Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches

Journal of Molecular Diagnostics

Volumn 11, Issue 4, 2009, Pages 311-318

  Voskarides, Konstantinos ^a   Deltas, Constantinos ^a,b  

^a UNIVERSITY OF CYPRUS   (Cyprus)

^b CYPRUS INSTITUTE OF NEUROLOGY AND GENETICS   (Cyprus)

Author keywords

[No Author keywords available]

Indexed keywords

HETERODUPLEX; NUCLEASE;

ARTICLE; BASE MISPAIRING; DIAGNOSTIC KIT; GENE; GENETIC HETEROGENEITY; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; KIDNEY; KIDNEY DISEASE; MUTATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEIN CLEAVAGE; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS;

BASE PAIR MISMATCH; BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; ENDONUCLEASES; GENETIC TESTING; HETERODUPLEX ANALYSIS; HUMANS; KIDNEY; KIDNEY DISEASES; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID HETERODUPLEXES; PLANT PROTEINS; SENSITIVITY AND SPECIFICITY;

EID: 69249086611     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2009.080144     Document Type: Article

References (42)

1. Oleykowski CA, Bronson Mullins CR, Godwin AK, Yeung AT: Mutation detection using a novel plant endonuclease. Nucleic Acids Res 1998, 26:4597-4602
2. Yang B, Wen X, Kodali NS, Oleykowski CA, Miller CG, Kulinski J, Besack D, Yeung JA, Kowalski D, Yeung AT: Purification, cloning, and characterization of CEL I nuclease. Biochemistry 2000, 39:3533-3541
3. Sokurenko EV, Tchesnokova V, Yeung AT, Oleykowski CA, Trintchina E, Hughes KT, Rashid RA, Brint JM, Moseley SL, Lory S: Detection of simple mutations and polymorphisms in large genomic regions. Nucleic Acids Res 2001, 29:e111
4. Qiu P, Shandilya H, D'Alessio JM, O'Connor K, Durocher J, Gerard GF: Mutation detection using Surveyor nuclease. BioTechniques 2004, 36:702-707
5. Smits BMG, van Zutphen BFM, Plasterk RHA, Cuppen E: Genetic variation in coding regions between and within commonly used inbred rat strains. Genome Res 2004, 14:1285-1290
6. Shi R, Otomo K, Yamada H, Tatsumi T, Sugawara I: Temperaturemediated heteroduplex analysis for the detection of drug-resistant gene mutations in clinical isolates of Mycobacterium tuberculosis by denaturing HPLC: SURVEYOR nuclease. Microbes Infect 2006, 8:128-135
7. Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Henikoff JG, Comai L, Henikoff S: Large-scale discovery of induced point mutations with high throughput TILLING. Genome Res 2003, 13:524-530
8. Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, Yoshida S, Parniske M: A TILLING reverse genetics tool and a Web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 2003, 131:866-871
9. Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RHA, Cuppen E: Efficient target-selected mutagenesis in zebrafish. Genome Res 2003, 13:2700-2707
10. Bannwarth S, Procaccio V, Paquis-Flucklinger V: Rapid identification of mitochondrial DNA (mtDNA) mutations in neuromuscular disorders by using surveyor strategy. Nat Protoc 2006, 1:2037-2047
11. Bannwarth S, Procaccio V, Rouzier C, Fragaki K, Poole J, Chabrol B, Desnuelle C, Pouget J, Azulay JP, Attarian S, Pellissier JF, Gargus JJ, Abdenur JE, Mozaffar T, Calvas P, Labauge P, Pages M, Wallace DC, Lambert JC, Paquis-Flucklinger V: Rapid identification of unknown heteroplasmic mutations across the entire human mitochondrial genome with mismatch-specific Surveyor nuclease. Mitochondrion 2008, 8:136-145
12. Qiu P, Shandilya H, Gerard GF: A method for clone confirmation using a mismatch-specific DNA endonuclease. Mol Biotechnol 2005, 29:11-18
13. Kulinski J, Besack D, Oleylowski CA, Godwin AK, Yeung AT: CEL I enzymatic mutation detection assay. BioTechniques 2000, 29:44-48
14. Janne PA, Borras AM, Kuang Y, Rogers AM, Joshi VA, Liyanage H, Lindeman N, Lee JC, Halmos B, Maher EA, Distel RJ, Meyerson M, Johnson BE: A rapid and sensitive enzymatic method for epidermal growth factor receptor mutation screening. Clin Cancer Res 2006, 12:751-758
15. Sattler M, Walz C, Crowley BJ, Lengfelder E, Janne PA, Rogers AM, Kuang Y, Distel RJ, Reiter A, Griffin JD: A sensitive high-throughput method to detect activating mutations of Jak2 in peripheral-blood samples. Blood 2006, 107:1237-1238
16. Nowak D, Mossner M, Baldus CD, Hopfer O, Hofmann WK: Mutation analysis of hCDC4 in AML cells identifies a new intronic polymorphism. Int J Med Sci 2006, 3:148-151
17. Wada T, Fukushima Y, Saitoh S: A new detection method for ATRX gene mutations using a mismatch-specific endonuclease. Am J Med Genet A 2006, 140:1519-1523
18. Shi Y, Terry SF, Terry PF, Bercovitch LG, Gerard GF: Development of a rapid, reliable genetic test for Pseudoxanthoma elasticum. J Mol Diagn 2007, 9:105-112
19. Mitani N, Niwa Y, Okamoto Y: Surveyor nuclease-based detection of p53 gene mutations in haematological malignancy. Ann Clin Biochem 2007, 44:557-559
20. Voskarides K, Makariou C, Papagregoriou G, Stergiou N, Printza N, Alexopoulos E, Elia A, Papachristou F, Georgaki E, Pierides A, Deltas C: NPHS2 screening with SURVEYOR nuclease in Hellenic children with steroid-resistant nephrotic syndrome. Pediatr Nephrol 2008, 23:1373-1375
21. Poeta ML, Manola J, Goldwasser MA, Forastiere A, Benoit N, Califano JA, Ridge JA, Goodwin J, Kenady D, Saunders J, Westra W, Sidransky D, Koch WM: TP53 mutations and survival in squamous-cell carcinoma of the head and neck. N Engl J Med 2007, 357:2552-2561
22. Voskarides K, Damianou L, Neocleous V, Zouvani I, Christodoulidou S, Hadjiconstantinou V, Ioannou K, Athanasiou Y, Patsias C, Alexopoulos E, Pierides A, Kyriakou K, Deltas C: COL4A3/COL4A4 mutations producing focal segmental glomerulosclerosis and renal failure in thin basement membrane nephropathy. J Am Soc Nephrol 2007, 18:3004-3016
23. Nollau P, Wagener C: Methods for detection of point mutations: performance and quality assessment. IFCC Scientific Division, Committee on Molecular Biology Techniques. Clin Chem 1997, 43:1114-1428
24. Mean R, Pierides A, Deltas C, Koptides M: Modification of the enzyme mismatch cleavage method using T7 endonuclease I and silver staining. BioTechniques 2004, 36:758-760
25. Yeung AT, Hattangadi D, Blakesley L, Nicolas E: Enzymatic mutation detection technologies. BioTechniques 2005, 38:749-758
26. Tsuji T, Niida Y: Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories. Electrophoresis 2008, 29:1473-1483
27. Kaplan JM, Kim SH, North KN, Rennke H, Correia LA, Tong HQ, Mathis BJ, Rodriguez-Perez JC, Allen PG, Beggs AH, Pollak MR: Mutations in ACTN4, encoding alpha-actinin-4, cause familial focal segmental glomerulosclerosis. Nat Genet 2000, 24:251-256
28. Winn MP, Conlon PJ, Lynn KL, Farrington MK, Creazzo T, Hawkins AF, Daskalakis N, Kwan SY, Ebersviller S, Burchette JL, Pericak-Vance MA, Howell DN, Vance JM, Rosenberg PB: A mutation in the TRPC6 cation channel causes familial focal segmental glomerulosclerosis. Science 2005, 308:1801-1804
29. Reiser J, Polu KR, Moller CC, Kenlan P, Altintas MM, Wei C, Faul C, Herbert S, Villegas I, Avila-Casado C, McGee M, Sugimoto H, Brown D, Kalluri R, Mundel P, Smith PL, Clapham DE, Pollak MR: TRPC6 is a glomerular slit diaphragm-associated channel required for normal renal function. Nat Genet 2005, 37:739-744
30. Lemmink HH, Nillesen WN, Mochizuki T, Schroder CH, Brunner HG, van Oost BA, Monnens LA, Smeets HJ: Benign familial. hematuria due to mutation of the type IV collagen α4 gene. J Clin Invest 1996, 98:1114-1118
31. Rana K, Wang YY, Buzza M, Tonna S, Zhang KW, Lin T, Sin L, Padavarat S, Savige J: The genetics of thin basement membrane nephropathy. Semin Nephrol 2005, 25:163-170
32. Christodoulou K, Tsingis M, Stavrou C, Eleftheriou A, Papapavlou P, Patsalis PC, Ioannou P, Pierides A, Constantinou Deltas C: Chromosome 1 localization of a gene for autosomal dominant medullary cystic kidney disease (ADMCKD). Hum Mol Genet 1998, 7:905-911
33. Boute N, Gribouval O, Roselli S, Benessy F, Lee H, Fuchshuber A, Dahan K, Gubler MC, Niaudet P, Antignac C: NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome. Nat Genet 2000, 24:349-354
34. Karle SM, Uetz B, Ronner V, Glaeser L, Hildebrandt F, Fuchshuber A: Novel mutations in NPHS2 detected in both familial and sporadic steroid-resistant nephrotic syndrome. J Am Soc Nephrol 2002, 13:388-393
35. Miller SA, Dykes DD, Polesky HF: A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988, 16:1215
36. Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999, 41:95-98
37. Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP, Ardlie K, Reich DE, Robinson E, Sklar P, Shah N, Thomas D, Fan JB, Gingeras T, Warrington J, Patil N, Hudson TJ, Lander ES: Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nat Genet 2000, 24:381-386
38. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, Weder A, Cooper R, Lipshutz R, Chakravarti A: Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 1999, 22:239-247
39. Bannwarth S, Procaccio V, Paquis-Flucklinger V: Surveyor nuclease: a new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects. Hum Mutat 2005, 25:575-582
40. Otto EA, Helou J, Allen SJ, O'Toole JF, Wise EL, Ashraf S, Attanasio M, Zhou W, Wolf MT, Hildebrandt F: Mutation analysis in nephronophthisis using a combined approach of homozygosity mapping: CEL I endonuclease cleavage, and direct sequencing. Hum Mutat 2008, 29:418-426
41. Scaffino MF, Pilotto A, Papadimitriou S, Sbalzarini M, Ansaldi S, Diegoli M, Porcu E, Grasso M, Brega A, Arbustini E: Heteroduplex detection with a plant DNA endonuclease for standard gel electrophoresis. Transgenics 2004, 4:157-166
42. Heidet L, Arrondel C, Forestier L, Cohen-Solal L, Mollet G, Gutierrez B, Stavrou C, Gubler MC, Antignac C: Structure of the human type IV collagen gene COL4A3 and mutations in autosomal Alport syndrome. J Am Soc Nephrol 2001, 12:97-106