Short Tandem Repeat Amplification Research Articles

Monitoring of Donor/recipient T-cell Engraftment Kinetics in Myeloablative Allogeneic Stem Cell Transplantation Using Short Tandem Repeat Amplification from Cell Lysates

Molecular monitoring of donor/recipient T-cell kinetics early post-transplant can provide clues to the immunological events that govern host-versus-graft reaction (HVGR) and graft versus-host-disease (GVHD). We have previously used fluorescence in situ hybridization (FISH) with X and Y probes to monitor recipient T (R-T) cell clearance early after myeloablative allogeneic stem cell transplantation (ASCT). We demonstrated that impaired clearance of residual host-T-cells in the early days post-transplant was associated with graft rejection, while enhanced clearance could be an indicator of increased donor anti-host alloreactivity and predictive of acute GVHD. Although FISH is the most accurate quantitative molecular tool for the determination of the exact donor/recipient-T-cell numbers at any time points post-transplant, it has the disadvantage of being limited to sex mismatched donor/recipient pairs. Our goal was to develop a molecular approach that, irrespective of gender, would be comparable to FISH in accurately determining host residual T-cell clearance after myeloablative conditioning for ASCT. We have genotyped DNA from cell lysates using polymerase chain reaction (PCR) amplification of short tandem repeats (STR) with fluorescently labeled oligonucleotide primers, and used the Genescan 672 software for accurate quantitative analysis of the amplified alleles. Here, we show that this approach allowed us to achieve in T-cells accurate quantitative analyses of amplified donor/recipient alleles in sex matched patients on days +5, +8 and +12 post-transplant, despite severe leukopenia.

Quality control of PCR primers used in multiplex STR amplification reactions

Reliable amplification of short tandem repeat (STR) DNA markers with the polymerase chain reaction (PCR) is dependent on high quality PCR primers. The particular primer combinations and concentrations are especially important with multiplex amplification reactions where multiple STR loci are simultaneously copied. Commercially available kits are now widely used for STR amplification and subsequent DNA typing. We present here the use of high performance liquid chromatography (HPLC) and time-of-flight mass spectrometry (TOF-MS) methods for characterization of commercially available STR kits.

Detection of male and female fetal DNA in maternal plasma by multiplex fluorescent polymerase chain reaction amplification of short tandem repeats.

The purpose of this study was to develop a fluorescent polymerase chain reaction (PCR) assay for the detection of circulating fetal DNA in maternal plasma. Maternal DNA extracted from plasma samples of pregnant women at term and newborn DNA isolated from cord blood were used to genotype 12 mother/child pairs at nine different polymorphic short tandem repeat loci. Multiplex fluorescent PCR was used to detect fetus-specific alleles in the corresponding maternal plasma samples. Fetus-specific alleles were found in all maternal plasma samples studied. Using these polymorphic repeat sequences, every mother/child pair was informative in at least four of nine loci. Paternally inherited fetal alleles were detected in 84% of informative short tandem repeats. This approach may have implications for non-invasive prenatal diagnosis. Compared with other fetal DNA detection systems that use fetus-derived Y sequences to detect only male fetal DNA in maternal plasma, our proposed technique can be applied to both female and male fetuses.

Detection of male and female fetal DNA in maternal plasma by multiplex fluorescent polymerase chain reaction amplification of short tandem repeats

Detection of male and female fetal DNA in maternal plasma by multiplex fluorescent polymerase chain reaction amplification of short tandem repeats

Clonal analysis of high-grade squamous intra-epithelial lesions of the uterine cervix.

We previously reported that invasive squamous cell carcinomas of the uterine cervix are of monoclonal composition. In the current study, we extended our previous work to determine the clonal composition of cases of high-grade squamous intra-epithelial lesion (HSIL). Clonal analysis targeting the HUMARA locus was performed on cervical tissue from 9 cases, 8 showing heterozygosity at the HUMARA locus and being, therefore, informative for clonality analysis. Uterine cervices were cut into 12 blocks, fixed with formalin and embedded in paraffin, and DNA was extracted from targeted lesions of each block. A total of 30 samples of cervical intra-epithelial neoplasia 3 (CIN3) (14 samples of carcinoma in situ and 16 samples of severe dysplasia) and 1 sample of CIN2 (moderate dysplasia) were analyzed. Monoclonal composition of the lesions was demonstrated in 30/30 cases of CIN3. Polyclonal composition was seen in the single case of CIN2. In 6 uterine cervices, in which dysplastic lesions were present in more than 3 blocks, the pattern of X-chromosome inactivation was the same in all lesions, suggesting that these individual lesions were derived from a single cell, with intraepithelial extension within the cervical mucosa. By contrast, one uterus contained 2 discontinuous dysplastic foci with different patterns of X-chromosome inactivation, indicating that the 2 lesions developed independently from each other. Our results demonstrate that (i) lesions of CIN3 (severe dysplasia and carcinoma in situ) are composed of a clonal neoplastic population of cells and (ii) most cases of HSIL are unifocal in origin.

Study of hematopoietic chimerism following allogeneic peripheral blood stem cell transplantation using PCR amplification of short tandem repeats.

Allogeneic peripheral blood progenitor cell transplantation (PBPCT) is increasingly being used to treat hematologic malignancies. However, the capacity of PBPC to maintain long-term hematopoiesis remains controversial. To add further information to this issue we studied the chimeric status in 12 patients receiving G-CSF-mobilized PBPC from HLA-identical sibling donors. All patients were conditioned with cyclophosphamide and total body irradiation. In six cases the apheresis product was partially T-cell depleted by counterflow centrifugation (n = 2) or the immunoadsorption biotin-avidin method (n = 4). The follow-up was longer than 6 months in five patients, with a maximum of 420 days. Molecular analysis of the engraftment was done using PCR amplification of short tandem repeats. Apparent complete donor chimerism was detected in all patients between 28 and 420 days after engraftment. This study indicates that full short-term engraftment is achieved in patients receiving allogeneic G-CSF-mobilized PBPC from healthy donors and suggests that this might also be true for long-term engraftment.

Validation of Multiplex Polymorphic STR Amplification Sets Developed for Personal Identification Applications

Polymorphic short tandem repeat (STR) loci, which typically consist of variations in the number of 3-7 base pair repeats present at a site, provide an effective means of personal identification. Typing can be accomplished by amplification of genomic DNA using the polymerase chain reaction (PCR) and locus-specific primers, separation of amplified alleles using gel electrophoresis and their display using silver staining or fluorescent detection. Primers for several STR loci can be combined in a single multiplex reaction so typing of multiple loci can be accomplished rapidly and with less DNA than required if each locus were analyzed separately. Before such muliplex systems are used in forensic or paternity applications, it is desirable that they undergo testing for their reliability. This study evaluates the performance of two STR triplex systems, one containing the loci HUMCSF1PO, HUMTPOX, and HUMTH01, and the other containing HUMHPRTB, HUMFESFPS, and HUMVWFA31. Protocols for amplification of these two triplexes, and their corresponding monoplexes, were evaluated for sensitivity of detection, resistance to changes in the annealing temperature of the amplification protocol, and the ability to identify the minority contributor in amplification of mixed samples. In addition, five laboratories determined the alleles of twenty DNA samples, each extracted by one of four different extraction methods. The results illustrate that the two STR triplex systems and the monoplex systems contained within them can be used with as little as 0.25 ng of DNA template. Both triplexes amplified with 100% success using the Perkin Elmer Model 480 thermal cycler. With the GeneAmp 9600 System, the CTT triplex amplified with 100% success and the HFv triplex in 95.6% of attempts. These experiments meet many requirements for use in validation of DNA typing systems for forensic cases and paternity identification.

Validation of highly discriminating multiplex short tandem repeat amplification systems for individual identification.

Short tandem repeat (STR) loci are routinely employed for individual identification. WE have examined the performance and reproducibility of a highly informative co-amplification system containing the tetranucleotide STR loci: HUMVWFA31/A, HUMTH01, D20S85, D8S1179, HUMFIBRA, D21S11, and D18S51, in conjunction with the amelogenin sex test, in addition to a modified system omitting the locus D20S85. Polymerase chain reaction (PCR) products were fluorescently detected on an automated sequencer and automatically sized against an internal size standard by Genescan software. Both systems were routinely able to type 500 pg of undegraded DNA. At DNA concentrations between 50-500 pg, partial profiles were produced, but no allelic drop-out was observed. Balanced amplification of all loci occurred over a wide range of DNA concentrations from 50 pg to 10 ng. Alteration of reagent concentrations and cycling parameters from optimal resulted in variation in the efficiency of individual locus amplification relative to the other loci within the system. This was also observed at high ionic strength or extreme pH. However, at all reagent concentrations and conditions, allelic drop-out was not observed. These multiplex systems have potential in both routine forensic and intelligence database applications.

Analysis of Clonality by Amplification of Short Tandem Repeats

The clonal composition of cancers of the female reproductive tract was evaluated by analysis of patterns of X-chromosome inactivation. Using DNA extracted from frozen tissues or paraffin-embedded archival specimens as template, polymerase chain reaction (PCR) was performed to generate amplified DNA fragments of exon 1 of the X-linked androgen receptor gene, which contains a highly polymorphic trinucleotide repeat. Predigestion of tumor DNA with methylation-sensitive restriction endonuclease Hha I or Hpa II permitted selective PCR amplification from the methylated (uncleaved) allele. Of a total of 54 tumors analyzed, 50 cases showed heterozygosity (93%) and were therefore informative for clonal analysis. Monoclonal composition of the tumors was suggested in a total of 49 of 50 cases, including 12 adenocarcinomas of the uterine endometrium, 13 squamous cell carcinomas of the uterine cervix, 6 adenocarcinomas of the uterine endocervix, and 18 epithelial tumors of the ovary. However, polyclonal composition was observed in one mucinous carcinoma of the ovary, in which we previously showed that both GGT-->GAT and GGT-->GTT mutations are present in > 20% of total K-ras copies in the tissue. Our studies demonstrate the utility of PCR amplification of highly polymorphic repetitive sequences for analysis of patterns of X-chromosome inactivation. This approach is practical for the analysis of clonal cell composition in a high proportion of both formalin-fixed and frozen archival tissues.