Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products

Developmental Dynamics

Volumn 243, Issue 12, 2014, Pages 1632-1636

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

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

Author keywords

Genome editing; Indel identification; Sanger sequencing

Indexed keywords

ALLELE; ARTICLE; CHROMATOGRAPHY; CLONING; DIPLOIDY; GENE IDENTIFICATION; GENE SEQUENCE; GENOTYPE; INDEL MUTATION; MUTANT; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; ZEBRA FISH; ALGORITHM; COMPUTER PROGRAM; HETEROZYGOTE; NUCLEOTIDE SEQUENCE; PROCEDURES;

ALGORITHMS; DNA MUTATIONAL ANALYSIS; HETEROZYGOTE; INDEL MUTATION; POLYMERASE CHAIN REACTION; SOFTWARE;

EID: 84924246056     PISSN: 10588388     EISSN: 10970177     Source Type: Journal    
DOI: 10.1002/dvdy.24183     Document Type: Article

References (13)

1. Bhangale TR, Stephens M, Nickerson DA. 2006. Automating resequencing-based detection of insertion-deletion polymorphisms. Nat Genet 38:1457-1462. doi:10.1038/ng1925.
2. Bibikova M, Golic M, Golic KG, Carroll D. 2002. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161:1169-1175.
3. Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. 2007. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res 17:659-666. doi:10.1101/gr.6151507.
4. Dahlem TJ, Hoshijima K, Jurynec MJ, Gunther D, Starker CG, Locke AS, Weis AM, Voytas DF, Grunwald DJ. 2012. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet 8:e1002861. doi:10.1371/journal.pgen.1002861.
5. Dmitriev DA, Rakitov RA. 2008. Decoding of superimposed traces produced by direct sequencing of heterozygous indels. PLoS Comput Biol 4:e1000113. doi:10.1371/journal.pcbi.1000113.
6. Gaj T, Gersbach CA, Barbas CF. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397-405. doi:10.1016/j.tibtech.2013.04.004.
7. Gupta A, Christensen RG, Rayla AL, Lakshmanan A, Stormo GD, Wolfe SA. 2012. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 9:588-590. doi:10.1038/nmeth.1994.
8. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh J-RJ, Joung JK. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227-229. doi:10.1038/nbt.2501.
9. Joung JK, Sander JD. 2013. TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14:49-55. doi:10.1038/nrm3486.
10. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ. 2011. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143-148. doi:10.1038/nbt.1755.
11. Parant JM, George SA, Pryor R, Wittwer CT, Yost HJ. 2009. A rapid and efficient method of genotyping zebrafish mutants. Dev Dyn 238:3168-3174. doi:10.1002/dvdy.22143.
12. Tenney AE, Wu JQ, Langton L, Klueh P, Quatrano R, Brent MR. 2007. A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. Genome Res 17:212-218. doi:10.1101/gr.5661407.
13. Zu Y, Tong X, Wang Z, Liu D, Pan R, Li Z, Hu Y, Luo Z, Huang P, Wu Q, Zhu Z, Zhang B, Lin S. 2013. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods 10:329-331. doi:10.1038/nmeth.2374.