메뉴 건너뛰기




Volumn 1167, Issue , 2014, Pages 303-315

Dealing with pseudogenes in molecular diagnostics in the next-generation sequencing era

Author keywords

Data analysis in NGS; Molecular diagnostics; Next generation sequencing (NGS); Pseudogenes of genes associated with monogenic disorders; Target enrichment in NGS

Indexed keywords

BRCA1 PROTEIN; OLIGONUCLEOTIDE; POLYCYSTIN 1;

EID: 84922326973     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0835-6_21     Document Type: Article
Times cited : (23)

References (46)
  • 3
    • 70449706229 scopus 로고    scopus 로고
    • Comprehensive analysis of the pseudo-genes of glycolytic enzymes in vertebrates: The anomalously high number of GAPDH pseu-dogenes highlights a recent burst of retrotrans-positional activity
    • Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB (2009) Comprehensive analysis of the pseudo-genes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseu-dogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics 10:480. doi: 10.1186/1471-2164-10-480
    • (2009) BMC Genomics , vol.10 , pp. 480
    • Liu, Y.J.1    Zheng, D.2    Balasubramanian, S.3    Carriero, N.4    Khurana, E.5    Robilotto, R.6    Gerstein, M.B.7
  • 4
    • 0036796620 scopus 로고    scopus 로고
    • Identification and analysis of over 2000 ribo-somal protein pseudogenes in the human genome
    • Zhang Z, Harrison P, Gerstein M (2002) Identification and analysis of over 2000 ribo-somal protein pseudogenes in the human genome. Genome Res 12(10):1466–1482. doi: 10.1101/gr.331902
    • (2002) Genome Res , vol.12 , Issue.10 , pp. 1466-1482
    • Zhang, Z.1    Harrison, P.2    Gerstein, M.3
  • 6
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467
    • (1977) Proc Natl Acad Sci U S A , vol.74 , Issue.12 , pp. 5463-5467
    • Sanger, F.1    Nicklen, S.2    Coulson, A.R.3
  • 8
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technolo-gies—the next generation
    • Metzker ML (2010) Sequencing technolo-gies—the next generation. Nat Rev Genet 11(1):31–46. doi: 10.1038/nrg2626
    • (2010) Nat Rev Genet , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 10
    • 84875457774 scopus 로고    scopus 로고
    • Detection of novel mutations that cause auto-somal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing
    • de Sousa DM, Hernan I, Pascual B, Borras E, Mane B, Gamundi MJ, Carballo M (2013) Detection of novel mutations that cause auto-somal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing. Mol Vis 19:654–664
    • (2013) Mol Vis , vol.19 , pp. 654-664
    • De Sousa, D.M.1    Hernan, I.2    Pascual, B.3    Borras, E.4    Mane, B.5    Gamundi, M.J.6    Carballo, M.7
  • 12
    • 84883790923 scopus 로고    scopus 로고
    • Deep intronic ‘mutations’ cause hemophilia A: Application of next generation sequencing in patients without detectable mutation in F8 cDNA
    • Pezeshkpoor B, Zimmer N, Marquardt N, Nanda I, Haaf T, Budde U, Oldenburg J, El-Maarri O (2013) Deep intronic ‘mutations’ cause hemophilia A: application of next generation sequencing in patients without detectable mutation in F8 cDNA. J Thromb Haemost. doi: 10.1111/jth.12339
    • (2013) J Thromb Haemost
    • Pezeshkpoor, B.1    Zimmer, N.2    Marquardt, N.3    Nanda, I.4    Haaf, T.5    Budde, U.6    Oldenburg, J.7    El-Maarri, O.8
  • 14
    • 79951805438 scopus 로고    scopus 로고
    • Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: Opportunities, challenges, and limitations
    • De Leeneer K, Hellemans J, De Schrijver J, Baetens M, Poppe B, Van Criekinge W, De Paepe A, Coucke P, Claes K (2011) Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations. Hum Mutat 32(3):335–344. doi: 10.1002/humu.21428
    • (2011) Hum Mutat , vol.32 , Issue.3 , pp. 335-344
    • De Leeneer, K.1    Hellemans, J.2    De Schrijver, J.3    Baetens, M.4    Poppe, B.5    Van Criekinge, W.6    De Paepe, A.7    Coucke, P.8    Claes, K.9
  • 16
    • 33845342557 scopus 로고    scopus 로고
    • Microfluidic digital PCR enables multigene analysis of individual environmental bacteria
    • Ottesen EA, Hong JW, Quake SR, Leadbetter JR (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314(5804):1464–1467. doi: 10.1126/science.1131370
    • (2006) Science , vol.314 , Issue.5804 , pp. 1464-1467
    • Ottesen, E.A.1    Hong, J.W.2    Quake, S.R.3    Leadbetter, J.R.4
  • 17
    • 45849087630 scopus 로고    scopus 로고
    • High throughput gene expression measurement with real time PCR in a micro-fluidic dynamic array
    • Spurgeon SL, Jones RC, Ramakrishnan R (2008) High throughput gene expression measurement with real time PCR in a micro-fluidic dynamic array. PLoS One 3(2):e1662. doi: 10.1371/journal.pone.0001662
    • (2008) Plos One , vol.3 , Issue.2 , pp. e1662
    • Spurgeon, S.L.1    Jones, R.C.2    Ramakrishnan, R.3
  • 21
    • 84859622645 scopus 로고    scopus 로고
    • Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy
    • Valencia CA, Rhodenizer D, Bhide S, Chin E, Littlejohn MR, Keong LM, Rutkowski A, Bonnemann C, Hegde M (2012) Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy. J Mol Diagn 14(3):233–246. doi: 10.1016/j. jmoldx.2012.01.009
    • (2012) J Mol Diagn , vol.14 , Issue.3 , pp. 233-246
    • Valencia, C.A.1    Rhodenizer, D.2    Bhide, S.3    Chin, E.4    Littlejohn, M.R.5    Keong, L.M.6    Rutkowski, A.7    Bonnemann, C.8    Hegde, M.9
  • 28
    • 0024376686 scopus 로고
    • Minimal homol-ogy requirements for PCR primers
    • Sommer R, Tautz D (1989) Minimal homol-ogy requirements for PCR primers. Nucleic Acids Res 17(16):6749
    • (1989) Nucleicacids Res , vol.17 , Issue.16 , pp. 6749
    • Sommer, R.1    Tautz, D.2
  • 29
    • 71549173409 scopus 로고    scopus 로고
    • RExPrimer: An integrated primer designing tool increases PCR effectiveness by avoiding 3′ SNP-in-primer and mis-priming from structural variation
    • Piriyapongsa J, Ngamphiw C, Assawamakin A, Wangkumhang P, Suwannasri P, Ruangrit U, Agavatpanitch G, Tongsima S (2009) RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3′ SNP-in-primer and mis-priming from structural variation. BMC Genomics 10 Suppl 3:S4. doi: 10.1186/1471-2164-10-S3-S4
    • (2009) BMC Genomics , vol.10 , pp. S4
    • Piriyapongsa, J.1    Ngamphiw, C.2    Assawamakin, A.3    Wangkumhang, P.4    Suwannasri, P.5    Ruangrit, U.6    Agavatpanitch, G.7    Tongsima, S.8
  • 31
    • 84871455595 scopus 로고    scopus 로고
    • Genotyping of fanconi anemia patientsby whole exome sequencing: Advantages and challenges
    • Knies K, Schuster B, Ameziane N, Rooimans M, Bettecken T, de Winter J, Schindler D (2012) Genotyping of fanconi anemia patients by whole exome sequencing: advantages and challenges. PLoS One 7(12):e52648. doi: 10.1371/journal.pone.0052648
    • (2012) Plos One , vol.7 , Issue.12 , pp. e52648
    • Knies, K.1    Schuster, B.2    Ameziane, N.3    Rooimans, M.4    Bettecken, T.5    De Winter, J.6    Schindler, D.7
  • 34
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8(3):186–194
    • (1998) Genome Res , vol.8 , Issue.3 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 35
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8(3):175–185
    • (1998) Genome Res , vol.8 , Issue.3 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 38
    • 56449095958 scopus 로고    scopus 로고
    • How segmental duplications shape our genome: Recent evolution of ABCC6 and PKD1 Mendelian disease genes
    • Symmons O, Varadi A, Aranyi T (2008) How segmental duplications shape our genome: recent evolution of ABCC6 and PKD1 Mendelian disease genes. Mol Biol Evol 25(12):2601–2613. doi: 10.1093/molbev/msn202
    • (2008) Mol Biol Evol , vol.25 , Issue.12 , pp. 2601-2613
    • Symmons, O.1    Varadi, A.2    Aranyi, T.3
  • 39
    • 0035874915 scopus 로고    scopus 로고
    • Homologues to the first gene for autosomal dominant poly-cystic kidney disease are pseudogenes
    • Bogdanova N, Markoff A, Gerke V, McCluskey M, Horst J, Dworniczak B (2001) Homologues to the first gene for autosomal dominant poly-cystic kidney disease are pseudogenes. Genomics 74(3):333–341. doi: 10.1006/geno.2001.6568
    • (2001) Genomics , vol.74 , Issue.3 , pp. 333-341
    • Bogdanova, N.1    Markoff, A.2    Gerke, V.3    McCluskey, M.4    Horst, J.5    Dworniczak, B.6
  • 42
    • 0036206745 scopus 로고    scopus 로고
    • Distinct BRCA1 rearrangements involving the BRCA1 pseudo-gene suggest the existence of a recombination hot spot
    • Puget N, Gad S, Perrin-Vidoz L, Sinilnikova OM, Stoppa-Lyonnet D, Lenoir GM, Mazoyer S (2002) Distinct BRCA1 rearrangements involving the BRCA1 pseudo-gene suggest the existence of a recombination hot spot. Am J Hum Genet 70(4):858–865. doi: 10.1086/339434
    • (2002) Am J Hum Genet , vol.70 , Issue.4 , pp. 858-865
    • Puget, N.1    Gad, S.2    Perrin-Vidoz, L.3    Sinilnikova, O.M.4    Stoppa-Lyonnet, D.5    Lenoir, G.M.6    Mazoyer, S.7
  • 43
    • 0030447834 scopus 로고    scopus 로고
    • The BRCA1 and 1A1.3B promoters are parallel elements of a genomic duplication at 17q21
    • Barker DF, Liu X, Almeida ER (1996) The BRCA1 and 1A1.3B promoters are parallel elements of a genomic duplication at 17q21. Genomics 38(2):215–222. doi: 10.1006/ geno.1996.0618
    • (1996) Genomics , vol.38 , Issue.2 , pp. 215-222
    • Barker, D.F.1    Liu, X.2    Almeida, E.R.3
  • 44
    • 0029934489 scopus 로고    scopus 로고
    • The 5′ end of the BRCA1 gene lies within a duplicated region of human chromosome 17q21
    • Brown MA, Xu CF, Nicolai H, Griffi ths B, Chambers JA, Black D, Solomon E (1996) The 5′ end of the BRCA1 gene lies within a duplicated region of human chromosome 17q21. Oncogene 12(12):2507–2513
    • (1996) Oncogene , vol.12 , Issue.12 , pp. 2507-2513
    • Brown, M.A.1    Xu, C.F.2    Nicolai, H.3    Griffi Ths, B.4    Chambers, J.A.5    Black, D.6    Solomon, E.7
  • 46
    • 73449142861 scopus 로고    scopus 로고
    • DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: Neurofi bromatosis type 1 gene as a model
    • Chou LS, Liu CS, Boese B, Zhang X, Mao R (2010) DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofi bromatosis type 1 gene as a model. Clin Chem 56(1):62–72. doi: 10.1373/clinc hem.2009.132639
    • (2010) Clin Chem , vol.56 , Issue.1 , pp. 62-72
    • Chou, L.S.1    Liu, C.S.2    Boese, B.3    Zhang, X.4    Mao, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.