Xác thực các biến thể nucleotid đơn bằng phân tích exon bổ sung với bộ sequencer bán dẫn để bổ sung dữ liệu về giải trình tự gen toàn bộ của một quần thể người

Gonzaga-Jauregui C, Lupski JR, Gibbs RA: Human genome sequencing in health and disease. Annu Rev Med. 2012, 63: 35-61. 10.1146/annurev-med-051010-162644. Berg JS, Khoury MJ, Evans JP: Deploying whole genome sequencing in clinical practice and public health: meeting the challenge one bin at a time. Genet Med. 2011, 13 (6): 499-504. 10.1097/GIM.0b013e318220aaba. Altshuler D, Durbin DR, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Collins FS, De La Vega FM, Donnelly P, Egholm M, Flicek P, Gabriel SB, Gibbs RA, Knoppers BM, Lander ES, Lehrach H, Mardis ER, McVean GA, Nickerson DA, Peltonen L, Schafer AJ, Sherry ST, Wang J, Wilson R, Gibbs RA, Deiros D, Metzker M, Muzny D, Reid J, Wheeler D, et al: A map of human genome variation from population-scale sequencing. Nature. 2010, 467 (7319): 1061-1073. 10.1038/nature09534. Altshuler DM, Durbin DR, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE, Flicek P, Gabriel SB, Gibbs RA, Green ED, Hurles ME, Knoppers BM, Korbel JO, Lander ES, Lee C, Lehrach H, Mardis ER, Marth GT, McVean GA, Nickerson DA, Schmidt JP, Sherry ST, Wang J, Wilson RK, Gibbs RA, Dinh H, Kovar C, Lee S, et al: An integrated map of genetic variation from 1,092 human genomes. Nature. 2012, 491 (7422): 56-65. 10.1038/nature11632. Wong LP, Ong RT, Poh WT, Liu X, Chen P, Li R, Lam KK, Pillai NE, Sim KS, Xu H, Sim NL, Teo SM, Foo JN, Tan LW, Lim Y, Koo SH, Gan LS, Cheng CY, Wee S, Yap EP, Ng PC, Lim WY, Soong R, Wenk MR, Aung T, Wong TY, Khor CC, Little P, Chia KS, Teo YY: Deep whole-genome sequencing of 100 southeast Asian Malays. Am J Hum Genet. 2013, 92 (1): 52-66. 10.1016/j.ajhg.2012.12.005. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al: Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008, 456 (7218): 53-59. 10.1038/nature07517. Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S: Sequencing studies in human genetics: design and interpretation. Nat Rev Genet. 2013, 14 (7): 460-470. 10.1038/nrg3455. Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC: Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS One. 2013, 8 (2): e55089-10.1371/journal.pone.0055089. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, et al: An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011, 475 (7356): 348-352. 10.1038/nature10242. Boland JF, Chung CC, Roberson D, Mitchell J, Zhang X, Im KM, He J, Chanock SJ, Yeager M, Dean M: The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Hum Genet. 2013, 132 (10): 1153-1163. 10.1007/s00439-013-1321-4. Li X, Buckton AJ, Wilkinson SL, John S, Walsh R, Novotny T, Valaskova I, Gupta M, Game L, Barton PJ, Cook SA, Ware JS: Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers. PLoS One. 2013, 8 (7): e67744-10.1371/journal.pone.0067744. Elliott AM, Radecki J, Moghis B, Li X, Kammesheidt A: Rapid detection of the ACMG/ACOG-recommended 23 CFTR disease-causing mutations using ion torrent semiconductor sequencing. J Biomol Tech. 2012, 23 (1): 24-30. 10.7171/jbt.12-2301-003. Chan M, Ji SM, Yeo ZX, Gan L, Yap E, Yap YS, Ng R, Tan PH, Ho GH, Ang P, Lee AS: Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J Mol Diagn. 2012, 14 (6): 602-612. 10.1016/j.jmoldx.2012.06.003. Kanagal-Shamanna R, Portier BP, Singh RR, Routbort MJ, Aldape KD, Handal BA, Rahimi H, Reddy NG, Barkoh BA, Mishra BM, Paladugu AV, Manekia JH, Kalhor N, Chowdhuri SR, Staerkel GA, Medeiros LJ, Luthra R, Patel KP: Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: promises and challenges for routine clinical diagnostics. Mod Pathol. 2014, 27: 314-327. Abou Tayoun AN, Tunkey CD, Pugh TJ, Ross T, Shah M, Lee CC, Harkins TT, Wells WA, Tafe LJ, Amos CI, Tsongalis GJ: A Comprehensive Assay for CFTR Mutational Analysis Using Next-Generation Sequencing. Clin Chem. 2013, 59 (10): 1481-1488. 10.1373/clinchem.2013.206466. Junemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, Goesmann A, Stoye J, Harmsen D: Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. PLoS One. 2012, 7 (8): e41606-10.1371/journal.pone.0041606. Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, Nusbaum C, Jaffe DB: Characterizing and measuring bias in sequence data. Genome Biol. 2013, 14 (5): R51-10.1186/gb-2013-14-5-r51. Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW: Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput Biol. 2013, 9 (4): e1003031-10.1371/journal.pcbi.1003031. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ: Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012, 30 (5): 434-439. 10.1038/nbt.2198. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y: A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012, 13: 341- Feliubadalo L, Lopez-Doriga A, Castellsague E, Del Valle J, Menendez M, Tornero E, Montes E, Cuesta R, Gomez C, Campos O, Pineda M, Gonzalez S, Moreno V, Brunet J, Blanco I, Serra E, Capella G, Lazaro C: Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. Eur J Hum Genet. 2013, 21 (8): 864-870. 10.1038/ejhg.2012.270. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, Boroevich KA, Nagasaki M, Yamaguchi R, Shibuya T, Kubo M, Miyano S, Nakamura Y, Tsunoda T: Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet. 2010, 42 (11): 931-936. 10.1038/ng.691. Thorvaldsdottir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013, 14 (2): 178-192. 10.1093/bib/bbs017. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol. 2011, 29 (1): 24-26. 10.1038/nbt.1754. Minoche AE, Dohm JC, Himmelbauer H: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 2011, 12 (11): R112-10.1186/gb-2011-12-11-r112. Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F: An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics. 2012, 13: 8-10.1186/1471-2105-13-8. Asan , Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, Wang J, Wu M, Liu X, Tian G, Wang J, Wang J, Yang H, Zhang X: Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 2011, 12 (9): R95-10.1186/gb-2011-12-9-r95. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M: Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011, 29 (10): 908-914. 10.1038/nbt.1975. Parla JS, Iossifov I, Grabill I, Spector MS, Kramer M, McCombie WR: A comparative analysis of exome capture. Genome Biol. 2011, 12 (9): R97-10.1186/gb-2011-12-9-r97. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, et al: Enterotypes of the human gut microbiome. Nature. 2011, 473 (7346): 174-180. 10.1038/nature09944. Daum LT, Rodriguez JD, Worthy SA, Ismail NA, Omar SV, Dreyer AW, Fourie PB, Hoosen AA, Chambers JP, Fischer GW: Next-generation ion torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains. J Clin Microbiol. 2012, 50 (12): 3831-3837. 10.1128/JCM.01893-12. Geurts-Giele WR, der Velden AW D-v, Bartalits NM, Verhoog LC, Hanselaar WE, Dinjens WN: Molecular diagnostics of a single multifocal non-small cell lung cancer case using targeted next generation sequencing. Virchows Arch. 2013, 462 (2): 249-254. 10.1007/s00428-012-1346-4. Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, Sanford T, Buddavarapu K, Krosting J, Garmire L, Wylie D, Shinde R, Beaudenon S, Alexander EK, Mambo E, Adai AT, Latham GJ: Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J Mol Diagn. 2013, 15 (2): 234-247. 10.1016/j.jmoldx.2012.11.006. Perkins TT, Tay CY, Thirriot F, Marshall B: Choosing a Benchtop Sequencing Machine to Characterise Helicobacter pylori Genomes. PLoS One. 2013, 8 (6): e67539-10.1371/journal.pone.0067539. Singh RR, Patel KP, Routbort MJ, Reddy NG, Barkoh BA, Handal B, Kanagal-Shamanna R, Greaves WO, Medeiros LJ, Aldape KD, Luthra R: Clinical Validation of a Next-Generation Sequencing Screen for Mutational Hotspots in 46 Cancer-Related Genes. J Mol Diagn. 2013, 15 (5): 607-622. 10.1016/j.jmoldx.2013.05.003. Yeo ZX, Chan M, Yap YS, Ang P, Rozen S, Lee AS: Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. PLoS One. 2012, 7 (9): e45798-10.1371/journal.pone.0045798. Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC: Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc Natl Acad Sci U S A. 2011, 108 (30): 12348-12353. 10.1073/pnas.1102838108. Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:13033997. 2013 Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011, 43 (5): 491-498. 10.1038/ng.806. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20 (9): 1297-1303. 10.1101/gr.107524.110. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007, 81 (3): 559-575. 10.1086/519795. Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093/bioinformatics/btq033. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352. Ihaka R, Gentleman R: R: a language for data analysis and graphics. J Comp Graph Stat. 1996, 5: 299-314.