Systematic evaluation of sanger validation of next-generation sequencing variants

Clinical Chemistry

Volumn 62, Issue 4, 2016, Pages 647-654

  Beck, Tyler F ^a   Mullikin, James C ^a,b   Biesecker, Leslie G ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTROLLED STUDY; EXOME; HUMAN; MAJOR CLINICAL STUDY; NEXT GENERATION SEQUENCING; VALIDATION PROCESS; ANIMAL; BLOOD; DNA SEQUENCE; GENETIC VARIATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; STANDARDS; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA;

DNA;

ANIMALS; DNA; GENETIC VARIATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, STATISTICAL; SEQUENCE ANALYSIS, DNA;

EID: 84962374976     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2015.249623     Document Type: Article

References (29)

1. de Souza F. EmTech: Illumina says 228,000 human genomes will be sequenced this year. MIT Technology Review. http://www.technologyreview.com/news/531091/emtech-illumina-says-228000-human-genomes-will-be-sequenced-this-year/ (Accessed July 2015).
2. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977;74:5463-7.
3. Sikkema-Raddatz B, Johansson LF, de Boer EN, Almomani R, Boven LG, van den Berg MP, et al. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Hum Mutat 2013;34: 1035-42.
4. McCourt CM, McArt DG, Mills K, Catherwood MA, Maxwell P, Waugh DJ, et al. Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS ONE 2013;8:e69604.
5. Strom SP, Lee H, Das K, Vilain E, Nelson SF, Grody WW, Deignan JL. Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory. Genet Med 2014;16: 510-5.
6. Baudhuin LM, Lagerstedt SA, Klee EW, Fadra N, Oglesbee D, Ferber MJ. Confirming variants in next-generation sequencing panel testing by Sanger sequencing. J Mol Diagn 2015;17:456-61.
7. Biesecker LG, Mullikin JC, Facio FM, Turner C, Cherukuri PF, Blakesley RW, et al. The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine. Genome Res 2009;19:1665-74.
8. Johnston JJ, Teer JK, Cherukuri PF, Hansen NF, Loftus SK; NIH Intramural Sequencing Center (NISC), et al. Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. Am J Hum Genet 2010; 86:743-8.
9. Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, et al. Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am J Hum Genet 2012;91:97-108.
10. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, et al. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 2010;20:1420-31.
11. Chines PS, Swift AJ, Bonnycastle LL, Erdos M, Mullikin JC; NIH Intramural Sequencing Center, et al. PrimerTile: designing overlapping PCR primers for resequencing. Am J Hum Genet 2005;77:A1257.
12. Gordon D, Green P. Consed: agraphical editor for next-generation sequencing. Bioinformatics 2013;29: 2936-7.
13. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res 2012;40:e115.
14. Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinforma Oxf Engl 2007;23:1289-91.
15. 2 from contingency tables, and the calculation of P. J R Stat Soc 1922:85:87-94. Available from: https://digital.library.adelaide.edu.au/dspace/handle/2440/15173 (Accessed December 2015).
16. Jaccard P. The distribution of the Flora in the Alpine Zone.1. New Phytol 1912;11:37-50.
17. Brown LD, Cai TT, DasGupta A. Interval estimation for a binomial proportion. Stat Sci 2001;16:101-33.
18. Leinonen R, Sugawara H, Shumway M. The sequence read archive. Nucleic Acids Res 2011;39:D19-21.
19. Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, et al. Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. Am J Hum Genet 2015;96:913-25.
20. Sen SK, Boelte KC, Barb JJ, Joehanes R, Zhao X, Cheng Q, et al. Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification. Am J Hum Genet 2014;95:66-76.
21. Pierson TM, Yuan H, Marsh ED, Fuentes-Fajardo K, Adams DR, Markello T, et al. GRIN2A mutation and early-onset epileptic encephalopathy: personalized therapy with memantine. Ann Clin Transl Neurol 2014;1: 190-8.
22. Yuan H, Hansen KB, Zhang J, Pierson TM, Markello TC, Fajardo KVF, et al. Functional analysis of a de novo GRIN2A missense mutation associated with early-onset epileptic encephalopathy. Nat Commun 2014;5:3251.
23. Gonsalves SG, Ng D, Johnston JJ, Teer JK, Stenson PD, Cooper DN, et al. Using exome data to identify malignant hyperthermia susceptibility mutations. Anesthesiology 2013;119:1043-53.
24. Gartner JJ, Parker SCJ, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A 2013;110: 13481-6.
25. Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, et al. Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet 2013; 6:337-46.
26. Le Gallo M, O'Hara AJ, Rudd ML, Urick ME, Hansen NF, O'Neil NJ, et al. Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiq-uitin ligase complex genes. Nat Genet 2012;44: 1310-5.
27. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of inci-dental findings in clinical exome and genome sequencing. Genet Med 2013;15:565-74.
28. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browserat UCSC. Genome Res 2002;12:996-1006.
29. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database ofgenomes, transcripts and proteins. Nucleic Acids Res 2007;35:D61-5.