Considerations for the development of a reference method for sequencing of haploid DNA -an opinion paper on behalf of the IFCC committee on molecular diagnostics

Clinical Chemistry and Laboratory Medicine

Volumn 47, Issue 11, 2009, Pages 1343-1350

  Rousseau, Francois ^a   Gancberg, David ^b   Schimmel, Heinz ^c   Neumaier, Michael ^d   Bureau, Alexandre ^a   Mamotte, Cyril ^e   Van Schaik, Ron ^f   Payne, Deborah ^g   Pazzagli, Mario ^h   Young, Ian ⁱ  

^a UNIVERSITÉ LAVAL   (Canada)

^b EUROPEAN COMMISSION   (Belgium)

^c JOINT RESEARCH CENTRE   (Italy)

^d Institute for Clinical Chemistry   (Germany)

^e CURTIN UNIVERSITY   (Australia)

^f ERASMUS MEDICAL CENTER   (Netherlands)

^g UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^h UNIVERSITY OF FLORENCE   (Italy)

ⁱ WELLCOME RESEARCH LABORATORIES   (United Kingdom)

Author keywords

DNA sequencing; Nucleic acids; Position paper; Reference method

Indexed keywords

DNA;

DNA SEQUENCE; HAPLOIDY; NOTE; PRIORITY JOURNAL; QUALITY CONTROL; REFERENCE VALUE;

ADVISORY COMMITTEES; CHEMISTRY, CLINICAL; CLINICAL LABORATORY TECHNIQUES; HAPLOIDY; HUMANS; INTERNATIONAL COOPERATION; MOLECULAR DIAGNOSTIC TECHNIQUES; REFERENCE STANDARDS; SEQUENCE ANALYSIS, DNA;

EID: 73349101866     PISSN: 14346621     EISSN: 14374331     Source Type: Journal    
DOI: 10.1515/CCLM.2009.319     Document Type: Note

References (27)

1. NCCLS. Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine; Approved Guideline. NCCLS document MM9-A [ISBN 1-56238-558-5]. NCCLS, 940 West Valley Road, Suite 1400, Wayne, Pennsylvania 19087-21898 USA, 2004.
2. American College of Medical Genetics; Standards and Guidelines for Clinical Genetics Laboratories; revised 02/ 2007 (http://www.acmg.net/AM/ Template.cfm?SectionsLaboratory-Standards-and-Guidelines&Templates/CM/ HTMLDisplay.cfm&ContentIDs3735).
3. CMGS guidelines, 2003 retired 2007.
4. College of American Pathologists. Checklist for Molecular Pathology. Chicago, IL.
5. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual, vol.1,2,3. New York: Cold Spring Harbor Laboratory Press, 1989.
6. ISO/IEC Guide 99:2007. International Vocabulary of Metrology - Basic and general concepts and associated terms (VIM). Geneva: International Organization for Standardization; 2007.
7. ISO/IEC 15193: 2002. In vitro diagnostic medical devices - measurement of quantities in samples of biological origin - presentation of reference measurement procedures. Int Org Standardization 2002.
8. Broothaerts W, Corbisier P, Emons H, Emteborg H, Linsinger TP, Trapmann S. Development of a certified reference material for genetically modified potato with altered starch composition. J Agric Food Chem 2007; 55:4728-4734
9. Orlando C, Verderio P, Maatman R, Danneberg J, Ramsden S, Neumaier M, et al. EQUAL-qual: a European program for external quality assessment of genomic DNA extraction and PCR amplification. Clin Chem 2007;53: 1349-1357
10. Wilfinger WW, Mackey K, Chomczynski P. Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechniques 1997;22:474-6, 478-481
11. Sahota A, Brooks AI, Tischfield JA. Preparing DNA from saliva for genotyping. Cold Spring Harb. Protoc., 2007. doi:10.1101/pdb.prot4831.
12. Kontanis EJ, Reed FA. Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors. J Forensic Sci 2006;51:795-804.
13. Eurachem Guide 1998: The fitness for purpose of analytical methods: a laboratory guide to method validation and related analysis. http://www.eurachem. org/guides/valid.pdf.
14. Ahmad-Nejad P, Dorn-Beineke A, Pfeiffer U, Brade J, Geilenkeuser WJ, Ramsden S, et al. Methodologic European external quality assurance for DNA sequencing: the EQUALseq program. Clin Chem 2006;52:716-727
15. 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;52:728-736
16. Rå dström P, Knutsson R, Wolffs P, Lövenklev M, Löfstro ̈m C. Pre-PCR processing: strategies to generate PCR-compatible samples. Mol Biotechnol 2004;26:133-146
17. Robertson JM, Walsh-Weller J. An introduction to PCR primer design and optimization of amplification reactions. Methods Mol Biol 1998;98:121-154
18. Grunenwald H. Optimization of polymerase chain reactions. Methods Mol Biol 2003;226:89-100.
19. Ewing B, Hillier L, Wendl M, Green P. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 1998;8:175-185
20. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998;8:186-194
21. ISO/IEC 17025:2005 General requirements for the competence of testing and calibration laboratories. Int Org Standardization, 2005.
22. Neumaier M, Gerhard M, Wagener C. Diagnosis of micrometastases by the amplification of tissue-specific genes. Gene 1995;159:43-47
23. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008;18:1851-1858
24. Ten Bosch JR, Grody WW. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diag 2008;6:484-492
25. Schuster SC. Next-generation sequencing transforms today's biology. Nature Methods 2008;5:16-18
26. Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet 2006;38:375-381
27. Ross SM. A first course in probability, 8th ed. Upper Saddle River. NJ: Pearson Prentice Hall, 2008.