We describe a novel method for rapidly identifying and distinguishing between different DNA sequences using short tandem repeat (STR) analysis and DNA microarrays. The method can be used to deduce identity, length, and number of STRs of the target molecule. We refer to this technique as the "variable-length probe array" method for STR profiling (VLPA). The method involves hybridization of the u...

AIM To find an association between Y chromosome polymorphisms and some ethnic groups. METHODS Short tandem repeats (STR) and single-nucleotide polymorphisms (SNP) on the Y chromosome were typed in 311 unrelated men from four different ethnic groups - Italians from northern Italy, Albanians, Africans from the Maghreb region, and Indo-Pakistanis, using the AmpFlSTR® Yfiler PCR Amplification Kit...

MOTIVATION Y-chromosome short tandem repeats (Y-STRs) are widely used for population studies, forensic purposes and, potentially, the study of disease, therefore knowledge of their mutation rate is valuable. Here we show a novel method for estimation of site-specific Y-STR mutation rates from partial phylogenetic information, via the maximum likelihood framework. RESULTS Given Y-STR data clas...

OBJECTIVES Epstein Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) are a useful biological resource, however, genomic variations can happen during the generation and immortalization processes of LCLs. The purpose of this study was to identify genomic variations in LCL DNA compared with matched blood DNA using short tandem repeats (STRs) analysis. METHODS We analyzed 15 STRs with...

Three types of sequence variations--single-nucleotide polymorphisms (SNPs), insertions and deletions (indels), and short tandem repeats (STRs)--have been extensively reported in mammalian genomes. In this study, we discovered a novel type of sequence variation, i.e., multiple-nucleotide length polymorphisms (MNLPs) in bovine UCN3 (Urocortin 3) and its receptor CRHR2 (corticotropin-releasing hor...

Length variation in short tandem repeats (STRs) is an important family of DNA polymorphisms with numerous applications in genetics, medicine, forensics, and evolutionary analysis. Several major diseases have been associated with length variation of trinucleotide (triplet) repeats including Huntington's disease, hereditary ataxias and spinobulbar muscular atrophy. Using the reference human genom...

Polymers of random 14 mer oligonucleotides are shown to detect discrete loci in the human genome. Eighteen different synthetic tandem repeats of random 14 base-pair units (STRs) have been generated and all of them turn out to detect polymorphic loci on southern blots of human DNA samples, presumably corresponding to a variable number of tandem repeats (VNTR). This finding suggests that minisate...

Y-chromosome diversity has been analyzed at a micro-geographical level, examining 10 binary polymorphisms and 7 short tandem repeats (STRs) in 443 samples belonging to 11 populations from two regions of Northern Spain, Galicia and Cantabria. Both regions, as a whole, cluster with other Iberian populations. However, some individual populations, particularly that from the Pas Valley in Cantabria,...

Short tandem repeats (STRs) or microsatellites are well-known sequence elements that may change the spacing between transcription factor binding sites (TFBSs) in promoter regions by expansion or contraction of repetitive units. Some of these mutations have the potential to contribute to phenotypic diversity by altering patterns of gene expression. To explore how repetitive sequence motifs withi...

BACKGROUND Autosomal and Y chromosome short tandem repeats (STRs) and mitochondrial DNA polymorphisms are the most commonly used molecular tools for determination of kinship. AIM To report a revision of 1,120 kinship cases (paternity and others) analyzed in our laboratory. MATERIAL AND METHODS Revision of all kinship cases analyzed between years 2001-2006. Autosomal and Y chromosome STRs an...