Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  de Leeneer, Kim ^a   de Schrijver, Joachim ^b   Clement, Lieven ^b   Baetens, Machteld ^a   Lefever, Steve ^a   de Keulenaer, Sarah ^b   van Criekinge, Wim ^b   Deforce, Dieter ^b   van Nieuwerburgh, Filip ^b   Bekaert, Sofie ^b   Pattyn, Filip ^a   de Wilde, Bram ^a   Coucke, Paul ^a,b   Vandesompele, Jo ^a,b   Claes, Kathleen ^a   Hellemans, Jan ^a,b  

^a GHENT UNIVERSITY HOSPITAL   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; CDH23 GENE; CONGENITAL DEAFNESS; CONTROLLED STUDY; DATA ANALYSIS; ESPN GENE; ESRRB GENE; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FBN1 GENE; GENE; GENE FREQUENCY; GENETIC SCREENING; GENETIC VARIABILITY; GJB2 GENE; HETEROZYGOSITY; HUMAN; MASSIVE PARALLEL PYROSEQUENCING; MATHEMATICAL COMPUTING; MYO15A GENE; MYO7A GENE; ONCOGENE; OTOF GENE; PCDH15 GENE; PJVK GENE; POLYMERASE CHAIN REACTION; PYROSEQUENCING; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SLC26A4 GENE; TECTA GENE; TGFBR1 GENE; TGFBR2 GENE; TMC1 GENE; TMIE GENE; TMPRSS3 GENE; TRIOBP GENE; HIGH THROUGHPUT SEQUENCING; INSTRUMENTATION; LABORATORY DIAGNOSIS; METHODOLOGY; MOLECULAR PATHOLOGY; NUCLEOTIDE SEQUENCE;

DNA MUTATIONAL ANALYSIS; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PATHOLOGY, MOLECULAR; POLYMERASE CHAIN REACTION; QUALITY CONTROL;

EID: 80053590678     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025531     Document Type: Article

References (18)

1. Chou LS, Lyon E, Wittwer CT, (2005) A comparison of high-resolution melting analysis with denaturing high-performance liquid chromatography for mutation scanning: cystic fibrosis transmembrane conductance regulator gene as a model. American journal of clinical pathology 124: 330-338.
2. De Leeneer K, Coene I, Poppe B, De Paepe A, Claes K, (2009) Genotyping of frequent BRCA1/2 SNPs with unlabeled probes: a supplement to HRMCA mutation scanning, allowing the strong reduction of sequencing burden. The Journal of molecular diagnostics: JMD 11: 415-419.
3. Wittwer CT, (2009) High-resolution DNA melting analysis: advancements and limitations. Human mutation 30: 857-859.
4. De Leeneer K, Coene I, Poppe B, De Paepe A, Claes K, (2008) Rapid and sensitive detection of BRCA1/2 mutations in a diagnostic setting: comparison of two high-resolution melting platforms. Clinical chemistry 54: 982-989.
5. Sanger F, Coulson AR, (1975) A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of molecular biology 94: 441-448.
6. Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nature biotechnology 26: 1135-1145.
7. Shendure JA, Porreca GJ, Church GM, (2008) Overview of DNA sequencing strategies. Current protocols in molecular biology/edited by Frederick M Ausubel [et al] Chapter 7: Unit 7 1.
8. De Leeneer K, Hellemans J, De Schrijver J, Baetens M, Poppe B, et al. (2011) Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations. Human mutation 32: 335-344.
9. Baetens M, Van Laer L, De Leeneer K, Hellemans J, De Schrijver J, et al. (2011) Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes. Human mutation 32: 1053-1062.
10. De Schrijver JM, De Leeneer K, Lefever S, Sabbe N, Pattyn F, et al. (2010) Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC bioinformatics 11: 269.
11. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nature methods 5: 887-893.
12. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
13. Harismendy O, Frazer K, (2009) Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. BioTechniques 46: 229-231.
14. Quinlan AR, Stewart DA, Stromberg MP, Marth GT, (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nature methods 5: 179-181.
15. Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4: 903-905.
16. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, et al. (2010) Target-enrichment strategies for next-generation sequencing. Nature methods 7: 111-118.
17. Carr IM, Morgan JE, Diggle CP, Sheridan E, Markham AF, et al. (2011) Illuminator, a desktop program for mutation detection using short-read clonal sequencing. Genomics (In press).
18. Morgan JE, Carr IM, Sheridan E, Chu CE, Hayward B, et al. (2010) Genetic diagnosis of familial breast cancer using clonal sequencing. Human mutation 31: 484-491.