Validation of copy number variation sequencing for detecting chromosome imbalances in human preimplantation embryos

Biology of Reproduction

Volumn 91, Issue 2, 2014, Pages

  Wang, Li ^a   Cram, David S ^b   Shen, Jiandong ^c   Wang, Xiaohong ^d   Zhang, Jianguang ^b   Song, Zhuo ^b   Xu, Genming ^b   Li, Na ^d   Fan, Junmei ^a   Wang, Shufang ^a   Luo, Yaning ^a   Wang, Jun ^d   Yu, Li ^a   Liu, Jiayin ^c   Yao, Yuanqing ^a  

^a CHINESE PLA GENERAL HOSPITAL   (China)

^b Limited   (China)

^c NANJING MEDICAL UNIVERSITY   (China)

^d FOURTH MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Array CGH; Blastomere biopsy; Copy number variation sequencing; Embryos; Preimplanation genetic diagnosis

Indexed keywords

ANEUPLOIDY; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CRYOPRESERVATION; DIAGNOSIS; DIAGNOSTIC ACCURACY; EMBRYO; FERTILIZATION IN VITRO; GENE AMPLIFICATION; GENE MAPPING; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN TISSUE; PREIMPLANTATION EMBRYO; PREIMPLANTATION GENETIC DIAGNOSIS; PRIORITY JOURNAL; RETROSPECTIVE STUDY; SENSITIVITY AND SPECIFICITY; SINGLE CELL ANALYSIS; VALIDATION STUDY; BLASTOCYST; POLYMERASE CHAIN REACTION; PRENATAL DIAGNOSIS; PROCEDURES; REPRODUCIBILITY;

ANEUPLOIDY; BLASTOCYST; FERTILIZATION IN VITRO; HUMANS; POLYMERASE CHAIN REACTION; PREIMPLANTATION DIAGNOSIS; REPRODUCIBILITY OF RESULTS;

EID: 84928823213     PISSN: 00063363     EISSN: 15297268     Source Type: Journal    
DOI: 10.1095/biolreprod.114.120576     Document Type: Article

References (36)

1. Hardy K, Handyside AH. Biopsy of cleavage stage human embryos and diagnosis of single gene defects by DNA amplification. Arch Pathol Lab Med 1992; 116:388-392.
2. Munne S. Preimplantation genetic diagnosis for aneuploidy and translocations using array comparative genomic hybridization. Curr Genomics 2012; 13:463-470.
3. Munne S, Weier HU. Simultaneous enumeration of chromosomes 13, 18, 21, X, and Y in interphase cells for preimplantation genetic diagnosis of aneuploidy. Cytogenet Cell Genet 1996; 75:263-270.
4. Munne S, Sandalinas M, Escudero T, Fung J, Gianaroli L, Cohen J. Outcome of preimplantation genetic diagnosis of translocations. Fertil Steril 2000; 73:1209-1218.
5. Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 1992; 13:718-725.
6. Wilton L, Williamson R, McBain J, Edgar D, Voullaire L. Birth of a healthy infant after preimplantation confirmation of euploidy by comparative genomic hybridization. N Engl J Med 2001; 345:1537-1541.
7. Fiorentino F, Spizzichino L, Bono S, Biricik A, Kokkali G, Rienzi L, Ubaldi FM, Iammarrone E, Gordon A, Pantos K. PGD for reciprocal and Robertsonian translocations using array comparative genomic hybridization. Hum Reprod 2011; 26:1925-1935.
8. Schoolcraft WB, TreffNR, Stevens JM, Ferry K, Katz-Jaffe M, Scott RT Jr. Live birth outcome with trophectoderm biopsy, blastocyst vitrification, and single-nucleotide polymorphism microarray-based comprehensive chromosome screening in infertile patients. Fertil Steril 2011; 96:638-640.
9. Tan YQ, Tan K, Zhang SP, Gong F, Cheng DH, Xiong B, Lu CF, Tang XC, Luo KL, Lin G, Lu GX. Single-nucleotide polymorphism microarraybased preimplantation genetic diagnosis is likely to improve the clinical outcome for translocation carriers. Hum Reprod 2013; 28:2581-2592.
10. TreffNR, Tao X, Ferry KM, Su J, Taylor D, Scott RT Jr. Development and validation of an accurate quantitative real-time polymerase chain reaction-based assay for human blastocyst comprehensive chromosomal aneuploidy screening. Fertil Steril 2012; 97:819-824.
11. Kuliev A, Zlatopolsky Z, Kirillova I, Spivakova J, Cieslak Janzen J. Meiosis errors in over 20,000 oocytes studied in the practice of preimplantation aneuploidy testing. Reprod Biomed Online 2011; 22:2-8.
12. Voet T, Vanneste E, Van der Aa N, Melotte C, Jackmaert S, Vandendael T, Declercq M, Debrock S, Fryns JP, Moreau Y, D'Hooghe T, Vermeesch JR. Breakage-fusion-bridge cycles leading to inv dup del occur in human cleavage stage embryos. Hum Mutat 2011; 32:783-793.
13. Voet T, Vanneste E, Vermeesch JR. The human cleavage stage embryo is a cradle of chromosomal rearrangements. Cytogenet Genome Res 2011; 133:160-168.
14. Vanneste E, Voet T, Le Caignec C, Ampe M, Konings P, Melotte C, Debrock S, Amyere M, Vikkula M, Schuit F, Fryns JP, Verbeke G, et al. Chromosome instability is common in human cleavage-stage embryos. Nat Med 2009; 15:577-583.
15. Hou Y, Fan W, Yan L, Li R, Lian Y, Huang J, Li J, Xu L, Tang F, Xie XS, Qiao J. Genome analyses of single human oocytes. Cell 2013; 155:1492-1506.
16. Wang L, Wang X, Zhang J, Song Z, Wang S, Gao Y, Wang J, Luo Y, Niu Z, Yue X, Xu G, Cram DS, et al. Detection of chromosomal aneuploidy in human preimplantation embryos by next-generation sequencing. Biol Reprod 2014; 90:95.
17. Fiorentino F, Biricik A, Bono S, Spizzichino L, Cotroneo E, Cottone G, Kokocinski F, Michel CE. Development and validation of a nextgeneration sequencing-based protocol for 24-chromosome aneuploidy screening of embryos. Fertil Steril 2014; 101:1375-1382.
18. Yin X, Tan K, Vajta G, Jiang H, Tan Y, Zhang C, Chen F, Chen S, Pan X, Gong C, Li X, Lin C, et al. Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts. Biol Reprod 2013; 88:69.
19. Song Y, Liu C, Qi H, Zhang Y, Bian X, Liu J. Noninvasive prenatal testing of fetal aneuploidies by massively parallel sequencing in a prospective Chinese population. Prenat Diagn 2013; 33:700-706.
20. Wang Y, Chen Y, Tian F, Zhang J, Song Z, Wu Y, Han X, Hu W, Ma D, Cram D, Cheng W. Maternal mosaicism is a significant contributor to discordant sex shromosomal aneuploidies associated with noninvasive prenatal testing. Clin Chem 2013; 60:251-259.
21. Wang Y, Zhu J, Chen Y, Lu S, Chen B, Zhao X, Wu Y, Han X, Ma D, Liu Z, Cram D, Cheng W. Two cases of placental T21 mosaicism: challenging the detection limits of non-invasive prenatal testing. Prenat Diagn 2013; 33:1207-1210.
22. Mao J, Wang T, Wang BJ, Liu YH, Li H, Zhang J, Cram D, Chen Y. Confined placental origin of the circulating cell free fetal DNA revealed by a discordant non-invasive prenatal test result in a trisomy 18 pregnancy. Clin Chim Acta 2014; 433:190-193.
23. Yu C, Wang L, Li J, Guo C, Guo X, Zhang X, Xu Y, Yao Y. Ovarian stimulation reduces IL-6 release from mouse and human pre-implantation embryos. Am J Reprod Immunol 2012; 68:199-204.
24. Shen J, Cram DS, Wu W, Cai L, Yang X, Sun X, Cui Y, Liu J. Successful PGD for late infantile neuronal ceroid lipofuscinosis achieved by combined chromosome and TPP1 gene analysis. Reprod Biomed Online 2013; 27:176-183.
25. Liang D, Lv W, Wang H, Xu L, Liu J, Li H, Hu L, Peng Y, Wu L. Noninvasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing. Prenat Diagn 2013; 33:409-415.
26. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25:1754-1760.
27. Hocking TD, Schleiermacher G, Janoueix-Lerosey I, Boeva V, Cappo J, Delattre O, Bach F, Vert JP. Learning smoothing models of copy number profiles using breakpoint annotations. BMC Bioinformatics 2013; 14:164.
28. Picard F, Robin S, Lavielle M, Vaisse C, Daudin JJ. A statistical approach for array CGH data analysis. BMC Bioinformatics 2005; 6:27.
29. TreffNR, Su J, Tao X, Northrop LE, Scott RT, Jr. Single-cell wholegenome amplification technique impacts the accuracy of SNP microarraybased genotyping and copy number analyses. Mol Hum Reprod 2011; 17:335-343.
30. Van der Aa N, Esteki MZ, Vermeesch JR, Voet T. Preimplantation genetic diagnosis guided by single-cell genomics. Genome Med 2013; 5:71.
31. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med 2010; 61:437-455.
32. Simpson JL, Samango-Sprouse C. Prenatal diagnosis and 47, XXY. Am J Med Genet C Semin Med Genet 2013; 163C:64-70.
33. Schoolcraft WB, Katz-Jaffe MG. Comprehensive chromosome screening of trophectoderm with vitrification facilitates elective single-embryo transfer for infertile women with advanced maternal age. Fertil Steril 2013; 100:615-619.
34. Liu J, Wang W, Sun X, Liu L, Jin H, Li M, Witz C, Williams D, Griffith J, Skorupski J, Haddad G, Gill J. DNA microarray reveals that high proportions of human blastocysts from women of advanced maternal age are aneuploid and mosaic. Biol Reprod 2012; 87:148.
35. Handyside AH. 24-chromosome copy number analysis: a comparison of available technologies. Fertil Steril 2013; 100:595-602.
36. Schaaf CP, Wiszniewska J, Beaudet AL. Copy number and SNP arrays in clinical diagnostics. Annu Rev Genomics Hum Genet2011; 12:25-51.