A modified method for whole exome resequencing from minimal amounts of starting DNA

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Kozarewa, Iwanka ^a   Rosa Rosa, Juan Manuel ^a   Wardell, Christopher P ^a   Walker, Brian A ^a   Fenwick, Kerry ^a   Assiotis, Ioannis ^a   Mitsopoulos, Costas ^a   Zvelebil, Marketa ^a   Morgan, Gareth J ^a   Ashworth, Alan ^a   Lord, Christopher J ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA;

ARTICLE; CONTROLLED STUDY; DNA FRAGMENTATION; DNA HYBRIDIZATION; DNA LIBRARY; DNA REPAIR; EXOME; FLOW CYTOMETRY; GENETIC ASSOCIATION; GENOTYPING TECHNIQUE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; POLYMERASE CHAIN REACTION; PROCESS DEVELOPMENT; QUALITY CONTROL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR BIOPSY; CELL LINE; DNA SEQUENCE; FEMALE; GENE LIBRARY; GENETICS; GENOMICS; GENOTYPE; ISOLATION AND PURIFICATION; LABORATORY; METHODOLOGY;

CELL LINE; DNA; EXOME; FEMALE; GENE LIBRARY; GENOMICS; GENOTYPE; HUMANS; LABORATORIES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84857765412     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0032617     Document Type: Article

References (15)

1. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, et al. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40: 722-729.
2. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, et al. (2010) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184-190.
3. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191-196.
4. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, et al. (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7: 111-118.
5. Rosa M, Mohammadi A, Masood S, (2010) The value of fine needle aspiration biopsy in the diagnosis and prognostic assessment of palpable breast lesions. Diagn Cytopathol.
6. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, et al. (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39: 1522-1527.
7. Adey A, Morrison HG, Asan, Xun X, Kitzman JO, et al. (2010) Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 11: R119.
8. The (2003) The International HapMap Project. Nature 426: 789-796.
9. Kozarewa I, Turner DJ, (2011) Amplification-free library preparation for paired-end Illumina sequencing. Methods Mol Biol 733: 257-266.
10. Li H, Durbin R, (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
11. 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.
12. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
13. Walker BA, Leone PE, Chiecchio L, Dickens NJ, Jenner MW, et al. (2010) A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value. Blood 116: e56-65.
14. Barber LJ, Rosa Rosa JM, Kozarewa I, Fenwick K, Assiotis I, et al. (2011) Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. PLoS One 6: e21639.
15. Ashworth A, Lord CJ, Reis-Filho JS, (2011) Genetic interactions in cancer progression and treatment. Cell 145: 30-38.