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PubMed2002

[The unusual typing of short tandem repeats].

Short tandem repeats (STRs) have been widely used in forensic sciences such as stain analysis and paternity testing. Although most of STR typing could give the reliable and clear results, some unusual typing have been observed in forensic practice. The anomalous typing could result from a lot of causes, including DNA genetic variation, poor quality or quantity of DNA template, different typing system or method, nonspecific reaction in PCR or anomalous electrophoresis migration. The unusual results may disturb the right interpretation of STR typing.

DNA Fingerprinting↗

PubMed1994

Rapid and efficient resolution of parentage by amplification of short tandem repeats.

Short tandem repeat (STR) loci are highly informative polymorphic loci that are gaining popularity for identity testing. We have conducted parentage testing by using nine STR loci on 50 paternity trios that had been previously tested using VNTR loci. These nine unlinked STR loci are amplified in three multiplex reactions and, when examined for genetic informativeness, provide a combined average power of exclusion of 99.73% (Caucasian data). The informative value of the selected loci is based on extensive STR typing of four racial/ethnic populations. In 37 of the 50 cases, paternity could not be excluded by any of the loci. In the remaining 13 cases, paternity was excluded by at least two of the STR markers. The probability of paternity calculated for the alleged father of each matching trio was > 99% in 36 of the 37 inclusion cases. All data agreed with the results reported using VNTR loci and conventional Southern technology. Our studies validate the use of DNA typing with STR loci for parentage testing, thus providing an accurate, highly sensitive, and rapid assay.

Alleles↗

PubMed2005

Comparison of variable number tandem repeat and short tandem repeat genetic markers for qualitative and quantitative chimerism analysis post allogeneic stem cell transplantation.

BACKGROUND: Analysis of donor chimerism has become a routine procedure for the documentation of engraftment after allogeneic hematopoietic stem cell transplantation. Quantitative analysis of chimerism kinetics has been shown to predict graft failure or relapse. In this study, we compared the use of variable number tandem repeats (VNTR) and short tandem repeats (STR) as polymorphic genetic markers in chimerism analysis. This study included qualitative and quantitative assessment of both techniques to assess informative yield and sensitivity. PATIENTS AND METHODS: We analyzed 206 samples representing 40 transplant recipients and their HLA-identical sibling donors. A panel of six VNTR loci, 15 STR loci and 1 sex chromosome locus was used. Amplified VNTR products were visualized in an ethidium bromide-stained gel. STR loci were amplified using fluorescent primers, and the products were analyzed by capillary electrophoresis. RESULTS: VNTR and STR analysis gave comparable qualitative results in the majority of cases. The incidence of mixed chimerism (MC) by STR analysis was 45% compared to 32% in cases evaluated by VNTR analysis. STR markers were more informative; several informative loci could be identified in all patients. Unique alleles for both patient and donor could be identified in all patients by STR versus 32/40 by VNTR analysis. The STR markers were also more sensitive in the detection of chimerism. The size of VNTR alleles and differences between the size of donor and recipient VNTR alleles affected the sensitivity of detection. With both techniques, quantitative assessment of chimerism showed some discrepancies between the estimated and the calculated percentage of donor DNA. Discordance between the two estimates was observed in 8/19 patients with MC. However, sequential monitoring of the relative band intensity of VNTR alleles offered some insight into the direction of change in engraftment over time. CONCLUSION: The higher yield of informative loci with STR and the automated measurement of amplified STR 103 products offered the advantages of more rapid and accurate quantitative assessment of chimerism. The choice between these two techniques depends on the need for quantitative or qualitative information, the availability of equipment, and the cost.

Chimerism↗

PubMed2005

Locus-specific brackets for reliable typing of Y-chromosome short tandem repeat markers.

Short tandem repeat (STR) loci, widely used as genetic markers in disease diagnostic studies and human identity applications, are traditionally genotyped through comparison of allele sizes to a sequenced allelic ladder. Allelic ladders permit a floating bin allele calling method to be utilized, which enables reliable allele calling across laboratories, instrument platforms, and electrophoretic conditions. Precise sizing methods for STR allele calling involving fixed bins can also be used when a high degree of precision has been demonstrated within an instrument platform and a set of electrophoretic conditions. An alternative method for reliable genotyping of STR markers, locus-specific brackets (LSBs), is introduced here. LSBs are artificial alleles created through molecular biology manipulations to be shorter or longer than alleles commonly seen in populations under investigation. The size and repeat number of measured alleles are interpolated between the two LSB products that are mixed with the polymerase chain reaction-amplified STR alleles. The advantages and limitations of the LSB approach are described along with a concordance study between the LSB typing approach and other STR typing methods. Complete agreement was observed with 162 samples studied at 5 Y-chromosome loci.

Alleles↗

PubMed1998

Spectral measurements of intercalated PCR-amplified short tandem repeat alleles.

Short tandem repeat (STR) alleles are popular for use as forensic markers due to their highly polymorphic nature. Commonly they are separated by gel electrophoresis and visualized using intercalation dyes. The purpose of this study was to determine the changes in absorbance and fluorescence of DNA-intercalation dye complexes as a function of base pair (bp)-to-dye ratio. The DNA samples consisted of STR alleles from loci THO1, F13A01, and vWFA31. The alleles were PCR amplified and HPLC purified to ensure that only the desired DNA fragment was present in each sample. Alleles ranged in size from 151 bp for locus vWFA (allele 17) to 199 bp for the locus F13A01 (allele 8). The adenine and thymine (AT) content varied from 48% for the THO1 locus to 69% for F13A01 and vWFA31 loci. The homozygous alleles of each locus were mixed individually with the bis-intercalators TOTO-1 and YOYO-1 and their corresponding monomeric dyes TOPRO-1 and YOPRO-1. The absorbance of the DNA-dye complex at 260 nm increased with addition of each intercalation dye. Subtraction of the dye absorbance rendered the DNA absorbance constant at 260 nm. Fluorescence emission increased dramatically upon intercalation of both the monomeric and dimeric dyes into the DNA helix. A plateau of fluorescence intensity was observed at base pair-to-dye ratios of 10/1 for the bis-intercalator TOTO-1 and 5/1 for YOYO-1 for all three loci. The greatest fluorescence intensity response was obtained with the intercalator YOYO-1 using allele 8 of the F13A01 locus, which had the greatest AT concentration.

Adenine↗

PubMed2006

Laser microdissection separation of pure spermatozoa from epithelial cells for short tandem repeat analysis.

Short tandem repeat (STR) analysis is a valuable tool in identifying the source of biological stains, particularly from the investigation of sexual assault crimes. Difficulties in analysis arise primarily in the interpretation of mixed genotypes when cell separation of the sexual assailant's sperm from the victim's cells is incomplete. The forensic community continues to seek improvements in cell separation methods from mixtures for DNA typing. The feasibility of applying laser microdissection (LMD) technology to precisely separate sexual assault cell mixtures by visual inspection coupled with laser dissection was assessed through three experiments. First, various histological stains were evaluated for use with LMD and DNA analysis. Second, different DNA isolation methods were evaluated on LMD-collected cells. Finally, STR analysis was performed on LMD-separated sperm cells from mixtures of semen and female buccal epithelial cells. The results indicated (a) hematoxylin/eosin staining performed best in its ability to differentiate sperm and epithelial cells while exhibiting the least negative effect on further downstream analysis; (b) both QIAamp and Lyse-N-Go methods were useful for recovery of DNA from LMD-collected sperm cells; and (c) LMD separation provided clear STR profiles of the male donor with the absence of any additional alleles from the female donor. This report describes an efficient, low-manipulation LMD method for the efficient separation of spermatozoa from two-donor sperm/epithelial cell mixtures.

Alleles↗

PubMed1997

Agarose-based system for separation of short tandem repeat loci.

Short tandem repeats (STRs) are traditionally analyzed on large polyacrylamide electrophoresis gels. We demonstrate in this study that a small (10-cm-long, 1-mm-thick) agarose gel is sufficient for analysis of multiplexed samples for several commonly used STR loci. A system was developed using a high-resolution agarose, MetaPhor. Within an hour of electrophoresis, sufficient resolution was obtained to allow discrimination of triple-multiplexed STR loci. We show that this agarose is capable of resolving di- as well as tetranucleotide ladders. Using PCR conditions similar to those routinely used with sensitive detection systems, we found that direct staining of gels with SYBR Green I stain was comparable with silver staining, autoradiography or fluorescently tagged primers for sample detection and was considerably easier. This procedure significantly simplifies STR analysis and is much faster than many standard protocols.

DNA↗

PubMed1996

Allele frequency distributions at several variable number of tandem repeat (VNTR) and short tandem repeat (STR) loci in a restricted Caucasian population from south Italy and their evaluation for paternity and forensic use.

Allele frequencies at six VNTR loci, 11 STR loci, and at the HLA-DQA1 locus were evaluated in a well-defined population from Campania (South Italy). The allele frequencies of three VNTR loci, 11 STR loci, and the HLA-DQA1 locus were compared with data obtained from a general Caucasian reference population in the USA. The aim of this study was to determine the power of each single locus and group of loci for forensic and paternity testing purposes. Significant differences between the allele frequencies of the two populations were found in two VNTR loci, four STR loci and in the HLA-DQA1 locus. The two populations were in Hardy-Weinberg equilibrium for the STR loci, but as expected, not for some VNTR loci. It was also found that: (i) the discriminatory power of two STR systems (nine and 11 loci, respectively) is similar in the two populations analysed; and (ii) that the allele frequencies for the STR systems of a large reference population can always be applied to subjects of a small subpopulation. In conclusion, for forensic purposes and for paternity testing, most of the 11 STR loci examined can be analysed using allele frequencies from a general Caucasian reference population without typing subpopulations, whereas the VNTR loci must be subtyped.

Adult↗

PubMed2002

Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats.

A procedure utilizing Chelex 100, chelating resin, was adapted to extract DNA from dental pulp. The procedure was simple and rapid, involved no organic solvents, and did not require multiple tube transfers. The extraction of DNA from dental pulp using this method was as efficient, or more so, than using proteinase K and phenol-chloroform extraction. In this study, the Chelex method was used with amplification and typing at Y-chromosomal loci to determine the effects of temperature on the sex determination of the teeth. The extracted teeth were incinerated in a dental furnace for 2 minutes at 100 degrees C, 200 degrees C, 300 degrees C, 400 degrees C, and 500 degrees C. After the isolation of DNA from the dental pulp by the Chelex method, alphoid repeats, and short tandem repeats, the human Y chromosome (DYZ3), DYS19, SYS389, DYS390, and DYS393 could be amplified and typed in all samples incinerated at up to 300 degrees C for 2 minutes. The DYS389 locus in some samples could not be amplified at 300 degrees C for 2 minutes. An autopsy case is described in which genotypings of DYS19, DYS390, and DYS393 from dental pulp obtained from a burned body were needed. The data presented in this report suggest that Chelex 100-based DNA extraction, amplification, and typing are possible in burned teeth in forensic autopsy cases.

Chelating Agents↗

PubMed1999

Survey of the Korean population for 9 short tandem repeat loci.

The short tandem repeats with repeat units ranging from two to several nucleotides became a powerful tool in the field of forensic identification and paternity determination as well as for research in human gene mapping. Allele and genotype frequencies for 9 short tandem repeats including HUMCSF1PO, HUMTH01, HUMPLA2A1, HUMF13A01, HUMCYAR04, HUMLIPOL, HUMHPRTB, HUMCD4, and HUMFABP were determined using PCR and subsequent analysis of the PCR products by denaturing polyacrylamide gel electrophoresis followed by silver-staining. DNA samples were obtained from about 100 Korean people and amplified in a thermocycler adopting glass capillaries rather than traditional tubes. We found that the bovine serum albumin was an essential additive for the capillary PCR, presumably to coat the inner surface of the capillary which may adsorb Taq DNA polymerase. The capillary thermocycler was very effective in reducing the cycling time such that most of the amplification reactions could be finished within 30 min albeit the PCR product was less than that for the tube systems. All loci except HUMHPRTB met the Hardy-Weinberg expectations according to the exact test. The cumulative power of discrimination (PD) was 0.9999998 and the power of exclusion (POE) for the paternity test was a little low, being 0.9873989.

Alleles↗

PubMed2001

When autosomal short tandem repeats fail: optimized primer and reaction design for Y-chromosome short tandem repeat analysis in forensic casework.

Y-chromosomal short tandem repeats (Y-STRs) are useful forensic DNA markers in investigation of sexual assault cases when a mixture of male and female DNA (e.g., in vaginal swabs) is present in a sample, especially when DNA of the male contributor is present only in very small amount compared to the DNA of the female victim. With autosomal STR analysis of male and female DNA, male DNA in mixtures can usually be detected and correctly interpreted only when it exceeds 5%. However, the amplification of some Y-STRs is known to result in polymerase chain reaction (PCR) products that are not associated with the Y-chromosome, but derive from the X-chromosome and/or autosomal regions. This can cause problems in the interpretation of results, particularly when female DNA is present in excess. Consequently, more specific and sensitive Y-STR primers and PCR conditions are needed. This paper presents two casework examples in which sensitive Y-STR multiplexes (with the addition of PCR enhancer) were successfully used in the analysis of mixtures of male and female DNA, the male component not interpretable by standard autosomal STR typing.

Adolescent↗

PubMed1994

High sensitive DNA typing approaches for the analysis of forensic evidence: comparison of nested variable number of tandem repeats (VNTR) amplification and a short tandem repeats (STR) polymorphism.

The approach of using nested primers for the APO B variable number of tandem repeats (VNTR) increases the sensitivity of the polymerase chain reaction (PCR) to single cell level. Different experiments and a comparison to the short tandem repeats (STR) system VWA were carried out, to determine the applicability of this method to forensic samples. Nested amplification of the Apo B VNTR was affected by a strong tendency towards preferential amplification of the shorter alleles. This phenomenon was observed for DNA quantities as low as 100 pg and impaired, depending on the allele length, the results for mixed samples. As expected, VWA polymorphism showed less preferential amplification. The high sensitivity of both PCR systems is accompanied by an increased susceptibility to contamination. Using artificially contaminated bloodstains, the bloodstain genotype, the contamination or both genotypes could be found on one piece of evidence. Here a single analysis can lead to an incorrect result. Therefore a strategy for obtaining reliable results should consist of multiple stain extractions and the amplification of different stepped dilutions of the DNA solution.

Base Sequence↗

PubMedDate not supplied

Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci.

Tetrameric short tandem repeat (STR) polymorphisms are widely used in population genetics, molecular evolution, gene mapping and linkage analysis, paternity tests, forensic analysis, and medical applications. This article provides allelic distributions of the STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TPOX, TH01, and D16S539 in 143 Mestizos from Northeastern Mexico, estimates of contributions of genes of European (Spanish), American Indian and African origin in the gene pool of this admixed Mestizo population (using 10 of these loci); and a comparison of the genetic admixture of this population with the previously reported two polymorphic molecular markers, D1S80 and HLA-DQA1 (n = 103). Genotype distributions were in agreement with Hardy-Weinberg expectations (HWE) for almost all 13 STR markers. Maximum likelihood estimates of admixture components yield a trihybrid model with Spanish, Amerindian, and African ancestry with the admixture proportions: 54.99% +/- 3.44, 39.99% +/- 2.57, and 5.02% +/- 2.82, respectively. These estimates were not significantly different from those obtained using D1S80 and HLA-DQA1 loci (59.99% +/- 5.94, 36.99% +/- 5.04, and 3.02% +/- 2.76). In conclusion, Mestizos of Northeastern Mexico showed a similar ancestral contribution independent of the markers used for evolutionary purposes. Further validation of this database supports the use of the 13 STR loci along with D1S80 and HLA-DQA1 as a battery of efficient DNA forensic markers in Northeastern Mestizo populations of Mexico.

Genetic Markers↗

PubMed1998

The short tandem repeat locus D3S1359.

Short tandem repeats (STRs) are used by many laboratories throughout the world performing paternity testing or criminal casework. Nevertheless, many of the established STRs have obvious disadvantages such as low number of common alleles (e.g., hTPO, THO1) or alleles with frequencies of nearly 50% (e.g., hTPO, FES). In this paper the new STR locus D3S1359 is described. In a population study which was carried out on 136 unrelated individuals from southwestern Germany, we have detected 17 different alleles. The most common allele was allele 13 (204 bp) with a frequency of 18.8%. Eight further alleles have frequencies higher than 5%. With a heterozygozity index of 90% and 60 different genotypes, D3S1359 has shown to be a highly polymorphic and informative marker. Sequencing data of this STR locus revealed further variation.

Alleles↗

PubMed2004

NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes.

Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.

Alleles↗

PubMed2000

Survey of the fragile X syndrome CGG repeat and the short-tandem-repeat and single-nucleotide-polymorphism haplotypes in an African American population.

Previous studies have shown that specific short-tandem-repeat (STR) and single-nucleotide-polymorphism (SNP)-based haplotypes within and among unaffected and fragile X white populations are found to be associated with specific CGG-repeat patterns. It has been hypothesized that these associations result from different mutational mechanisms, possibly influenced by the CGG structure and/or cis-acting factors. Alternatively, haplotype associations may result from the long mutational history of increasing instability. To understand the basis of the mutational process, we examined the CGG-repeat size, three flanking STR markers (DXS548-FRAXAC1-FRAXAC2), and one SNP (ATL1) spanning 150 kb around the CGG repeat in unaffected (n=637) and fragile X (n=63) African American populations and compared them with unaffected (n=721) and fragile X (n=102) white populations. Several important differences were found between the two ethnic groups. First, in contrast to that seen in the white population, no associations were observed among the African American intermediate or "predisposed" alleles (41-60 repeats). Second, two previously undescribed haplotypes accounted for the majority of the African American fragile X population. Third, a putative "protective" haplotype was not found among African Americans, whereas it was found among whites. Fourth, in contrast to that seen in whites, the SNP ATL1 was in linkage equilibrium among African Americans, and it did not add new information to the STR haplotypes. These data indicate that the STR- and SNP-based haplotype associations identified in whites probably reflect the mutational history of the expansion, rather than a mutational mechanism or pathway.

Black or African American↗

PubMed2006

Least-square deconvolution: a framework for interpreting short tandem repeat mixtures.

Interpreting mixture short tandem repeat DNA data is often a laborious process, involving trying different genotype combinations mixed at assumed DNA mass proportions, and assessing whether the resultant is supported well by the relative peak-height information of the mixture sample. If a clear pattern of major-minor alleles is apparent, it is feasible to identify the major alleles of each locus and form a composite genotype profile for the major contributor. When alleles are shared between the two contributors, and/or heterozygous peak imbalance is present, it becomes complex and difficult to deduce the profile of the minor contributor. The manual trial and error procedures performed by an analyst in the attempt to resolve mixture samples have been formalized in the least-square deconvolution (LSD) framework reported here for two-person mixtures, with the allele peak height (or area) information as its only input. LSD operates on the peak-data information of each locus separately, independent of all other loci, and finds the best-fit DNA mass proportions and calculates error residual for each possible genotype combination. The LSD mathematical result for all loci is then to be reviewed by a DNA analyst, who will apply a set of heuristic interpretation guidelines in an attempt to form a composite DNA profile for each of the two contributors. Both simulated and forensic peak-height data were used to support this approach. A set of heuristic guidelines is to be used in forming a composite profile for each of the mixture contributors in analyzing the mathematical results of LSD. The heuristic rules involve the checking of consistency of the best-fit mass proportion ratios for the top-ranked genotype combination case among all four- and three-allele loci, and involve assessing the degree of fit of the top-ranked case relative to the fit of the second-ranked case. A different set of guidelines is used in reviewing and analyzing the LSD mathematical results for two-allele loci. Resolution of two-allele loci is performed with less confidence than for four- and three-allele loci. This paper gives a detailed description of the theory of the LSD methodology, discusses its limitations, and the heuristic guidelines in analyzing the LSD mathematical results. A 13-loci sample case study is included. The use of the interpretation guidelines in forming composite profiles for each of the two contributors is illustrated. Application of LSD in this case produced correct resolutions at all loci. Information on obtaining access to the LSD software is also given in the paper.

Algorithms↗

PubMed1999

Extraction of DNA from decomposed human tissue. An evaluation of five extraction methods for short tandem repeat typing.

Hyperpolymorphic short tandem repetitive DNA sequences, STRs or microsatellites, have become widely used in human identification, particularly in criminal cases and in mass disasters. In such cases the substrates for the analyses may be decomposed biological material, a fact that has to be taken into account when choosing the appropriate casework methods. In this paper we report the evaluation of five different DNA extraction methods, namely the phenol-chloroform, the silica based, the InstaGene Matrix (BioTest), the glass fiber filter, and the Chelex based methods. The substrates for the analyses are decomposed human liver tissue specimens from forensic autopsy cases. Extracted DNA was quantified and DNA profiled by a set of seven STRs. We have compared laboratory time consumption and costs of the five methods, showing that the Chelex method is the more rapid and less expensive of the methods, the phenol-chlorophorm and silica extractions being the most time consuming and resource demanding ones. A full profile was obtained by the silica method in nine out of ten cases and this method failed to give a reliable type in four out of 70 STR analyses. The phenol-chlorophorm and the glass fiber filter methods failed in 16 analyses, the InstaGene Matrix (BioTest) in 25 and the Chelex extracts in 56 of the 70 STR analyses. By multiple logistic regression we show that the difference between the silica procedure and the other methods are statistically significant. In our hands, the silica gel extraction procedure is an obvious choice when the biological material available is decomposed human tissue--even if this procedure is one of the more laborious ones.

Autolysis↗