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 nonradioac...

This article reviews new genetic markers on the Y-chromosome and methods for analyzing these short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci. Relative chromosomal locations for over 50 Y-chromosome STRs (Y-STRs) are described along with their repeat motif and allele range characteristics based on published population studies. Multiplex assays for typing many of these mar...

A major end point of nonmyeloablative hematopoietic stem cell transplantation is the attainment of either mixed chimerism or full donor hematopoiesis. Because the majority of human genetic disparity is generated by single nucleotide polymorphisms (SNPs), direct measurement of SNPs should provide a robust tool for the detection and quantitation of chimerism. Using pyrosequencing, a rapid quantit...

Background: Human identification requires the maintenance of population databases of short tandem repeat (STR) loci that allow for their correct interpretation during paternity testing and forensic cases. Material and Methods: We analyzed 15 STR loci with the AmpFlSTR® Identifiler kit in a Mestizo (admixed) population sample from the state of Guerrero (South Mexico). Results: We estimated the a...

DNA sequence variation is known to exist in and around the repeat region of short tandem repeat (STR) loci used in human identity testing. While the vast majority of STR alleles measured in forensic DNA laboratories worldwide type as "normal" alleles compared with STR kit allelic ladders, a number of variant alleles have been reported. In addition, a sequence difference at a polymerase chain re...

A multiplex PCR assay capable of amplifying 20 Y-chromosome short tandem repeat (STR) markers simultaneously has been developed. These markers include all of the Y STRs that make up the ‘‘extended haplotype’’ used in Europe (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAII) plus additional polymorphic Y STRs (DYS437, DYS438, DYS439, DYS447, DYS448, DYS388, DYS426, GATA A7.1,...

The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the "raw material" for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decrea...

Repetitive sequences are abundant in the human genome. Different classes of repetitive DNA sequences, including simple repeats, tandem repeats, segmental duplications, interspersed repeats, and other elements, collectively span more than 50% of the genome. Because repeat sequences occur in the genome at different scales they can cause various types of sequence analysis errors, including in alig...

Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. He...

Two distinct classes of repetitive sequences, interspersed mobile elements and satellite DNAs, shape eukaryotic genomes and drive their evolution. Short arrays of tandem repeats can also be present within nonautonomous miniature inverted repeat transposable elements (MITEs). In the clam Donax trunculus, we characterized a composite, high copy number MITE, named DTC84. It is composed of a centra...