Single-cell whole-genome amplification technique impacts the accuracy of SNP microarray-based genotyping and copy number analyses

Molecular Human Reproduction

Volumn 17, Issue 6, 2011, Pages 335-343

  Treff, Nathan R ^a,b   Su, Jing ^a   Tao, Xin ^a   Northrop, Lesley E ^a,b   Scott, Richard T ^a,b  

^a REPRODUCTIVE MEDICINE ASSOCIATES OF NEW JERSEY   (United States)

^b ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

Aneuploidy screening; Copy number; Single cell genotyping; SNP microarray; Whole genome amplification

Indexed keywords

ACCURACY; CONTROLLED STUDY; GENE AMPLIFICATION; GENE DOSAGE; GENOTYPE; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

CELL LINE; DNA FINGERPRINTING; FIBROBLASTS; GENE DOSAGE; GENOME, HUMAN; GENOTYPE; HUMANS; KARYOTYPING; NUCLEIC ACID AMPLIFICATION TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79957532985     PISSN: 13609947     EISSN: 14602407     Source Type: Journal    
DOI: 10.1093/molehr/gaq103     Document Type: Review

References (56)

1. Barker DL, Hansen MST, Faruqi AF, Giannola D, Irsula OR, Lasken RS, Latterich M, Makarov V, Oliphant A, Pinter JH. et al. Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res 2004;14:901-907.
2. Brukner I, Paquin B, Belouchi M, Labuda D, Krajinovic M. Self-priming arrest by modified random oligonucleotides facilitates the quality control of whole genome amplification. Anal Biochem 2005; 339:345-347.
3. Burlet P, Frydman N, Gigarel N, Kerbrat V, Tachdijian G, Feyereisen E, Bonnefont J, Frydman R, Munnich A, Steffann J. Multiple displacement amplification improves PGD for fragile X syndrome. Mol Hum Reprod 2006;12:647-652.
4. Cui XF, Li HH, Goradia TM, Lange K, Kasasian HH Jr, Galas D, Arnheim N. Single-sperm typing: determination of genetic distance between the G gamma-globin and parathyroid hormone loci by using the polymerase chain reaction and allele-specific oligomers. Proc Natl Acad Sci USA 1989;86:9389-9393.
5. Dean F, Hosono S, Fang L, Wu X, Faruqi A, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 2002; 99:5261-5266.
6. Dolezel J, Bartos J, Voglmayr H, Greihuber J. Nuclear DNA content and genome size of trout and human. Cytometry A 2003;51:127-128.
7. Escudero T, Pere C, Fischer J, Prates R, Tormasi S, Santiago M. Preimplantation genetic diagnosis (PGD) for reciprocal translocations using array comparative genome hybridization (aCGH). Fertil Steril 2010;94:S80-S81.
8. Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, Carter NP, Speicher MR. High resolution array-CGH analysis of single cells. Nucleic Acids Res 2007;35:1-10.
9. Fragouli E, Lensi M, Ross R, Katz-Jaffe M, Schoolcraft WB, Wells D. Comprehensive molecular cytogenetic analysis of the human blastocyst stage. Hum Reprod 2008;23:2596-2608.
10. Fritz MA. Perspectives on the efficacy and indications for preimplantation genetic screening: where are we now? Hum Reprod 2008; 23:2617-2621.
11. Gianaroli L, Magli MC, Ferraretti A, Fiorentino A, Garrisi J, Munne S. Preimplantation genetic diagnosis increases the implantation rate in human in vitro fertilization by avoiding the transfer of chromosomally abnormal embryos. Fertil Steril 1997;68:1128-1131.
12. Gutierrez-Mateo C, Colls P, Sanchez-Casas Padilla E, Escudero T, Prates R, Ketterson K, Wells D, Munne S. Validation of microarray comparative genomic hybridization for comprehensive chromosome analysis of embryos. Fertil Steril 2010; Oct. 23 [Epub ahead of print].
13. Handyside AH, Robinson MD, Simpson RJ, Omar MB, Shaw MA, Grudzinskas JG, Rutherford A. Isothermal whole genome amplification from single and small numbers of cells: a new era for preimplantation genetic diagnosis of inherited disease. Mol HumReprod 2004; 10:767-772.
14. Handyside AH, Harton GL, Mariani B, Thornhill AR, Affara NA, Shaw MA, Griffin DK. Karyomapping: a universal method for genome wide analysis of genetic disease based on mapping crossovers between parental haplotypes. J Med Genet 2009.
15. Handyside AH, Grifo J, Prates R, Tormasi S, Fisher JM, Munne S. Validation and first clinical application of karyomapping for preimplantation diagnosis (PGD) of Gaucher disease combined with 24 chromosome screening. Fertil Steril 2010;94:S79-S80.
16. Hellani A. Clinical application of multiple displacement amplification in preimplantation genetic diagnosis. RBM Online 2005;10:376-380.
17. Hellani A, Sammour A, Johansson L, El-Sheikh A. Delivery of a normal baby after preimplantation genetic diagnosis for non-ketotic hyperglycinaemia. Reprod Biomed Online 2008a;16:893-897.
18. Hellani A, Abu-Amero K, Azouri J, El-Akoum S. Successful pregnancies after application of array-comparative genomic hybridization in PGS-aneuploidy screening. Reprod Biomed Online 2008b;17: 841-847.
19. Johnson DS, Gemelos G, Baner J, Ryan A, Cinnioglu C, Banjevic M, Ross R, Alper M, Barrett B, Frederick J. et al. Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24 h protocol. Hum Reprod 2010a;25:1066-1075.
20. Johnson DS, Hill M, Abae M, Frederick J, Swanson M, Rabinowitz M. First clinical application of DNA microarrays for translocations and inversions. Fertil Steril 2010b;93:S13-S14.
21. Kahraman S, Bahce M, Samli H, Imirzahoglu N, Yakism K, Cengiz G, Donmez E. Healthy births and ongoing pregnancies obtained by preimplantation genetic diagnosis in patients with advanced maternal age and recurrent implantation failure. Hum Reprod 2000; 15:2003-2007.
22. Keskintepe L, Sher G, Keskintepe M. Reproductive oocyte/embryo genetic analysis: comparison between fluorescence in-situ hybridization and comparative genomic hybridization. Reprod Biomed Online 2007;15:303-309.
23. Lage JM, Leamon JH, Pejovic T, Hamann S, Lacey M, Dillon D, Segraves R, Vossbrinck B, González A, Pinkel D. et al. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 2003; 13:294-307.
24. Le Caignec C, Spits C, Sermon K, De Rycke M, Thienpont B, Debrock S, Staessen C, Moreau Y, Fryns JP, Van Steirteghem A. et al. Single-cell chromosomal imbalances detection by array CGH. Nucleic Acids Res 2006;34:e68.
25. Lledo B, Ten J, Galan F, Bernabeu R. Preimplantation genetic diagnosis of Marfan syndrome using multiple displacement amplification. Fertil Steril 2006;86:949-955.
26. Lledo B, Bernabeu R, Ten J, Galan F, Cioffi L. Preimplantation genetic diagnosis of X-linked adrenoleukodystrophy with gender determination using multiple displacement amplification. Fertil Steril 2007;88:1327-1333.
27. Lovmar L, Fredriksson M, Liljedahl U, Sigurdsson S, Syvanen AC. Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res 2003;31:129-139.
28. Munne S, Magli MC, Cohen J, Morton NE, Sadowy S, Gianaroli L, Tucker M, Marquez C, Sable D, Ferraretti A. et al. Positive outcome after preimplantation diagnosis of aneuploidy in human embryos. Hum Reprod 1999;14:2191-2199.
29. Munne S, Sandalinas M, Escudero T, Velilla E, Walmsley R, Sadowy S, Cohen J, Sable D. Improved implantation after preimplantation genetic diagnosis of aneuploidy. Reprod Biomed Online 2003;7:91-97.
30. Munne S, Fisher JM, Warner A, Chen S, Zouves C, Cohen J, Group at RCP. Preimplantation genetic diagnosis significantly reduces pregnancy loss in infertile couples: a multicenter study. Fertil Steril 2006;85:S178-S179.
31. Munne S, Surrey ES, Grifo J, Marut E, Opsahl M, Taylor TH. Preimplantation genetic diagnosis using a-CGH significantly increases ongoing pregnancy rates per transfer. Fertil Steril 2010;94:S81.
32. Northrop LE, Treff NR, Levy B, Scott RT Jr. SNP microarray-based 24 chromosome aneuploidy screening demonstrates that cleavage-stage FISH poorly predicts aneuploidy in embryos that develop to morphologically normal blastocysts. Mol Hum Reprod 2010;16: 590-600.
33. Panelli S, Damiani G, Espen L, Micheli G, Sgaramella V. Towards the analysis of the genomes of single cells: Further characterisation of the multiple displacement amplification. Gene 2006;372:1-7.
34. Park JW, Beaty TH, Boyce P, Scott AF, McIntosh I. Comparing whole-genome amplification methods and sources of biological samples for single-nucleotide polymorphism genotyping. Clin Chem 2005;5:1520-1523.
35. Rabinowitz M, Behr D, Potter D, Ross R, Alper M, Banjevic M. Parental support for single gene PGD and simultaneous 24-chromosome screening reduces risks of allele misdiagnosis and transfer of aneuploid embryos. Fertil Steril 2009;92:S202.
36. Rabinowitz M, Beltsos A, Potter D, Bush M, Givens C, Smotrich D. Effects of advanced maternal age are abrogated in 122 patients undergoing transfer of embryos with euploid microarray screening results at cleavage stage. Ferti Steril 2010;94:S80.
37. Ren Z, Zhou C, Xu Y, Deng J, Zeng H, Zeng Y. Mutation and haplotype analysis of Duchene muscular dystrophy by single cell multiple displacement amplification. Mol Hum Reprod 2007;13:431-436.
38. Renwick P, Lewis C, Abbs S, Ogilivie C. Determination of the genetic status of cleavage-stage human embryos by microsatellite marker analysis following multiple displacement amplification. Prenat Diagn 2007;27:206-215.
39. Saiki R, Gelfand D, Stoffel S, Scharf S, Higuchi R, Horn G, Mullis K, Erlich H. Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988;239:487-491.
40. Schoolcraft WB, Treff NR, Ferry K, Stevens JM, Katz-Jaffe MG, Scott RT. Clinical application of comprehensive chromosomal screening at the blastocyst stage. Fert Steril 2010a;94:S23.
41. Schoolcraft WB, Treff NR, Ferry K, Stevens JM, Katz-Jaffe MG, Scott RT. First clinical application of SNP microarray based 24 chromosome aneuploidy screening of human blastocysts. Fertil Steril 2010b;4:S23-S24.
42. Scott RT Jr, Treff NR. Assessing the reproductive competence of individual embryos: a proposal for the validation of new '-omics' technologies. Fertil Steril 2010;94:791-794.
43. Scott RT Jr, Miller KA, Olivares R, Su J, Fratterelli J, Treff NR. Microarray based 24 chromosome preimplantation genetic diagnosis (mPGD) is highly predictive of the reproductive potential of human embryos: a prospective blinded non-selection trial. Fertil Steril 2008;90:22.
44. Scott RT Jr, Tao X, Taylor D, Ferry K, Treff N. A prospective randomized controlled trial demonstrating significantly increased clinical pregnancy rates following 24 chromosome aneuploidy screening: biopsy and analysis on day 5 with fresh transfer. Fertil Steril 2010;94:S2.
45. Sher G, Keskintepe L, Keskintepe M, Ginsburg M, Maassarani G, Yakut T, Baltaci V, Kotze D, Unsal E. Oocyte karyotyping by comparative genomic hybridization provides a highly reliable method for selecting 'competent' embryos, markedly improving in vitro fertilization outcome: a multiphase study. Fertil Steril 2007;87:1033-1040.
46. Sher G, Keskintepe L, Keskintepe M, Maassarani G, Tortoriello D, Brody S. Genetic analysis of human embryos by metaphase comparative genomic hybridization (mCGH) improves efficiency of IVF by increasing embryo implantation rate and reducing multiple pregnancies and spontaneous miscarriages. Fertil Steril 2009;92:1886-1894.
47. Treff NR, Su J, Tao X, Miller K, Scott RT. First IVF babies born after rapid 24 chromosome embryo aneuploidy screening and fresh embryo transfer. Fertil Steril 2009a;92:S49.
48. Treff N, Tao X, Su J, Northrop LE, Kamani M, Bergh P, Miller K, Levy B, Scott R. SNP microarray based concurrent screening of 24 chromosome aneuploidy, unbalanced translocations, and single gene disorders in human embryos: first application of comprehensive triple factor PGD. Biol Reprod 2009b;81:188.
49. Treff NR, Tao X, Lonczak A, Su J, Taylor D, Scott R. Four hour 24 chromosome aneuploidy screening using high throughput PCR SNP allele ratio analyses. Fertil Steril 2009c;92:S49-S50.
50. Treff NR, Su J, Tao X, Levy B, Scott RT Jr. Accurate single cell 24 chromosome aneuploidy screening using whole genome amplification and single nucleotide polymorphism microarrays. Fertil Steril 2010a; 94:2017-2021.
51. Treff NR, Levy B, Su J, Northrop LE, Tao X, Scott RT Jr. SNP microarray-based 24 chromosome aneuploidy screening is significantly more consistent than FISH. Mol Hum Reprod 2010b; 16:583-589.
52. Treff N, Northrop LE, Kasabwala K, Su J, Levy B, Scott RT. SNP microarray based concurrent screening of 24 chromosome aneuploidy and unbalanced translocations in preimplantation human embryos. Fertil Steril 2010c; Nov. 29 [Epub ahead of print].
53. Vanneste E, Voet T, Le Caignec C, Ampe M, Konings P, Melotte C, Debrock S, Amyere M, Vikkula M, Schuit F. et al. Chromosome instability is common in human cleavage-stage embryos. Nat Med 2009;15:577-583.
54. Wells D, Delhanty JD. Comprehensive chromosomal analysis of human preimplantation embryos using whole genome amplification and single cell comparative genomic hybridization. Mol Hum Reprod 2000; 6:1055-1062.
55. Wells D, Sherlock JK, Handyside AH, Delhanty JD. Detailed chromosomal and molecular genetic analysis of single cells by whole genome amplification and comparative genomic hybridization. Nucleic Acids Res 1999;27:1214-1218.
56. Wells D, Fragouli E, Alfarawaty S, Munne S, Schoolcraft WB, Katz-Jaffe M. Highly significant improvement in embryo implantation and increased live birth rate achieved after comprehensive chromosomal screening: implications for single embryo transfer. Fertil Steril 2009;94:S79.