Small Tandem Repeat Research Articles

Rapid detection of trisomies 21 and 18 and sexing by quantitative fluorescent multiplex PCR.

Aneuploidies involving chromosomes 21, 18, 13, X and Y account for over 95% of all chromosomal abnormalities in live-born infants. Prenatal diagnosis of these disorders is usually accomplished by cytogenetic analysis of amniotic or chorionic cells but this is a lengthy procedure requiring great technical expertise. In this paper, we assess the diagnostic value of using a quantitative fluorescent polymerase chain reaction (PCR) suitable for the simultaneous and rapid diagnosis of trisomies 21 and 18 together with the detection of DNA sequences derived from the X and Y chromosomes. Samples of DNA, extracted from amniotic fluid, fetal blood or tissues, and peripheral blood from normal adults were investigated by quantitative fluorescent PCR amplification of polymorphic small tandem repeats (STRs) specific for two loci on each of chromosomes 21 and 18. Quantitative analysis of the amplification products allowed the diagnosis of trisomies 21 and 18, while sexing was performed simultaneously using PCR amplification of DNA sequences derived from the chromosomes X and Y. These results indicate the advantages of using two sets of STR markers for the detection of chromosome 21 trisomies and confirmed the usefulness of quantitative fluorescent multiplex PCR for the rapid prenatal diagnosis of selected chromosomal abnormalities.

Gene dosage in capillary electrophoresis: Pre-natal diagnosis of Down's syndrome

Modern proposals for pre-natal genetic analysis of Down's syndrome consist in isolating DNA from amniotic cells and amplifying a highly polymorphic small tandem repeat region of the chromosome 21-specific D21S11 marker. The polymerase-chain-reaction-amplified fragments are typically 5′-end labelled with a green or blue fluorescent reporter and data acquisition occurs on-lane in DNA sequencing gel-slabs and equipment. The following patterns are expected: for normal individuals, 1 peak or two peaks in a 1:1 ratio. In the case of trisomy 21, the following patterns are found: either three peaks in a 1:1:1 ratio or a two-peak profile with a 2:1 gene ratio. We have developed a capillary electrophoretic system, offering precise diagnostic value by exploiting the intrinsic DNA absorbance at 254 nm. The separation occurs in capillaries coated with an extremely stable and hydrophilic layer of poly(N-acroyloyl amino ethoxy ethanol) and filled with a background electrolyte consisting of 89 m M Tris-borate, 2 m M EDTA, 2.5 μM ethidium bromide and 8% short-chain, low-viscosity, replaceable, liquid, linear, sieving polyacrylamide. The technique offers high reproducibility and precise on-liine, automated peak acquisition and quantitation.

Detection of fetal cells in transcervical samples and prenatal diagnosis of chromosomal abnormalities.

Transcervical samples collected by lavage, aspiration, and cytobrush from women between 6 and 13 weeks of gestation were tested for the presence of fetal cells using fluorescence in situ hybridization (FISH) with probes for chromosomes X, Y, 1, and 21, and by polymerase chain reaction (PCR) amplification of DNA sequences derived from chromosomes X, Y, and 21. With a few exceptions, a good correlation was observed between the results of sexing the fetuses using FISH or PCR on transcervical cell (TCC) samples retrieved by lavage and those obtained by testing fetal (placental) tissue. In a comparative study between TCC samples collected by lavage or cytobrush, the sex of the fetus was correctly diagnosed by PCR amplification of a Y-derived DNA sequence. Variable results were observed with samples obtained by aspiration, mainly because this procedure was found to be more prone to failure to remove thick mucus without previous injection of physiological saline. Chromosome 21-derived small tandem repeats (STRs) of fetal origin were successfully detected in about 40 per cent of TCC samples recovered by lavage. Two cases of chromosomal abnormalities, one of trisomy 21 and one of triploidy, were detected in TCC samples in the course of our investigations.

Detection of trophoblast cells in transcervical samples collected by lavage or cytobrush

To compare two methods of obtaining fetal cells from the endocervical canal for prenatal diagnosis during the first trimester: lavage with physiologic saline, and the endocervical passage of a cytobrush. Fetal cells were identified morphologically using conventional and immunohistochemical staining. Y-specific sequences were detected using polymerase chain reaction (PCR) and fluorescent in situ hybridization. The presence of fetal DNA was also demonstrated by PCR amplification of a polymorphic short tandem repeat marker. Syncytiotrophoblast cells were identified in four of 11 lavage samples and in one of 11 brush samples. Sex determination using fluorescent in situ hybridization was achieved in all 11 lavage samples and in nine of 11 cytobrush samples; no Y sequences were located in two brush samples from male embryos. Sex determination was achieved successfully in all 22 samples using PCR of X- and Y-specific DNA sequences. Small tandem repeat pattern analysis indicated the presence of fetal DNA in five of 11 lavage samples and in one of eight cytobrush samples, which were informative because the maternal and fetal small tandem repeat patterns differed. Although lavage retrieves more trophoblast cells than does brushing, both methods are potentially suitable for molecular prenatal diagnosis.

Rapid detection of selected aneuploidies by quantitative fluorescent PCR.

Selected aneuploidies can be rapidly diagnosed by the analysis of fluorescent polymerase chain reaction (PCR) products of chromosome-specific and highly polymorphic small tandem repeats (STRs). The quantitative STR patterns obtained from samples of normal individuals are markedly different from those seen when patients with aneuploidies involving chromosome X, or trisomies of chromosomes 21 and 18, are tested. For example, while samples from normal subjects--tested with a chromosome 21-derived STR (D21S11)--show two fluorescent PCR peaks with similar activities in a 1:1 ratio, the analysis of samples from patients with trisomy 21 reveals the presence of either three peaks (ratio 1:1:1), or two peaks with a ratio of 2:1. The use of an internal non-polymorphic marker allows identification of trisomic samples with three copies of the same allele. This rapid approach (24 hours) is particularly valuable when applied to prenatal diagnosis of chromosomal abnormalities since it reduces the time of anxiety of the parents waiting for the results of the conventional cytogenetic tests, which require several weeks.

Molecular evidence of fetal‐derived chromosome 21 markers (STRs) in transcervical samples

Transcervical cells (TCCs), collected by flushing or aspiration at 8-13 weeks of gestation, were analysed for the presence of fetal-derived DNA sequences. DNA extracted from maternal peripheral blood, TCC samples, and placental tissue was amplified by the polymerase chain reaction (PCR) to detect small tandem repeat (STR) markers specific to chromosome 21. STR products of fetal origin could be clearly observed in four TCC samples. TCC samples collected by flushing or aspiration were also analysed by fluorescent in situ hybridization (FISH) using X and Y probes simultaneously: 46,XY cells could be detected in all TCC samples obtained from mothers with male fetuses.

Rapid molecular method for prenatal detection of Down's syndrome

We have evaluated a rapid method that allows prenatal detection of Down's syndrome in less than 24 hours. DNA from uncultured amniotic fluid, fetal blood, and tissue samples was amplified with the small tandem repeat (STR) marker D21S11. Quantitative analysis of fluorescent STR products with evaluation of their sizes provided clear evidence for trisomy 21. Whilst most normal samples showed two amplification peaks of equal size, Down's syndrome samples were characterised by either three STR peaks or two peaks with a ratio of 2:1. Co-amplification with a non-polymorphic sequence allowed analysis of samples that were homozygous for the 21–derived STRs. Lancet 1994; 343: 1197–98

Conventional protein coding genes in the Drosophila Y chromosome: is the puzzle of the fertility gene function solved?

Conventional protein coding genes in the Drosophila Y chromosome: is the puzzle of the fertility gene function solved?

Fluorescent approaches to diagnosis of Lesch-Nyhan syndrome and quantitative analysis of carrier status

Lesch-Nyhan syndrome is an X-linked recessive disorder caused by molecular defects within the HPRT gene. Deletional forms of this syndrome, most of which are inherited, account for 15% of the cases. In addition, a large percentage of cases are due to de novo point mutations. We have used complementary fluorescence-based PCR assays to analyse disease-causing mutations in three unrelated families: (1) inheritance of dye-labelled PCR products of linked polymorphic loci mapping within and flanking the HPRT gene; (2) dye-labelled exon dosage analysis and (3) automated fluorescence-based DNA sequence analysis. Our results using fluorescent, dye-tagged PCR products show that inheritance of two polymorphic small tandem repeat, HPRTB (AGAT)n′ mapping within intron 3 of the HPRT gene, and the CA-repeat at DXS294 can be used to establish linkage to the disease. In addition, we modified a previously described PCR protocol to use fluorescent dye-labelled oligoprimers and an ABI Gene Scanner™ in order to rapidly quantitate deletional forms of Lesch-Nyhan syndrome. Quantitative PCR analysis of individual exons followed by dosage analysis confirmed a deletion encompassing exon 9. A similar approach was used to confirm a previously described HPRT gene duplication involving exons 2 and 3. In this analysis, we co-amplified the HPRTB [AGAT]n and HUMARA [AGC]n repeats and confirmed increased exon dosage in carriers for the duplication. DNA sequence analysis remains the method of choice for delineating new disease-causing mutations, most of which are non-deletional forms of Lesch-Nyhan syndrome. We have also used a cycle-sequencing strategy employing dye-labelled dideoxy terminators and a laser-activated, fluorescence-emission DNA sequencer in order to define carrier status in 10 family members at risk for Lesch-Nyhan syndrome due to a splice donor mutation in intron 7. Our DNA sequence analyses corroborate small tandem repeat (STR) inheritance patterns in this family. Multiple fluorescence-based strategies should facilities rapid diagnosis of the various Lesch-Nyhan disease-causing mutations.

Diagnosis of Down syndrome and other aneuploidies using quantitative polymerase chain reaction and small tandem repeat polymorphisms.

Pregnant women over 35 years of age are routinely offered screening tests and karyotyping to detect Down syndrome and certain other aneuploidies because the risk of these disorders increases exponentially with maternal age. It is, however, only cost-effective to karyotype high-risk pregnancies and a substantial number of remaining aneuploidy cases go undetected. We describe a rapid, inexpensive method to detect trisomy using polymorphic small tandem repeat (STR) markers and the polymerase chain reaction (PCR) to amplify amniocyte DNA. STR patterns obtained on patients with trisomy 21, trisomy 18 and triplo-X syndromes are distinct from controls. Polymorphic trisomy genotypes either show three fragment peaks of equal intensity or two fragments at a 2:1 dosage ratio. In addition, Turner syndrome (45, X0) DNA can be distinguished from normal male DNA because it fails to amplify a Y-chromosome specific PCR marker yet contains only a single dose of X-specific STR markers. Quantitative analysis of peak heights and areas from STR markers show that the two peak patterns separate into completely non-overlapping groups. The high level of heterozygosity of most STR markers result in a predominance of heterozygous controls and trisomy patterns with multiple alleles, the easiest patterns to differentiate. Homozygosity, and hence an uninformative STR pattern, is more common in controls than in trisomy samples. We anticipate as few as three STR markers per chromosome should be over 99% informative.

Organization of the Epstein-Barr virus DNA molecule. II. Fine mapping of the boundaries of the internal repeat cluster of B95-8 and identification of additional small tandem repeats adjacent to the HR-1 deletion.

We used cloned BamHI fragments from Epstein-Barr virus strain B95-8 [EBV(B95-8)]DNA to obtain detailed restriction maps of the region of the genome adjacent to the large internal repeat cluster. These maps together with the results of hybridization experiments using a 3.1-kilobase repeat probe defined more precisely the location of the injection between the internal repeat cluster and the flanking unique-sequence DNA. On one side (UL), the repeat sequences extended 600 +/- 80 base pairs (bp) into BamHI-Y; on the other side (US), they extended 1,300 +/- 200 bp into BamHI-C. Therefore, EBV(B95-8) DNA contained a nonintegral number of 3.1-kilobase repeat units, namely, 12.6 copies. The mapping studies also revealed a second series of internal tandem repetitions in EBV(B95-8) DNA located within the BamHI-H fragment. This cluster comprised 11 copies of a 135-bp repeat unit which contained a single site for the NotI restriction endonuclease. Hybridization to these cloned EBV(B95-8) fragments using total EBV(HR-1) DNA as probe indicated that the deletion in EBV(HR-1) removed all 3,000 bp of unique-sequence DNA which lay between the large 3.1-kilobase and the small 135-bp repeat clusters. Thus, the deletion which destroyed the transforming ability in the EBV(HR-1) virus was bounded on either side by tandem repetitions.

Human U1 loci: genes for human U1 RNA have dramatically similar genomic environments.

We have cloned and sequenced several distinct loci from the human genome whose sequences agree exactly and are colinear with the sequence of the small nuclear RNA U1. There appear to be 100-150 such U1 loci in the human genome. Although these loci are not in close clusters or in small tandem repeats in the genome, the majority of them have remarkably similar genomic environments. Several potential RNA polymerase termination sites exist in the immediate 3' flanking regions of the loci studied; however, no TATA box is found in the immediate 5' flanking sequences. These observations, with the findings of others concerning the transcription of U1, suggest that U1 RNA is synthesized from a family of transcription units. These data are consistent with the proposal that RNA polymerase II may synthesize primary transcripts from these transcription units, which are processed at both the 5' and 3' ends to yield mature U1 RNA and possibly other RNA species of unknown function.

Two distant regions of the Epstein-Barr virus genome with sequence homologies have the same orientation and involve small tandem repeats.

The two regions of the Epstein-Barr virus genome (DSL and DSR) carrying homologous sequences at distant parts of the long unique region are described. Cleavage of cloned DNA containing the DSR region with restriction endonucleases revealed a so far unrecognized small tandem repeat of approximately 120 base pairs present in approximately 20 copies. Heteroduplexes of the DNA of two clones containing DSL and DSR respectively, visualized in the electron microscope by cytochrome c spreading, revealed that the region of homology is approximately 2.5 kb long, involves small tandem repeats, and has the same orientation in the viral genome. Mica adsorption of the heteroduplex showed, that the homologous region consists of approximately 1.5 kb with only partial homology including the small internal repeats and 0.9 kb with well-matched duplexes. When DNA containing the DSL region reanneals, it can give rise to two single-stranded loops of the same size at different positions suggesting the presence of a row of tandem repeats also in this region.

Evolutionary variants of simian virus 40: Nucleotide sequence of a conserved SV40 DNA segment containing the origin of viral DNA replication as an inverted repetition

Abstract Evolutionary variants of simian virus 40 (SV40), generated during serial passage of the virus at high multiplicity of infection, retain viral DNA sequences functioning as cis elements required for propagation, including the origin of DNA replication. To help define the SV40 origin signal, we have determined the nucleotide sequence of an SV40 segment present in a variant cloned from the 45th passage stock. The variant genome consists of SV40 DNA joined to cellular DNA and is made up of three tandemly arranged repeats of a basic DNA segment that is 28% of the length of wild-type SV40 DNA. Within each basic segment, the SV40 sequences derived from the region of the replication origin are present as an inverted repetition. On one side of the inverted sequence are 164 nucleotides of SV40 DNA and on the other side are 198 nucleotides. The variant sequence is the same as that found in parental SV40 DNA except for the presence of small tandem repeats within the variant segment. These data, together with the results of other studies of SV40 variants and deletion mutants, localize the SV40 ori signal to a segment of DNA of about 80 nucleotides between map units 0.66 and 0.68.