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Journal of Thyroid Research
Volume 2012, Article ID 318232, 9 pages
http://dx.doi.org/10.1155/2012/318232
Research Article

Determination of RET Sequence Variation in an MEN2 Unaffected Cohort Using Multiple-Sample Pooling and Next-Generation Sequencing

1Research & Development, ARUP Institute for Clinical and Experimental Pathology, 500 Chipeta Way, Salt Lake City, UT 84108, USA
2Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA

Received 7 October 2011; Accepted 23 January 2012

Academic Editor: Gary L. Francis

Copyright © 2012 R. L. Margraf et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. T. Kloos, C. Eng, D. B. Evans et al., “Medullary thyroid cancer: management guidelines of the American thyroid association,” Thyroid, vol. 19, no. 6, pp. 565–612, 2009. View at Google Scholar · View at Scopus
  2. M. A. Kouvaraki, S. E. Shapiro, N. D. Perrier et al., “RET proto-oncogene: a review and update of genotype-phenotype correlations in hereditary medullary thyroid cancer and associated endocrine tumors,” Thyroid, vol. 15, no. 6, pp. 531–544, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. C. Eng, D. Clayton, I. Schuffenecker et al., “The relationship between specific ret proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2: international RET mutation consortium analysis,” Journal of the American Medical Association, vol. 276, no. 19, pp. 1575–1579, 1996. View at Publisher · View at Google Scholar · View at Scopus
  4. J. W. de Groot, T. P. Links, J. T. Plukker, C. J. Lips, and R. M. Hofstra, “RET as a diagnostic and therapeutic target in sporadic and hereditary endocrine tumors,” Endocrine Reviews, vol. 27, no. 5, pp. 535–560, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. P. J. Morrison and N. C. Nevin, “Multiple endocrine neoplasia type 2B (mucosal neuroma syndrome, Wagenmann-Froboese syndrome),” Journal of Medical Genetics, vol. 33, no. 9, pp. 779–782, 1996. View at Google Scholar · View at Scopus
  6. G. Wiesner and K. Snow-Bailey, “GeneReviews: Multiple Endocrine Neoplasia Type 2,” 2005, http://www.geneclinics.org/servlet/access?db=geneclinics&site=gt&id=8888892&key=2paoNNdpDmi-r &gry=&fcn=y&fw=ZVFB&filename=/profiles/men2/indexhtml.
  7. C. J. Wray, T. A. Rich, S. G. Waguespack, J. E. Lee, N. D. Perrier, and D. B. Evans, “Failure to recognize multiple endocrine neoplasia 2B: more common than we think?” Annals of Surgical Oncology, vol. 15, no. 1, pp. 293–301, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. R. L. Margraf, D. K. Crockett, P. M. Krautscheid et al., “Multiple endocrine neoplasia type 2 RET protooncogene database: repository of MEN2-associated RET sequence variation and reference for genotype/phenotype correlations,” Human Mutation, vol. 30, no. 4, pp. 548–556, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. C. Eng, D. Clayton, I. Schuffenecker et al., “The relationship between specific ret proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2: international RET mutation consortium analysis,” Journal of the American Medical Association, vol. 276, no. 19, pp. 1575–1579, 1996. View at Publisher · View at Google Scholar · View at Scopus
  10. A. Z. Lai, T. S. Gujral, L. M. Mulligan et al., “RET signaling in endocrine tumors: delving deeper into molecular mechanisms,” Endocrine Pathology, vol. 18, no. 2, pp. 57–67, 2007. View at Google Scholar
  11. V. Bansal, O. Harismendy, R. Tewhey et al., “Accurate detection and genotyping of SNPs utilizing population sequencing data,” Genome Research, vol. 20, no. 4, pp. 537–545, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  12. T. E. Druley, F. L. Vallania, D. J. Wegner et al., “Quantification of rare allelic variants from pooled genomic DNA,” Nature Methods, vol. 6, no. 4, pp. 263–265, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. D. C. Koboldt, K. Chen, T. Wylie et al., “VarScan: variant detection in massively parallel sequencing of individual and pooled samples,” Bioinformatics, vol. 25, no. 17, pp. 2283–2285, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. A. A. Out, I. J. van Minderhout, J. J. Goeman et al., “Deep sequencing to reveal new variants in pooled DNA samples,” Human Mutation, vol. 30, no. 12, pp. 1703–1712, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. S. E. Calvo, E. J. Tucker, A. G. Compton et al., “High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex i deficiency,” Nature Genetics, vol. 42, no. 10, pp. 851–858, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  16. V. Bansal, “A statistical method for the detection of variants from next-generation resequencing of DNA pools,” Bioinformatics, vol. 26, no. 12, pp. i318–i324, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  17. R. L. Margraf, J. D. Durtschi, S. Dames et al., “Multi-sample pooling and illumina genome analyzer sequencing methods to determine gene sequence variation for database development,” Journal of Biomolecular Techniques, vol. 21, no. 3, pp. 126–140, 2010. View at Google Scholar · View at Scopus
  18. R. L. Margraf, J. D. Durtschi, S. Dames, D. C. Pattison, J. E. Stephens, and K. V. Voelkerding, “Variant identification in multi-sample pools by illumina genome analyzer sequencing,” Journal of Biomolecular Techniques, vol. 22, no. 2, pp. 74–84, 2011. View at Google Scholar
  19. J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer, “Substantial biases in ultra-short read data sets from high-throughput DNA sequencing,” Nucleic Acids Research, vol. 36, no. 16, article e105, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  20. R. Li, Y. Li, X. Fang et al., “SNP detection for massively parallel whole-genome resequencing,” Genome Research, vol. 19, no. 6, pp. 1124–1132, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  21. R. L. Margraf, R. Mao, W. E. Highsmith, L. M. Holtegaard, and C. T. Wittwer, “Mutation scanning of the RET protooncogene using high-resolution melting analysis,” Clinical Chemistry, vol. 52, no. 1, pp. 138–141, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. R. A. Palais, M. A. Liew, and C. T. Wittwer, “Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping,” Analytical Biochemistry, vol. 346, no. 1, pp. 167–175, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. D. W. Craig, J. V. Pearson, S. Szelinger et al., “Identification of genetic variants using bar-coded multiplexed sequencing,” Nature Methods, vol. 5, no. 10, pp. 887–893, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. O. Harismendy, P. C. Ng, R. L. Strausberg et al., “Evaluation of next generation sequencing platforms for population targeted sequencing studies,” Genome Biology, vol. 10, no. 3, article R32, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  25. C. T. Wittwer, G. H. Reed, C. N. Gundry, J. G. Vandersteen, and R. J. Pryor, “High-resolution genotyping by amplicon melting analysis using LCGreen,” Clinical Chemistry, vol. 49, no. 6, part 1, pp. 853–860, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Liew, R. Pryor, R. Palais et al., “Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons,” Clinical Chemistry, vol. 50, no. 7, pp. 1156–1164, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  27. S. F. Dobrowolski, J. T. McKinney, C. A. di San Filippo, G. S. Keow, B. Wilcken, and N. Longo, “Validation of dye-binding/high-resolution thermal denaturation for the identification of mutations in the SLC22A5 gene,” Human Mutation, vol. 25, no. 3, pp. 306–313, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  28. C. Willmore, J. A. Holden, L. Zhou, S. Tripp, C. T. Wittwer, and L. J. Layfield, “Detection of c-kit-activating mutations in gastrointestinal stromal tumors by high-resolution amplicon melting analysis,” American Journal of Clinical Pathology, vol. 122, no. 2, pp. 206–216, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  29. G. H. Reed and C. T. Wittwer, “Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis,” Clinical Chemistry, vol. 50, no. 10, pp. 1748–1754, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  30. D. K. Crockett, S. R. Piccolo, P. G. Ridge et al., “Predicting phenotypic severity of uncertain gene variants in the RET proto-oncogene,” Plos ONE, vol. 6, no. 3, 2011. View at Publisher · View at Google Scholar · View at PubMed