AmpFlSTR Identifiler PCR Amplification Kit Research Articles

The distribution of allele frequencies of the 15 Short Tandem Repeats loci in Elaziğ population, Türkiye

The DNA within the Human Genome involves loci with high polymorphism such as short tandem repeats (STR). The STR polymorphism analysis is extensively used for numerous purposes such as identification studies in forensic sciences, paternity tests, genome mapping, and population studies. In this study, blood and swab samples were obtained from 200 unrelated healthy individuals living in Elazig province. DNA was amplified via the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems, USA) to analyze the 15 STR loci. Using the ABI PRISM310 Genetic Analyzer capillary electrophoresis, the samples were analyzed and the allelic ladder was used to compare and identify the alleles of the samples, the distribution of the allele frequencies and peak values were examined. For statistical analysis Arlequin v.3.11 and PowerStats v.1.2 were used to assess the data. To determine if the allele frequencies were compatible with the Hardy-Weinberg (HW) equilibrium, the Markov chain and the Fisher's exact test p-value (p<0.05) were examined. It was determined that the D8S1179 (0.00002), D21S11 (0.00593) and vWA (0.04939) loci were not compatible with the HW equilibrium, but the rest of the loci were compatible. For the loci, the combined power of exclusion is 0.9999995, the combined power of discrimination is 0.9999999999998. The probability of matching for the 15 STR loci was calculated to be 1 in 1.364x10ˉ17. The power of discrimination was quite high when all the loci were considered. The results of this study indicate that the populations residing in the Elaziğ province may benefit from paternity testing, forensic identification, and genomic mapping using the data as an appropriate marker.

Effectiveness of whole genome amplification prior to short tandem repeat analysis for degraded DNA

Short tandem repeat (STR) analysis is prone to failure as DNA is frequently damaged by various environmental factors; hence, increasing the number of starting templates may constitute a feasible approach to improve STR profiling success. Whole genome amplification (WGA) is often applied to bolster starting template quantity. Moreover, WGA can reportedly be used on degraded DNA samples in forensics. Therefore, we utilized a PCR-based WGA method, termed “modified improved primer extension preamplification” (mIPEP), prior to STR analysis of degraded DNA, as this method is less affected by DNA quantity and quality than most others. Saliva from four volunteers was dried on glass fiber filter papers (paper) and glass slides (glass) and irradiated with UVA light (365 nm). The mIPEP method was initiated using 5, 0.5, and 0.05 ng of DNA following DNA extraction. The DNA degradation index (DI) was calculated based on the ratio of 129 to 41 bp DNA fragments; lower numbers indicate higher degradation. Following mIPEP, STR analysis was performed using the AmpFlSTR Identifiler PCR amplification kit. The number of detectable STR loci, with and without mIPEP, decreased according to reduced DI in a different manner for the various DNA concentrations extracted from paper and glass. Specifically, for the 5 ng DNA sample on paper, at a DI < 0.2, the number of detectable STR loci was greater with mIPEP than without it, owing to fewer locus drop-outs. Similarly, the 0.05 ng DNA sample deposited on paper, at DI ≥ 0.7, exhibited higher numbers of detectable STR loci when prepared using mIPEP owing to fewer allele drop-outs. Moreover, among samples deposited on glass, the 0.05 ng DNA sample at DI ≥ 0.4 afforded a larger number of detectable STR loci when prepared using mIPEP than those without mIPEP, owing to fewer locus drop-outs. These findings suggest that performing mIPEP in accordance with sample DNA condition (e.g., quantity and quality) may lead to increased success of STR analysis. Notably, the conditions identified as most responsive to mIPEP were consistent across both UVA-irradiated and environmentally-damaged sample states. Taken together, our results suggest that applying mIPEP would be beneficial to obtain improved STR profiles under conditions involving severely degraded samples with large quantities of DNA, or with small quantities of DNA albeit with slight degradation.

Investigation of the efficiency of whole genome amplification prior to short tandem repeat analysis using degraded DNA

Short tandem repeat (STR) analysis is prone to failure because DNA is frequently degraded by various environmental factors. Increasing the number of starting templates may improve success in STR profiling. One approach to increase the number of DNA templates is whole genome amplification (WGA); however, few studies have demonstrated that WGA can be used on degraded DNA samples in forensics. Therefore, we performed a PCR-based WGA termed “modified improved primer extension preamplification” (mIPEP) prior to STR analysis of degraded DNA, since this method was less affected by DNA quantity and quality than other approaches are.Saliva from four volunteers was dried onto filter papers. These samples were irradiated with UVA light (365 nm) for 3, 7, 14, and 30 days. The mIPEP method was initiated using 5, 0.5, and 0.05 ng of DNA after DNA extraction. Following mIPEP, STR analysis was performed using the AmpFlSTR Identifiler PCR Amplification Kit. This study was approved by the ethics committee at Tokyo Women’s Medical University.The number of detectable STR loci in 0.05 ng DNA sample was greater in those prepared by mIPEP than those prepared without mIPEP, when no radiation was applied. After 3 days of irradiation, the number of detectable STR loci in 0.5 ng DNA sample was smaller in those treated with mIPEP than in samples without mIPEP. There was no significant difference between the number of detectable STR loci with and without mIPEP after 7 and 14 days of irradiation. However, after 30 days of irradiation, the number of detectable STR loci in 5 ng DNA samples prepared with mIPEP was greater than in those without mIPEP. Hence, mIPEP was not necessary for STR loci detection in moderately degraded samples, but it did improve the success of STR profiling in severely degraded samples.

Multiplex STR panel for assessment of chimerism following hematopoietic stem cell transplantation (HSCT)

Short tandem repeat (STR) analysis is used in chimerism monitoring after allogeneic hematopoietic stem cell transplantation (HSCT) for patients with various hematologic malignancies. Commercial forensic STR kits often contain loci with huge differences in power of discrimination (PD) across populations, causing some loci to be less informative for chimerism analysis in certain populations. This study aimed to construct a new STR multiplex panel with highly informative loci for efficient chimerism analysis. Thirteen STR markers which exhibit high PD (> 0.9) in at least 80% of 50 populations globally were selected to form a new panel and used in STR analysis of 253 Malaysian subjects. Cumulative power of discrimination (CPD) and combined power of exclusion (CPE) were determined from 253 Malaysian individuals. Loci informativity was assessed and compared to the commercial AmpFLSTR Identifiler PCR Amplification kit in 14 donor-recipient pairs. The new panel had detected 202 unique alleles including five novel alleles from the 253 individuals with high CPD and CPE (> 0.99999999999999999 and > 0.999999997 respectively). All loci from the new panel in the donor-recipient pair analysis showed higher than 50% informativity, while five loci from the commercial kit demonstrated lower than 50% informativity. Four loci from the new panel ranked the highest informativity. A sequenced allelic ladder which consists of 202 unique alleles from the 253 subjects was also developed to ensure accurate allele designation. The new 13-loci STR panel, thus, could serve as an additional powerful, accurate, and highly informative panel for chimerism analysis for HSCT patients.

RETRACTED ARTICLE: Forensic characterization of 15 autosomal STRs in four populations from Xinjiang, China, and genetic relationships with neighboring populations

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors 47 ethnic groups including the Manchu (MCH: 0.11%), Mongols (MGL: 0.81%), Kyrgyz (KGZ: 0.86%) and Uzbek (UZK: 0.066%). To establish DNA databases for these populations, allele frequency distributions for 15 autosomal short tandem repeat (STR) loci were determined using the AmpFlSTR Identifiler PCR amplification kit. There was no evidence of departures from Hardy–Weinberg equilibrium (HWE) in any of the four populations and minimal departure from linkage equilibrium (LE) for a very small number of pairwise combinations of loci. The probabilities of identity for the different populations ranged from 1 in 1.51 × 1017 (MCH) to 1 in 9.94 × 1018 (MGL), the combined powers of discrimination ranged from 0.99999999999999999824 (UZK) to 0.9999999999999999848 (MCH) and the combined probabilities of paternal exclusion ranged from 0.9999979323 (UZK) to 0.9999994839 (MCH). Genetic distances, a phylogenetic tree and principal component analysis (PCA) revealed that the MCH, KGZ and UZK are genetically closer to the Han population of Liaoning and the Mongol population of Mongolia while the MGL are closer to Han, Japanese, Korean, Malaysian, Hong Kong Han and Russians living in China.

Analysis of paternity exclusions in the material collected by the Department of Forensic Medicine, Medical University of Bialystok in 2008-2017.

Analysis of frequency and structure of paternity exclusions in the material collected by the Department of Forensic Medicine, Medical University of Bialystok in 2008-2017. The paper is based on paternity test reports involving alleged father-child-mother trios. In atotal of reviewed 958 cases, 187 exclusions were identified. The analysis was carried out on the basis of the results of DNA tests. DNA extraction was performed using QIAamp DNA Mini Kit (Qiagen) and DNA quantitation using Quantifiler Human DNA Quantification Kit and 7500 Real-Time PCR System (Applied Biosystems). AmpFLSTR Identifiler PCR Amplification Kit and aPCR System 9700 thermal cycler (Applied Biosystems) were used for DNA amplification. Over the analyzed period, the number of paternity tests was nearly halved, whereas the percentage of exclusions in individual years varied significantly (33.9-13.3%), with the average of 26.3%. The highest efficiency of exclusions was observed for D18S51 (0.7166) and FGA (0.7059), and the least effective system was TPOX (0.3048). The applied set of markers has been demonstrated to be an efficient tool in genetic paternity tests in the context of the recommended rules of exclusion.

Genetic analysis of the Saraiki population living in Pakistan

ABSTRACTAutosomal short tandem repeat (STR) markers are a powerful tool used in forensic sciences for profile matching and paternity testing, sibship and kinship analysis. This study represents the allele frequency distribution of 15 autosomal STR multiplex of the Saraiki population living in Pakistan. Allele frequencies of this population were compared with the other populations living in Pakistan. Buccal swabs were taken from 150 unrelated individuals of the Saraiki population living in different regions of Pakistan and profiles were generated using an AmpFlSTR Identifiler PCR Amplification kit. Population genetic calculations were performed on this population. Allele frequencies of the Saraiki population showed that this population is at Hardy Weinberg Equilibrium except at loci D3S1358, TH01, D13S317, TPOX and FGA, with distinct differences in HObs and HExp values. The average heterozygosity and polymorphism information content (PIC) at all loci were 0.77 and 0.766, respectively. Each STR marker showed a high degree of polymorphism and a high power of discrimination (PD). A phylogenetic tree shows that the Saraiki population living in Pakistan is genetically distinct from other geographically neighboring populations of the country. The population data presented in this study can be used as a reference database for the Saraiki population in forensic casework.

Genetic polymorphism of 15 STR loci in El Salvador.

The aim of this study was to estimate the allelic frequencies of the 15 short tandem repeat (STR) loci included in AmpFlSTRIdentifiler PCR Amplification Kit. Biological samples were obtained from 109 unrelated individuals from El Salvador. Allelic frequencies and forensic parameters were calculated. All loci showed no departure from Hardy-Weinberg equilibrium after Bonferroni correction. The obtained frequencies were compared with other previously reported population data. The multidimensional scaling plot and the neighbor-joining phylogeny supported a high native Mesoamerican contribution.

Identification of new primer binding site mutations at TH01 and D13S317 loci and determination of their corresponding STR alleles by allele-specific PCR

Several commercial multiplex PCR kits for the amplification of short tandem repeat (STR) loci have been extensively applied in forensic genetics. Consequently, large numbers of samples have been genotyped, and the number of discordant genotypes observed has also increased. We observed allele dropout with two novel alleles at the STR loci TH01 and D13S317 during paternity testing using the AmpFℓSTR Identifiler PCR Amplification Kit. The lost alleles reappeared when alternative PCR primer pairs were used. A sequence analysis revealed a G-to-A substitution 82 bases downstream of the last TCAT motif of the repeat region at the TH01 locus (GenBank accession: D00269) and a G-to-T substitution 90 bases upstream of the first TATC motif of the repeat region at the D13S317 locus (GenBank accession: G09017). The frequencies of these two point mutations were subsequently investigated in the Chinese population using sequence-specific primer PCR (SSP-PCR), but neither of these mutations was detected in any of the samples tested. In addition, the DNA samples in which the mutations were identified were amplified to type the point mutations by SSP-PCR to determine the corresponding STR alleles at the two loci. Subsequently, the amplified PCR products with different point mutations and STR repeat numbers were directly sequenced because this strategy overcomes the appearance overlapping peaks generated by different STR alleles and accurately characterizes genotypes. Thus, our findings not only provide useful information for DNA databases and forensic identification but also establish an effective strategy for typing STR alleles with primer binding site mutations.

Differences of PCR efficiency between two-step PCR and standard three-step PCR protocols in short tandem repeat amplification

The effects on STR typing results, using a two-step PCR protocol that combines the annealing and extension steps, were determined using samples at various DNA concentrations. DNA samples ranging from 62.5 to 500 pg were amplified using the reagents contained within the AmpFlSTR Identifiler PCR Amplification Kit. At 250–500 pg of DNA template, the rates of detecting alleles were close to those found when using three-step PCR (the standard Identifiler protocol) and two-step PCR protocols. The two-step PCR increased by 8.1% and 64.2% the average number of amplified alleles compared with the three-step PCR at 125 pg and 62.5 pg of template DNA, respectively. At 62.5–500 pg of DNA, the average peak heights were 23.3–65.0% higher than heights using the three-step PCR protocol. When two different PCR protocols were applied to old bones, the average number of amplified loci was similar. These results suggested that the two-step PCR protocol can generate more STR alleles in low template DNA samples; however, the method may be limited with samples of very low-quality, i.e., degraded DNA, compared with the three-step protocol. A better understanding of the effects of the two-step PCR protocol on amplification conditions might help researchers improve STR typing.

Genetic polymorphism of 15 STR loci in Chinese Han population from Shanghai municipality in East China

The aim of this study was to estimate the allelic frequencies of the fifteen STRs included in AmpFlSTR(®) Identifiler(®) PCR Amplification Kit (Applied Biosystems, USA) in a sample of 186 unrelated individuals resident in Shanghai. Allelic frequencies and forensic parameters were calculated. All loci showed no departure from Hardy-Weinberg equilibrium. The obtained frequencies were compared with other previously reported population data.

Comparison of Two Methods for Isolating DNA from Human Skeletal Remains for STR Analysis

The quality and efficiency of a standard organic DNA isolation method and a silica-based method using the QIAGEN Blood Maxi Kit were compared to obtain human DNA and short tandem repeats (STRs) profiles from 39 exhumed bone samples for paternity testing. DNA samples were quantified by real-time PCR, and STR profiles were obtained using the AmpFlSTR(®) Identifiler(®) PCR amplification kit. Overall, the silica-based method recovered less DNA ranging from 0 to 147.7 ng/g (average 7.57 ng/g, median = 1.3 ng/g) than did the organic method ranging from 0 to 605 ng/g (average 44.27 ng/g, median = 5.8 ng/g). Complete profiles (16/16 loci tested) were obtained from 37/39 samples (95%) using the organic method and from 9/39 samples (23%) with the silica-based method. Compared with a standard organic DNA isolation method, our results indicate that the published silica-based method does not improve neither the quality nor the quantity of DNA for STR profiling.

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database.

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

Identification of dual false indirect exclusions on the D5S818 and FGA loci

Here, we present a case in which the result of a maternity test was obscured due to two false indirect exclusions that occurred in two out of 15 genetic loci through the use of the AmpFlSTR Identifiler PCR Amplification kit (Applied Biosystems, Foster City, CA). The Identifiler kit failed to amplify allele 11 of the D5S818 system on the child and failed to capture the existence of allele 13 on the FGA system on both mother and child. The situation was remedied through use of the PowerPlex 16 PCR Amplification Kit (Promega, Madison, WI) which used different primers with a different allele range than that of the Identifiler kit. Maternity was confirmed through sequencing and it was found that the failure of the Identifiler kit to amplify allele 11 on the D5S818 system was the result of an incompatibility to the primer-binding site due to a mutation that changed a guanine (G) into a thymine (T) 55 base pairs (bp) downstream of the repeat. The inability of the Identifiler kit to pick up allele 13 of the FGA system was due to the out-of-range location of the allele. Indirect exclusions can be misleading if they are not fully investigated since allele range as well as primer-binding affinity are two confounders that must be addressed to ensure accuracy of the test results.

5-Azacytidine as Salvage Treatment in Relapsed Myeloid Tumors after Allogeneic Bone Marrow Transplantation

Relapse after allogeneic blood or marrow transplantation carries a very poor prognosis. Current strategies for management that include donor lymphocyte infusions (DLIs) and salvage chemotherapies are usually toxic and ineffective. Here we report the outcome of 10 patients with myeloid malignancies that received 5-azacytidine after a failed allogeneic bone marrow transplant. Of the 10 patients, 6 achieved a complete remission, 1 had stable disease, and 3 progressed after a median of 6 cycles administered. Only 1 patient has died (of disease progression), and no flares of graft-versus-host disease (GVHD) were observed with 5-azacytidine. As of latest follow-up, the median overall survival (OS) for the group was 422.5 days (127-1411). These results further suggest that 5-azacytidine is an active agent after failing an allogeneic bone marrow transplant, and prospective studies are warranted.

Utility of Chimerism Analysis to Determine Tissue of Origin in Post Transplant Lymphoproliferative Disorder (PTLD).

Abstract 4305Post-transplant lymphoproliferative disorder (PTLD) is one of the major complications of organ transplantation. Most PTLDs are associated with Epstein-Barr virus (EBV) infection of B-lineage lymphocytes. Central nervous system (CNS) involvement is rare. Although most PTLDs following solid organ transplants is of recipient origin, PTLDs following bone marrow or stem cell transplant are mostly of donor cell origin. Origin of the tumor cells are of crucial importance in deciding treatment and predicting prognosis. Here we report a case of PTLD of diffuse large B cell Lymphoma of donor tissue origin determined by chimerism analysis. The patient was a 52-year-old woman with myelofibrosis (Myeloproliferative disorder) who received unrelated donor peripheral blood stem cell transplantation. The donor was an ABO compatible, HLA matched unrelated donor. Post transplant immunosuppression therapy was administered. The post transplant history was complicated by multiple viral infections, including BK, CMV and EB virus. Four months after transplantation, the patient developed fever and mental status changes, MRI of brain showed multiple enhancing lesions. Brain biopsy revealed brain tissue with dense infiltration of large atypical lymphoid cells predominantly perivascular in location. Immunohistochemical stains reveal that the large atypical lymphoid cells are of B-cell origin and these cells are 100% positive for Ebstein Barr virus by EBV encoded RNA by in-situ hybridization. The flowcytometry study revealed a monoclonal population of B cells with Kappa light chain restriction. These findings support the diagnosis of post transplant lymphoproliferative disorder (PTLD) of diffuse large B-cell lymphoma type. To determine the origin of tumor cells, chimerism analysis of the host DNA (buccal) and tumor DNA were performed. Short tandem repeat (STR) multiplex PCR assay were performed using the AmpFlSTR Identifiler PCR amplification kit (Applied Biosystems, Foster City, CA). After amplification, samples were analyzed on an ABI 310 DNA Sequencer (Applied Biosystems). The allele distribution was significantly different between the recipient DNA (from buccal swab) compared to tumor DNA indicating donor origin of the tumor (PTLD). The patient was then placed on high dose methotrexate and dexamethasome, however her condition deteriorated dramatically and the patient expired shortly following the diagnosis. It is known that the major pathogenetic defect of PTLD is the insufficient EBV-specific cytotoxic T-cell control of EBV-driven B-cell proliferations. Despite this understanding, determining the right therapy for any given patient with PTLD remains a major clinical issue. It is important to identify patients who will benefit from reduction of immunosuppression, who will benefit from Rituximab. It is also important to develop more effective, less toxic chemotherapies for resistant or aggressive disease. The chimerism analysis performed on our patient to identify tumor cell origin is an unique and reliable method to help directing clinical management of PTLD. Disclosures:No relevant conflicts of interest to declare.

DNA recovery from different evidences in 300 cases of sexual assault

Almost 60% of the DNA evidences analyzed in our laboratory correspond to sexual assault cases. With the aim to assess the efficiency of the DNA IQ System (Promega) in recovering the perpetrator DNA profile, the statistical analysis of results obtained in 300 casework was performed. In such cases, 850 evidence samples were processed. In 71% of the cases the perpetrator DNA profile was detected in at least one of the submitted casework samples, with a minimum of 13 STRs markers typed using the AmpFlSTR Identifiler PCR amplification kit (Applied Biosystem). When the suspect DNA profile was available, 67% matched with the evidence. With regard to the type of evidence, the best performance corresponded to panties, with more than 70% of success in recovering male profile, whereas the efficiency of vaginal swabs was almost 60%, with a higher incidence of victim/perpetrator mixed profiles.

Integration of the AmpFlSTR Identifiler PCR Amplification Kit with SRY-specific primers for gender identification

Dropout of the amelogenin Y-specific allele due to an interstitial deletion of the Yp involving the amelogenin Y locus (AMELY) can cause misidentification of sex genotype with potentially serious consequences in personal identification processes and criminal investigations. Inclusion of additional sex-defining markers in forensic DNA typing kits is therefore advisable. In this study, the co-amplification of the sex-determining region Y (SRY) gene and 16 STR loci included in the AmpFlSTR Identifiler PCR Amplification Kit was evaluated. Combination of SRY and Identifiler primers did not compromise the amplification outcome and generated a 90 bp male-specific SRY fragment, showing a reproducible peak height ratio in comparison with the AMELY peak. The SRY peak was detectable in presence of amounts of template DNA as low as 125 pg, and in mixed samples with a male/female DNA ratio of 1:100.

Validation of the AMPFℓSTR® MiniFilerTM PCR Amplification Kit for Use in Forensic Casework*

The AmpFlSTR MiniFiler PCR Amplification Kit is designed to genotype degraded and/or inhibited DNA samples when the AmpFlSTR Identifiler PCR Amplification Kit is incapable of generating a complete genetic profile. Validation experiments, following the SWGDAM guidelines, were designed to evaluate the performance of MiniFiler. Data obtained demonstrated that MiniFiler, when used in conjunction with Identifiler, provided an increased ability to obtain genetic profiles from challenged samples. The optimum template range was found to be between 0.2 and 0.6 ng, with 0.3 ng yielding the best results. Full concordance was achieved between the MiniFiler kit and Identifiler kit except in a single case of a null allele at locus D21S11. Numerous instances of severe heterozygous peak imbalance (<50%) were observed in single source samples amplified within the optimum range of input DNA suggesting that caution be taken when attempting to deduce component genotypes in a mixture.

Loss of heterozygosity (LOH)--implications for human genetic identification.

The aim of this study was assessment of possible effects of loss of heterozygosity on human genetic identification of histolopathogical tissue sections. DNA templates were extracted from tumour tissue specimens excised from oncological patients and from reference blood samples. AmpFlSTR Identifiler PCR Amplification Kit and ABI 310 Genetic Analyzer (Applera) were used to obtain genetic profiles. Frequency of LOH was calculated for respective samples. Fisher's exact test was performed for statistical analysis. Forty-two percent of the 101 cancer cases analysed were found to possess alterations of the microsatellites manifesting with allelic loss. The most frequently altered loci were D3S1358 and D18S51. The alteration was detected in 47% of cases with larynx carcinoma, 44% of cases with uveal melanoma, 60% of cases with cervical cancers, one case of liposarcoma G3 and one case od neurofibrosarcoma. No LOH was found in liposarcoma G1, dermatofibrosarcoma and cystosarcoma protuberans in either primary or recurrent tumours. In benign tumours (lipoma and fibroma) LOH was also absent. During genotyping of DNA extracted from histopathological tissue sections caution should be taken when non-match or exclusion based on few discrepancies is concluded.