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Items: 1 to 20 of 110

1.

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.

Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB.

J Mol Diagn. 2018 Jan;20(1):4-27. doi: 10.1016/j.jmoldx.2017.11.003. Epub 2017 Nov 21. Review.

PMID:
29154853
2.

Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.

Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN.

J Mol Diagn. 2017 May;19(3):341-365. doi: 10.1016/j.jmoldx.2017.01.011. Epub 2017 Mar 21. Review.

PMID:
28341590
3.

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. 2015 Apr;139(4):481-93. doi: 10.5858/arpa.2014-0250-CP. Epub 2014 Aug 25.

PMID:
25152313
4.

Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment.

Roy S, LaFramboise WA, Nikiforov YE, Nikiforova MN, Routbort MJ, Pfeifer J, Nagarajan R, Carter AB, Pantanowitz L.

Arch Pathol Lab Med. 2016 Sep;140(9):958-75. doi: 10.5858/arpa.2015-0507-RA. Epub 2016 Feb 22. Review.

PMID:
26901284
5.

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.

Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN.

J Mol Diagn. 2017 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002. Review.

6.

Pipeliner: software to evaluate the performance of bioinformatics pipelines for next-generation resequencing.

Nevado B, Perez-Enciso M.

Mol Ecol Resour. 2015 Jan;15(1):99-106. doi: 10.1111/1755-0998.12286. Epub 2014 Jun 28.

PMID:
24890372
7.

Designing and Implementing NGS Tests for Inherited Disorders: A Practical Framework with Step-by-Step Guidance for Clinical Laboratories.

Santani A, Simen BB, Briggs M, Lebo M, Merker JD, Nikiforova M, Vasalos P, Voelkerding K, Pfeifer J, Funke B.

J Mol Diagn. 2019 May;21(3):369-374. doi: 10.1016/j.jmoldx.2018.11.004. Epub 2018 Dec 31. Review.

PMID:
30605766
8.

Next-Generation Sequencing for Infectious Disease Diagnosis and Management: A Report of the Association for Molecular Pathology.

Lefterova MI, Suarez CJ, Banaei N, Pinsky BA.

J Mol Diagn. 2015 Nov;17(6):623-34. doi: 10.1016/j.jmoldx.2015.07.004. Epub 2015 Sep 30. Review.

PMID:
26433313
9.

Multi-Institutional FASTQ File Exchange as a Means of Proficiency Testing for Next-Generation Sequencing Bioinformatics and Variant Interpretation.

Davies KD, Farooqi MS, Gruidl M, Hill CE, Woolworth-Hirschhorn J, Jones H, Jones KL, Magliocco A, Mitui M, O'Neill PH, O'Rourke R, Patel NM, Qin D, Ramos E, Rossi MR, Schneider TM, Smith GH, Zhang L, Park JY, Aisner DL.

J Mol Diagn. 2016 Jul;18(4):572-9. doi: 10.1016/j.jmoldx.2016.03.002. Epub 2016 May 4.

PMID:
27155050
10.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

Kim B, Ali T, Lijeron C, Afgan E, Krampis K.

Gigascience. 2017 Aug 1;6(8):1-7. doi: 10.1093/gigascience/gix048.

11.

Principles of analytical validation of next-generation sequencing based mutational analysis for hematologic neoplasms in a CLIA-certified laboratory.

Kanagal-Shamanna R, Singh RR, Routbort MJ, Patel KP, Medeiros LJ, Luthra R.

Expert Rev Mol Diagn. 2016;16(4):461-72. doi: 10.1586/14737159.2016.1142374. Epub 2016 Feb 15. Review.

PMID:
26765348
12.

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. doi: 10.1309/AJCPR88WDJJLDMBN.

PMID:
26386089
13.

Molecular Pathology Informatics.

Roy S.

Surg Pathol Clin. 2015 Jun;8(2):187-94. doi: 10.1016/j.path.2015.02.013. Epub 2015 Apr 7. Review.

PMID:
26065793
14.

ACMG clinical laboratory standards for next-generation sequencing.

Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, Friez MJ, Funke BH, Hegde MR, Lyon E; Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee.

Genet Med. 2013 Sep;15(9):733-47. doi: 10.1038/gim.2013.92. Epub 2013 Jul 25.

15.

Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus.

Ji H, Enns E, Brumme CJ, Parkin N, Howison M, Lee ER, Capina R, Marinier E, Avila-Rios S, Sandstrom P, Van Domselaar G, Harrigan R, Paredes R, Kantor R, Noguera-Julian M.

J Int AIDS Soc. 2018 Oct;21(10):e25193. doi: 10.1002/jia2.25193.

16.

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL.

Deans ZC, Costa JL, Cree I, Dequeker E, Edsjö A, Henderson S, Hummel M, Ligtenberg MJ, Loddo M, Machado JC, Marchetti A, Marquis K, Mason J, Normanno N, Rouleau E, Schuuring E, Snelson KM, Thunnissen E, Tops B, Williams G, van Krieken H, Hall JA; IQN Path ASBL.

Virchows Arch. 2017 Jan;470(1):5-20. doi: 10.1007/s00428-016-2025-7. Epub 2016 Sep 27. Review.

17.

A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome.

Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA.

BMC Microbiol. 2017 Sep 13;17(1):194. doi: 10.1186/s12866-017-1101-8.

18.

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):420-31. doi: 10.1016/j.cancergen.2013.11.003. Epub 2013 Nov 22. Review.

PMID:
24388712
19.

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform.

Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, Fochler ET, Hill JM, Liem AT, Wiley MR, Ladner JT, Pfeffer BP, Elliot O, Petrosov A, Jima DD, Vallard TG, Melendrez MC, Skowronski E, Quan PL, Lipkin WI, Gibbons HS, Hirschberg DL, Palacios GF, Rosenzweig CN.

BMC Bioinformatics. 2015 Dec 29;16:416. doi: 10.1186/s12859-015-0840-5.

20.

Standards for Clinical Grade Genomic Databases.

Yohe SL, Carter AB, Pfeifer JD, Crawford JM, Cushman-Vokoun A, Caughron S, Leonard DG.

Arch Pathol Lab Med. 2015 Nov;139(11):1400-12. doi: 10.5858/arpa.2014-0568-CP.

PMID:
26516938

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