MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq

Genome Research

Volumn 23, Issue 4, 2013, Pages 687-697

  Hill, Jonathon T ^a   Demarest, Bradley L ^a   Bisgrove, Brent W ^a   Gorsi, Bushra ^a   Su, Yi Chu ^a   Yost, H Joseph ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NKX2.5; TRANSCRIPTION FACTOR TBX1; UNCLASSIFIED DRUG;

ARTICLE; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE FREQUENCY; GENE MAPPING; GENE MUTATION; GENETIC ANALYSIS; GENETIC SCREENING; MUTATION MAPPING ANALYSIS PIPELINE FOR POOLED RNA SEQUENCE; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; ZEBRA FISH;

ALLELES; ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENES, RECESSIVE; INTERNET; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; RNA; SELECTION, GENETIC; SEQUENCE ANALYSIS, RNA; SOFTWARE; ZEBRAFISH;

CAENORHABDITIS ELEGANS; DANIO RERIO;

EID: 84875990159     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.146936.112     Document Type: Article

References (45)

1. Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, Lee SGP, Lim AYM, Hajan HS, Collas P, Bourque G, et al. 2011. Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res 21: 1328-1338.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
3. Arnold CN, Xia Y, Lin P, Ross C, Schwander M, Smart NG, Müller U, Beutler B. 2011. Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. Genetics 187: 633-641.
4. Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, et al. 2011. Next-generation mapping of Arabidopsis genes. Plant J 67: 715-725.
5. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
6. Beis D, Bartman T, Jin SW, Scott IC, D'Amico LA, Ober EA, Verkade H, Frantsve J, Field HA, Wehman A, et al. 2005. Genetic and cellular analyses of zebrafish atrioventricular cushion and valve development. Development 132: 4193-4204.
7. Bowen ME, Henke K, Siegfried KR, Warman ML, Harris MP. 2012. Efficient mapping and cloning of mutations in zebrafish by low-coverage wholegenome sequencing. Genetics 190: 1017-1024.
8. Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik Ela W, Smith Jr. 2011. An SNP-based linkage map for zebrafish reveals sex determination loci. G3 (Bethesda) 1: 3-9.
9. Brenner S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71-94.
10. Chen JN, van Bebber F, Goldstein AM, Serluca FC, Jackson D, Childs S, Serbedzija G,Warren KS, Mably JD, Lindahl P, et al. 2001. Genetic steps to organ laterality in zebrafish. Comp Funct Genomics 2: 60-68.
11. Christodoulou DC, Gorham JM, Herman DS, Seidman JG. 2011. Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr Protoc Mol Biol 94: 4.12.1-4.12.11.
12. ClevelandW. 1988. Locally weighted regression: An approach to regression analysis by local fitting. J Am Stat Assoc 83: 596-610.
13. Cuperus JT, Montgomery TA, Fahlgren N, Burke RT, Townsend T, Sullivan CM, Carrington JC. 2010. Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc Natl Acad Sci 107: 466-471.
14. Doitsidou M, Poole RJ, Sarin S, Bigelow H, Hobert O. 2010. C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy. PLoS ONE 5: e15435.
15. DrieverW, Solnica-Krezel L, Schier AF, Neuhauss SC, Malicki J, Stemple DL, Stainier DY, Zwartkruis F, Abdelilah S, Rangini Z, et al. 1996. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123: 37-46.
16. García-García MJ, Eggenschwiler JT, Caspary T, Alcorn HL, Wyler MR, Huangfu D, Rakeman AS, Lee JD, Feinberg EH, Timmer JR, et al. 2005. Analysis of mouse embryonic patterning and morphogenesis by forward genetics. Proc Natl Acad Sci 102: 5913-5919.
17. Geoffrey Burns C, MacRae C. 2006. Purification of hearts from zebrafish embryos. BioTechniques 40: 278-282.
18. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, et al. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29: 644-652.
19. Haffter P, Granato M, Brand M, Mullins M, Hammerschmidt M, Kane D, Odenthal J, van Eeden F, Jiang Y, Heisenberg C, et al. 1996. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123: 1-36.
20. Hughes SE, Huang C, Kornfeld K. 2011. Identification of mutations that delay somatic or reproductive aging of Caenorhabditis elegans. Genetics 189: 341-356.
21. Hurvich CM, Simonoff JS, Tsai C-L. 1998. Smoothing parameter selection in nonparametric regression using an improved Akaike information criterion. J R Stat Soc Series B Stat Methodol 60: 271-293.
22. Lawson ND, Weinstein BM. 2002. In vivo imaging of embryonic vascular development using transgenic zebrafish. Dev Biol 248: 307-318.
23. Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin C, Cooney J, Anderson H, King M, Stottman R, Ha S, et al. 2012. Mutation mapping and identification by whole genome sequencing. Genome Res 22: 1541-1548.
24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
25. Lin X, TangW, Ahmad S, Lu J, Colby CC, Zhu J, Yu Q. 2012. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res 288: 67-76.
26. Liu S, Yeh C-T, Tang HM, Nettleton D, Schnable PS. 2012. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS ONE 7: e36406.
27. Medina PMB, Swick LL, Andersen R, Blalock Z, Brenman JE. 2006. A novel forward genetic screen for identifying mutations affecting larval neuronal dendrite development in Drosophila melanogaster. Genetics 172: 2325-2335.
28. Mohideen MA, Moore JL, Cheng KC. 2000. Centromere-linked microsatellite markers for linkage groups 3, 4, 6, 7, 13, and 20 of zebrafish (Danio rerio). Genomics 67: 102-106.
29. Moore JL, Rush LM, Breneman C, Mohideen M-APK, Cheng KC. 2006. Zebrafish genomic instability mutants and cancer susceptibility. Genetics 174: 585-600.
30. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, et al. 2011. Sequencespecific error profile of Illumina sequencers. Nucleic Acids Res 39: e90.
31. Nix DA, Courdy SJ, Boucher KM. 2008. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9: 523.
32. Nüsslein-Volhard C, Wieschaus E. 1980. Mutations affecting segment number and polarity in Drosophila. Nature 287: 795-801.
33. Pan W, Pham VN, Stratman AN, Castranova D, Kamei M, Kidd KR, Lo BD, Shaw KM, Torres-Vazquez J,Mikelis CM, et al. 2012. CDP-diacylglycerol synthetase-controlled phosphoinositide availability limits VEGFA signaling and vascular morphogenesis. Blood 120: 489-498.
34. Piotrowski T, Ahn DG, Schilling TF, Nair S, Ruvinsky I, Geisler R, Rauch GJ, Haffter P, Zon LI, Zhou Y, et al. 2003. The zebrafish van gogh mutation disrupts tbx1, which is involved in the DiGeorge deletion syndrome in humans. Development 130: 5043-5052.
35. Rösel TD, Hung L-H, Medenbach J, Donde K, Starke S, Benes V, Rätsch G, Bindereif A. 2011. RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation. EMBO J 30: 1965-1976.
36. Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jørgensen J-E,Weigel D, Andersen SU. 2009. SHOREmap: Simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6: 550-551.
37. Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, Kaplan S, Jackson D, de Sauvage F, Jacob H, Fishman MC. 1999. Zebrafish genetic map with 2000 microsatellite markers. Genomics 58: 219-232.
38. Tabernero MD, Maíllo A, Nieto AB, Diez-Tascón C, Lara M, Sousa P, Otero A, Castrillo A, Patino-Alonso MDC, Espinosa A, et al. 2012. Delineation of commonly deleted chromosomal regions in meningiomas by highdensity single nucleotide polymorphism genotyping arrays. Genes Chromosomes Cancer 51: 606-617.
39. Uchida N, Sakamoto T, Kurata T, Tasaka M. 2011. Identification of EMSinduced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing. Plant Cell Physiol 52: 716-722.
40. Vesterlund L, Jiao H, Unneberg P, Hovatta O, Kere J. 2011. The zebrafish transcriptome during early development. BMC Dev Biol 11: 30.
41. Voz ML, Coppieters W, Manfroid I, Baudhuin A, Von Berg V, Charlier C, Meyer D, Driever W, Martial JA, Peers B. 2012. Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing. PLoS ONE 7: e34671.
42. Warren LL, Li L, Nelson MR, Ehm MG, Shen J, Fraser DJ, Aponte JL, Nangle KL, Slater AJ, Woollard PM, et al. 2012. Deep resequencing unveils genetic architecture of ADIPOQ and identifies a novel low-frequency variant strongly associated with adiponectin variation. Diabetes 61: 1297-1301.
43. Xiao T, Roeser T, StaubW, Baier H. 2005. A GFP-based genetic screen reveals mutations that disrupt the architecture of the zebrafish retinotectal projection. Development 132: 2955-2967.
44. Yu Q, Shen Y, Chatterjee B, Siegfried BH, Leatherbury L, Rosenthal J, Lucas JF, Wessels A, Spurney CF, Wu Y-J, et al. 2004. ENU induced mutations causing congenital cardiovascular anomalies. Development 131: 6211-6223.
45. Zuryn S, Le Gras S, Jamet K, Jarriault S. 2010. A strategy for direct mapping and identification of mutations by whole-genome sequencing. Genetics 186: 427-430.