Bibliography for STR methods
1. Hammond, H.A., Jin, L., Zhong, Y., Caskey, C.T., and Chakraborty, R. Evaluation of 13 short tandem repeat loci for use in personal identification applications [see comments]. Am. J. Hum. Genet., 55: 175-189, 1994.
Comment in: Am J Hum Genet 1995 Apr;56(4):1005-6 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 0002-9297 ENGLISH UNITED-STATES Personal identification by using DNA typing methodologies has been an issue in the popular and scientific press for several years. We present a PCR-based DNA-typing method using 13 unlinked short tandem repeat (STR) loci. Validation of the loci and methodology has been performed to meet standards set by the forensic community and the accrediting organization for parentage testing. Extensive statistical analysis has addressed the issues surrounding the presentation of "match" statistics. We have found STR loci to provide a rapid, sensitive, and reliable method of DNA typing for parentage testing, forensic identification, and medical diagnostics. Valid statistical analysis is generally simpler than similar analysis of RFLP-VNTR results and provides powerful statistical evidence of the low frequency of random multilocus genotype matching JOURNAL-ARTICLE 0; 9007-49-2 1994295585 199410, (Ref ID:4990)
2. Alford, R.L., Hammond, H.A., Coto, I., and Caskey, C.T. Rapid and efficient resolution of parentage by amplification of short tandem repeats [see comments]. Am. J. Hum. Genet., 55: 190-195, 1994.
Comment in: Am J Hum Genet 1995 Jun;56(6):1503-6 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 0002-9297 ENGLISH UNITED-STATES 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 JOURNAL-ARTICLE 9007-49-2 1994295586 199410, (Ref ID:4991)
3. Edwards, A., Hammond, H.A., Jin, L., Caskey, C.T., and Chakraborty, R. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics, 12: 241-253, 1992.
Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030 0888-7543 ENGLISH UNITED-STATES Trimeric and tetrameric short tandem repeats (STRs) represent a rich source of highly polymorphic markers in the human genome that may be studied with the polymerase chain reaction (PCR). We report the analysis of a multilocus genotype survey of 97-380 chromosomes in U.S. Black, White, Mexican-American, and Asian populations at five STR loci located on chromosomes 1, 4, 11, and X. The heterozygote frequencies of the loci ranged from 0.36 to 0.91 and the number of alleles from 6 to 20 for the 20 population and locus combinations. Relative allele frequencies exhibited differences between populations and unimodal, bimodal, and complex distributions. Although deviations were noted at some locus-population test combinations, genotype data from the loci were consistent overall with Hardy-Weinberg equilibrium by three tests. Population subheterogeneity within each ethnic group was not detected by two additional tests. No mutations were detected in a total of 860 meioses for two loci studied in the CEPH kindreds and five loci studied in other families. An indirect estimate of the mutation rates gave values from 2.3 x 10(-5) to 15.9 x 10(-5) for the five loci. Higher mutation rates appear to be associated with greater numbers of tandem repeats in the core motif. The most frequent genotype for all five loci combined appears to have a frequency of 7.59 x 10(-4). Together, these results suggest that trimeric and tetrameric STR loci are useful markers for the study of new mutations and genetic linkage analysis and for application to personal identification in the medical and forensic sciences JOURNAL-ARTICLE GM41399GMNIGMS 0; 9007-49-2 1992155713 199205, (Ref ID:4992)
4. Huang, T.H., Hejtmancik, J.F., Edwards, A., Pettigrew, A.L., Herrera, C.A., Hammond, H.A., Caskey, C.T., Zoghbi, H.Y., and Ledbetter, D.H. Linkage of the gene for an X-linked mental retardation disorder to a hypervariable (AGAT)n repeat motif within the human hypoxanthine phosphoribosyltransferase (HPRT) locus (Xq26). Am. J. Hum. Genet., 49: 1312-1319, 1991.
Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030 0002-9297 ENGLISH UNITED-STATES We recently reported a new X-linked mental retardation (XLMR) disorder in a four-generation family of Dutch descent. Features included Dandy-Walker malformation, basal ganglia disease, and seizures. Twenty-six family members, including two living affected males and two obligate carriers, were available for study. No evidence of linkage was observed between the disease locus and RFLPs from several X-chromosome regions, including Xp21-p22 (13 markers), proximal Xq (four markers), and Xq28 (three markers). However, a new hypervariable short tandem repeat (STR) within the HPRT gene at Xq26 showed positive linkage to the disease locus, with a maximum lod score of 2.19 at a recombination fraction of 0. A second hypervariable marker in Xq26, the dinucleotide repeat XL90A3 (DXS425), showed a lod score of .84 at a recombination fraction of .11. Both the HPRT and DXS425 markers were typed in 40 CEPH families, and subsequent multipoint linkage analysis showed the following order: Xcen-DXS425-(HPRT,XLMR)-F9-qter. HPRT and these flanking markers are therefore useful for carrier detection and prenatal diagnosis in this family. This study illustrates that hypervariable STRs will be powerful tools for linkage analysis and genetic diagnosis, particularly when relatively small families are involved H; P; R; T; XLMR JOURNAL-ARTICLE DK31428DKNIDDK EC 2.4.2.8; 0; 0; 0 1992081777 199203, (Ref ID:4993)
5. Edwards, A., Civitello, A., Hammond, H.A., and Caskey, C.T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet., 49: 746-756, 1991.
Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030 0002-9297 ENGLISH UNITED-STATES Tandemly reiterated sequences represent a rich source of highly polymorphic markers for genetic linkage, mapping, and personal identification. Human trimeric and tetrameric short tandem repeats (STRs) were studied for informativeness, frequency, distribution, and suitability for DNA typing and genetic mapping. The STRs were highly polymorphic and inherited stably. A STR-based multiplex PCR for personal identification is described. It features fluorescent detection of amplified products on sequencing gels, specific allele identification, simultaneous detection of independent loci, and internal size standards. Variation in allele frequencies were explored for four U.S. populations. The three STR loci (chromosomes 4, 11, and X) used in the fluorescent multiplex PCR have a combined average individualization potential of 1/500 individuals. STR loci appear common, being found every 300-500 kb on the X chromosome. The combined frequency of polymorphic trimeric and tetrameric STRs could be as high as 1 locus/20 kb. The markers should be useful for genetic mapping, as they are sequence based, and can be multiplexed with the PCR. A method enabling rapid localization of STRs and determination of their flanking DNA sequences was developed, thus simplifying the identification of polymorphic STR loci. The ease by which STRs may be identified, as well as their genetic and physical mapping utility, give them the properties of useful sequence tagged sites (STSs) for the human genome initiative JOURNAL-ARTICLE 1991377737 199112, (Ref ID:4994)
6. Puers, C., Hammond, H.A., Caskey, C.T., Lins, A.M., Sprecher, C.J., Brinkmann, B., and Schumm, J.W. Allelic ladder characterization of the short tandem repeat polymorphism located in the 5' flanking region to the human coagulation factor XIII A subunit gene. Genomics, 23: 260-264, 1994.
Promega Corporation Madison, Wisconsin 53711-5399 0888-7543 ENGLISH UNITED-STATES The short tandem repeat (STR) polymorphism present within the 5' untranslated region of the human coagulation factor XIII A subunit gene, HUMF13A01[AAAG]n, was evaluated using an allelic ladder, i.e., a standard size marker consisting of amplified alleles from the locus. The allelic ladder was constructed by pooling 12 polymerase chain reaction (PCR)-amplified alleles identified by their differential migration in denaturing polyacrylamide gel electrophoresis. This standard marker was used to distinguish 14 different alleles observed at this locus. Sequence analyses indicate that 13 of the alleles contain 4 through 16 iterations of the tandemly repeated AAAG sequence, respectively. The remaining allele carries four repeats and displays a deletion of two consecutive nucleotides (GT), one base distal to the repeat region. The allelic ladder was employed to type 326 F13A01 chromosomes rapidly and reliably in representatives of a German Caucasian population. Population data were analyzed with respect to Hardy-Weinberg Equilibrium (HWE) and compared with those of a previously studied Houston, Texas, Caucasian population HUMF13A JOURNAL-ARTICLE 9007-49-2; 9013-56-3 1995130094 199504, (Ref ID:4995)
7. Tanabe,H., Takada,Y., Minegishi,D., Kurematsu,M., Masui,T., and Mizusawa,H. Cell line individualization by STR multiplex system in the cell bank found cross contamination between ECV304 and EJ-1/T24. Tiss. Cult. Res. Commun., 18: 329-338, 1999.
Notes:
Short tandem repeat (STR) regions represent highly polymorphic micro satellite markers in the human genome that have tandemly repetitive sequence elements of 2 to 7 bp in length as a unit The application of STR regions to population genetics and personal identification has been well studied. Recent technical advances have enabled us to analyze multilocus STR regions simultaneously by a method, called the STR Multiplex system, that uses a single PCR amplification in one tube. We established a new evaluation system for the identification of cell lines based on an STR Multiplex method that uses 9 different loci: D5S81 8. D13S31 7, D7S820, D16S539, vWA. THOI , Amelogenin, TPOX, and CSFIPO The STR profiling data from 96 cell lines were examined and an efficiency of this approach for cell standardization was found. Using this method, we have analyzed the STR profiles of human cell lines. ECV304, EJ-1, and T24, reoently reported by the DSMZ-German Collection of Microorganisms and Cell Cultures to have been cross-contaminated. Our results clearly detect the cross-contamination between ECV304 and EJ-1/T24. The cross-contamination was estimated to be derived from the T24 cells. Collectively, the STR Multipiex system provides a rapid, precise, and powerful method in cell line identification for quality control at the JCRB Cell Bank.
Reference ID: 5018