Processed pseudogene confounding deletion/duplication assays for SMAD4

Journal of Molecular Diagnostics

Volumn 17, Issue 5, 2015, Pages 576-582

  Millson, Alison ^a   Lewis, Tracey ^a   Pesaran, Tina ^b   Salvador, David ^b   Gillespie, Katrina ^b   Gau, Chia Ling ^b   Pont Kingdon, Genevieve ^a   Lyon, Elaine ^a,c   Bayrak Toydemir, Pinar ^a,c  

^a ARUP INSTITUTE FOR CLINICAL AND EXPERIMENTAL PATHOLOGY   (United States)

^b AMBRY GENETICS   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

SMAD4 PROTEIN; SMAD4 PROTEIN, HUMAN;

ARTICLE; ASSAY; CHROMOSOME; CONTROLLED STUDY; DIAGNOSTIC TEST; EXON; FOLLOW UP; GENE AMPLIFICATION; GENE DELETION; GENE DUPLICATION; GENE SEQUENCE; HUMAN; LABORATORY; MICROARRAY ANALYSIS; PSEUDOGENE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; DIFFERENTIAL DIAGNOSIS; DNA MUTATIONAL ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; INTESTINAL POLYPOSIS; LABORATORY DIAGNOSIS; MULTIPLEX POLYMERASE CHAIN REACTION; NEOPLASTIC SYNDROMES, HEREDITARY; PROCEDURES; SEQUENCE ALIGNMENT; TELANGIECTASIA, HEREDITARY HEMORRHAGIC;

DIAGNOSIS, DIFFERENTIAL; DNA MUTATIONAL ANALYSIS; FALSE POSITIVE REACTIONS; GENE DELETION; GENE DUPLICATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTESTINAL POLYPOSIS; MULTIPLEX POLYMERASE CHAIN REACTION; NEOPLASTIC SYNDROMES, HEREDITARY; PSEUDOGENES; SEQUENCE ALIGNMENT; SMAD4 PROTEIN; TELANGIECTASIA, HEREDITARY HEMORRHAGIC;

EID: 84952660134     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2015.05.005     Document Type: Article

References (16)

1. J.R. Howe, S. Roth, J.C. Ringold, R.W. Summers, H.J. Järvinen, P. Sistonen, I.P.M. Tomlinson, R.S. Houlston, S. Bevan, F.A. Mitros, E.M. Stone, and L.A. Aaltonen Mutations in the SMAD4/DPC4 gene in juvenile polyposis Science 280 1998 1086 1088
2. J.R. Howe, J.L. Bair, M.G. Sayed, M.E. Anderson, F.A. Mitros, G.M. Petersen, V.E. Velculescu, G. Traverso, and B. Volgelstein Germline mutations of the gene encoding bone morphogenetic protein receptor 1A in juvenile polyposis Nat Genet 28 2001 184 187
3. J.R. Howe, M.G. Sayed, A.F. Ahmed, J. Ringold, J. Larsen-Haidle, A. Merg, F.A. Mitros, C.A. Vaccaro, G.M. Petersen, F.M. Giardiello, S.T. Tinley, L.A. Aaltonen, and H.T. Lynch The prevalence of MADH4 and BMPR1A mutations in juvenile polyposis and absence of BMPR2, BMPR1B, and ACVR1 mutations J Med Genet 41 2004 484 491
4. C.J. Gallione, G.M. Repetto, E. Legius, A.K. Rustgi, S.L. Schelley, S. Tejpar, G. Mitchell, É. Drouin, C.J.J. Westermann, and D.A. Marchuk A combined syndrome of juvenile polyposis and hereditary haemoffhagic telangiectasia associated with mutation in MADH4 (SMAD4) Lancet 363 2004 852 859
5. E.F. Vanin Processed pseudogenes: characteristics and evolution Annu Rev Genet 19 1985 253 272
6. D.D. Luan, M.H. Korman, J.L. Jakubczak, and T.H. Eickbush Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition Cell 72 1993 595 605
7. C. Esnault, J. Maestre, and T. Heidmann Human LINE retrotransposons generate processed pseudogenes Nat Genet 24 2000 363 367
8. H. LaDuca, A.J. Stuenkel, J.S. Dolinsky, S. Keiles, S. Tandy, T. Pesaran, E. Chen, C.-L. Gau, E. Palmaer, K. Shoaepour, D. Shah, V. Speare, S. Gandomi, and E. Chao Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more that 2,000 patients Genet Med 16 2014 830 837
9. K.J. Livak, and T.D. Schmittgen Analysis of relative gne expression data using real-time quantitative PCR and the 2-ΔΔCT method Methods 25 2001 402 408
10. C.P. Vaughn, E. Lyon, and W.S. Samowitz Confirmation of single exon deletions in MLH1 and MSH2 using quantitative polymerase chain reaction J Mol Diagn 10 2008 355 360
11. N.C. Nicolaides, K.C. Carter, B.K. Shell, N. Papadopoulos, B. Vogelstein, and K.W. Kinzler Genomic organization of the human PMS2 gene family Genomics 30 1995 195 206
12. M. De Vos, B.E. Hayward, S. Picton, E. Sheridan, and D.T. Bonthron Novel PMS2 pseudogenes can conceal recessive mutations causing a distinctive childhood cancer syndrome Am J Hum Genet 74 2004 954 964
13. H. Nakagawa, J.C. Lockman, W.L. Frankel, H. Hampel, K. Steenblock, L.J. Burgart, S.N. Thibodeau, and A. de la Chapelle Mismatch repair gene PMS2: disease-causing germline mutations are frequent in patients whose tumors stain negative for PMS2 protein, but paralogous genes obscure mutation detection and interptertation Cancer Res 64 2004 4721 4727
14. C.P. Vaughn, J. Robles, J.J. Swensen, C.E. Miller, E. Lyon, R. Mao, P. Bayrak-Toydemir, and W.S. Samowitz Clinical analysis of PMS2 mutation detection and avoidance of pseudogenes Hum Mutat 31 2010 588 593
15. C.F. Vaughn, K.J. Hart, W.S. Samowitz, and J.J. Swensen Avoidance of pseudogene interference in the detection of 3′ deletions in PMS2 Hum Mutat 32 2011 1063 1071
16. Z. Zhang, P.M. Harrison, Y. Lui, and M. Gerstein Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome Genome Res 13 2003 2541 2558