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PubMed2002

Characterization of two New York City Jewish populations at six short tandem repeat loci.

The Hasidic and non-Hasidic Jewish communities of New York City represent two subpopulations with long-documented histories of restrictive marriage patterns and a high degree of endogamy. As part of a continuing study into their genetic structure, allele frequencies were determined for the six tetrameric short tandem repeat (STR) loci: FESFPS, F13AO1, vWA, CSF1PO, TPOX, and THO1. All loci were tested for Hardy-Weinberg equilibrium (HWE) by three tests: chi-square analysis, Monte Carlo chi-square analysis. and the exact test. The non-Hasidic population failed to meet HWE at the F13A01, FESFPS, and CSF1PO loci by all three tests. The Hasidic population also failed to meet HWE at the same loci by some of the tests. Comparison of the Hasidic to the non-Hasidic population using an R x C contingency table demonstrated a similarity at only the vWA locus. Significant differences exist when comparing the two Jewish populations to a reference Caucasian population.

Alleles↗
PubMedDate not supplied

Polymorphism of T-cell receptor gamma short tandem repeats as a susceptibility risk factor of hepatocellular carcinoma.

BACKGROUND: T-cells play a critical role in the immunological surveillance network against cancer formation. The activation of T-cells is initiated by binding of T-cell receptors (TCR) with antigen epitopes. Polymorphisms of TCR-gamma microsatellite (short tandem repeats, STR) marker has been associated with early-onset colorectal cancer. The aim of this study was to test the relationship of TCR-gamma STR genetic polymorphisms and hepatocellular carcinoma (HCC). MATERIALS AND METHODS: A total of 225 chronic hepatitis B- or C-related HCC and liver cirrhosis patients were enrolled in this study. The other 225 sex-matched cirrhotic patients without HCC were recruited as controls. Their TCR-ygammaSTR polymorphisms at loci D7S1818 and D7S2206 were measured by polymerase chain reaction. Dietary habits and other possible risk factors for HCC were also assessed by a structured questionnaire. RESULTS: Compared to controls, the HCC patients were older in age (64.9 +/- 10.3 vs. 53.5 +/- 10.1 years, p < 0.001) and had a higher percentage of family history of HCC (13.3% vs. 7.6%, p = 0.045) and habitual alcohol use (23.1% vs. 15.6%, p= 0.042). A total of 20 genotypes of TCR-gamma D7S1818 STR were detected. Of these, the genotype 16 (13/14 of repeat number of GA A) had a higher percentage in the HCC groups than in the controls (13.8% vs. 6.7%, p = 0.013). After adjustment for age, family history of HCC and habitual alcohol use, the TCR-gamma genotype 16 remained a significant risk factor for HCC (OR: 2.18, 95% CI: 1.02-4.65, p= 0.045). CONCLUSION: The TCR-gamma STR polymorphism may be associated with HCC susceptibility.

Aged↗
PubMed1998

Polymorphisms of twelve short tandem repeat loci in a Taiwanese population and their application in parentage testing.

With the advancement of techniques in molecular biology, rapid, sensitive, and reliable methods of DNA typing for parentage testing have become available. In this study, we evaluated the usefulness of multiplex polymerase chain reaction (PCR) with 12 unlinked short tandem repeat (STR) loci for paternity testing in Taiwan. The genetic informativeness of this test was then compared with that of conventional human leukocyte antigen (HLA) analysis in 167 parentage studies. The 12 STR loci alone provided a cumulative power of exclusion of up to 0.9998. Paternity was excluded in 59 (35.3%) cases, including 40 of 112 paternity trios and 19 of 55 paternity duos. In the 40 trios in which paternity was excluded, a mean of 6 (range, 3-9) incompatible STR markers were in the 19 duos in which paternity was excluded, a mean of 4 (range, 1-8) incompatible STR markers were noted. In the 72 trios in which the alleged paternity could not be excluded, the mean probabilities of paternity (PP) were 90.6863% with HLA testing alone, 99.9847% with STR analysis alone, and 99.9972% with combined HLA and STR analysis. In the 36 duos in which the alleged paternity could not be excluded, the mean PPs were 81.4768% with HLA testing alone, 99.6124% with STR analysis alone, and 99.9145% with combined HLA and STR analysis. These results suggest that STR analysis is very powerful when used alone for paternity trio testing and when combined with conventional serologic HLA typing for duo parentage testing in the Taiwan population.

Chromosome Mapping↗
PubMed1995

Mass disasters: rapid molecular screening of human remains by means of short tandem repeats typing.

Human remains identification represents a challenging situation and constitutes a difficult task associated with mass disasters. The only highly efficient means for individual and family group reconstruction is that based on DNA typing. On July 18, 1994 an explosion destroyed the A.M.I.A. (Argentine Israeli Association). Over 100 people died; however, the exact number of victims is still being investigated. Our Service received over 70 remains to be characterized by DNA typing in order to determine the number of victims and to try to reconstruct the family groups to which they belonged. DNA was extracted by a cetyltrimethylammonium bromide (CTAB) based protocol, a rapid molecular screening of all samples was carried out by multiplex STR amplifications including HUMTH01, HUMFABP, HUMHPRTB, HUMRENA4, HUMVWA, HUMFES/FPS and Y27H39LR. Samples with identical genotypes were HaeIII-digested. Southern blotted and probed with YNH-24 (D2S44). PH-30 (D4S139). LH-1 (D5S110) and MS-1 (D1S7) for variable number of tandem repeats (VNTR) evaluation. The minisatellite variant repeat (MVR) approach was used in those cases in which band or profile shift were detected in Southern blot assays. Kinship between victims and putative relatives was initially evaluated by comparison of short tandem repeat (STR) profiles and then confirmed by VNTR with the above probes. The high identification efficiency attained in this case is, in part, supported by a previous experience, the DNA-based molecular characterization of human remains caused by the explosion of the Israeli Embassy in Buenos Aires, March 1992.

Blotting, Southern↗
PubMed2006

Molecular crowding increases the amplification success of multiple displacement amplification and short tandem repeat genotyping.

Multiple displacement amplification (MDA) can generate large quantities of genomic DNA product from small amounts of template. We investigated the ability of MDA to amplify samples containing very small amounts of target DNA (5 pg to 1 ng) in the presence of a second, larger DNA sample for downstream short tandem repeat (STR) multiplex genotyping. We observed that STR amplification success of the minor fraction was increased in these mixed samples when compared with standard PCR only or MDA containing only the single trace DNA sample. Increased numbers of alleles were detected, with less amplification bias between loci than in single source samples undergoing the same protocol. To improve the STR genotyping accuracy, animal DNA was substituted for the additional human DNA, maintaining the increase in the number and quality of human-specific STR loci amplified. Polyethylene glycol 400, a commonly used crowding agent, was used as a replacement for the added genomic DNA in the MDA reaction and produced very similar results. Therefore, we suggest that additional DNA is acting as a molecular crowding agent during MDA. Performing MDA on trace amounts of DNA under crowded conditions results in greater numbers of alleles being amplified and more balanced amplification occurring between alleles.

Alleles↗
PubMed1997

[Allelic polymorphism of short tandemly repeating sequences of the HUMF13A01 and HUMCD4 loci in Russian populations from Moscow and Tomsk].

In samples from populations of the cities of Moscow and Tomsk, analysis of allelic polymorphism of microsatellite loci HUMF13A01 and HUMCD4 was performed by polymerase chain reaction (PCR). Eight HUMCD4 alleles (115-165 bp) and nine alleles (180-230 bp) of locus HUMF13A01 were identified. In both populations, the distributions of allelic frequencies for these loci did not differ significantly. The distribution of observed genotype frequencies fitted Hardy-Weinberg equilibrium in both populations. Mendelian inheritance of these tandem repeats was demonstrated by analysis of two large families. Parameters of polymorphism information content (PIC) for the loci studied were detected; comparative analysis of allelic frequencies with similar data on several populations was performed. These short tandem repeats (STR) were proposed for use in personal identification and paternity tests.

Alleles↗
PubMed2004

[Genetic polymorphism of 6 short tandem repeat loci in Mongolian population of China].

OBJECTIVE: To clarify the distribution of genetic polymorphism of D3S1358, D13S317, D5S818, D6S1043, D2S1772, D7S3048 loci of the Mongolian population in Ximeng pastoral area and construct the relevant genetic database. METHODS: Multiplex PCR and polyacrylamide gel electrophoresis were used to investigate the polymorphism of 6 short tandem repeat (STR) loci in 286 individuals of the Mongolian population. RESULTS: In this study, 6, 9, 8, 11, 14, 11 alleles were observed at the 6 STR loci respectively. The genotypes distributions in Mongolian population were in accordance with Hardy-Weinberg equilibrium (P>0.05), the cumulative expected heterozygosities (H), discriminating probability (DP) and the polymorphism information contents (PIC) for the 6 loci were 0.9998, 09999, 0.9998 respectively. These data were compared with those of the Han population. The results showed there were significant difference in D3S1358, D13S317, D5S818, D2S1772, D7S3048 loci between the Mongolian population and Han population (P<0.05). However, no significant difference in D6S1043 locus was seen between the two populations (P>0.05). CONCLUSION: The results demonstrate that these 6 STR loci can serve as genetic marks and provide valuable data which are beneficial to studying the population genetics and ethnology.

China↗
PubMed2000

Identification of the origin of a vesical mass occurring after cadaveric renal transplantation using short tandem repeat markers.

We report a case of polypoid cystitis in a 54-year-old female occurring 4 years after cadaveric kidney transplantation. Endoscopic exploration revealed a polypoid tumor near the stoma opened for the transplanted ureter. The diagnosis of polypoid cystitis was confirmed histopathologically. Genotyping of cells from the tumor with polymorphic short tandem repeat (STR) and amelogenin loci revealed that the tumor contained alleles from both the donor and recipient. Molecular genetic analysis provided strong evidence that the tumor cells arose from the donor tissue.

Cadaver↗
PubMed2003

[Analysis of short tandem repeat polymorphism in a female patient with Duchenne muscular dystrophy].

OBJECTIVE: To understand the mechanism of Duchenne/Becker muscular dystrophy (DMD) in a female patient. METHODS: A multiplex PCR (mPCR) protocol was applied to detect the dystrophin gene of the female DMD patient and her family members, whose haplotypes were analyzed in light of short tandem repeat polymorphism (STR) of five microsatellite markers (located in 5' terminus and introns 44, 45, 49, and 50). RESULTS: No deletion was detected in the affected female patient and her affected son. Examination of the female DMD patient's STR haplotypes identified in the female patient and her affected son the same haplotype inherited from her unaffected mother, who was a likely germinal mosaicism. The female patient has different haplotype from her affected son and her mother as a deletion was identified in the intron 45 of the affected son, and the female patient and her mother were probably heterozygous for this deletion. CONCLUSION: STR haplotype may not be responsible for the pathogenesis of DMD in the female patient and her affected son.

Female↗
PubMed2001

Identification of a compound short tandem repeat stretch in the 5'-upstream region of the cholecystokinin gene, and its association with panic disorder but not with schizophrenia.

The cholecystokinin gene (CCK) is thought to play a role in the pathogenesis of both panic disorder and schizophrenia. In this study, we have extended the 5'-upstream sequence of the CCK gene, and identified a compound short tandem repeat (STR), located approximately -2.2 to -1.8 kb from the cap site. This STR was found to be polymorphic with ten different allele lengths. Case-control studies using 73 panic patients, 305 schizophrenics and 252 controls showed a significant allelic association with panic disorder (P = 0.025), but not with schizophrenia. Dividing the STR alleles into three classes according to length, Long (L), Medium (M) and Short (S), produced strong genotypic (MM) (nominal P = 0.0014) and allelic (M) (nominal P = 0.0079) associations with panic disorder. screening the newly extended promoter region detected not only the previously identified -36c>t and -188a>g single nucleotide polymorphisms (SNPs) but a new rare snp, -345g>C. Neither of the former two SNPs showed significant association with either panic disorder or schizophrenia. Haplotypic distributions of the STR and SNPs -188 and -36 were significantly different between panic samples and controls (P = 0.0003). These findings suggest that the novel STR or a nearby variant may confer susceptibility to the development of panic disorder.

5' Untranslated Regions↗
PubMed1999

Gene deletion and carrier detection in the family of Becker muscular dystrophy by short tandem repeat sequence polymorphism.

OBJECTIVE: To type haplotypes among the patients, carriers and normal offspring in a family of males with Becker muscular dystrophy in one generation by allelic fragment length polymorphism analysis. METHODS: Deletion analysis of the patients were performed using multiplex polymerase chain reaction (PCR) of amplification with 9 dystrophin exon primers. Intragenic short tandem repeat (STR) sequence (STR44, STR45, STR49 and STR50) were amplified by PCR to analyse allelic fragment length polymorphisms in the members of the family. RESULTS: The deletions of exons 17, 19 and 45, as well as deletions of allelic fragments at the loci of STR44 and STR45 were determined in the patients. Hemizygosity at those two loci were detected and carrier status ascertained in the mother of the patients. The normal haplotypes were typed in the sister of the patients. CONCLUSION: The method of STR sequence polymorphism analysis can determine haplotypes at normal status or at risk status. It would be used in prenatal diagnosis and carrier detection in the families of Duchenne and Becker muscular dystrophy.

Adolescent↗
PubMed2005

[Detection of fetal short tandem repeat genotype in maternal plasma by multiplex fluorescent polymerase chain reaction].

OBJECTIVE: To study the feasibility of using free fetal DNA in maternal plasma for non-invasive prenatal diagnosis. METHODS: Maternal DNA extracted from plasma samples of 10 pregnant women at early pregnancy, medium pregnancy and late pregnancy and their husband's DNA isolated from whole blood samples were used to detect genotype by multiplex fluorescent PCR at nine different polymorphic short tandem repeat(STR) loci. RESULTS: Fetus-specific alleles were found in maternal plasma samples studied. By the application of these polymorphic short repeat sequences, every pregnant women/husband pair was informative in at least three of nine loci. Paternally inherited fetal alleles were detected in 23 of 30 plasma samples. They are 6/10 cases in early pregnancy, 8/10 cases in middle pregnancy and 9/10 cases in late pregnancy respectively. CONCLUSION: Fluorescent multiplex PCR can be used for amplification of male and female fetal STRs in maternal plasma to obtain genetic information, which may have implication for non-invasive prenatal diagnosis of certain hereditary diseases independent of the fetal sex.

Adult↗
PubMed2006

Short tandem repeat polymorphism in the flanking region of the human phosphoglycerate kinase gene in a Japanese population.

The human phosphoglycerate kinase (PGK1) gene is located within Xqll-Xql3 and is closely linked to the androgen receptor gene within a region implicated in a number of X-chromosome-linked urologic disorders. A polymorphism of a TATC short tandem repeat (STR) is present downstream from the PGK1 3' nuclease-sensitive site. We present the PGK1 flanking STR sequence and population genetic data for 190 Japanese males and 83 Japanese females. Ten STR alleles and 29 genotypes were identified in the population. Five alleles--*10, *11, *12, *13, and *14--were common in the Japanese with frequencies greater than 10%. No significant deviations from Hardy-Weinberg equilibrium were established. The power of discrimination was 0.993 for females and 0.819 for males; heterozygosity was 0.759 for females; and the polymorphic information content was 0.936. These data indicate that this STR locus shows a high degree of polymorphism in this Japanese population and may prove to be a useful genetic marker in forensic medicine, in determining the clonality of neoplasms, and potentially in studying predisposition to prostate cancer and other urologic diseases.

Female↗
PubMed2005

Von Willebrand gene tracking by single-tube automated fluorescent analysis of four short tandem repeat polymorphisms.

Molecular diagnosis of von Willebrand disease (VWD) has been hampered by the large size and complex genomic characteristics of the gene involved. For this reason, indirect methods using intragenic polymorphic markers described along the von Willebrand factor (VWF) gene are valuable tools for gene monitoring and linkage analysis. Several studies have demonstrated the four commonly utilized short tandem repeats (STRs), three located in intron 40 and one in the promoter region of the VWF gene, to be highly informative for this task. Our objective was t o develop a rapid, automated method to simultaneously analyze these four STRs for VWF gene tracking. Amplification of the four loci is achieved in a single multiplex fluorescent PCR which is then analyzed in the same run by capillary electrophoresis. Data processing with GeneScan and Genotyper software has simplified management and tabulation of the resulting haplotypes. Analysis of the VWF gene in DNA from 102 individuals (204 chromosomes) revealed that the three STRs within intron 40 showed significant linkage disequilibrium against each other but not against the VWP locus. Moreover, the combination of the four markers offers a high heterozygosity rate (>99%) that improves tracing VWF gene inheritance. In conclusion, the automated fluorescent capillary electrophoresis method presented here is an extremely rapid, simple and highly informative technique for association studies between VWD and the VWF gene in addition to genetic counseling and prenatal diagnosis by precise linkage analysis in VWD-affected families.

Alleles↗
PubMed1995

A highly discriminating octoplex short tandem repeat polymerase chain reaction system suitable for human individual identification.

Through the use of fluorescence-based polymerase chain reaction systems, a highly discriminating multiplex with the potential for individual identification has been developed. The use of multiple dye technology enabling loci with overlapping size ranges to be co-amplified has enabled us to successfully amplify seven tetranucleotide short tandem repeat loci within a single reaction resulting in a discriminating power in the region of 1 x 10(9). Three out of the seven loci employed exhibit alleles differing in size by only 2 bp as opposed to the conventional 4 bp, which results in such loci being more powerful in terms of distinguishing between samples, particularly when co-amplified in this manner. The size ranges of the loci contained within the system are such that windows still exist for the inclusion of additional loci at a later stage, which could increase the discriminating power of the system still further. In addition, further weight and utility is lent to the system through the incorporation of a simple and reliable sex test involving the amplification of a segment of the X-Y homologous gene Amelogenin.

Amelogenin↗
PubMed2001

Detection of maternal DNA in umbilical cord plasma by fluorescent PCR amplification of short tandem repeat sequences.

Recently, maternal DNA was detected in umbilical cord blood using PCR amplification of minisatellite sequences. The presence of maternal DNA was demonstrated in 1% to 100% of umbilical cord blood samples. The objective of this study was to determine the frequency of cord blood contamination by maternal genetic material. We used fluorescent PCR amplification of highly polymorphic short tandem repeat (STR) markers to detect maternal DNA in umbilical cord plasma.

DNA↗
PubMed2001

Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era.

The recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make-up; however, the post-genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs.

Alleles↗