Functional constraint and small insertions and deletions in the ENCODE regions of the human genome

Genome Biology

Volumn 8, Issue 9, 2007, Pages

  Clark, Taane G ^a   Andrew, Toby ^b   Cooper, Gregory M ^c   Margulies, Elliott H ^c   Mullikin, James C ^c   Balding, David J ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b STANFORD UNIVERSITY   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMALDEHYDE;

ARTICLE; BASE PAIRING; CHROMATIN; CONTROLLED STUDY; EXON; GENE DELETION; GENE FUNCTION; GENE INSERTION; GENE NUMBER; GENE SEQUENCE; GENE STRUCTURE; GENETIC POLYMORPHISM; GENETIC REGULATION; HUMAN; HUMAN GENOME; MAMMAL; MOLECULAR EVOLUTION; NONHUMAN; REGULATORY SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENOME; PROTEIN TERTIARY STRUCTURE; REGRESSION ANALYSIS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

MAMMALIA;

ANIMALS; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; MODELS, GENETIC; MUTAGENESIS, INSERTIONAL; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN STRUCTURE, TERTIARY; REGRESSION ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE DELETION; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 44049101638     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-9-r180     Document Type: Article

References (38)

1. Mills RE Luttig CT Larkins CE Beauchamp A Tsui C Pittard WS Devine SE An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 2006, 16:1182-1190. 1557762 16902084
2. Bhangale TR Rieder MJ Livingston RJ Nickerson DA Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet 2005, 14:59-69. 15525656
3. Strachan T Read AP Human Molecular Genetics Garland Science/Taylor & Francis Group 2006
4. Wasserman WW Sandelin A Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5:276-287. 15131651
5. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005, 437:69-87. 16136131
6. Weber JL David D Heil J Fan Y Zhao C Marth G Human diallelic insertion/ deletion polymorphisms. Am J Hum Genet 2002, 71:854-862. 378541 12205564
7. Lunter G Ponting CP Hein J Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2006, 2:e5. 1326222 16410828
8. Snir S Pachter L Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. Research in Computational Molecular Biology Berlin, Heidelberg: Springer 2006, 265-280.
9. Kuroki Y Toyoda A Noguchi H Taylor TD Itoh T Kim DS Kim DW Choi SH Kim IC Choi HH Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. Nat Genet 2006, 38:158-167. 16388311
10. Li WH Saunders MA News and views: The chimpanzee and us. Nature 2005, 437:50-51. 16136126
11. ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640. 15499007
12. ENCODE project target selection process and target regions http://genome.gov/10506161
13. Eddy SR Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001, 2:919-929. 11733745
14. Giresi PG Gupta M Lieb JD Regulation of nucleosome stability as a mediator of chromatin function. Curr Opin Genet Dev 2006, 16:171-176. 16503136
15. Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 12748633
16. Maquat LE Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 2004, 5:89-99. 15040442
17. Pagani F Baralle FE Genomic variants in exons and introns: Identifying the splicing spoilers. Nat Rev Genet 2004, 5:389-396. 15168696
18. Waterston RH Lindblad-Toh K Birney E Rogers J Abril JF Agarwal P Agarwala R Ainscough R Alexandersson M An P Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562. 12466850
19. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 17571346
20. Bhangale TR Stephens M Nickerson DA Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet 2006, 38:1457-1462. 17115056
21. Conrad DF Andrews TD Carter NP Hurles ME Pritchard JK A high-resolution survey of deletion polymorphism in the human genome. Nat Genet 2006, 38:75-81. 16327808
22. Locke DP Sharp AJ McCarroll SA McGrath SD Newman TL Cheng Z Schwartz S Albertson DG Pinkel D Altshuler DM Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am J Hum Genet 2006, 79:275-290. 1559496. 16826518
23. Redon R Ishikawa S Fitch KR Feuk L Perry GH Andrews TD Fiegler H Shapero MH Carson AR Chen W Global variation in copy number in the human genome. Nature 2006, 444:444-454. 17122850
24. Wong KK deLeeuw RJ Dosanjh NS Kimm LR Cheng Z Horsman DE MacAulay C Ng RT Brown CJ Eichler EE A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 2007, 80:91-104. 1785303 17160897
25. Margulies EH Cooper GM Asimenos G Thomas DJ Dewey CN Siepel A Birney E Keefe D Schwartz AS Hou M Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007, 17:760-774. 1891336 17567995
26. Cooper GM Stone EA Asimenos G Green ED Batzoglou S Sidow A Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005, 15:901-913. 1172034 15965027
27. Ellegren H Smith NG Webster MT Mutation rate variation in the mammalian genome. Curr Opin Genet Dev 2003, 13:562-568. 14638315
28. Bailey JA Eichler EE Primate segmental duplications: Crucibles of evolution, diversity and disease. Nat Rev Genet 2006, 7:552-564. 16770338
29. Guigo R Flicek P Abril JF Reymond A Lagarde J Denoeud F S Ashburner M Bajic VB Birney E EGASP: The human ENCODE Genome Annotation Assessment Project. Genome Biol 2006, 7(Suppl 1):S2-S31. 1810551 16925836
30. Reese MG Guigo R EGASP: Introduction. Genome Biol 2006, (Suppl 1):S1-S3
31. A haplotype map of the human genome. Nature 2005, 437:1299-1320. 1880871 16255080
32. Ning Z Cox AJ Mullikin JC SSAHA: A fast search method for large DNA databases. Genome Res 2001, 11:1725-1729. 311141 11591649
33. The International HapMap Project http://www.hapmap.org/
34. The ENCODE project at UCSC http://genome.ucsc.edu/cgi-bin/hgTables
35. The ENCODE project at UCSC http://hgdownload.cse.ucsc.edu/goldenPath/ hg17/encode/database/encodeIndels.txt.gz
36. Venables WN Ripley BD Modern Applied Statistics with S New York: Springer 2002.
37. Hardison RC Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 2000, 16:369-372. 10973062
38. Giresi PG Kim J McDaniell RM Iyer VR Lieb JD FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 2007, 17:877-885. 1891346 17179217