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J. Clin. Microbiol. 51, 745–51. Efficient depletion of host DNA contamination in malaria clinical sequencing. 2013

Oyola, S.O. et al.

Notes: Human Genomic DNA: Male was used to construct a reference mock clinical sample. (4545)

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Clin. Chem. 58, 580–9. COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing. 2012

Milbury, C.A. et al.

Notes: Human Genomic DNA: Male was used to dilute experimental genomic DNA from cell lines and tumor samples for PCR before sequencing. (4543)

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DNA Research 19, 395-406. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer 2012

Murphy, S.J., Cheville, J.C., Zarei, S., Johnson, S.H., Sikkink, R.A., Kosari, F., Feldman, A.L., Eckloff, B.W., Karnes, R.J. and Vasmatzis, G.

Notes: Genomic rearrangements detected by NGS were mapped and confirmed by PCR. Human Genomic DNA: Male was used as a control for the confirmatory experiments. (4539)

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Nucl. Acids Res. 39, e81. A method for counting PCR template molecules with application to next-generation sequencing. 2011

Casbon, J.A., Osborne, R.J., Brenner, S. and Lichtenstein, C.P.

Notes: DNA templates are often amplified by PCR during library generation prior to next-generation sequencing, but amplification can introduce biases and duplications that are not easily corrected. In this paper, the authors developed a simple method to count the number of input template molecules to reduce these PCR-related problems: The ligation of a degenerate base region to all fragments during library creation. To evaluate their approach to correct for biases and duplications, the authors created a library using Human Genomic DNA, amplified the library by inverse PCR using the GoTaq® Hot Start Polymerase and 1X Colorless GoTaq® Flexi Buffer, sequenced the resulting DNA fragments and assessed the quality of the next-generation sequencing data. (4160)

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Nucl. Acids Res. 39, e81. A method for counting PCR template molecules with application to next-generation sequencing.

J.A. Casbon, R. J. Osborne, S. Brenner and C.P. Lichtenstein

Notes: Human Genomic DNA used as the starting material in the NGS workflow.  GoTaq® Flexi Colorless Buffer and GoTaq® Flexi Polymerase were used in amplification of template in step added to the beginning of library preparation. (4531)

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Nucl. Acids Res. 38, 6985-96. Targeted next-generation sequencing of DNA regions proximal to a conserved CXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer 2010

Chmielecki,J., Peifer, M., Socci, N.D., Hutchinson, K., Viale, A., Zhao, Z., Thomas, R.K. and Pao, W.

Notes: Human Genomic DNA:Male was used as a negative control in standard PCR and Sanger Sequencing to confirm fusion genomic breakpoints identified by NGS experiments. (4534)

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Clin. Chem. 55, 748–56. Coamplification at lower denaturation temperature-PCR increases mutation-detection selectivity of TaqMan-based real-time PCR. 2009

Li, J., Wang, L., Jänne, P.A. and Makrigiorgos, GM.

Notes: The authors describe a new form of PCR, co-amplification at lower denaturation temperature PCR (COLD-PCR), to detect low-level somatic mutations. This technique is based on the facts that a) each DNA sequence has a critical denaturation temperature (Tc), which is lower than the melting temperature (Tm) and below which PCR efficiency decreases dramatically and b) Tc depends on DNA sequence. The authors used GoTaq® Flexi DNA Polymerase and mutation-specific TaqMan® probes for tumor protein 53 (TP53) and epidermal growth factor receptor (EGFR) to detect low-level somatic mutations in a mixture of wildtype and mutant DNAs. Conventional TaqMan® technology can detect mutant alleles at an abundance of 10–20% of that of the wildtype allele; using COLD-PCR the authors were able to increase selectivity 15- to 30-fold, detecting as little as 0.8% mutuant alleles. (4038)

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