cerebral infarction (CI). The DNA samples were collected from patients with CI (n = 72) and people over the age of 90 years without CI (n = 59). Alleles of the STR loci were determined using the STR Profiler Plus PCR amplification kit. The relationship between the age of onset and heterozygosity was determined with the Cox regression method. A correlation between the age of onset and heterozygosity was observed for the D8S1179 locus (p < 0.05). It implied that regions in the vicinity of locus D8S1179 may harbor susceptibility genes for CI. The analysis of heterozygosity for particular loci as genetic markers using our new study design may be an efficient and reliable approach to estimate genetic predispositions.

Applications of Cell-Free Fetal DNA in Maternal Serum

Cell-free fetal DNA (cffDNA) is available in the maternal circulation throughout pregnancy and can be used for noninvasive prenatal diagnosis including, determination of fetal sex, identification of specific single gene disorders, typing of fetal blood groups (RhD), paternity determination and potentially routine use for Down's syndrome (DS) testing of all pregnancies. I searched published literature on the PubMed and databases on Scopus interface systematically using keyword's cffDNA, noninvasive diagnosis, fetal DNA in the maternal serum. Reference lists from the papers were also searched. cffDNA representing only 3% of the total cell-free circulating DNA in early and rising to 12% in late pregnancy, clinical investigations has already demonstrated the potential advantage, such as improving safety, earlier diagnosis and comparative ease of testing using cffDNA technology. The discovery of cffDNA circulating in the maternal serum has opened the door to noninvasive prenatal diagnosis testing with novel clinical implications.

How to cite this article

Ghorbian S. Applications of Cell-Free Fetal DNA in Maternal Serum. Int J Infertility Fetal Med 2012;3(2):33-39.

Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3.

Developing criteria and data to determine best options for expanding the core CODIS loci

BACKGROUND

Recently, the Combined DNA Index System (CODIS) Core Loci Working Group established by the US Federal Bureau of Investigation (FBI) reviewed and recommended changes to the CODIS core loci. The Working Group identified 20 short tandem repeat (STR) loci (composed of the original CODIS core set loci (minus TPOX), four European recommended loci, PentaE, and DYS391) plus the Amelogenin marker as the new core set. Before selecting and finalizing the core loci, some evaluations are needed to provide guidance for the best options of core selection.

METHOD

The performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large datasets under single-source profile comparisons, mixture comparisons and kinship searches, and for international data sharing. Informativeness (for example, match probability, average kinship index (AKI)) and mutation rates of each locus were some of the criteria to consider for loci selection. However, the primary factor was performance with challenged forensic samples.

RESULTS

The current battery of loci provided in already validated commercial kits meet the needs for single-source profile comparisons and international data sharing, even with relatively large databases. However, the 13 CODIS core loci are not sufficiently powerful for kinship analyses and searching potential contributors of mixtures in larger databases; 19 or more autosomal STR loci perform better. Y-chromosome STR (Y-STR) loci are very useful to trace paternal lineage, deconvolve female and male mixtures, and resolve inconsistencies with Amelogenin typing. The DYS391 locus is of little theoretical or practical use. Combining five or six Y-chromosome STR loci with existing autosomal STR loci can produce better performance than the same number of autosomal loci for kinship analysis and still yield a sufficiently low match probability for single-source profile comparisons.

CONCLUSION

A more comprehensive study should be performed to provide the necessary information to decision makers and stakeholders about the construction of a new set of core loci for CODIS. Finally, selection of loci should be driven by the concept that the needs of casework should be supported by the processes of CODIS (or for that matter any forensic DNA database).

Autosomal short tandem repeat genetic variation of the Basques in Spain

Aim

To examine population genetic structure and hypotheses of the origin of the modern Basque population in Spain using autosomal short tandem repeat (STR) data from individuals living in 27 mountain villages in the provinces of Alava, Vizcaya, Guipuzcoa, and Navarre, by comparing Basque autosomal STR variation with that of neighboring populations in Europe, as well as proposed ancestral populations in North Africa and the Caucasus.

Methods

Allele frequencies for 9 autosomal STR loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA, and vWA) and several population genetic parameters were determined for the 4 provinces in the Basque region of Spain (n = 377). Heterozygosity within the Basque population was measured using a locus-by-locus analysis of molecular variance. Relationships between the Basques and other populations were examined using a multidimensional scaling (MDS) plot of Shriver’s D_SW distance matrix.

Results

Heterozygosity levels in the Basque provinces were on the low end of the European distribution (0.805-0.812). The MDS plot of genetic distances revealed that the Basques differed from both the Caucasian and North African populations with respect to autosomal STR variation.

Conclusions

Autosomal STR analysis does not support the hypotheses of a recent common ancestor between the Basques and populations either from the Caucasus or North Africa.

Variants observed for STR locus SE33: a concordance study

Discordance of STR typing results can be expected between kits that employ different primers for amplification. The complex motif of the SE33 locus and its flanking regions can contribute to the degree of discordant results. Sequence-dependent conformational changes can manifest as length differences under certain electrophoretic conditions and/or use of different primers. The AmpFlSTR® NGM SElect™ PCR Amplification Kit (Life Technologies, Carlsbad, CA), PowerPlex® ESX 17 system (Promega Corporation, Madison, WI), and PowerPlex® ESI 17 system (Promega Corporation) were compared for concordance of allele calls for the SE33 marker in selected samples. A total of 16 samples were identified that were discordant at one of the SE33 alleles by an apparent one nucleotide in size. While the ESX 17 and NGM SElect™ kits yielded concordant results for these 16 samples, the ESI 17 kit generated alleles that differed. The discordant alleles were observed in individuals of African and European descent. Sequence analysis revealed that the one-base difference in size is not due to an indel but is instead the result of a single nucleotide polymorphism (SNP) in the flanking region of the SE33 repeat region. Three different SNPs were observed, one of which is novel. Although these migration anomalies were observed only with the ESI 17 kit, one cannot preclude that a similar phenomenon may occur with the other kits as data sets increase. The type and degree of discordance of STR allele calls among STR kits is an important issue when comparing STR profiles among laboratories and when determining search parameters for identifying candidate associations in national databases.

Novel association analysis between 9 short tandem repeat loci polymorphisms and coronary heart disease based on a cross-validation design

OBJECTIVE

To investigate genes associated with coronary heart disease (CHD) screened with a novel cross-validation design.

METHODS

On the basis of age at the onset of the first episode of CHD, stratified sampling by age (<50 years, 50-59 years, 60-69 years, 70-79 years and >80 years) was performed. Alleles of the nine CODIS STR loci including D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820, were determined using the STR Profiler Plus PCR amplification kit. Allele frequencies were compared with a control population. The mean age of patients with and without the alleles was compared. Cross-validation was based on differences in both frequency values and ages instead of adjustment procedure for multiple testing.

RESULTS

There were statistical differences in frequency values between the CHD group and the control population for three alleles, and also statistical differences in the age at first onset of CHD for two alleles; at least one allele, D21S11-28.2, was statistically different with regards to both frequency values and age. It was confirmed that D21S11-28.2 is truly related with CHD.

CONCLUSIONS

A single true CHD-related allele could be discriminated from the sampling errors through cross-validation. It appears that CHD-related genes may be located near to loci D21S11.

A simple method for establishing concordance between short-tandem-repeat allele frequency databases

BACKGROUND

Current paternity and forensic accreditation standards do not require concordance to be established between short-tandem-repeat allele frequency databases representing the same population. The current statistical methods for evaluating databases do not establish concordance. Although acceptable under current forensic statistical methods, databases representing the same population may have sufficient variation to influence the outcome of a nondirect relationship testing result (i.e., siblingship). Hence there is a need for a quantitative method to determine concordance between databases.

STUDY DESIGN AND METHODS

Local allele frequency databases were generated for major US ethnic groups. Statistical analysis was performed as recommended by international forensic standards. A new method was developed and used for evaluating concordance between the locally developed and published databases. Smaller deviation values signify greater concordance between compared databases. The results were quantitatively confirmed against data obtained from a multidimensional scaling analysis system (SPSS, SPSS, Inc.).

RESULTS

The locally developed database deviated from the mean of the published data by approximately 0.1073 for Caucasians, 0.1341 for US Hispanics, and 0.1287 for African Americans. Upon pairwise comparison, the published databases deviated from one another by 0.1210 in US Caucasians, 0.1457 in US Hispanics, and 0.1228 in African Americans. The local database was observed to be more concordant to published databases than some of the published data to themselves.

CONCLUSION

The developed database was shown to be concordant with four previously published databases using the new method. The results were confirmed by comparison to qualitative data obtained from the multidimensional scaling analysis system.

STR sequence analysis for characterizing normal, variant, and null alleles

DNA sequence variation is known to exist in and around the repeat region of short tandem repeat (STR) loci used in human identity testing. While the vast majority of STR alleles measured in forensic DNA laboratories worldwide type as "normal" alleles compared with STR kit allelic ladders, a number of variant alleles have been reported. In addition, a sequence difference at a polymerase chain reaction (PCR) primer binding site in the DNA template can cause allele drop-out (i.e., a "null" or "silent" allele) with one set of primers and not with another. Our group at the National Institute of Standards and Technology (NIST) has been sequencing variant and null alleles supplied by forensic labs and cataloging this information on the NIST STRBase website for the past decade. The PCR primer sequences and strategy used for our STR allele sequencing work involving 23 autosomal STRs and 17 Y-chromosome STRs are described along with the results from 111 variant and 17 null alleles.

Rare sequence variation in the genome flanking a short tandem repeat locus can lead to a question of "nonmaternity"

Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed.

Donor cell leukemia in umbilical cord blood transplant patients: a case study and literature review highlighting the importance of molecular engraftment analysis

Donor cell neoplasms are rare complications of treatment regimens that involve stem cell transplantation for hematological malignancies, myelodysplastic processes, or certain genetic or metabolic disorders. We report a case of donor cell leukemia in a pediatric patient with a history of acute myeloid leukemia that manifested as recurrent AML FAB type M5 fourteen months after umbilical cord blood transplantation. Although there was some immunophenotypic drift from the patient's original AML and their posttransplant presentation, the initial pathological impression was of recurrent disease. Bone marrow engraftment analysis by multiplex PCR of short tandem repeat markers performed on the patient's diagnostic specimen showed complete engraftment by donor cells, with a loss of heterozygosity in the donor alleles on chromosome 7. This led to the reinterpretation of this patient's disease as donor-derived leukemia. This interpretation was supported by a routine karyotype and fluorescence in situ hybridization analysis showing loss of chromosome 7 and a male (donor) chromosome complement in this female patient. Also noted was a loss of the patient's presenting chromosomal abnormality, t(11;19)(q23;p13). This case highlights the need for close coordination between all aspects of clinical testing for the transplant patient, including molecular engraftment studies, when distinguishing the very common complication of recurrent disease from the exceedingly rare complication of donor cell leukemia.

Developmental validation of the PowerPlex 16 HS System: an improved 16-locus fluorescent STR multiplex

STR multiplexes remain the cornerstone of genotyping forensic samples. The PowerPlex 16 HS System contains the core CODIS loci: D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, and vWA. Additional loci amplified in the multiplex reaction are the sex-determinant locus, amelogenin, and two pentanucleotide STR loci, Penta D and Penta E. The PowerPlex 16 HS System is an updated version of the PowerPlex 16 System; while the primers and dyes remain unchanged, it introduces an enhanced buffer system that includes hot-start Taq DNA polymerase and ensures robust performance. Due to the modification of the reaction mix, a multi-laboratory developmental validation study was completed to document performance capabilities and limitations for the revised assay. Data within this validation was generated by eight laboratories and served as the basis for the following conclusions: genotyping of single-source samples was consistent across a large range of template DNA concentrations with most laboratories obtaining complete profiles at 62.5pg. Mixture analyses showed that over 90% of minor alleles were detected at 1:9 ratios. Optimum amplification cycle number was ultimately dependent on the sensitivity of the detection instrument and could be adjusted to accommodate a range of DNA template concentrations. Reaction conditions including volume and annealing temperature as well as the concentrations of primers, Taq DNA polymerase, and magnesium were shown to be optimal and able to withstand moderate variations without affecting multiplexed STR amplification. Finally, data from non-probative samples and concordance studies showed consistent results when comparing the PowerPlex 16 HS System with the PowerPlex 16 System as well as other commercially available systems.

False homozygosities at CSF1PO loci revealed by discrepancies between two kits in Chinese population

During the course of paternity test, three samples in two cases were apparently homozygous at the CSF1PO locus using AmpFlSTRs Identifiler PCR Amplification kits, but using the PowerPlexs 16 kit, the three individuals were found to be heterozygous. This puzzling problem was solved by using multiple analytical approaches, including the use of different primer pairs and the characterization of the mutation causing the ''null allele.'' Dropout was caused by a single mutation event in the presumptive binding site of the forward primer. While the frequency of these silent alleles remains low (0.5% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.

Forensic analysis of autosomal STR markers using Pyrosequencing

Short tandem repeats (STRs) are highly variable, and therefore routinely used in forensic investigations for a DNA-based individual identification. The routine assay is commonly performed by size separation using capillary electrophoresis, but alternative technologies can also be used. In this study, a Pyrosequencing assay was developed for analysis of STR markers useful in forensic DNA analysis. The assay was evaluated for 10 different STR loci (CSF1PO, TH01, TPOX, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539 and Penta E) and a total of 114 Swedish individuals were genotyped. This genotyping strategy reveal the actual sequence and variant alleles were seen at several loci, providing additional information compared to fragment size analysis. At the D13S317 locus a T/A SNP located in the last repeat unit was observed in 92% of the genotypes. Moreover, an upstream flanking SNP at locus D7S820, a SNP within the repeats at D3S1358 and D8S1179 and a deletion in the flanking region at locus D5S818 were observed. The Pyrosequencing method was first developed for SNP typing and sequencing of shorter DNA fragments but the method also provides an alternative method for STR analysis of less complex repeats. This assay is suitable for investigation of new markers, a rapid compilation of population data and for confirmation of variant and new alleles.

An INDEL polymorphism at the X-STR GATA172D05 flanking region

A new polymorphic INDEL was detected at the X-STR GATA172D05 flanking region, which corresponds to an 18-bp deletion, 141 bp upstream the TAGA repeat motif. This INDEL was found to be polymorphic in different population samples from Native Americans, Africans, and Europeans as well as in an admixed population from the Amazonia (Belém). Gene diversities varied between 37.5% in Native Americans and 49.9% in Africans. Comparison between human and chimpanzee sequences showed that the ancestral state corresponds to the presence of two copies of 18 bp, detected in both species; and the mutated allele has lost one of these two copies. The simultaneous analysis of the short tandem repeat (STR) and INDEL variation showed an association between the INDEL ancestral allele with the shorter STR alleles. High diversities were found in all population groups when combining the information provided by the INDEL and STR variation. Gene diversities varied between 76.7% in Native Americans and 80.6% in both Portugal and Belém.

A D19S433 primer binding site mutation and the frequency in Japanese of the silent allele it causes

Short tandem repeat studies are powerful tools for parentage analysis and for identification of missing persons, victims of murder, and victims of mass fatalities when reference samples are unavailable. The primer in the Identifiler kit failed to amplify an allele at the D19S433 locus, producing a silent ("null") allele. The causal mutation is a base change (G>A) 32 nucleotides downstream from the 3' end of the AAGG repeats. The silent alleles are problematical in parentage analysis because when transmitted, they can cause a parent-child inconsistency that is unrelated to Mendelian genetics. The inconsistency is sometimes termed an "apparent opposite homozygosity" and it produces false evidence of nonparentage. Alternative primers were designed to amplify the D19S433 locus alleles and they detect the silent allele. Frequencies of the (no longer) silent allele were determined to be 0.0114 in 176 people from Shizuoka (Honshu) and 0.0128 in 156 people from Okinawa.

Identification of a rare mutation in a TH01 primer binding site

We experienced a difficult case of TH01 typing. Instability of TH01 allele 9.3 was observed using GenePrint STR System TH01. Allele dropout was observed when an AmpFlSTR Profiler Kit was subsequently used for confirmation of the TH01 type. Use of the PowerPlex 16 System made it possible to detect allele 9.3. As a result of sequencing, a single point mutation (G-to-A transition) located 37 bases upstream of the first TCAT motif of the repeat region was identified as the cause of the allele dropout during use of the AmpFlSTR Profiler Kit. This mutation was located at the 3' end of the forward primers of the AmpFlSTR Profiler Kit and GenePrint STR System TH01.

Number of STR repeats as a potential new quantitative genetic marker for complex diseases, illustrated by schizophrenia

It has proved difficult to find strong and replicable genetic linkages for complex diseases, since each susceptibility gene makes only a modest contribution to onset. This is partly because high-efficacy genetic markers are not usually available. The aim of this article is to explore the possibility that the total number of tandem repeats in one STR locus, rather than the frequencies of different alleles, is a higher efficacy quantitative genetic marker. DNA samples were collected from schizophrenic patients and from a control population. Alleles of the short tandem repeats (STR) loci D3S1358, vWA, and FGA were determined using the STR Profiler Plus PCR amplification kit. The two groups did not differ statistically in the frequencies of alleles at the D3S1358, vWA, or FGA loci. However, a significant difference was obtained in the vWA locus when the total number of core unit repeats was compared between the schizophrenia and control groups (33.28+/-2.61 vs. 32.35+/-2.58, P<0.05). It seems that the number of STR repeats may be a new, quantitative, and higher efficacy genetic marker for directly indicating genetic predisposition to complex hereditary diseases such as schizophrenia.

Concordance Study Between the AmpF?STR�MiniFilerTMPCR Amplification Kit and Conventional STR Typing Kits

The AmpFlSTR MiniFiler polymerase chain reaction amplification kit developed by Applied Biosystems enables size reduction on eight of the larger STR loci amplified in the Identifiler kit, which will aid recovery of information from highly degraded DNA samples. The MiniFiler Kit amplifies CSF1PO, FGA, D2S1338, D7S820, D13S317, D16S539, D18S51, and D21S11 as well as the sex-typing locus amelogenin. A total of 1308 samples were evaluated with both the MiniFiler and Identifiler STR kits: 449 African American, 445 Caucasian, 207 Hispanic, and 207 Asian individuals. Full concordance between Identifiler and MiniFiler Kits was observed in 99.7% (10,437 out of 10,464) STR allele calls compared. The 27 differences seen are listed in Table 1 and encompass the loci D13S317 (n = 14) and D16S539 (n = 10) as well as D18S51 (n = 1), D7S820 (n = 1), and CSF1PO (n = 1). Genotyping discrepancies between the Identifiler and MiniFiler kits were confirmed by reamplification of the samples and further testing using the PowerPlex 16 kit in many cases. DNA sequence analysis was also performed in order to understand the nature of the genetic variations causing the allele dropout or apparent repeat unit shift.

A single mutation in the FGA locus responsible for false homozygosities and discrepancies between commercial kits in an unusual paternity test case

We report an unusual paternity test case showing multiple peculiarities. Using AmpFlSTR Profiler Plus and AmpFlSTR Identifiler PCR Amplification kits, the alleged father and the two children were apparently homozygous at the FGA locus, but using the PowerPlex 16 kit the three individuals were found to be heterozygous. Drop-out was caused by a single mutation event in the presumptive binding site of the reverse primer. In addition, three inconsistencies were detected between the daughter and the alleged father among 18 STR markers. The occurrence of the rare null allele at the FGA locus and case history suggested that the true father was the brother of the alleged father. Furthermore, a single-step repeat maternal mutation was also detected at D16S539. This puzzling case was solved by using multiple analytical approaches, including the use of different primer pairs, the use of a high number of STR markers, and the characterization of the mutation causing the "null allele."

Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus and PowerPlex 16

During duplicate analysis of buccal swabs from 1,377 individuals with 2 commercial short tandem repeat (STR) kits, we observed 8 discordant phenotypes with SGM Plus (SGM, second generation multiplex) for the STRs THO1 (2), vWA (4) and D18S51 (2), and 1 discrepancy with PowerPlex 16 for D18S51. One individual even showed two discrepancies (vWA and THO1) for SGM Plus. In each case, the difference observed was due to the non-amplification or allele dropout of the second allele in a heterozygous genotype. Sequence analysis revealed each time the presence of a mutation that probably coincided with the primer-binding site. Primer-binding site mutations for vWA and D18S51 have been reported previously, while the mutation for THO1 (C-to-T substitution at position 1286 of GenBank sequence D00269) is reported here for the first time. While the frequency of these silent alleles remains low (0.58% in our study), it is suggested that appropriate measures should be taken for database comparisons and that allelic dropout should be further investigated by sequence analysis and be reported to the forensic community.

Profiling and authentication of human cell lines using short tandem repeat (STR) loci: Report from the National Cell Bank of Iran

Assurance of cell line homogeneity and capability of cell contamination detection are among the most essential steps of cell based research. Due to high discriminatory efficiency, low cost and reliability, analysis of short tandem repeats (STR) has been introduced as a method of choice for human cell line authentication. In the present study 13 Combined DNA Index System (CODIS) based STRs along with the gender determination (Amelogenin) gene were utilized to establish a reproducible approach for the authentication of 100 human cell lines deposited in the National Cell Bank of Iran (NCBI), using the polymerase chain reaction (PCR) method. PCR products were subsequently analyzed by polyacrylamide gel electrophoresis (PAGE) and visualized by silver staining followed by gel documentation and software analysis. STR profiles obtained were compared with those of the American Type Culture Collection (ATCC) and the Japanese Collection of Research Bioresource (JCRB) as STR references. We detected 18.8% cross contamination among the NCBI human cell lines. To our knowledge, this is the first report of authentication of human cell lines using the 13 CODIS core STRs combined with Amelogenin.

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

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

Genetic data for the 13 CODIS STR loci in Singapore Chinese

Allele frequencies for the 13 CODIS STR loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 209 unrelated Chinese in Singapore. The combined random match probability for the 13 loci is about 6.6 x10(-15) and the overall probability of excluding paternity is 0.9999899. The results demonstrate that the loci are useful for forensic human identification and parentage testing for the Chinese population in Singapore.

Discovery and identification of new D13S317 primer binding site mutations

During the course of conventional testing of CODIS standards at the Alabama Department of Forensic Sciences, a sample with a heterozygous null genotype at D13S317 was discovered using the PowerPlex 1.1 kit (Promega, Madison, WI). The loss of both alleles was confirmed when the sample was amplified using PowerPlex 1.2 primers and resulted in a 9, 10 genotype at this locus. To determine the cause of the silent alleles, the ADFS designed D13S317 primers which encompassed the PowerPlex 1.1 D13S317 primer binding sites and sequenced the region. Both alleles showed the presence of two substitutions (T-->A and G-->T) at positions 1 and 5 (5'-->3') of the reverse primer (positions 196 and 200 of the sequence in GenBank accession number ). Since the mutations were identical on both alleles, they may be assumed to be of ancestral origin.

Forensic aspects of mass disasters: Strategic considerations for DNA-based human identification

Many mass disasters result in loss of lives. Law enforcement and/or public safety and health officials often have the responsibility for identifying the human remains found at the scene, so they can be returned to their families. The recovered human remains range from being relatively intact to highly degraded. DNA-based identity testing is a powerful tool for victim identification in that the data are not restricted to any particular one to one body landmark comparison and DNA profile comparisons can be used to associate separated remains or body parts. Even though DNA typing is straightforward, a disaster is a chaotic environment that can complicate effective identification of the remains. With some planning, or at least identification of the salient features to consider, stress can be reduced for those involved in the identification process. General guidelines are provided for developing an action plan for identification of human remains from a mass disaster by DNA analysis. These include: (1) sample collection, preservation, shipping and storage; (2) tracking and chain of custody issues; (3) laboratory facilities; (4) quality assurance and quality control practices; (5) parsing out work; (6) extraction and typing; (7) interpretation of results; (8) automation; (9) software for tracking and managing data; (10) the use of an advisory panel; (11) education and communication; and (12) privacy issues. In addition, key technologies that may facilitate the identification process are discussed, such as resin based DNA extraction, real-time PCR for quantitation of DNA, use of mini-STRs, SNP detection procedures, and software. Many of the features necessary for DNA typing of human remains from a mass disaster are the same as those for missing persons' cases. Therefore, developing a missing persons DNA identification program would also provide the basis for a mass disaster human remains DNA identification program.

Genetic data for the 13 CODIS STR loci in Singapore Indians

Allele frequencies for the 13 CODIS short tandem repeat (STR) loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 174 unrelated Indians in Singapore.

STR data for the 13 CODIS loci in Singapore Malays

Allele frequencies for the 13 CODIS (Combined DNA Index System, USA) STR loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 197 unrelated Malays in Singapore.

Identification of more sequence variations in the D8S1179 locus

Routine STR-typing of 10,293 buccal swabs using different multiplex kits presented discordant D8S1179 profiles in four cases. Sequencing analysis identified a G-to-A transition upstream to the repeat, and an A-to-T transversion and a G-to-A transition downstream to the repeat. In the fourth case a four-base pair deletion downstream resulted in altered genotypes using different primer pairs. Current searching algorithms of the German DNA database are not capable of matching profiles that are divergent in only one STR-locus. Thus, to accommodate matching requirements and to avoid errors in individual genetic characterization for D8S1179, as described here, it is suggested that alternative primer pairs be used for routine genotyping as a matter of course.

Twelve short tandem repeat loci Y chromosome haplotypes: Genetic analysis on populations residing in North America

A total of 2443 male individuals, previously typed for the 13 CODIS STR loci, distributed across the five North American population groups African American, Asian, Caucasian, Hispanic, and Native American were typed for the Y-STR loci DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 using the PowerPlex Y System. All population samples were highly polymorphic for the 12 Y-STR loci with the marker DYS385a/b being the most polymorphic across all sample populations. The Native American population groups demonstrated the lowest genetic diversity, most notably at the DYS393 and DYS437 loci. Almost all of the 12-locus haplotypes observed in the sample populations were represented only once in the database. Haplotype diversities were greater than 99.6% for the African Americans, Caucasians, Hispanics, and Asians. The Native Americans had the lowest haplotype diversities (Apaches, 97.0%; Navajo, 98.1%). Population substructure effects were greater for Y-haplotypes, compared with that for the autosomal loci. For the apportionment of variance for the 12 Y-STRs, the within sample population variation was the largest component (>98% for each major population group and approximately 97% in Native Americans), and the variance component contributed by the major population groups was less than the individual component, but much greater than among sample populations within a major group (11.79% versus 1.02% for African Americans/Caucasians/Hispanics and 15.35% versus 1.25% for all five major populations). When each major population is analyzed individually, the R(ST) values were low but showed significant among group heterogeneity. In 692 confirmed father-son pairs, 14 mutation events were observed with the average rate of 1.57x10(-3)/locus/generation (a 95% confidence bound of 0.83x10(-3) to 2.69x10(-3)). Since the Y-STR loci reside on the non-recombining region of the Y chromosome, the counting method is one approach suggested for conveying an estimate of the rarity of the Y-haplotype. Because the Y-STR loci are not all in disequilibrium to the same extent, the counting method is a very conservative approach. The data also support that autosomal STR frequencies can be multiplied by the upper bound frequency estimate of a Y-haplotype in the individual population group or those pooled into major population groups (i.e., Caucasian, African American, Hispanic, and Asian). These analyses support use of the haplotype population data for estimating Y-STR profile frequencies for populations residing in North America.