Ultra high throughput sequencing in human DNA variation detection: A comparative study on the NDUFA3-PRPF31 region

PLoS ONE

Volumn 5, Issue 9, 2010, Pages

  Benaglio, Paola ^a   Rivolta, Carlo ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENE PRODUCT; PROTEIN NDUFA3; PROTEIN PRPF31; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE DELETION; GENE INSERTION; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC SCREENING; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; ULTRA HIGH THROUGHPUT SEQUENCING;

BASE SEQUENCE; EYE PROTEINS; GENETIC VARIATION; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NADH DEHYDROGENASE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 77958575588     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013071     Document Type: Article

References (23)

1. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
2. Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24: 142-149.
3. Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11: 31-46.
4. Rio Frio T, McGee TL, Wade NM, Iseli C, Beckmann JS, et al. (2009) A singlebase substitution within an intronic repetitive element causes dominant retinitis pigmentosa with reduced penetrance. Hum Mutat 30: 1340-1347.
5. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
6. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
7. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19: 1527-1541.
8. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10: R32.
9. 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.
10. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18: 1638-1642.
11. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876.
12. Ikegawa S, Mabuchi A, Ogawa M, Ikeda T (2002) Allele-specific PCR amplification due to sequence identity between a PCR primer and an amplicon: is direct sequencing so reliable? Hum Genet 110: 606-608.
13. Richard GF, Kerrest A, Dujon B (2008) Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 72: 686-727.
14. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 8: R143.
15. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
16. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, et al. (2010) Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 42: 400-405.
17. Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F, et al. (2010) Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods 7: 485-486.
18. Ingman M, Gyllensten U (2009) SNP frequency estimation using massively parallel sequencing of pooled DNA. European Journal of Human Genetics 17: 383-386.
19. Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, et al. (2009) Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 30: 1703-1712.
20. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5: 887-893.
21. Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M (2007) Targeted highthroughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 35: e97.
22. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35: e130.
23. Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, et al. (2010) A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol 11: R15.