Methods for routine diagnosis of genomic rearrangements: Multiplex PCR-based methods and future perspectives

Expert Review of Molecular Diagnostics

Volumn 8, Issue 1, 2008, Pages 41-52

  De Lellis, Laura ^a   Curia, Maria Cristina ^a   Veschi, Serena ^a   Aceto, Gitana Maria ^a   Morgano, Annalisa ^a   Cama, Alessandro ^a  

^a UNIVERSITY OF CHIETI   (Italy)

Author keywords

Balanced rearrangement; Copy number; Locus specific; Molecular diagnosis; Routine application; Structural alteration; Unbalanced rearrangement; Whole genome

Indexed keywords

CAPILLARY ELECTROPHORESIS; DIAGNOSTIC PROCEDURE; GENE REARRANGEMENT; GENETIC DISORDER; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; IN SITU HYBRIDIZATION; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATIONAL ANALYSIS; POLYMERASE CHAIN REACTION; REVIEW; SCREENING; DNA MICROARRAY; GENOME; GERM CELL; METHODOLOGY;

GENE REARRANGEMENT; GENOME, HUMAN; GERM CELLS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION;

EID: 38149077389     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.8.1.41     Document Type: Review

References (57)

1. Shaw CJ, Lupski JR. Implications of human genome architecture for rearrangement based disorders: the genomic basis of disease. Hum. Mol. Genet. 13(1), R57-R64 (2004).
2. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat. Rev. Genet. 7, 85-97 (2006). •• Comprehensive and detailed review that discusses the different types of structural variants discovered in the human genome, the methods employed to detect them and the most relevant studies lead in this field.
3. Lupski JR, Stankiewicz P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 1, e49 (2005).
4. Seabright M. A rapid banding technique for human chromosomes. Lancet 2, 971-2 (1971).
5. Pinkel D, Straume T, Gray JW. Cytogenetic analysis using quantitative, high sensitivity, fluorescence hybridization. Proc. Natl Acad. Sci. USA 83, 2934-2938 (1986).
6. Mundle SD, Sokolova I. Clinical implications of advanced molecular cytogenetics in cancer. Expert Rev. Mol. Diagn. 4, 71-81 (2004). • Excellent review on advantages and limitations of FISH and other cytogenetic methods.
7. Parra I, Windle B. High resolution visual mapping of stretched DNA by fluorescent hybridization. Nat. Genet. 5, 17-21 (1993).
8. Schrock E, du Manoir S, Veldman T et al. Multicolor spectral karyotyping of human chromosomes. Science 273, 494-497 (1996).
9. Wijnen J, van der Klift H, Vasen H et al. MSH2 genomic deletions are a frequent cause of HNPCC. Nat. Genet. 20, 326-328 (1998).
10. Nakagawa H, Hampel H, de la Chapelle A. Identification and characterization of genomic rearrangements of MSH2 and MLH1 in Lynch syndrome (HNPCC) by novel techniques. Hum. Mutat. 22, 258 (2003).
11. Sebat J, Lakshmi B, Troge J et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004). •• One of the earliest studies that reports a global view about the distribution of copy number polymorphisms in the human genome using high-density representional oligonucleotide microarray analysis.
12. Iafrate AJ, Feuk L, Rivera MN et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949-51 (2004). •• Extensive analysis of large-scale copy number variations throughout the genome of control individuals, which collected all the variations detected into the available Genome Variation Database.
13. Dhami P, Coffey AJ, Abbs S et al. Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. Am. J. Hum. Genet. 76, 750-762 (2005).
14. Vissers LE, Veltman JA, van Kessel AG, Brunner HG. Identification of disease genes by whole genome CGH arrays. Hum. Mol. Genet. 14 Spec No. 2, R215-R223 (2005).
15. Lucito R, Healy J, Alexander J et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291-305 (2003).
16. Barrett MT, Scheffer A, Ben-Dor A et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl Acad. Sci. USA 101, 17765-17770 (2004).
17. Solinas-Toldo S, Lampel S, Stilgenbauer S et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20, 399-407 (1997).
18. De Lellis L, Curia MC, Catalano T et al. Combined use of MLPA and nonfluorescent multiplex PCR analysis by high performance liquid chromatography for the detection of genomic rearrangements. Hum. Mutat. 27, 1047-1056 (2006).
19. Hall N. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210, 1518-1525 (2007). •• Detailed overview about features, applications, advantages and limitations of new technologies for genomic high-throughput sequencing.
20. Bieche I, Olivi M, Champeme MH, Vidaud D, Lidereau R, Vidaud M. Novel approach to quantitative polymerase chain reaction using real-time detection: application to the detection of gene amplification in breast cancer. Int. J. Cancer 78, 661-666 (1998).
21. Armour JA, Barton DE, Cockburn DJ, Taylor GR. The detection of large deletions or duplications in genomic DNA. Hum. Mutat. 20, 325-337 (2002).
22. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30, e57 (2002).
23. Armour JA, Sismani C, Patsalis PC, Cross G. Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res. 28, 605-609 (2000).
24. Charbonnier F, Raux G, Wang Q et al. Detection of exon deletions and duplications of the mismatch repair genes in hereditary nonpolyposis colorectal cancer families using multiplex polymerase chain reaction of short fluorescent fragments. Cancer Res. 60, 2760-2763 (2000).
25. Dehainault C, Lauge A, Caux-Moncoutier V et al. Multiplex PCR/liquid chromatography assay for detection of gene rearrangements: application to RB1 gene. Nucleic Acids Res. 32, e139 (2004).
26. Gibbons B, Datta P, Wu Y, Chan A, Al Armour J. Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA. BMC Genomics 7, 163 (2006).
27. Houdayer C, Gauthier-Villars M, Lauge A et al. Comprehensive screening for constitutional RB1 mutations by DHPLC and QMPSF. Hum. Mutat. 23, 193-202 (2004).
28. White S, Kalf M, Liu Q et al. Comprehensive detection of genomic duplications and deletions in the DMD gene, by use of multiplex amplifiable probe hybridization. Am. J. Hum. Genet. 71, 365-374 (2002).
29. Combes P, Bonnet-Dupeyron MN, Gauthier-Barichard F et al. PLP1 and GPM6B intragenic copy number analysis by MAPH in 262 patients with hypomyelinating leukodystrophies: identification of one partial triplication and two partial deletions of PLP1. Neurogenetics 7, 31-37 (2006).
30. Patsalis PC, Kousoulidou L, Mannik K et al. Detection of small genomic imbalances using microarray-based multiplex amplifiable probe hybridization. Eur. J. Hum. Genet. 15, 162-172 (2007).
31. Casilli F, Di Rocco ZC, Gad S et al. Rapid detection of novel BRCA1 rearrangements in high-risk breast-ovarian cancer families using multiplex PCR of short fluorescent fragments. Hum. Mutat. 20, 218-226 (2002).
32. Rovelet-Lecrux A, Hannequin D, Raux G et al. APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat. Genet. 38, 24-26 (2006).
33. Audrézet MP, Chen JM, Raguenes O et al. Genomic rearrangements in the CFTR gene: extensive allelic heterogeneity and diverse mutational mechanisms. Hum. Mutat. 23, 343-357 (2004).
34. Duponchel C, Di Rocco C, Cicardi M, Tosi M. Rapid detection by fluorescent multiplex PCR of exon deletions and duplications in the C1 inhibitor gene of hereditary angioedema patients. Hum. Mutat. 17, 61-70 (2001). • Study that extensively discusses the useful addition of universal hexadecamer sequences on the 5′-end of multiplex PCR primers in order to improve the linearity and reproducibility of multiplex PCR reactions.
35. Su YN, Hung CC, Li H et al. Quantitative analysis of SMN1 and SMN2 genes based on DHPLC: a highly efficient and reliable carrier-screening test. Hum. Mutat. 25, 460-467 (2005).
36. Kumar J, Kumar A, Das SK, Shukla G, Sengupta S. Detection of differential gene copy number using denaturing high performance liquid chromatography. J. Biochem. Biophys. Methods 64, 226-234 (2005).
37. Naimi M, Tardieu S, Depienne C et al. Detection of genomic rearrangements by DHPLC: a prospective study of 90 patients with inherited peripheral neuropathies associated with 17p11.2 rearrangements. Am. J. Med. Genet. 136, 136-139 (2005).
38. Hung CC, Su YN, Lin CY et al. Denaturing HPLC coupled with multiplex PCR for rapid detection of large deletions in Duchenne muscular dystrophy carriers. Clin. Chem. 51, 1252-1256 (2005).
39. Charbonnier F, Olschwang S, Wang Q et al. MSH2 in contrast to MLH1 and MSH6 is frequently inactivated by exonic and promoter rearrangements in hereditary nonpolyposis colorectal cancer. Cancer Res. 62, 848-853 (2002).
40. Wang Y, Friedl W, Sengteller M et al. A modified multiplex PCR assay for detection of large deletions in MSH2 and MLH1. Hum. Mutat. 19, 279-286 (2002).
41. Tournier I, Paillerets BB, Sobol H et al. Significant contribution of germline BRCA2 rearrangements in male breast cancer families. Cancer Res. 64, 8143-8147 (2004).
42. Bellanne-Chantelot C, Clauin S, Chauveau D et al. Large genomic rearrangements in the hepatocyte nuclear factor-1β (TCF2) gene are the most frequent cause of maturity-onset diabetes of the young type 5. Diabetes 54, 3126-3132 (2005).
43. Spentchian M, Brun-Heath I, Taillandier A et al. Characterization of missense mutations and large deletions in the ALPL gene by sequencing and quantitative multiplex PCR of short fragments. Genet. Test. 10, 252-257 (2006).
44. Wehner M, Mangold E, Sengteller M et al. Hereditary nonpolyposis colorectal cancer: pitfalls in deletion screening in MSH2 and MLH1 genes. Eur. J. Hum. Genet. 13, 983-986 (2005).
45. Udaka T, Kurosawa K, Izumi K et al. Screening for partial deletions in the CREBBP gene in Rubinstein-Taybi syndrome patients using multiplex PCR/liquid chromatography. Genet. Test. 10, 265-271 (2006).
46. Kurahashi H, Shaikh TH, Zackai EH et al. Tightly clustered 11q23 and 22q11 breakpoints permit PCR-based detection of the recurrent constitutional t(11;22). Am. J. Hum. Genet. 67, 763-768 (2000).
47. Liu YT, Carson DA. A novel approach for determining cancer genomic breakpoints in the presence of normal DNA. PLoS ONE 2, e380 (2007).
48. Guillaud-Bataille M, Valent A, Soularue P et al. Detecting single DNA copy number variations in complex genomes using one nanogram of starting DNA and BAC-array CGH. Nucleic Acids Res. 32, e112 (2004).
49. Thomas RK, Nickerson E, Simons JF et al. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat. Med. 12, 852-855 (2006).
50. Charbonnier F, Baert-Desurmont S, Liang P et al. The 5′ region of the MSH2 gene involved in hereditary non-polyposis colorectal cancer contains a high density of recombinogenic sequences. Hum. Mutat. 26, 255-261 (2005).
51. Urban AE, Korbel JO, Selzer R et al. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc. Natl Acad. Sci. USA 103, 4534-4539 (2006). •• First high-resolution array-CGH method for accurate detection of DNA copy number changes in chromosome 22 using isothermal high-density tiling arrays and genomic DNA from patient with complex genetic disorders.
52. Pinkel D, Segraves R, Sudar D et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20, 207-211 (1998).
53. Bertone P, Stolc V, Royce TE et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242-2246 (2004).
54. MRC-Holland www.mrc-holland.com
55. PamGene www.pamgene.com
56. Primer Premier 5 www.premierbiosoft.com/primerdesign/index.html
57. FastPCR www.biocenter.helsinki.fi/bi/Programs/fastpcr.htm