Affiliation: Stanford University
- Multigene amplification and massively parallel sequencing for cancer mutation discoveryFredrik Dahl
Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
Proc Natl Acad Sci U S A 104:9387-92. 2007..Seven cancer cell lines and one normal genomic DNA sample were studied with multiple mutations and polymorphisms identified among the 10 genes. Mutations and polymorphisms in the TP53 gene were confirmed by traditional sequencing...
- Multiplex amplification of all coding sequences within 10 cancer genes by Gene-CollectorSimon Fredriksson
Stanford Genome Technology Center, Bio X, Stanford, California 94305, USA
Nucleic Acids Res 35:e47. 2007..Gene-Collector has utility for numerous applications such as high throughput resequencing, SNP analyses, and pathogen detection...
- Multiplex amplification of large sets of human exonsGregory J Porreca
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
Nat Methods 4:931-6. 2007..We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing...
- Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragmentsFredrik Dahl
Department of Genetics and Pathology, Rudbeck Laboratory Se 75185 Uppsala, Sweden
Nucleic Acids Res 33:e71. 2005..Eighty-nine percent of the selectors generated PCR products that hybridized to the expected positions on the array, while little or no amplification artifacts were observed...
- PieceMaker: selection of DNA fragments for selector-guided multiplex amplificationJohan Stenberg
Department of Genetics and Pathology, Rudbeck Laboratory Se 751 85, Uppsala, Sweden
Nucleic Acids Res 33:e72. 2005..The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes...
- Analyzing genes using closing and replicating circlesMats Nilsson
Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
Trends Biotechnol 24:83-8. 2006..This review describes the recent developments in the technologies that use specific DNA circularization, coupled to DNA amplification through PCR or rolling-circle amplification, and addresses the great potential of these tools...
- Real-time monitoring of rolling-circle amplification using a modified molecular beacon designMats Nilsson
Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
Nucleic Acids Res 30:e66. 2002..The method allows highly accurate quantification of circularized DNA over a broad concentration range by relating the signal from the test DNA circle to an internal reference DNA circle reporting in a distinct fluorescence color...
- MLGA--a rapid and cost-efficient assay for gene copy-number analysisMagnus Isaksson
Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE 751 85 Uppsala, Sweden
Nucleic Acids Res 35:e115. 2007..We have developed a technique based on multiplex amplification of size-coded selectively circularized genomic fragments, which is robust, cheaper and more rapid than current multiplex targeted copy-number assays...
- Evaluation of beta globin mRNA as an early marker of haemoglobin response to epoetin treatmentGunnar Birgegard
Department of Haematology, University Hospital, Uppsala 751 85, Sweden
Med Oncol 24:318-22. 2007..Compared to reticulocyte count, beta-globin mRNA is more reliable in the individual patient, but the clinical usefulness of the assay needs to be evaluated in further studies...
- Making ends meet in genetic analysis using padlock probesMats Nilsson
Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
Hum Mutat 19:410-5. 2002..We argue that the probes have the potential to render high-throughput genetic analyses precise and affordable...