Considerations for standardizing predictive molecular pathology for cancer prognosis

References

• Available from: https://wwwn.cdc.gov/clia/
   Google Scholar
• Available from: https://www.iso.org/obp/ui/#iso:std:iso:15189:ed-3:v2:en
   Google Scholar
• Available from: http://ukgtn.nhs.uk/
   Google Scholar
• Volmar KE, Idowu MO, Souers RJ, et al. Molecular testing in anatomic pathology and adherence to guidelines: a College of American pathologists Q-Probes study of 2230 testing events reported by 26 Institutions. Arch Pathol Lab Med. 2015 Sep;139(9):1115–1124.
   PubMed Web of Science ®Google Scholar
• Cree IA, Deans Z, Ligtenberg MJ, et al. European society of pathology task force on quality assurance in molecular pathology; Royal College of pathologists. Guidance for laboratories performing molecular pathology for cancer patients. J Clin Pathol. 2014 Nov;67(11):923–931.
   PubMed Web of Science ®Google Scholar
• Altimari A, de Biase D, De Maglio G, et al. 454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples. Onco Targets Ther. 2013 Aug 5;6:1057–1064.
   PubMed Web of Science ®Google Scholar
• Aslanzadeh J. Preventing PCR amplification carryover contamination in a clinical laboratory. Ann Clin Lab Sci. 2004 Autumn;34(4):389–396.
   PubMed Web of Science ®Google Scholar
• Platt E, Sommer P, McDonald L, et al. Tissue floaters and contaminants in the histology laboratory. Arch Pathol Lab Med. 2009 Jun;133(6):973–978.
   PubMed Web of Science ®Google Scholar
• Bass BP, Engel KB, Greytak SR, et al. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen? Arch Pathol Lab Med. 2014 Nov;138(11):1520–1530.
   PubMed Web of Science ®Google Scholar
• Howat WJ, Wilson BA. Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods. 2014 Nov;70(1):12–19.
   PubMed Web of Science ®Google Scholar
• Chen H, Luthra R, Goswami RS, et al. Analysis of pre-analytic factors affecting the success of clinical next-generation sequencing of solid organ malignancies. Cancers (Basel). 2015 Aug 28;7(3):1699–1715.
   PubMedGoogle Scholar
• Schrijver WA, van der Groep P, Hoefnagel LD, et al. Influence of decalcification procedures on immunohistochemistry and molecular pathology in breast cancer. Mod Pathol. 2016 Dec;29(12):1460–1470.
   PubMedGoogle Scholar
• Srinivasyaiah A, Nitin P, Hegde U. Comparison of microwave versus conventional decalcification of teeth using three different decalcifying solutions. J Lab Physicians. 2016 Jul-Dec;8(2):106–111.
   PubMedGoogle Scholar
• Do H, Dobrovic A. Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization. Clin Chem. 2015 Jan;61(1):64–71.
   PubMed Web of Science ®Google Scholar
• Lou JJ, Mirsadraei L, Sanchez DE, et al. A review of room temperature storage of biospecimen tissue and nucleic acids for anatomic pathology laboratories and biorepositories. Clin Biochem. 2014 Mar;47(4–5):267–273.
   PubMed Web of Science ®Google Scholar
• Nakayama Y, Yamaguchi H, Einaga N, et al. Pitfalls of DNA quantification using DNA-binding fluorescent dyes and suggested solutions. Plos One. 2016 Mar 3;11(3):e0150528.
   Web of Science ®Google Scholar
• Cheng L, Zhang S, MacLennan GT, et al. Laser-assisted microdissection in translational research: theory, technical considerations, and future applications. Appl Immunohistochem Mol Morphol. 2013 Jan;21(1):31–47.
   PubMedGoogle Scholar
• Loghavi S, Routbort MJ, Patel KP, et al. How do we make clinical molecular testing for cancer standard of care for pathology departments? J Natl Compr Canc Netw. 2016 Jun;14(6):787–792.
   PubMed Web of Science ®Google Scholar
• Hicks DG, Whitney-Miller CL. The evolving role of HER2 evaluation for diagnosis and clinical decision making for breast and gastric adenocarcinoma. Biotech Histochem. 2013 May;88(3–4):121–131.
   PubMed Web of Science ®Google Scholar
• Hiley CT, Le Quesne J, Santis G, et al. Challenges in molecular testing in non-small-cell lung cancer patients with advanced disease. Lancet. 2016 Sep 3;388(10048):1002–1011.
   PubMed Web of Science ®Google Scholar
• Alix-Panabières C, Pantel K. Clinical applications of circulating tumor cells and circulating tumor DNA as liquid biopsy. Cancer Discov. 2016 May;6(5):479–491.
   PubMed Web of Science ®Google Scholar
• Heitzer E, Ulz P, Geigl JB. Circulating tumor DNA as a liquid biopsy for cancer. Clin Chem. 2015 Jan;61(1):112–123.
   PubMed Web of Science ®Google Scholar
• Seekhuntod S, Thavarungkul P, Chaichanawongsaroj N. Validation of a multiplex allele-specific polymerase chain reaction assay for detection of KRAS gene mutations in formalin-fixed, paraffin-embedded tissues from colorectal cancer patients. Plos One. 2016 Jan 26;11(1):e0147672.
   Google Scholar
• Barbano R, Pasculli B, Coco M, et al. Competitive allele-specific TaqMan PCR (Cast-PCR) is a sensitive, specific and fast method for BRAF V600 mutation detection in Melanoma patients. Sci Rep. 2015 Dec 22;5:18592.
   PubMed Web of Science ®Google Scholar
• Nguyen A, Legrain M, Noel G, et al. An innovative fluorescent semi-quantitative methylation-specific PCR method for the determination of MGMT promoter methylation is reflecting intra-tumor heterogeneity. Curr Cancer Drug Targets. 2015;15(7):624–640.
   PubMed Web of Science ®Google Scholar
• Weber B, Meldgaard P, Hager H, et al. Detection of EGFR mutations in plasma and biopsies from non-small cell lung cancer patients by allele-specific PCR assays. BMC Cancer. 2014 Apr 28;14:294.
   PubMed Web of Science ®Google Scholar
• Beau-Faller M, Blons H, Domerg C, et al. A multicenter blinded study evaluating EGFR and KRAS mutation testing methods in the clinical non-small cell lung cancer setting–IFCT/ERMETIC2 project part 1: comparison of testing methods in 20 French molecular genetic National Cancer Institute platforms. J Mol Diagn. 2014 Jan;16(1):45–55.
   PubMed Web of Science ®Google Scholar
• Harrington CT, Lin EI, Olson MT, et al. Fundamentals of pyrosequencing. Arch Pathol Lab Med. 2013 Sep;137(9):1296–1303.
   PubMed Web of Science ®Google Scholar
• Kriegsmann J, Kriegsmann M, Casadonte R. MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review). Int J Oncol. 2015 Mar;46(3):893–906.
   PubMed Web of Science ®Google Scholar
• Kriegsmann M, Arens N, Endris V, et al. Detection of KRAS, NRAS and BRAF by mass spectrometry - a sensitive, reliable, fast and cost-effective technique. Diagn Pathol. 2015 Jul;30(10):132.
   Web of Science ®Google Scholar
• Paolillo C, Londin E, Fortina P. Next generation sequencing in cancer: opportunities and challenges for precision cancer medicine. Scand J Clin Lab Invest Suppl. 2016;245:S84–S91.
   Google Scholar
• Schenkel LC, Kerkhof J, Stuart A, et al. Clinical next-generation sequencing pipeline outperforms a combined approach using sanger sequencing and multiplex ligation-dependent probe amplification in targeted gene panel analysis. J Mol Diagn. 2016 Sep;18(5):657–667.
   PubMed Web of Science ®Google Scholar
• Gao J, Wu H, Shi X, et al. Comparison of next-generation sequencing, quantitative PCR, and sanger sequencing for mutation profiling of EGFR, KRAS, PIK3CA and BRAF in clinical lung tumors. Clin Lab. 2016;62(4):689–696.
   PubMed Web of Science ®Google Scholar
• Hinrichs JW, van Blokland WT, Moons MJ, et al. Comparison of next-generation sequencing and mutation-specific platforms in clinical practice. Am J Clin Pathol. 2015 Apr;143(4):573–578.
   PubMed Web of Science ®Google Scholar
• Prichard JW. Overview of automated immunohistochemistry. Arch Pathol Lab Med. 2014 Dec;138(12):1578–1582.
   PubMed Web of Science ®Google Scholar
• Sholl LM. Protein correlates of molecular alterations in lung adenocarcinoma: immunohistochemistry as a surrogate for molecular analysis. Semin Diagn Pathol. 2015 Sep;32(5):325–333.
   PubMed Web of Science ®Google Scholar
• Bubendorf L, Büttner R, Al-Dayel F, et al. Testing for ROS1 in non-small cell lung cancer: a review with recommendations. Virchows Arch. 2016 Aug 17;469:489–503.
   PubMed Web of Science ®Google Scholar
• Falzarano SM, Magi-Galluzzi C. ERG protein expression as a biomarker of prostate cancer. Biomark Med. 2013 Dec;7(6):851–865.
   PubMed Web of Science ®Google Scholar
• Mahajan A. Practical issues in the application of p16 immunohistochemistry in diagnostic pathology. Hum Pathol. 2016 May;51:64–74.
   PubMed Web of Science ®Google Scholar
• Fiore C, Bailey D, Conlon N, et al. Utility of multispectral imaging in automated quantitative scoring of immunohistochemistry. J Clin Pathol. 2012 Jun;65(6):496–502.
   PubMed Web of Science ®Google Scholar
• Polley MY, Leung SC, Gao D, et al. An international study to increase concordance in Ki67 scoring. Mod Pathol. 2015 Jun;28(6):778–786.
   PubMed Web of Science ®Google Scholar
• Singh S, Hallet J, Rowsell C, et al. Variability of Ki67 labeling index in multiple neuroendocrine tumors specimens over the course of the disease. Eur J Surg Oncol. 2014 Nov;40(11):1517–1522.
   PubMed Web of Science ®Google Scholar
• Polley MY, Leung SC, McShane LM, et al. International Ki67 in Breast Cancer Working Group of the Breast International Group and North American Breast Cancer Group. An international Ki67 reproducibility study. J Natl Cancer Inst. 2013 Dec 18;105(24):1897–1906.
   PubMedGoogle Scholar
• Endrullat C, Glökler J, Franke P, et al. Standardization and quality management in next-generation sequencing. Appl Transl Genom. 2016 Jul;1(10):2–9.
   Web of Science ®Google Scholar
• Long-Mira E, Washetine K, Hofman P. Sense and nonsense in the process of accreditation of a pathology laboratory. Virchows Arch. 2016 Jan;468(1):43–49.
   PubMed Web of Science ®Google Scholar
• Elliott K, McQuaid S, Salto-Tellez M, et al. Immunohistochemistry should undergo robust validation equivalent to that of molecular diagnostics. J Clin Pathol. 2015 Oct;68(10):766–770.
   PubMed Web of Science ®Google Scholar
• Petersen I, Blind C, Koepenik A, et al. iCon-TMA for control and quantitation of immunohistochemistry and in situ molecular pathology analysis. Pathol Res Pract. 2007;203(8):629–631.
   PubMed Web of Science ®Google Scholar
• Rakha EA, Pinder SE, Bartlett JM, et al. National coordinating committee for breast pathology. Updated UK recommendations for HER2 assessment in breast cancer. J Clin Pathol. 2015 Feb;68(2):93–99.
   PubMed Web of Science ®Google Scholar
• Lyon E, Schrijver I, Weck KE, et al. CAP/ACMG biochemical and molecular genetics committee. Molecular genetic testing for cystic fibrosis: laboratory performance on the College of American Pathologists external proficiency surveys. Genet Med. 2015 Mar;17(3):219–225.
   PubMed Web of Science ®Google Scholar
• Marchetti A, Barberis M, Papotti M, et al. ALK rearrangement testing by FISH analysis in non-small-cell lung cancer patients: results of the first italian external quality assurance scheme. J Thorac Oncol. 2014 Oct;9(10):1470–1476.
   PubMed Web of Science ®Google Scholar
• Normanno N, Pinto C, Castiglione F, et al. The Italian external quality assessment for RAS testing in colorectal carcinoma identifies methods-related inter-laboratory differences. J Transl Med. 2015 Sep;3(13):287.
   Web of Science ®Google Scholar
• Patton S, Normanno N, Blackhall F, et al. Assessing standardization of molecular testing for non-small-cell lung cancer: results of a worldwide external quality assessment (EQA) scheme for EGFR mutation testing. Br J Cancer. 2014 Jul 15;111(2):413–420.
   PubMed Web of Science ®Google Scholar
• Aumann K, Niermann K, Asberger J, et al. Structured reporting ensures complete content and quick detection of essential data in pathology reports of oncological breast resection specimens. Breast Cancer Res Treat. 2016 Apr;156(3):495–500.
   PubMed Web of Science ®Google Scholar
• Słodkowska J, Cierniak S, Patera J, et al. Functional assessment of synoptic pathology reporting for ovarian cancer. Pathobiology. 2016;83(2–3):70–78.
   PubMed Web of Science ®Google Scholar
• Ellis DW, Srigley J. Does standardised structured reporting contribute to quality in diagnostic pathology? The importance of evidence-based datasets. Virchows Arch. 2016 Jan;468(1):51–59.
   PubMed Web of Science ®Google Scholar
• Haroske G, Schrader T. A reference model based interface terminology for generic observations in anatomic pathology structured reports. Diagn Pathol. 2014;9(Suppl 1):S4.
   Google Scholar
• Simpson RW, Berman MA, Foulis PR, et al. Cancer biomarkers: the role of structured data reporting. Arch Pathol Lab Med. 2015 May;139(5):587–593.
   PubMed Web of Science ®Google Scholar
• Kench JG, Delahunt B, Griffiths DF, et al. Dataset for reporting of prostate carcinoma in radical prostatectomy specimens: recommendations from the international collaboration on cancer reporting. Histopathology. 2013 Jan;62(2):203–218.
   PubMed Web of Science ®Google Scholar
• Casati B, Bjugn R. Structured electronic template for histopathology reporting on colorectal carcinoma resections: five-year follow-up shows sustainable long-term quality improvement. Arch Pathol Lab Med. 2012 Jun;136(6):652–656.
   PubMed Web of Science ®Google Scholar
• Lewis C, McQuaid S, Hamilton PW, et al. Building a ‘repository of science’: the importance of integrating biobanks within molecular pathology programmes. Eur J Cancer. 2016 Sep 23;67:191–199.
   PubMed Web of Science ®Google Scholar