Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches

Human Genetics

Volumn 132, Issue 8, 2013, Pages 899-911

  Chen, Geng ^a   Wang, Charles ^b   Shi, Leming ^c   Tong, Weida ^c   Qu, Xiongfei ^a   Chen, Jiwei ^a   Yang, Jianmin ^a   Shi, Caiping ^a   Chen, Long ^a   Zhou, Peiying ^a   Lu, Bingxin ^a   Shi, Tieliu ^a  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^c NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COPY NUMBER VARIATION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTOMICS;

MACACA; MAMMALIA; PAN;

ANIMALS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; PAN TROGLODYTES; REFERENCE VALUES; RNA; SEQUENCE ANALYSIS, RNA; TISSUE DISTRIBUTION;

EID: 84880918628     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-013-1300-9     Document Type: Article

References (49)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Baker M (2012) De novo genome assembly: what every biologist should know. Nat Method 9:333-337
4. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25:1915-1927
5. Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C et al (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956-963
6. Chen G, Li R, Shi L, Qi J, Hu P, Luo J, Liu M, Shi T (2011a) Revealing the missing expressed genes beyond the human reference genome by RNA-Seq. BMC Genomics 12:590
7. Chen G, Wang C, Shi T (2011b) Overview of available methods for diverse RNA-Seq data analyses. Sci China Life Sci 54:1121-1128
8. Chen G, Yin K, Wang C, Shi T (2011c) De novo transcriptome assembly of RNA-Seq reads with different strategies. Sci China Life Sci 54:1129-1133
9. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P et al (2010) Origins and functional impact of copy number variation in the human genome. Nature 464:704-712
10. Consortium IHGS (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945
11. Eichler EE, Clark RA, She X (2004) An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet 5:345-354
12. Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7:85-97
13. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29-W37
14. Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Method 8:469-477
15. Harris RS (2007) Improved pairwise alignment of genomic DNA. PhD Thesis, The Pennsylvania State University, Pennsylvania
16. Istrail S, Sutton GG, Florea L, Halpern AL, Mobarry CM, Lippert R, Walenz B, Shatkay H, Dew I, Miller JR et al (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci USA 101:1916-1921
17. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12:656-664
18. Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L et al (2006) Genome assembly comparison identifies structural variants in the human genome. Nat Genet 38:1413-1418
19. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F et al (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453:56-64
20. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G et al (2010) Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Method 7:365-371
21. Kielbasa SM, Wan R, Sato K, Horton P, Frith MC (2011) Adaptive seeds tame genomic sequence comparison. Genome Res 21:487-493
22. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L et al (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318:420-426
23. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
24. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5:e254
25. Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J et al (2010) Building the sequence map of the human pan-genome. Nat Biotechnol 28:57-63
26. Li Y, Zheng H, Luo R, Wu H, Zhu H, Li R, Cao H, Wu B, Huang S, Shao H et al (2011) Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol 29:723-730
27. Lorenc A, Makalowski W (2003) Transposable elements and vertebrate protein diversity. Genetica 118:183-191
28. Mackie Ogilvie C, Scriven PN (2002) Meiotic outcomes in reciprocal translocation carriers ascertained in 3-day human embryos. Eur J Hum Genet 10:801-806
29. Marguerat S, Bahler J (2010) RNA-seq: from technology to biology. Cell Mol Life Sci 67:569-579
30. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509-1517
31. Nagalakshmi U, Waern K, Snyder M (2010) RNA-Seq: a method for comprehensive transcriptome analysis. In: Frederick M Ausubel et al (eds) Current protocols in molecular biology. Chaps 4: Unit 4 11, pp 11-13
32. Noe L, Kucherov G (2005) YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Res 33:W540-W543
33. Oliver-Bonet M, Navarro J, Carrera M, Egozcue J, Benet J (2002) Aneuploid and unbalanced sperm in two translocation carriers: evaluation of the genetic risk. Mol Hum Reprod 8:958-963
34. Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87-98
35. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J et al (2012) The Pfam protein families database. Nucleic Acids Res 40:D290-D301
36. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W et al (2006) Global variation in copy number in the human genome. Nature 444:444-454
37. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ et al (2010) De novo assembly and analysis of RNA-seq data. Nat Method 7:909-912
38. Saha S, Bridges S, Magbanua ZV, Peterson DG (2008) Empirical comparison of ab initio repeat finding programs. Nucleic Acids Res 36:2284-2294
39. Surget-Groba Y, Montoya-Burgos JI (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20:1432-1440
40. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111
41. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511-515
42. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562-578
43. Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D et al (2005) Fine-scale structural variation of the human genome. Nat Genet 37:727-732
44. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al (2001) The sequence of the human genome. Science 291:1304-1351
45. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y et al (2008) The diploid genome sequence of an Asian individual. Nature 456:60-65
46. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
47. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973-982
48. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-829
49. Zerbino DR, Paten B, Haussler D (2012) Integrating genomes. Science 336:179-182