Publications

GPS-driven publications

  1. Utility of Clinical High-Depth Next Generation Sequencing for Somatic Variant Detection in the PIK3CA Related Overgrowth Spectrum. Hucthagowder V, Shenoy A, Corliss M, Vigh-Conrad KA, Storer C, Grange DK, Cottrell CE. Clin Genet. 2016 Jun 16. doi: 10.1111/cge.12819. PubMedID 27307077
  2. Concurrent MPLW515L and Y591D mutations in a patient with myelofibrosis. Rashidi A, Heusel JW, Oh ST. Blood Cells Mol Dis. 60 (2016) 1-2. Article link

  3. Occult Specimen Contamination in Routine Clinical Next-Generation Sequencing Testing. Sehn JK, Spencer DH, Pfeifer JD, Bredemeyer AJ, Cottrell CE, Abel HJ, Duncavage EJ. Am J Clin Pathol. 2015 Oct;144(4):667-74. PubMedID 26386089
  4. Diagnostic yield of targeted next generation sequencing in various cancer types: An information-theoretic approach. Hagemann IS, O’Neill PK, Erill I, Pfeifer JD. Cancer Genet. 2015 May 29 [Epub ahead of print]. PubMedID 26227479
  5. Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS). Al-Kateb H, Nguyen TT, Steger-May K, Pfeifer JD. Mol Oncol. 2015 May 29 [Epub ahead of print]. PubMedID 26071350
  6. MET Mutation Associated with Responsiveness to Crizotinib. Waqar SN, Morgensztern D, Sehn J. J Thorac Oncol. 2015 May;10(5):e29-31. PubMedID 25898962
  7. Clinical next-generation sequencing in patients with non-small cell lung cancer. Hagemann IS, Devarakonda S, Lockwood CM, Spencer DH, Guebert K, Bredemeyer AJ, Al-Kateb H, Nguyen TT, Duncavage EJ, Cottrell CE, Kulkarni S, Nagarajan R, Seibert K, Baggstrom M, Waqar SN, Pfeifer JD, Morgensztern D, Govindan R. Cancer. 2014 Oct 24. [Epub ahead of print]. PubMedID 25345567
  8. Clinical Genomics: A Guide to Clinical Next-Generation Sequencing. Shashikant Kulkarni (editor) and John Pfeifer (editor). Academic Press, December 2014. Print. ISBN-13: 978-0124047488
  9. Aggressive congenital juvenile myelomonocytic leukemia associated with somatic KRAS p.G13D mutation and concurrent germline IGF1R duplication. Kothari A, Hulbert ML, Cottrell CE, Nguyen TT. Leuk Lymphoma. 2014 Aug 11:1-8. [Epub ahead of print]. PubMedID 25110823
  10. Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing. Abel HJ, Al-Kateb H, Cottrell CE, Bredemeyer AJ, Pritchard CC, Grossmann AH, Wallander ML, Pfeifer JD, Lockwood CM, Duncavage EJ. J Mol Diagn. 2014 Jul;16(4):405-17. PubMedID 24813172
  11. Copy number variants in clinical next-generation sequencing data can define the relationship between simultaneous tumors in an individual patient. Sehn JK, Abel HJ, Duncavage EJ. Exp Mol Pathol. 2014 Jun 2;97(1):69-73. PubMedID 24886963
  12. Detection of viral pathogens in high grade gliomas from unmapped next-generation sequencing data. Cimino PJ, Zhao G, Wang D, Sehn JK, Lewis JS Jr, Duncavage EJ. Exp Mol Pathol. 2014 Jun;96(3):310-5. PubMedID 24704430
  13. Diagnostic Utility of Targeted Next-generation Sequencing in Problematic Cases. Sehn JK, Hagemann IS, Pfeifer JD, Cottrell CE, Lockwood CM. Am J Surg Pathol. 2014 Apr;38(4):534-41. PubMedID 24451277
  14. Targeted next-generation sequencing using fine-needle aspirates from adenocarcinomas of the lung. Karnes HE, Duncavage EJ, Bernadt CT. Cancer Cytopathol. 2014 Feb;122(2):104-13. PubMedID 24227699
  15. Clinical next generation sequencing in cancer. Pfeifer JD. Cancer Genet. 2013 Dec;206(12):409-12. PubMedID 24345338
  16. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Abel HJ, Duncavage EJ. Cancer Genet. 2013 Dec;206(12):432-440. PubMedID 24405614
  17. Design of targeted, capture-based, next generation sequencing tests for precision cancer therapy. Hagemann IS, Cottrell CE, Lockwood CM. Cancer Genet. 2013 Dec;206(12):420-431. PubMedID 24388712
  18. Stabilization of Disease after Targeted Therapy in a Thymic Carcinoma with KIT Mutation Detected by Clinical Next-Generation Sequencing. Hagemann IS, Govindan R, Javidan-Nejad C, Pfeifer JD, Cottrell CE. J Thorac Oncol. 2014 Feb;9(2). PubMedID 24419427
  19. Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology. Cottrell CE, Al-Kateb H, Bredemeyer AJ, Duncavage EJ, Spencer DH, Abel HJ, Lockwood CM, Hagemann IS, O’Guin SM, Burcea LC, Sawyer CS, Oschwald DM, Stratman JL, Sher DA, Johnson MR, Brown JT, Cliften PF, George B, McIntosh LD, Shrivastava S, Nguyen TT, Payton JE, Watson MA, Crosby SD, Head RD, Mitra RD, Nagarajan R, Kulkarni S, Seibert K, Virgin HW 4th, Milbrandt J, Pfeifer JD. J Mol Diagn. 2014 Jan;16(1):89-105. PubMedID 24211365
  20. Commentary: Genomic technologies and the new era of genomic medicine. Ankala A, Hegde M. J Mol Diagn. 2014 Jan;16(1):7-10. PubMedID 24269227
  21. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. Spencer DH, Tyagi M, Vallania F, Bredemeyer AJ, Pfeifer JD, Mitra RD, Duncavage EJ. J Mol Diagn. 2014 Jan;16(1):75-88. PubMedID 24211364
  22. Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens. Spencer DH, Sehn JK, Abel HJ, Watson MA, Pfeifer JD, Duncavage EJ.J Mol Diagn. 2013 Sep;15(5):623-33. PubMedID 23810758
  23. Clinical genomicist workstation. Sharma MK, Phillips J, Agarwal S, Wiggins WS, Shrivastava S, Koul SB, Bhattacharjee M, Houchins CD, Kalakota RR, George B, Meyer RR, Spencer DH, Lockwood CM, Nguyen TT, Duncavage EJ, Al-Kateb H, Cottrell CE, Godala S, Lokineni R, Sawant SM, Chatti V, Surampudi S, Sunkishala RR, Darbha R, Macharla S, Milbrandt JD, Virgin HW, Mitra RD, Head RD, Kulkarni S, Bredemeyer A, Pfeifer JD, Seibert K, Nagarajan R. AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:156-7. PubMedID 24303327
  24. Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data. Spencer DH, Abel HJ, Lockwood CM, Payton JE, Szankasi P, Kelley TW, Kulkarni S, Pfeifer JD, Duncavage EJ. J Mol Diagn. 2013 Jan;15(1):81-93. PubMedID 23159595
  25. Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia. Duncavage EJ, Abel HJ, Szankasi P, Kelley TW, Pfeifer JD.Mod Pathol. 2012 Jun;25(6):795-804. PubMedID 22425908
  26. Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. Duncavage EJ, Magrini V, Becker N, Armstrong JR, Demeter RT, Wylie T, Abel HJ, Pfeifer JD.J Mol Diagn. 2011 May;13(3):325-33. PubMedID 21497292
  27. Characterization of translocations in mesenchymal hamartoma and undifferentiated embryonal sarcoma of the liver. Mathews J, Duncavage EJ, Pfeifer JD.Exp Mol Pathol. 2013 Dec;95(3):319-24. PubMedID 24120702

GPS-associated publications

  1. Identification of Medically Actionable Secondary Findings in the 1000 Genomes. Olfson E, Cottrell CE, Davidson NO, Gurnett CA, Heusel JW, Stitziel NO, Chen LS, Hartz S, Nagarajan R, Saccone NL, Bierut LJ. PLoS One. 2015 Sep 2;10(9). PubMedID 26332594
  2. College of American Pathologists’ Laboratory Standards for Next-Generation Sequencing Clinical Tests. Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DG, Merker JD, Nagarajan R, Palicki LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV. Arch Pathol Lab Med. 2014 Aug 25. [Epub ahead of print]. PubMedID 25152313
  3. The Human Epigenome Browser at Washington University. Zhou X, Maricque B, Xie M, Li D, Sundaram V, Martin EA, Koebbe BC, Nielsen C, Hirst M, Farnham P, Kuhn RM, Zhu J, Smirnov I, Kent WJ, Haussler D, Madden PA, Costello JF, Wang T. Nat Methods. 2011 Nov 29;8(12):989-90. PubMedID 22127213
  4. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, Bender RH, Fulton LL, Delehaunty KD, Fronick CC, Appelbaum EL, Schmidt H, Abbott R, O’Laughlin M, Chen K, McLellan MD, Varghese N, Nagarajan R, Heath S, Graubert TA, Ding L, Ley TJ, Zambetti GP, Wilson RK, Mardis ER. JAMA. 2011 Apr 20;305(15):1568-76. PubMedID 21505135
  5. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, Wallis J, Chen K, Payton JE, Fulton RS, Veizer J, Schmidt H, Vickery TL, Heath S, Watson MA, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Ley TJ, Wilson RK. JAMA. 2011 Apr 20;305(15):1577-84. PubMedID 21505136
  6. The genetic landscape of the childhood cancer medulloblastoma. Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. Science. 2011 Jan 28;331(6016):435-9. PubMedID 21163964
  7. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O’Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Nat Biotechnol. 2010 Oct;28(10):1097-105. PubMedID 20852635
  8. Conserved role of intragenic DNA methylation in regulating alternative promoters. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D’Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Nature. 2010 Jul 8;466(7303):253-7. PubMedID 20613842
  9. DNMT3A mutations in acute myeloid leukemia. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O’Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK. N Engl J Med. 2010 Dec 16;363(25):2424-33. PubMedID 21067377
  10. Recurring mutations found by sequencing an acute myeloid leukemia genome. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ. N Engl J Med. 2009 Sep 10;361(11):1058-66. PubMedID 19657110
  11. The genomic landscapes of human breast and colorectal cancers. Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. Science. 2007 Nov 16;318(5853):1108-13. PubMedID 17932254

Other publications related to GPS products and services

  1. Variation in genome-wide mutation rates within and between human families. Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project. Nat Genet. 2011 Jun 12;43(7):712-4. PubMedID 21666693
  2. High-throughput discovery of rare insertions and deletions in large cohorts. Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD. Genome Res. 2010 Dec;20(12):1711-8. PubMedID 21041413
  3. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, Turner DJ, Hurles ME. Nat Genet. 2010 May;42(5):385-91. PubMedID 20364136
  4. Origins and functional impact of copy number variation in the human genome. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. Nature. 2010 Apr 1;464(7289):704-12. PubMedID 19812545
  5. Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation. Xue Y, Zhang X, Huang N, Daly A, Gillson CJ, Macarthur DG, Yngvadottir B, Nica AC, Woodwark C, Chen Y, Conrad DF, Ayub Q, Mehdi SQ, Li P, Tyler-Smith C. Genetics. 2009 Nov;183(3):1065-77. PubMedID 19737746
  6. Quantification of rare allelic variants from pooled genomic DNA. Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. Nat Methods. 2009 Apr;6(4):263-5. PubMedID 19252504
  7. Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. Chang LW, Payton JE, Yuan W, Ley TJ, Nagarajan R, Stormo GD. Genome Biol. 2008;9(2):R38. PubMedID 18291030