Standardization and quality management in next-generation sequencing.
DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.
Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
Christoph
C
Endrullat
Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
Jörn
J
Glökler
Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
Philipp
P
Franke
Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
Marcus
M
Frohme
ABRF, Association of Biomolecular Resource Facilities; BAM, binary alignment/map; CAP, College of American Pathologist's; CEN, European Committee for Standardization; CLIA, Clinical Laboratory Improvement Amendments; Data quality; ERCC, External RNA Controls Consortium; FDA, Food and Drug Administration; FFPE, formalin-fixed, paraffin-embedded; FMEA, failure mode and effects analysis; GATK, genome analysis toolkit; GSC, Genomic Standards Consortium; Guideline; HGP, Human Genome Project; Indel, insertion or deletion; MAQC, MicroArray Quality Control Project; MIGS, minimum information about a genome sequence; MOL, molecular pathology checklist; NGS, next-generation sequencing; NIST, National Institute of Standards and Technology; NTC, no-template control; Nex-StoCT, next generation sequencing — standardization of clinical testing; Next-generation sequencing; PT, proficiency testing; QA, quality assurance; QC, quality control; QM, quality management; QMS, quality management system; Quality management; RIN, RNA integrity number; SAM, sequence alignment/map; SEQC, sequencing quality control; SNP, single nucleotide polymorphism; SOP, standard operating procedure; Standardization; TN, technical note; VCF, variant call format; Validation; ddPCR, digital droplet PCR; mtDNA, mitochondrial DNA; qPCR, quantitative PCR
Cancer Gene Ther. 2015 Sep;22(9):417-30
26358176
Am J Clin Pathol. 2011 Oct;136(4):527-39
21917674
Genome Res. 2008 May;18(5):763-70
18212088
Nucleic Acids Res. 2007;35(18):6227-37
17855400
Genome Res. 2011 Sep;21(9):1543-51
21816910
PLoS One. 2016 Feb 22;11(2):e0149743
26901863
Genomics. 2008 Nov;92(5):255-64
18703132
J Mol Diagn. 2008 Nov;10(6):484-92
18832462
Nat Biotechnol. 2014 Sep;32(9):903-14
25150838
Nat Rev Genet. 2010 Jan;11(1):31-46
19997069
PLoS One. 2013 Jul 26;8(7):e69604
23922754
Nat Biotechnol. 2006 Sep;24(9):1151-61
16964229
PLoS One. 2014 Mar 20;9(3):e92192
24651575
PLoS One. 2013;8(4):e60234
23565205
PLoS One. 2013 Jun 06;8(6):e62692
23762227
Genome Res. 2010 Sep;20(9):1297-303
20644199
Nat Biotechnol. 2008 May;26(5):541-7
18464787
PLoS One. 2011 Apr 27;6(4):e19119
21589638
Bioinformatics. 2009 Aug 15;25(16):2078-9
19505943
Clin Biochem Rev. 2011 Nov;32(4):177-95
22147957
J Mol Diagn. 2010 Jul;12 (4):425-32
20431034
J Appl Genet. 2011 Nov;52(4):413-35
21698376
Arch Pathol Lab Med. 2015 Apr;139(4):481-93
25152313
Appl Environ Microbiol. 2010 Nov;76(21):7310-3
20833781
Genet Med. 2013 Sep;15(9):733-47
23887774
Bioinformatics. 2011 Aug 1;27(15):2156-8
21653522
Nat Biotechnol. 2012 Nov;30(11):1033-6
23138292
Genet Mol Res. 2008 Sep 23;7(3):861-71
18949705
BMC Bioinformatics. 2016 Feb 03;17 :58
26842848
BMC Mol Biol. 2006 Jan 31;7:3
16448564
Nat Methods. 2008 Jan;5(1):16-8
18165802
PLoS One. 2012;7(2):e30619
22312429
Nat Methods. 2005 Oct;2(10):731-4
16179916
J Invest Dermatol. 2013 Aug;133(8):e11
23856935
Am J Clin Pathol. 2006 Mar;125(3):343-54
16613337
Sci Rep. 2016 Apr 06;6:24067
27048884
Cancers (Basel). 2014 Nov 18;6(4):2296-312
25412366
Nucleic Acids Res. 2010 Apr;38(6):1767-71
20015970
Nature. 2004 May 27;429(6990):365-8
15164052
Nat Rev Genet. 2013 Oct;14(10):681-91
23999272
Forensic Sci Int Genet. 2013 Sep;7(5):543-9
23948325
Trends Genet. 2015 Feb;31(2):61-6
25579994
Science. 2009 Oct 9;326(5950):236-7
19815760
Brief Bioinform. 2011 Sep;12(5):489-97
21245079
Biotechniques. 2014 Feb 01;56(2):61-4, 66, 68, passim
24502796