Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Rieber, Nora ^a   Zapatka, Marc ^a   Lasitschka, Bärbel ^a   Jones, David ^a   Northcott, Paul ^b   Hutter, Barbara ^a   Jäger, Natalie ^a   Kool, Marcel ^a   Taylor, Michael ^b,c   Lichter, Peter ^a   Pfister, Stefan ^a,d   Wolf, Stephan ^a   Brors, Benedikt ^a   Eils, Roland ^a,e  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

^d UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^e UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ANALYTICAL EQUIPMENT; ARTICLE; CASE REPORT; CONTROLLED STUDY; CPG ISLAND; DIAGNOSTIC TEST ACCURACY STUDY; FALSE POSITIVE RESULT; FEMALE; GC RICH SEQUENCE; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC VARIABILITY; GENOMICS; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; MALE; MEDULLOBLASTOMA; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; SINGLE NUCLEOTIDE VARIANT; WHOLE GENOME SEQUENCING;

ANIMALS; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 84878825544     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066621     Document Type: Article

References (22)

1. Meyerson M, Gabriel S, Getz G, (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11: 685-696.
2. Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
3. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, et al. (2010) Diversity of human copy number variation and multicopy genes. Science 330: 641-646.
4. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, et al. (2011) Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 30: 78-82.
5. Nothnagel M, Herrmann A, Wolf A, Schreiber S, Platzer M, et al. (2011) Technology-specific error signatures in the 1000 Genomes Project data. Hum Genet 130: 505-516.
6. Kircher M, Heyn P, Kelso J, (2011) Addressing challenges in the production and analysis of Illumina sequencing data. BMC Genomics 12: 382.
7. Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T, (2011) Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS ONE 6: e19534.
8. Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol 10: R94.
9. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT, (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7: e30087.
10. Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, et al. (2012) A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms. Mol Plant 5: 1020-1028.
11. Wang W, Wei Z, Lam TW, Wang J, (2011) Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions. Sci Rep 1: 55.
12. Benjamini Y, Speed TP, (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40: e72.
13. Cheung MS, Down TA, Latorre I, Ahringer J, (2011) Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res 39: e103.
14. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12: R18.
15. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
16. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
18. Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, et al. (2012) Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature 488: 49-56.
19. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: 178-186.
20. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
21. Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH, (2011) Accurate and comprehensive sequencing of personal genomes. Genome Res 21: 1498-1505.
22. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, et al. (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327: 78-81.