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PubMed1993

The human D11S554 locus: four distinct families of repeat pattern alleles at one locus.

We have sequenced amplified products of 44 short tandem repeat alleles at the human D11S554 locus. The sequences revealed four distinct, but related, families of consensus repeat patterns. Six alleles deviated from the consensus patterns. Alleles differed in size by as little as one base pair, and precise sizing is required for analysis of alleles at this highly polymorphic locus. The evolution of alleles at the D11S554 locus and related short tandem repeat loci is discussed.

Alleles↗
PubMed1999

Transmission of de novo mutations of the deleted in azoospermia genes from a severely oligozoospermic male to a son via intracytoplasmic sperm injection.

OBJECTIVE: To investigate the transmission of microdeletions in the deleted in azoospermia (DAZ) genes to a male offspring via intracytoplasmic sperm injection (ICSI). DESIGN: Case report. SETTING: Reproductive unit of a university teaching hospital. PATIENT(S): A 29-year-old, severely oligozoospermic male with microdeletions of the DAZ genes in Yq interval 6 and his son, who was conceived via ICSI. INTERVENTION(S): DNA screening for the microdeletions in Yq interval 6 with 24 sequence tagged sites with the use of polymerase chain reaction amplification for the patient, the patient's father, and the patient's son. Paternity identification was performed using nine hypervariable short tandem repeats. MAIN OUTCOME MEASURE(S): Deletion mapping of Yq interval 6 from sequence tagged sites and electropherogram of short tandem repeats for DNA fingerprinting. RESULT(S): The son had the same microdeletions of the DAZ genes as the patient, and the patient's father had normal DAZ genes. The paternity of the patient, the patient's father, and the patient's son was verified. CONCLUSION(S): De novo DAZ microdeletions in an infertile male can be transmitted to a male offspring via ICSI. DNA screening tests for DAZ genes before ICSI may help in the genetic counseling of patients with idiopathic azoospermia or severe oligozoospermia.

Adult↗
PubMed2003

Allele frequencies for 15 STR loci in Van-Ağri districts of the Eastern Anatolia region of Turkey.

Allele frequencies of 13 tetrameric short tandem repeat (STR) loci (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA) and 2 pentameric short tandem repeat loci (Penta E and Penta D) included in the PowerPlex 16 kit were obtained from a sample of 116 unrelated individuals in Van-Ağri districts of the Eastern Anatolia region of Turkey. The expected performance of these loci for personal identification and paternity testing in this population was estimated.

Alleles↗
PubMed2003

Extraction and analysis of human nuclear and mitochondrial DNA from electron beam irradiated envelopes.

The United States Postal Service is considering methods such as electron beam irradiation to neutralize biological agents sent through the mail. While this is proven to reduce/eliminate pathogenic organisms, it may also degrade human genomic DNA and therefore hinder the ability to garner forensically informative genetic profiles. To determine the effects of electron beam irradiation on DNA typing, 16 white, standard letter-sized envelopes were licked. Half of the envelopes served as nonirradiated controls while the other half underwent irradiation at dosages sufficient to kill anthrax spores (29.3 and 51.6 kGy). Total cellular DNA was extracted from all envelopes; nuclear short tandem repeat loci, as well as the hypervariable region I from mitochondrial DNA, were amplified by means of the polymerase chain reaction. Short tandem repeat profiles and mitochondrial DNA sequence haplotypes were acquired on an ABI Prism 310 Genetic Analyzer platform. Analysis of data from irradiated samples revealed evidence of DNA degradation; however, the ability to construct full genetic profiles from both nuclear and mitochondrial DNA remained largely unaffected. The use of the polymerase chain reaction, coupled with florescent fragment analysis and mitochondrial DNA sequencing, should be considered to profile biological material from evidence enduring irradiation to inactivate infectious agents.

Complementarity Determining Regions↗
PubMed1999

Accurate characterization of the tyrosine hydroxylase forensic allele 9.3 through development of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Accurate and precise determination of the number of repeats from a short tandem repeat (STR) sequence for a human gene locus is demonstrated for the first time by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). Specifically, the polymorphic human tyrosine hydroxylase (HUMTHO1) gene, a tetranucleotide STR forensic allele, was chosen as a model system to evaluate our approach for future characterization of both STRs and variable number of tandem repeats (VNTRs) by development of an ESI-FTICR-MS approach. The coding and noncoding strands from the HUMTHO1 9.3 allele are simultaneously resolved obtaining accurate (better than 70 ppm) average mass measurements of 25,783.23 and 24,754.55 Da for the coding and noncoding strands, respectively. The mass measurements are used to calculate the number of repeats for each strand, 'n', of 9.75169 and 9.75001 for the coding and noncoding strands, respectively. It will be shown how the value of 'n' can be used to directly determine the number of pure repeats and accurately determine the exact nature of the polymorphism within the repeat (if any). The single nucleotide deletion in the coding strand (adenine) and noncoding strand (thymine) were accurately identified using this approach. Interestingly, we observed the conversion of single-stranded to double-stranded DNA while the PCR product in the ESI buffer was being infused; the issues related to this observation will be presented. Previous results by other researchers investigating the HUMTHO1 9.3 allele using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) are directly compared with our results. Our results indicate that ESI-FTICR-MS is a powerful approach to rapidly and accurately characterize tandem repeating sequences which will ultimately lead towards the understanding of a complex class of diseases and in human identity determination.

Alleles↗
PubMed2000

Application of electrophoresis technology to DNA analysis.

We used the variable number tandem repeat (VNTR) polymorphism and the ten short tandem repeat (STR) polymorphisms to study a number of disputed paternity cases in the Japanese population. For the determination of VNTR locus (D1S80) and the ten STR loci (vWA, F13B, TH01, TPOX, CSF1PO, F13A01, LPL, D3S1744, D12S1090, D18S849) we used polymerase chain reaction (PCR) amplification and the vertical polyacrylamide gel electrophoresis technique followed by SYBR green I staining. The irregular repeats were analyzed by sequencing from bands of vertical polyacrylamide gel electrophoresis using the latest gene analyzing equipment, the ABI PRISM 310 Genetic Analyzer. The probable genotypes of the deceased putative father were deduced by Komatu's method from the genotypes of the widow and the genotypes of their children. The calculation of paternity probability used the Essen-Moller formula and Bayes's theorem. Calculated in eleven loci, the distinguishing probabilities (DP) and the mean exclusion chance (MEC) were 0.9999 and 0.9989, respectively. Therefore, information obtained from eleven DNA polymorphisms is enough to determine paternity plausibility.

DNA↗
PubMed2003

Understanding the dynamics of Spinocerebellar Ataxia 8 (SCA8) locus through a comparative genetic approach in humans and apes.

Spinocerebellar Ataxia 8 (SCA8) is a neurodegenerative disorder caused by expansion of a trinucleotide repeat. We undertake a comparative genetic analysis among human populations and primate species in the normal variation range, where forces that shaped present diversity can be recognised. We determinate number of repeats of the short tandem repeat through allele length sizing and sequencing methods. Human allele distributions are very similar among populations, ruling out ethnicity as a genetic risk for allele expansion. Primate comparison shows human-specific features, with longer human alleles due to a novel variable trinucleotide repeat, not present in non-human primates, which increased the disease-causing expansion likelihood. SCA8 seems to be a human specific disease.

Alanine↗
PubMed1997

Basic issues in forensic DNA typing.

DNA analysis has become the standard method in forensic stain typing (termed DNA profiling). In contrast to conventional serological methods, any human tissue or body fluid can be analysed by DNA profiling as long as it contains nucleated cells. The majority of genetic systems studied at the DNA level are derived from "non-coding" portions from the human genome, and are located either in the vicinity of expressed (coding) genes or in stretches of DNA sequences interspersing with the genes. The typing results are usually recorded as DNA fragment lengths or "alleles" indicating the number of core repeat elements for short tandem repeat systems. These typing results do not contain any useful information which might reveal genetic traits or predispositions for inherited disease about the individual studied. Typing systems for DNA profiling are predominantly selected according to criteria related to the robustness for typing of (potentially degraded) forensic specimens, the degree of genetic polymorphism (which influences the chance to exclude a wrongfully accused person), and the amenability to standardisation as a basis to obtain reproducible results.

Alleles↗
PubMed1998

Microsatellite enrichment in organisms with large genomes (Allium cepa L.).

To exploit the polymorphism of repeat numbers in short tandem repeat (STR) sequences (microsatellites) as molecular markers, STRs must be isolated and PCR primers must be developed in flanking sequences. In species with large genomes such as Allium cepa L. (onion and shallot), an efficient selection procedure for genomic fragments containing STRs is a crucial step. Here we describe a nonradioactive method for microsatellite isolation based on affinity capture of single-stranded restriction fragments annealed to biotinylated microsatellite oligonucleotides (CA)10, (GAA)8 and (AAC)8 followed by adapter-mediated genomic PCR. Cloning of the products in E. coli and plasmid sequencing revealed more than 60% positive clones. Primers were designed in STR-flanking regions, and one or two bands were amplified in 13 diploid onion and five shallot accessions. Allelism of the bands was confirmed by product sequencing.

Dinucleotide Repeats↗
PubMed2001

[Allele sequences and population genetics of pentanucleotide tandem repeat D6S957].

OBJECTIVE: Pentanucleotide tandem repeat loci are useful markers of short tandem repeat (STR) for genetic analysis. We focused on the analysis of the DNA sequence for each allele at the pentanucleotide STR locus D6S957 in order to understand their structures in the human genome and to construct human allelic ladder, which is necessary for forensic DNA typing. In order to evaluate the forensic applicability of D6S957, we investigated the genotype distributions and allele frequencies in major ethnic groups. METHODS: A total of 230 samples from unrelated individuals were analyzed by PCR. Allele determination was carried out by comparison with a sequenced human allelic ladder made in-house. An example of each allele was sequenced on an ABI 377 automated sequencer. RESULTS: This pentanucleotide STR exhibited a minimal amount of stutter and provided easily interpretable results. Eight alleles were found in these populations. No evidence of deviation from Hardy-Weinberg equilibrium was observed. In 64 confirmed father/mother/child triplets no mutation events were observed. The mutation rate was indirectly estimated at 2.5 x 10(-5) using a maximum likelihood method. CONCLUSION: D6S957 is a useful marker for forensic casework and paternity analysis.

Alleles↗
PubMed2002

Molecular diagnosis of Duchenne/Becker muscular dystrophy by polymerase chain reaction and microsatellite analysis.

Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive genetic disorders resulting from mutations in the dystrophin gene. About two-thirds of the affected patients have large deletions or duplications, which occur in the 5' and central region of the gene. The remaining DMD/BMD cases show no deletions, so they cannot be easily identified by current strategies. In these DMD/BMD families, a linkage analysis that involves DNA markers of the flanking and intragenic dystrophin gene are necessary for carrier and prenatal diagnosis. We analyzed eighteen deletion-prone exons of the gene by a polymerase chain reaction (PCR) in order to characterize the molecular defects of the dystrophin gene in Korean DMD/BMD families. We also performed a linkage analysis to assess the usefulness and application of six short tandem repeat markers for molecular diagnosis in the families. We observed a deletion that eliminated the exon 50. Also, a linkage analysis in the families with six short tandem repeat (STR) markers showed heterozygosity at most of the STR markers. The haplotype analysis was useful for detecting the carrier status. This study will be helpful for a molecular diagnosis of DMD/BMD families in the Korean population.

Dystrophin↗
PubMed2005

[Therapy of Duchenne muscular dystrophy with umbilical cord blood stem cell transplantation].

OBJECTIVE: To analyze a Duchenne muscular dystrophy(DMD) patient's muscular regeneration, dystrophin expression and locomotive variation before and after he underwent umbilical cord blood stem cell transplantation in order to assess the therapeutic effect. METHODS: A 12-year-old DMD boy who could not walk for 3 years was confirmed by gene analysis and dystrophin protein immune test on his muscle. He had no other chronic disease. By HLA matching, a piece of umbilical cord blood stem cell with 6 HLA sites matching to the boy was found in Guangdong Umbilical Cord Blood Bank. The number of the nucleated cells of the umbilical cord blood stem cell was 24.08x 10(8). After pretreatment for the DMD boy with busulfan, cyclophosphamide and rabbit anti-human thymocyte globulin, the allergenic cord blood stem cells were transplanted into him by intravenous injection. Cyclosporin A, methylprednisolone, MMF, prostaglandin E1 and ganciclovir were given after the transplantation. At the same time, Gran, the granulocytic cell stimulating factor, and gamma globulin were administered. The biochemistry profile including serum creatine kinase (CK), the reconstruction of blood making, the deletion exon of DMD gene, the regenerating muscles, the dystrophin protein expression, and the locomotive function of the DMD boy were tested regularly. RESULTS: (1) The white blood cells (WBC) of peripheral blood decreased gradually to zero after pretreatment. In a period of 15 days after transplantation, the neutrophil increased to 0.5x 10(9)/L; at 25 days, WBC increased to normal level. Blood platelet was more than 20x 10(9)/L at 22 days. The hemoglobin rose to 85-100 g/L. At 140 days, sternal puncture revealed the rapid growth of neutrophil, blood platelet and hemoglobin. (2)At 140 days, the blood type of the DMD boy transformed from type O to type AB (the donor's blood type being AB). There was no grafe versus host reaction. (3) At 18, 30, 43, 55, 74 and 233 days after transplantation, the PCR-short tandem repeat test of the boy's peripheral blood DNA showed that his genotype was completely the same as the donor's. The results of PCR-short tandem repeat tests of the bone marrow cells DNA by sternal puncture at 140, 183 and 235 days were the same as those of the blood DNA. (4) At 60 days, DMD gene analysis by PCR showed that the defected DMD gene (exon 19 deletion) had been corrected by the umbilical cord stem cells transplantation. (5) At 75 days, the biopsy of calf muscle showed there were myoblast cells and muscular tubes growing. The dystrophin expressions were weak, but a few of them were strong. DNA analysis showed that the donor's gene DNA accounted for 1%-13%. At 126 days, obviously increased dystrophin positive muscular fibers of the boy were found. The donor's fibers rose to 2.5%-25%. (6) The serum CK of the boy declined from 5735 U/L to 274 U/L. (7) At 100 days, physical examination revealed improvement in his arms and legs. CONCLUSION: The therapy of Duchenne muscular dystrophy with allogeneic umbilical cord blood hematopoietic stem cell transplantation may reset up the blood-making function, decrease the serum CK level, restore the dystrophin in muscles, and improve the locomotive function of the DMD boy. These data suggest that the allogeneic umbilical cord blood hematopoietic stem cell transplantation may benefit the DMD boys.

Alprostadil↗
PubMed2003

Double incompatibility at human alpha fibrinogen and penta E loci in paternity testing.

We present a paternity testing case in which a double incompatibility was found for two short tandem repeat (STR) markers, human fibrinogen alpha (FGA) and Penta E. Analysis of the trio (mother, father, and daughter) included the amplification with a battery of 15 autosomal short tandem repeats (STR) by using a commercially available PowerPlex 16 System kit, and the detection with an ultraviolet-automatic sequencer. The biological paternity was confirmed with 12 additional markers. Reanalysis of the trio for the same markers with different primers was carried out by using an infrared automated sequencer and infrared-fluorescent primers. High paternity index confirmed that the observed inconsistencies were due to a double mutation, which was confirmed by sequence analysis at FGA and Penta E loci. Amplification and detection results obtained by the infrared-protocol showed consistent results with those obtained by ultraviolet-protocol and a commercially available kit. This has been our first case of double mutation at FGA and Penta E in a paternity testing. The use of our approach, based on two amplification and detection formats and on the sequence analysis, confirmed the observed meiotic paternal mutations.

Female↗
PubMed2002

Trends in DNA forensic analysis.

The paper gives a historical perspective of forensic DNA analysis and overviews existing technologies implemented in forensic laboratories for DNA profiling. Short tandem repeat analysis, mitochondrial DNA and Y-chromosome analysis are described. The review also focuses on emerging new technologies, which represent an interest for the DNA forensic community. Short tandem repeat analysis, by microelectronic chip device, electrophoretic microdevice and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry are reviewed in this context.

Chromosomes, Human, Y↗
PubMed2006

Chromatin diminution in the copepod Mesocyclops edax: diminution of tandemly repeated DNA families from somatic cells.

Chromatin diminution, i.e., the loss of selected chromosomal regions during the differentiation of early embryonic cells into somatic cells, has been described in taxa as varied as ciliates, copepods, insects, nematodes, and hagfish. The nature of the eliminated DNA has been extensively studied in ciliate, nematode, and hagfish species. However, the small size of copepods, which makes it difficult to obtain enough DNA from early embryonic cells for cloning and sequencing, has limited such studies. Here, to identify the sequences eliminated from the somatic cells of a copepod species that undergoes chromatin diminution, we randomly amplified DNA fragments from germ line and somatic line cells of Mesocyclops edax, a freshwater cyclopoid copepod. Of 47 randomly amplified germ line clones, 45 (96%) contained short, tandemly repeated sequences composed of either 2 bp CA-repeats, 8 bp CAAATAGA-repeats, or 9 bp CAAATTAAA-repeats. In contrast, of 83 randomly amplified somatic line clones, only 47 (57%) contained such short, tandemly repeated sequences. As previously observed in some nematode species, our results therefore show that there is partial elimination of chromosomal regions containing (CAAATAGA and CAAATTAAA) repeated sequences during the chromatin diminution observed in the somatic cells of M. edax. We speculate that chromatin diminution might have evolved repeatedly by recruitment of RNAi-related mechanisms to eliminate nonfunctional tandemly repeated DNA sequences from the somatic genome of some species.

Animals↗
PubMed1995

Microsatellite instability in adenocarcinoma of the prostate.

Instability of dinucleotide tandem repeat sequences has been reported to play a major role in the carcinogenic pathway of familial colon cancer, as well as a potential role in the carcinogenesis of other sporadic neoplasms. To determine the frequency of short tandem repeat instability in adenocarcinoma of the prostate, we studied 40 tumors that were stratified according to tumor grade. The tissue samples were screened with di-, tri- and tetranucleotide markers spanning a wide range of chromosomal loci, including an androgen receptor gene trinucleotide repeat. Microsatellite instability was observed overall in only one of the 40 (2.5%) prostate adenocarcinomas studied. This replication error-positive tumor demonstrated repeat length alterations at two loci. Five other tumors showed an alteration in microsatellite size at a single locus. These tumors were not considered to have the microsatellite instability phenotype. All changes were identified either within tetranucleotide sequences or within the androgen receptor gene repeat (4 or 20 total markers analyzed). Both repeat length expansions and contractions were identified. The replication error-positive case also included separate metastatic nodal tissue. Additional microsatellite analysis of the metastatic tumor tissue revealed allelic patterns identical with the normal tissue control. Our data indicate that microsatellite instability is rare in prostate adenocarcinoma. Therefore, observation of this low replication error frequency suggests that most prostate carcinomas develop in the absence of widespread accumulation of somatic mutations in short tandem repeat sequences. Additionally, these genetic alterations appear to occur more often in tetranucleotide repeat sequences as well as in an androgen receptor gene trinucleotide repeat.

Adenocarcinoma↗
PubMed1996

Nucleotide sequence of a cDNA clone (SUBT1) partly homologous to a human subtelomeric repeat sequence.

Telomeres contains short tandem repeats (TTAGGG)n that are usually several kilobases in size. DNA sequences located next to the repeats are called telomere-associated or subtelomeric sequences. In this report we describe isolation and characterization of a new cDNA sequence isolated with a telomere specific, chromosome 17 genomic clone. No open reading frame of notable length could be detected. However comparison with sequences in the EMBL/Genbank revealed a 897 bp of close to perfect match, in the 3'end with the centromeric end of a genomic clone containing subtelomeric repeat sequences. The potential function of the SUBT1 transcript remains to be elucidated.

Chromosomes, Human, Pair 17↗
PubMedDate not supplied

An adenine trimer precedes a C/G polymorphism in the 3'-amplimer region of the human platelet glycoprotein IIIa intron 6 CT repeat.

Restriction enzyme and short tandem repeat polymorphisms are often used to link a particular allele with an inheritable disease-related gene in the absence of the information regarding the DNA mutation or defect. Polymorphic markers within the gene in question are particularly useful and can provide sufficient information for genetic counselling to potential carriers of the disease. Using a published method for the CT repeat in intron 6 of the GP3A gene, it was found that a single nucleotide deletion in the published genomic GP3A sequence in the region of the antisense amplimer and a C/G nucleotide polymorphism (allele frequencies, G = 0.883, C = 0.117) immediately adjacent to the deletion were responsible for the lack of PCR amplification. The absence of amplification has important implications for the assignment of a particular CT repeat to a given allele and for the population frequencies of the various CT repeats.

Adenine↗