Tri-nucleotide Threading for parallel amplification of minute amounts of genomic DNA
2006 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 34, no 6, 9- p.Article in journal (Refereed) Published
Efforts to correlate genetic variations with phenotypic differences are intensifying due to the availability of high-density maps of single nucleotide polymorphisms (SNPs) and the development of high throughput scoring methods. These recent advances have led to an increased interest for improved multiplex preparations of genetic material to facilitate such whole genome analyses. Here we propose a strategy for the parallel amplification of polymorphic loci based on a reduced set of nucleotides. The technique denoted Tri-nucleotide Threading (TnT), allows SNPs to be amplified via controlled linear amplification followed by complete removal of the target material and subsequent amplification with a pair of universal primers. A dedicated software tool was developed for this purpose and variable positions in genes associated with different forms of cancer were analyzed using sub-nanogram amounts of starting material. The amplified fragments were then successfully scored using a microarray-based PrASE technique. The results of this study, in which 75 SNPs were analyzed, show that the TnT technique circumvents potential problems associated with multiplex amplification of SNPs from minute amounts of material. The technique is specific, sensitive and can be readily adapted to equipment and genotyping techniques used in other research laboratories without requiring changes to the preferred typing method.
Place, publisher, year, edition, pages
2006. Vol. 34, no 6, 9- p.
genomic DNA; trinucleotide; cytidine triphosphate; guanosine triphosphate; pyrimidine nucleotide; thymidine 5'-triphosphate; thymidine triphosphate; article; cancer; computer program; DNA microarray; gene amplification; gene locus; genetic variability; genotype; high throughput screening; human; phenotype; priority journal; scoring system; sensitivity and specificity; single nucleotide polymorphism; chemistry; evaluation; genome; genomics; methodology; polymerase chain reaction; Cytidine Triphosphate; Genome, Human; Genomics; Genotype; Guanosine Triphosphate; Humans; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Software; Thymine Nucleotides
IdentifiersURN: urn:nbn:se:kth:diva-7687DOI: 10.1093/nar/gkl103ISI: 000237002900005ScopusID: 2-s2.0-33645832164OAI: oai:DiVA.org:kth-7687DiVA: diva2:12787
QC 201008132007-11-212007-11-212010-08-13Bibliographically approved