Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis

Mammalian Genome

Volumn 25, Issue 3-4, 2014, Pages 120-128

  Damerla, Rama Rao ^a   Chatterjee, Bishwanath ^a   Li, You ^a   Francis, Richard J B ^a   Fatakia, Sarosh N ^a   Lo, Cecilia W ^a  

^a CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BIOINFORMATICS; C57BL 6 MOUSE; CHROMOSOME 4; CONGENITAL HEART DISEASE; FEMALE; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENOME ANALYSIS; GENOTYPE; INBRED STRAIN; MALE; MOUSE MUTANT; MUTAGENESIS; MUTATIONAL ANALYSIS; NONHUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; C57BL MOUSE; CHROMOSOMAL MAPPING; CROSS BREEDING; DISEASE MODEL; DNA MUTATIONAL ANALYSIS; GENETIC PREDISPOSITION; GENETICS; HEART DISEASES; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; MOUSE; MUTANT MOUSE STRAIN; NUCLEOTIDE SEQUENCE; PROCEDURES;

MUS;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CROSSES, GENETIC; DISEASE MODELS, ANIMAL; DNA MUTATIONAL ANALYSIS; GENETIC PREDISPOSITION TO DISEASE; HEART DISEASES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICE; MICE, INBRED C57BL; MICE, MUTANT STRAINS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84897109315     PISSN: 09388990     EISSN: 14321777     Source Type: Journal    
DOI: 10.1007/s00335-013-9494-7     Document Type: Article

References (21)

1. Arnold CN, Xia Y, Lin P, Ross C, Schwander M, Smart NG, Muller U, Beutler B (2011) Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. Genetics 187:633-641
2. Bode VC, McDonald JD, Guenet JL, Simon D (1988) hph-1: a mouse mutant with hereditary hyperphenylalaninemia induced by ethylnitrosourea mutagenesis. Genetics 118:299-305 (Pubitemid 18066647)
3. Bull KR, Rimmer AJ, Siggs OM, Miosge LA, Roots CM, Enders A, Bertram EM, Crockford TL, Whittle B, Potter PK, Simon MM, Mallon AM, Brown SD, Beutler B, Goodnow CC, Lunter G, Cornall RJ (2013) Unlocking the bottleneck in forward genetics using whole-genome sequencing and identity by descent to isolate causative mutations. PLoS Genet 9:e1003219
4. Caruana G, Farlie PG, Hart AH, Bagheri-Fam S, Wallace MJ, Dobbie MS, Gordon CT, Miller KA, Whittle B, Abud HE, Arkell RM, Cole TJ, Harley VR, Smyth IM, Bertram JF (2013) Genome-wide ENU mutagenesis in combination with high density SNP analysis and exome sequencing provides rapid identification of novel mouse models of developmental disease. PLoS One 8:e55429
5. Chan M, Ji SM, Yeo ZX, Gan L, Yap E, Yap YS, Ng R, Tan PH, Ho GH, Ang P, Lee AS (2012) Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J Mol Diagn 14:602-612
6. Daum LT, Rodriguez JD, Worthy SA, Ismail NA, Omar SV, Dreyer AW, Fourie PB, Hoosen AA, Chambers JP, Fischer GW (2012) Next-generation ion torrent sequencing of drug resistance mutations in Mycobacterium tuberculosis strains. J Clin Microbiol 50:3831-3837
7. Damerla R, Cui C, Gabriel G, Liu X, Gibbs B, Francis R, LI Y, Chatterjee B, Michaud J, Pazour G, Lo C (2013) Abstract#3162W, Mutation in the mouse homolog of C5ORF42 disrupts ciliogenesis and causes cerebellar defects and other Joubert Syndrome phenotypes associated with the disruption of Shh signaling. In: 63rd Annual meeting of the American Society of Human Genetics, Boston, 23 Oct 2013
8. Francis RJ, Christopher A, Devine WA, Ostrowski L, Lo C (2012) Congenital heart disease and the specification of left-right asymmetry. Am J Physiol Heart Circ Physiol 302:H2102-H2111
9. Guenet JL (2004) Chemical mutagenesis of the mouse genome: an overview. Genetica 122:9-24
10. Guichard C, Harricane MC, Lafitte JJ, Godard P, Zaegel M, Tack V, Lalau G, Bouvagnet P (2001) Axonemal dynein intermediate-chain gene (DNAI1) mutations result in situs inversus and primary ciliary dyskinesia (Kartagener syndrome). Am J Hum Genet 68:1030-1035 (Pubitemid 32289746)
11. Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Su YC, Yost HJ (2013) MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res 23:687-697
12. Nadeau JH (2001) Modifier genes in mice and humans. Nat Rev Genet 2:165-174
13. Neuhaus IM, Beier DR (1998) Efficient localization of mutations by interval haplotype analysis. Mamm Genome 9:150-154 (Pubitemid 28165383)
14. Ostrowski LE, Yin W, Rogers TD, Busalacchi KB, Chua M, O'Neal WK, Grubb BR (2010) Conditional deletion of dnaic1 in a murine model of primary ciliary dyskinesia causes chronic rhinosinusitis. Am J Respir Cell Mol Biol 43:55-63
15. Otto EA, Ramaswami G, Janssen S, Chaki M, Allen SJ, Zhou W, Airik R, Hurd TW, Ghosh AK, Wolf MT, Hoppe B, Neuhaus TJ, Bockenhauer D, Milford DV, Soliman NA, Antignac C, Saunier S, Johnson CA, Hildebrandt F (2011) Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy. J Med Genet 48:105-116
16. Pennarun G, Escudier E, Chapelin C, Bridoux AM, Cacheux V, Roger G, Clement A, Goossens M, Amselem S, Duriez B (1999) Loss-of-function mutations in a human gene related to Chlamydomonas reinhardtii dynein IC78 result in primary ciliary dyskinesia. Am J Hum Genet 65:1508-1519 (Pubitemid 30468663)
17. Shen Y, Leatherbury L, Rosenthal J, Yu Q, Pappas MA, Wessels A, Lucas J, Siegfried B, Chatterjee B, Svenson K, Lo CW (2005) Cardiovascular phenotyping of fetal mice by noninvasive high-frequency ultrasound facilitates recovery of ENU-induced mutations causing congenital cardiac and extracardiac defects. Physiol Genomics 24:23-36
18. Wang C, Krishnakumar S, Wilhelmy J, Babrzadeh F, Stepanyan L, Su LF, Levinson D, Fernandez-Vina MA, Davis RW, Davis MM, Mindrinos M (2012) High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci USA 109:8676-8681
19. Xia Y, Won S, Du X, Lin P, Ross C, La Vine D, Wiltshire S, Leiva G, Vidal SM, Whittle B, Goodnow CC, Koziol J, Moresco EM, Beutler B (2010) Bulk segregation mapping of mutations in closely related strains of mice. Genetics 186:1139-1146
20. Yu Q, Shen Y, Chatterjee B, Siegfried BH, Leatherbury L, Rosenthal J, Lucas JF, Wessels A, Spurney CF, Wu YJ, Kirby ML, Svenson K, Lo CW (2004) ENU induced mutations causing congenital cardiovascular anomalies. Development 131:6211-6223 (Pubitemid 40123933)
21. Zhang Z, Alpert D, Francis R, Chatterjee B, Yu Q, Tansey T, Sabol SL, Cui C, Bai Y, Koriabine M, Yoshinaga Y, Cheng JF, Chen F, Martin J, Schackwitz W, Gunn TM, Kramer KL, De Jong PJ, Pennacchio LA, Lo CW (2009) Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy. Proc Natl Acad Sci USA 106:3219-3224