Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

BMC Genomics

Volumn 16, Issue 8, 2015, Pages

  Frankish, Adam ^a   Uszczynska, Barbara ^b   Ritchie, Graham R S ^a,c   Gonzalez, Jose M ^a   Pervouchine, Dmitri ^b,d   Petryszak, Robert ^c   Mudge, Jonathan M ^a   Fonseca, Nuno ^c   Brazma, Alvis ^c   Guigo, Roderic ^b   Harrow, Jennifer ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; EXON SKIPPING; GENCODE DATABASE; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; INTRON; LOSS OF FUNCTION MUTATION; MISSENSE MUTATION; REFSEQ GENE DATABASE; RNA STABILITY; RNA TRANSLATION; ALTERNATIVE RNA SPLICING; BIOLOGY; GENETICS; HUMAN GENOME; METABOLISM; MOLECULAR GENETICS; SOFTWARE;

ISOPROTEIN; TRANSCRIPTOME;

ALTERNATIVE SPLICING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENOME, HUMAN; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN ISOFORMS; SOFTWARE; TRANSCRIPTOME;

EID: 84964425617     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-16-S8-S2     Document Type: Article

References (37)

1. Genomes Project C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA: An integrated map of genetic variation from 1,092 human genomes. Nature. 2012, 491 (7422): 56-65. 10.1038/nature11632.
2. UK10K: Rare Genetic Variants in Health and Disease (2010-2013). [ http://www.uk10k.org ]
3. Futema M, Plagnol V, Li K, Whittall RA, Neil HA, Seed M, Simon Broome C, Bertolini S, Calandra S, Descamps OS, et al: Whole exome sequencing of familial hypercholesterolaemia patients negative for LDLR/APOB/PCSK9 mutations. J Med Genet. 2014, 51 (8): 537-544. 10.1136/jmedgenet-2014-102405.
4. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, et al: Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013, 493 (7431): 216-220.
5. 100,000 Genomes Project. [ http://www.genomicsengland.co.uk ]
6. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010, 26 (16): 2069-2070. 10.1093/bioinformatics/btq330.
7. Wang K, Li M, Hakonarson H: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010, 38 (16): e164-10.1093/nar/gkq603.
8. Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG: A probabilistic disease-gene finder for personal genomes. Genome Res. 2011, 21 (9): 1529-1542. 10.1101/gr.123158.111.
9. Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M: VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics. 2012, 28 (17): 2267-2269. 10.1093/bioinformatics/bts368.
10. Kumar P, Henikoff S, Ng PC: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009, 4 (7): 1073-1081.
11. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR: A method and server for predicting damaging missense mutations. Nat Methods. 2010, 7 (4): 248-249. 10.1038/nmeth0410-248.
12. McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier JB, Donnelly P: Choice of transcripts and software has a large effect on variant annotation. Genome Med. 2014, 6 (3): 26-10.1186/gm543.
13. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, et al: GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006, 7 (Suppl 1): S4 1-9.
14. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, et al: GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22 (9): 1760-1774. 10.1101/gr.135350.111.
15. Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, et al: RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014, 42 (Database): D756-763.
16. Consortium EP, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, et al: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038/nature05874.
17. Consortium EP: An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489 (7414): 57-74. 10.1038/nature11247.
18. Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, et al: The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res. 2014, 42 (Database): D771-779.
19. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al: Ensembl 2015. Nucleic Acids Res. 2014
20. Cheng J, Maquat LE: Nonsense codons can reduce the abundance of nuclear mRNA without affecting the abundance of pre-mRNA or the half-life of cytoplasmic mRNA. Mol Cell Biol. 1993, 13 (3): 1892-1902.
21. Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M: PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics. 2006, 22 (12): 1437-1439. 10.1093/bioinformatics/btl116.
22. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D: Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA. 2003, 100 (20): 11484-11489. 10.1073/pnas.1932072100.
23. Lin MF, Jungreis I, Kellis M: PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011, 27 (13): i275-282. 10.1093/bioinformatics/btr209.
24. Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML: APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. 2013, 41 (Database): D110-117.
25. Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, et al: Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res. 2012, 22 (9): 1698-1710. 10.1101/gr.134478.111.
26. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006. 10.1101/gr.229102. Article published online before print in May 2002.
27. Thierry-Mieg D, Thierry-Mieg J: AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 2006, S12 11-14. 7 Suppl 1
28. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. Nature. 2008, 456 (7221): 470-476. 10.1038/nature07509.
29. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, et al: Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012, 337 (6090): 64-69. 10.1126/science.1219240.
30. Laguette MJ, Abrahams Y, Prince S, Collins M: Sequence variants within the 3'-UTR of the COL5A1 gene alters mRNA stability: implications for musculoskeletal soft tissue injuries. Matrix Biol. 2011, 30 (5-6): 338-345. 10.1016/j.matbio.2011.05.001.
31. Akdeli N, Riemann K, Westphal J, Hess J, Siffert W, Bachmann HS: A 3'UTR polymorphism modulates mRNA stability of the oncogene and drug target Polo-like Kinase 1. Mol Cancer. 2014, 13: 87-10.1186/1476-4598-13-87.
32. Lukowski SW, Bombieri C, Trezise AE: Disrupted post-transcriptional regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) by a 5'UTR mutation is associated with a CFTR-related disease. Hum Mutat. 2011, 32 (10): E2266-2282. 10.1002/humu.21545.
33. Li Q, Makri A, Lu Y, Marchand L, Grabs R, Rousseau M, Ounissi-Benkalha H, Pelletier J, Robert F, Harmsen E, et al: Genome-wide search for exonic variants affecting translational efficiency. Nat Commun. 2013, 4: 2260-
34. Wong JJ, Ritchie W, Ebner OA, Selbach M, Wong JW, Huang Y, Gao D, Pinello N, Gonzalez M, Baidya K, et al: Orchestrated intron retention regulates normal granulocyte differentiation. Cell. 2013, 154 (3): 583-595. 10.1016/j.cell.2013.06.052.
35. Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ: Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014, 24 (11): 1774-1786. 10.1101/gr.177790.114.
36. UniProt C: Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014, 42 (Database): D191-198.
37. Pakseresht N, Alako B, Amid C, Cerdeno-Tarraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, et al: Assembly information services in the European Nucleotide Archive. Nucleic Acids Res. 2014, 42 (Database): D38-43.