Current landscape and new paradigms of proficiency testing and external quality assessment for molecular genetics

Archives of Pathology and Laboratory Medicine

Volumn 137, Issue 7, 2013, Pages 983-988

  Kalman, Lisa V ^a   Lubin, Ira M ^a   Barker, Shannon ^a,b   Du Sart, Desiree ^c   Elles, Rob ^d   Grody, Wayne W ^e   Pazzagli, Mario ^f   Richards, Sue ^g   Schrijver, Iris ^h   Zehnbauer, Barbara ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c MURDOCH CHILDREN'S RESEARCH INSTITUTE   (Australia)

^d ST MARY S HOSPITAL   (United Kingdom)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF FLORENCE   (Italy)

^g OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^h STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC DISORDER; GOOD LABORATORY PRACTICE; HEALTH CARE QUALITY; HUMAN; METHODOLOGY; MOLECULAR DIAGNOSIS; MOLECULAR PATHOLOGY; REVIEW; STANDARD;

GENETIC DISEASES, INBORN; HUMANS; LABORATORY PROFICIENCY TESTING; MOLECULAR DIAGNOSTIC TECHNIQUES; PATHOLOGY, MOLECULAR; QUALITY ASSURANCE, HEALTH CARE;

EID: 84879618534     PISSN: 00039985     EISSN: 15432165     Source Type: Journal    
DOI: 10.5858/arpa.2012-0311-RA     Document Type: Review

References (77)

1. National Center for Biotechnology Information. GeneTests. http://www.ncbi.nlm.nih.gov/projects/GeneTests/static/about/data/summary.shtml. Updated March 22, 2012. Accessed May 14, 2012.
2. Dequeker E, Ramsden S, Grody WW, Stenzel TT, Barton DE. Quality control in molecular genetic testing. Nat Rev Genet. 2001;2(9):717-723.
3. International Organization for Standardization. Medical Laboratories - Particular Requirements for Quality And Competence. Geneva, Switzerland: International Organization for Standardization; 2007. Report No.: ISO 15189.
4. Clinical & Laboratory Standards Institute. Quality Management System: A Model for Laboratory Services; Approved Guideline - Fourth Edition. Wayne, PA: Clinical and Laboratory Standards Institute; 2011. Report No.: GP26-A4.
5. American College of Medical Genetics. ACMG Standards & Guidelines for Clinical Genetics Laboratories. http://www.acmg.net/AM/Template.cfm?Section= Laboratory-Standards-and-Guidelines&Template=/CM/HTMLDisplay. cfm&ContentID=6958MD. Accessed May 15, 2012.
6. Clinical and Laboratory Standards Institute. Molecular Diagnostics Methods for Genetic Disease; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2006. Report No.: MM01-A2.
7. New York State Department of Health. Clinical Laboratory Evaluation Program. http://www.wadsworth.org/labcert/clep/clep.html. Accessed May 15, 2012.
8. Department of Health and Human Services Health Care Financing Administration. Clinical Laboratory improvement amendments of 1998 - laboratory requirements. Fed Regist. 1992;57(40):7146. Codified at 42 CFR §493. 2004. http://wwwn.cdc.gov/clia/regs/toc.aspx. Accessed May 15, 2012.
9. Clinical and Laboratory Standards Institute. Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2004. Report No.: MM9-A.
10. Clinical and Laboratory Standards Institute. Diagnostic Nucleic Acid Microarrays; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2006. Report No.: MM12-A.
11. Clinical and Laboratory Standards Institute. Verification and Validation of Multiplex Nucleic Acid Assays; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2008. Report No.: MM17-A.
12. Clinical and Laboratory Standards Institute. Establishing Molecular Testing in Clinical Laboratory Environments; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2011. Report No.: MM19-A.
13. Mattocks CJ, Morris MA, Matthijs G, et al; EuroGentest Validation Group. A standardized framework for the validation and verification of clinical molecular genetic tests. Eur J Hum Genet. 2010;18(12):1276-1288.
14. EuroGentest 2 Coordination Action. Eurogentest Web site: Laboratories. http://www.eurogentest.org/laboratories/. Updated April 17, 2011. Accessed May 14, 2012.
15. Chen B, Gagnon M, Shahangian S, et al Centers for Disease Control and Prevention. Good laboratory practices for molecular genetic testing for heritable diseases and conditions. MMWR Recomm Rep. 2009;58(RR-6):1-35. http://www.cdc.gov/mmwr/pdf/rr/rr5806.pdf. Accessed May 10, 2012.
16. Anderson MW, Schrijver I. Next generation DNA sequencing and the future of genomic medicine. Genes. 2010;1(1):38-69.
17. Kearney HM, South ST, Wolff DJ, et al Working Group of the American College of Medical Genetics. American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet Med. 2011;13(7):676-679.
18. International Organization for Standardization-International Electrotechnical Commission. Conformity Assessment - General Requirements for Proficiency Testing. Geneva, Switzerland: International Organization for Standardization; 2010. ISO/IEC 17043.
19. Clinical and Laboratory Standards Institute. Assessment of Laboratory Tests When Proficiency Testing is Not Available; Approved Guideline. Wayne, PA:. Clinical and Laboratory Standards Institute 2008. Report No.: GP29-A2.
20. McGovern MM, Benach MO, Wallenstein S, Desnick RJ, Keenlyside R. Quality assurance in molecular genetic testing laboratories. JAMA. 1999;281(9): 835-840.
21. McGovern MM, Elles R, Beretta I, et al. Report of an international survey of molecular genetic testing laboratories. Community Genet. 2007;10(3):123-131.
22. College of American Pathologists. CAP Web site: Genetics. http://www.cap.org. Updated July 27, 2012. Accessed May 14, 2012.
23. Hudson KL, Murphy JA, Kaufman DJ, Javitt GH, Katsanis SH, Scott J. Oversight of US genetic testing laboratories. Nat Biotechnol. 2006;24(9):1083-1090.
24. Libeer JC. Role of external quality assurance schemes in assessing and improving quality in medical laboratories. Clin Chim Acta. 2001;309(2):173-177.
25. Ehrmeyer SS, Laessig RH. Has compliance with CLIA requirements really improved quality in US clinical laboratories? Clin Chim Acta. 2004;346(1):37-43.
26. Hofgartner WT, Tait JF. Frequency of problems during clinical moleculargenetic testing. Am J Clin Pathol. 1999;112(1):14-21.
27. Keenlyside RA, Collins CL, Hancock JS, et al. Do proficiency test results correlate with the work performance of screeners who screen Papanicolaou smears? Am J Clin Pathol. 1999;112(6):769-776.
28. LaMotte LC, Guerrant GO, Lewis DS, Hall CT. Comparison of laboratory performance with blind and mail-distributed proficiency testing samples. Public Health Rep. 1977;92(6):554-550.
29. Jenny RW, Jackson KY. Proficiency test performance as a predictor of accuracy of routine patient testing for theophylline. Clin Chem. 1993;39(1):76-81.
30. Howerton D, Krolak JM, Manasterski A, Handsfield JH. Proficiency testing performance in US laboratories: results reported to the Centers for Medicare & Medicaid Services, 1994 through 2006. Arch Pathol Lab Med. 2010;134(5):751-758.
31. Clinical and Laboratory Standards Institute. Proficiency Testing (External Quality Assessment) For Molecular Methods; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2005. Report No.: MM14-A.
32. Clinical and Laboratory Standards Institute. Using Proficiency Testing to Improve the Clinical Laboratory; Approved Guideline. Wayne, PA: Clinical and Laboratory Standards Institute; 2007. Report No.: GP27-A2.
33. Secretary's Advisory Committee on Genetics, Health, and Society.U.S. System of Oversight of Genetic Testing: A Response to the Charge of the Secretary of Health and Human Services. Bethesda, MD: Department of Health & Human Services; 2008. http://oba.od.nih.gov/oba/SACGHS/reports/SACGHS- oversight-report.pdf. Accessed May 10, 2012.
34. National Center for Biotechnology. GeneTests Web site. http://www.ncbi.nlm.nih.gov/sites/GeneTests/. Accessed May 14, 2012.
35. INSERM. Orphanet Web site. http://www.orpha.net/consor/cgi-bin/index.php. Last updated: May 13, 2012. Accessed May 14, 2012.
36. National Center for Biotechnology. Genetic Testing Registry Web site. http://www.ncbi.nlm.nih.gov/gtr/. Accessed May 15, 2012.
37. The Centers for Disease Control and Prevention. Newborn screening quality assurance program Web site. http://www.cdc.gov/labstandards/nsqap.html. Last updated May 9, 2012. Accessed May 14, 2012.
38. European Molecular Genetics Quality Network. The European Molecular Genetics Quality Network Web site. http://www.emqn.org/emqn/Home. Accessed May 14, 2012.
39. CF Network. Cystic Fibrosis European Network Web site. http://cf.eqascheme.org/. Accessed May 14, 2012.
40. The United Kingdom National External Quality Assessment Service Website.http://www.ukneqas.org.uk/content/PageServer.asp?S=99359106&C= 1252&CID=1&type=G. Updated July 6, 2010. Accessed May 14, 2012.
41. EuroGentest. External Quality Assessment. http://www.eurogentest.org/ laboratories/qau/eqa/. Updated November 23, 2011. Accessed May 14, 2012.
42. The Deutsche Vereinte Gesellschaft für Klinische Chemie und Laboratoriumsmedizin e.V. (DGKL) Web site. http://www.dgkl-rfb.de/index-E.shtml. Accessed May 14, 2012.
43. Human Genetics Society of Australasia Molecular Genetics Quality Assurance Program (HGSA MGQAP) Web site. http://www.hgsa.org.au/resources/ quality-assessment/. Updated January 10, 2012. Accessed May 14, 2012.
44. Ramsden SC, Deans Z, Robinson DO, et al. Monitoring standards for molecular genetic testing in the United Kingdom, The Netherlands and Ireland. Genetic Test. 2006;10(3):147-156.
45. Richards CS, Grody WW. Alternative approaches to proficiency testing in molecular genetics. Clin Chem. 2003;49(5):717-718.
46. Organization for Economic Cooperation and Development. OECD Guidelines for Quality Assurance in Molecular Genetic Testing. Paris, France: OECD, 2007:1-38.
47. Bellissimo DB: Practice guidelines and proficiency testing for molecular assays. Transfusion. 2007;47(1)(suppl):79S-84S.
48. Korn K, Reil H, Walter H, Schmidt B. Quality control trial for human immunodeficiency virus type 1 drug resistance testing using clinical samples reveals problems with detecting minority species and interpretation of test results. J. Clin. Microbiol. 2003;41(8):3559-3565.
49. Fae I, Lau M, Voorter C, Mayr WR, Fischer GF. HLA-B*8102, a new allele found in an external proficiency testing scheme. Tissue Antigens. 2004;64(5): 608-610.
50. Longhi E, Frison S, Colombini I, Malagoli A, Crespiatico L, Poli F. HLA-A* 2626, a new allele identified through external proficiency-testing exercise. Tissue Antigens. 2005;66(4):325-326.
51. Perry DJ, Goodeve A, Hill M, Jennings I, Kitchen S, Walker I; UK NEQAS for Blood Coagulation. The UK National External Quality Assessment Scheme (UK NEQAS) for molecular genetic testing in haemophilia. Thromb Haemost. 2006;96(5):597-601.
52. Weck KE, Zehnbauer B, Datto M, Schrijver I; CAP/ACMG Biochemical and Molecular Genetics Resource Committee. Molecular genetic testing for fragile X syndrome: laboratory performance on the College of American Pathologists proficiency surveys (2001-2009). Genet Med. 2012;14(3)306-312. doi:10.1038/gim.2011.11.
53. Palomaki GE, Richards CS. Assessing the analytic validity of molecular testing for Huntington disease using data from an external proficiency testing survey. Genet Med. 2012;14(1):69-75. doi: 10.1038/gim.0b013e3182310bb5.
54. Dequeker E, Cassiman JJ. Evaluation of CFTR gene mutation testing methods in 136 diagnostic laboratories: report of a large European external quality assessment. Eur J Hum Genet. 1998;6(2):165-175.
55. Noll, WW, Belloni, DR, Stenzel T, Grody. WW. Polymorphism in intron 4 of HFE does not compromise haemochromatosis mutation results [correspondence]. Nature Genet. 1999;23(3):271-272. doi:10.1038/15722.
56. Spector EB, Kathryn Kronquist; Fragile X Working Group of the Laboratory Quality Assurance Committee. Technical Standards and Guidelines for Fragile X Testing: A Revision to the Disease-Specific Supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics. Standards and Guidelines for Clinical Genetics Laboratories 2006 Edition. Bethesda, MD: American College of Medical Genetics; 2006. http://www.acmg.net/Pages/ACMG-Activities/stds-2002/fx.htm. Accessed May 14, 2012.
57. Mueller CR, Kristoffersson U, Stoppa-Lyonnet D. External quality assessment for mutation detection in the BRCA1 and BRCA2 genes: EMQN's experience of 3 years. Ann Oncol. 2004; 15(suppl 1): i14-i17. doi:10.1093/annonc/mdh652.
58. Hoeltge FA, Phillips MG, Styer PE, Mockridge P. Detection and correction of systematic laboratory problems by analysis of clustered proficiency testing failures. Arch Pathol Lab Med. 2005;129(2):186-189.
59. Lum G, Tholen DW, Floering DA. The usefulness of calibration verification and linearity surveys in predicting acceptable performance in graded proficiency tests. Arch Pathol Lab Med. 1995;119(5):401-408.
60. Kroll MH, Styer PE, Vasquez DA. Calibration verification performance relates to proficiency testing performance. Arch Pathol Lab Med. 2004;128(5): 544-548.
61. Watson MS, Cutting GR, Desnick RJ, et al. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Genet Med. 2004;6(5):387-391. Erratum Genet Med. 2005;7(4): 286; Genet Med. 2004;6(6):548.
62. Ahmad-Nejad P, Dorn-Beineke A, Pfeiffer U, et al. Methodologic European external quality assurance for DNA sequencing: the EQUALseq program. Clin Chem. 2006;52(4):716-727.
63. Patton SJ, Wallace AJ, Elles R. Benchmark for evaluating the quality of DNA sequencing: proposal from an international external quality assessment scheme. Clin Chem. 2006;52(4):728-736.
64. Raggi CC, Pizani R, Paradiso A, Pazzagli M, Orlando C. External quality assurance program for PCR amplification of genomic DNA: an Italian experience. Clin Chem. 2003;49(5):782-791.
65. Orlando C, Verderio P, Maatmanet R, et al. EQUAL-qual: a European program for external quality assessment of genomic DNA extraction and PCR amplification. Clin Chem. 2007;53(7):1349-1357.
66. Ramsden SC, Daly S, Geilenkeuser WJ, et al. EQUAL-quant: an international external quality assessment scheme for real-time PCR. Clin Chem. 2006;52(8):1584-1591.
67. Dorn-Beineke A, Ahmad-Nejad P, Pfeiffer U, et al. Improvement of technical and analytical performance in DNA sequencing by external quality assessment-based molecular training. Clin Chem. 2006;52(11):2072-2078.
68. Berwouts S, Gordon JT, Rundell CA, Barton DE, Dequeker E. Evaluation and use of a synthetic quality control material included in the European external quality assessment scheme for cystic fibrosis. Hum Mutat. 2008;29(8):1063-1070.
69. Jarvis M, Iyer RK, Williams LO, Noll WW, Thomas K, Grody WW. A novel method for creating artificial mutant samples for performance evaluation and quality control in clinical molecular genetics. J. Mol Diagn. 2005;7(2):247-251.
70. Seneca S, Morris MA, Patton S, Elles R, Sequeiros J. Experience and outcome of 3 years of a European EQA scheme for genetic testing of the spinocerebellar ataxias. Eur J Hum Genet. 2008;16(8):913-920.
71. Falbo V, Floridia G, Tosto F, et al. The Italian external quality assessment scheme for fragile x syndrome: the results of a 5-year survey. Genetic Test. 2008; 12(2):279-288.
72. Taruscio D, Falbo V, Floridia G, et al. Quality assessment in cytogenetic and molecular genetic testing: the experience of the Italian Project on Standardisation and Quality Assurance. Clin Chem Lab Med. 2004;42(8):915-921.
73. Tosto F, Salvatore M, Falbo V, et al. The Italian scheme of external quality assessment for b-thalassemia: genotyping and reporting results and testing strategies in a 5-year survey. Genet Test Mol Biomarkers. 2009;13(1):31-36.
74. Hertzberg M, Neville S, McDonald D. External quality assurance of molecular analysis of haemochromatosis gene mutations. J Clin Pathol. 2006; 59(7):744-747.
75. Brothman AR, Dolan MM, Goodman BK, et al. College of American Pathologists/American College of Medical Genetics proficiency testing for constitutional cytogenomic microarray analysis. Genet Med. 2011;13(9):765-769.
76. Birch L, English CA, Burns M, Keer JT. Generic scheme for independent performance assessment in the molecular biology laboratory. Clin Chem. 2004; 50(9):1553-1559.
77. Raggi CC, Verderi P, Pazzagli M, et al. An Italian program of external quality control for quantitative assays based on real-time PCR with Taq-Mane probes. Clin Chem Lab Med. 2005;43(5):542-548.