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Cited by 52Prenatal Screening and DiagnosticsGenomics and Rare DiseasesGenomics and Phylogenetic Studies

Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing

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Volozonoka, Ludmila, Miskova, Anna, Gailite, Linda·2022·International Journal of Molecular Sciences
DOI 10.3390/ijms23094819PMC PMC9102663
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Abstract

Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim of this review is to provide insight into the performance and drawbacks of DOP-PCR, MDA and MALBAC, as well as the hybrid WGA techniques most widely used in PGT. As the field of PGT is moving towards a wide adaptation of comprehensive massively parallel sequencing (MPS)-based approaches, we especially focus our review on MPS parameters and detection opportunities of WGA-amplified material, i.e., mappability of reads, uniformity of coverage and its influence on copy number variation analysis, and genomic coverage and its influence on single nucleotide variation calling. The ability of MDA-based WGA solutions to better cover the targeted genome and the ability of PCR-based solutions to provide better uniformity of coverage are highlighted. While numerous comprehensive PGT solutions exploiting different WGA types and adjusted bioinformatic pipelines to detect copy number and single nucleotide changes are available, the ones exploiting MDA appear more advantageous. The opportunity to fully analyse the targeted genome is influenced by the MPS parameters themselves rather than the solely chosen WGA.

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  • The complexity of genomes, including structural variations and non-coding regions, presents a significant challenge for alignment.

    “The complexity of genomes, including structural variations and non-coding regions, presents a significant challenge for alignment [79].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [79]

    Section 5.1 (Mappability of Reads; page unavailable) discusses reads that fail to align to a reference genome, but attributes them to factors such as primer dimers, short fragments and non-target DNA. Our copy does not say that structural variations or non-coding regions make genome alignment difficult. Searched for those terms and for mapping-related passages. (LLM, conf=0.76)

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  1. [1]Coutelle C. Williams C. Handyside A. Hardy K. Winston R. Williamson R. Genetic analysis of DNA from single human oocytes: A model for preimplantation diagnosis of cystic fibrosis Br. Med. J. 1989 299 22 24 10.1136/bmj.299.6690.22 2503195 PMC1837017 · DOI
  2. [2]Zhang L. Cui X. Schmitt K. Hubert R. Navidi W. Arnheim N. Whole genome amplification from a single cell: Implications for genetic analysis Proc. Natl. Acad. Sci. USA 1992 89 5847 5851 10.1073/pnas.89.13.5847 1631067 PMC49394 · DOI
  3. [3]Telenius H. Carter N.P. Bebb C.E. Nordenskjöld M. Ponder B.A.J. Tunnacliffe A. Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single degenerate primer Genomics 1992 13 718 725 10.1016/0888-7543(92)90147-K 1639399 · DOI
  4. [4]Toft C.L.F. Ingerslev H.J. Kesmodel U.S. Diemer T. Degn B. Ernst A. Okkels H. Kjartansdóttir K.R. Pedersen I.S. A systematic review on concurrent aneuploidy screening and preimplantation genetic testing for hereditary disorders: What is the prevalence of aneuploidy and is there a clinical effect from aneuploidy screening? Acta Obstet. Gynecol. Scand. 2020 99 696 706 10.1111/aogs.13823 32039470 · DOI
  5. [5]Kuliev A. Rechitsky S. Preimplantation genetic testing: Current challenges and future prospects Expert Rev. Mol. Diagn. 2017 17 1071 1088 10.1080/14737159.2017.1394186 29039978 · DOI
  6. [6]ESHRE PGT-M Working Group Carvalho F. Moutou C. Dimitriadou E. Dreesen J. Giménez C. Goossens V. Kakourou G. Vermeulen N. Zuccarello D. ESHRE PGT Consortium good practice recommendations for the detection of monogenic disorders Hum. Reprod. Open 2020 2020 hoaa018 10.1093/hropen/hoaa018 32500103 PMC7257022 · DOI
  7. [7]Harper J.C. Wilton L. Traeger-Synodinos J. Goossens V. Moutou C. SenGupta S.B. Pehlivan Budak T. Renwick P. De Rycke M. Geraedts J.P.M. The ESHRE PGD consortium: 10 years of data collection Hum. Reprod. Update 2012 18 234 247 10.1093/humupd/dmr052 22343781 · DOI
  8. [8]Rechitsky S. Pakhalchuk T. San Ramos G. Goodman A. Zlatopolsky Z. Kuliev A. First systematic experience of preimplantation genetic diagnosis for single-gene disorders, and/or preimplantation human leukocyte antigen typing, combined with 24-chromosome aneuploidy testing Fertil. Steril. 2015 103 503 512 10.1016/j.fertnstert.2014.11.007 25516085 · DOI
  9. [9]Cimadomo D. Capalbo A. Ubaldi F.M. Scarica C. Palagiano A. Canipari R. Rienzi L. The Impact of Biopsy on Human Embryo Developmental Potential during Preimplantation Genetic Diagnosis BioMed Res. Int. 2016 2016 7193075 10.1155/2016/7193075 26942198 PMC4749789 · DOI
  10. [10]Scott K.L. Hong K.H. Scott R.T. Selecting the optimal time to perform biopsy for preimplantation genetic testing Fertil. Steril. 2013 100 608 614 10.1016/j.fertnstert.2013.07.004 23993663 · DOI
  11. [11]Czyz Z.T. Kirsch S. Polzer B. Principles of whole-genome amplification Whole Genome Amplification: Methods and Protocols Springer Berlin/Heidelberg, Germany 2015
  12. [12]Kristjansson K. Chong S.S. Van den Veyver I.B. Subramanian S. Snabes M.C. Hughes M.R. Preimplantation single cell analyses of dystrophin gene deletions using whole genome amplification Nat. Genet. 1994 6 19 23 10.1038/ng0194-19 8136827 · DOI
  13. [13]Sermon K. Lissens W. Joris H. Van Steirteghem A. Liebaers I. Adaptation of the primer extension preamplification (PEP) reaction for preimplantation diagnosis: Single blastomere analysis using short PEP protocols Mol. Hum. Reprod. 1996 2 209 212 10.1093/molehr/2.3.209 9238681 · DOI
  14. [14]Snabes M.C. Chong S.S. Subramanian S.B. Kristjansson K. DiSepio D. Hughes M.R. Preimplantation single-cell analysis of multiple genetic loci by whole- genome amplification Proc. Natl. Acad. Sci. USA 1994 91 6181 6185 10.1073/pnas.91.13.6181 7517043 PMC44162 · DOI
  15. [15]Xu K. Tang Y. Grifo J.A. Rosenwaks Z. Cohen J. Preimplantation diagnosis: Primer extension preamplification for detection of multiple genetic loci from single human blastomeres Hum. Reprod. 1993 8 2206 2210 10.1093/oxfordjournals.humrep.a138004 8150925 · DOI
  16. [16]Telenius H. Ponder B.A. Tunnacliffe A. Pelmear A.H. Carter N.P. Ferguson-Smith M.A. Behmel A. Nordenskjöld M. Pfragner R. Cytogenetic analysis by chromosome painting using dop-pcr amplified flow-sorted chromosomes Genes Chromosom. Cancer 1992 4 257 263 10.1002/gcc.2870040311 1382568 · DOI
  17. [17]Cheung V.G. Nelson S.F. Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA Proc. Natl. Acad. Sci. USA 1996 93 14676 14679 10.1073/pnas.93.25.14676 8962113 PMC26194 · DOI
  18. [18]Bonnette M.D. Pavlova V.R. Rodier D.N. Thompson L.P. Boone E.L. Brown K.L. Meyer K.M. Trevino M.B. Champagne J.R. Cruz T.D. dcDegenerate oligonucleotide primed-PCR for multilocus, genome-wide analysis from limited quantities of DNA Diagn. Mol. Pathol. 2009 18 165 175 10.1097/PDM.0b013e31818d34d1 19704262 · DOI
  19. [19]Kittler R. Stoneking M. Kayser M. A whole genome amplification method to generate long fragments from low quantities of genomic DNA Anal. Biochem. 2002 300 237 244 10.1006/abio.2001.5460 11779116 · DOI
  20. [20]Wells D. Sherlock J.K. Handyside A.H. Delhanty J.D.A. Detailed chromosomal and molecular genetic analysis of single cells by whole genome amplification and comparative genomic hybridisation Nucleic Acids Res. 1999 27 1214 1218 10.1093/nar/27.4.1214 9927758 PMC148305 · DOI
  21. [21]Fragouli E. Lenzi M. Ross R. Katz-Jaffe M. Schoolcraft W.B. Wells D. Comprehensive molecular cytogenetic analysis of the human blastocyst stage Hum. Reprod. 2008 23 2596 2608 10.1093/humrep/den287 18664475 · DOI
  22. [22]Del Rey J. Vidal F. Ramírez L. Borràs N. Corrales I. Garcia I. Martinez-Pasarell O. Fernandez S.F. Garcia-Cruz R. Pujol A. Novel double factor PGT strategy analyzing blastocyst stage embryos in a single NGS procedure PLoS ONE 2018 13 e0205692 30332465 PMC6192598
  23. [23]Dean F.B. Nelson J.R. Giesler T.L. Lasken R.S. Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification Genome Res. 2001 11 1095 1099 10.1101/gr.180501 11381035 PMC311129 · DOI
  24. [24]Esteban J.A. Salas M. Blanco L. Fidelity of φ29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization J. Biol. Chem. 1993 268 2719 2726 10.1016/S0021-9258(18)53833-3 8428945 · DOI
  25. [25]Huang L. Ma F. Chapman A. Lu S. Xie X.S. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications Annu. Rev. Genom. Hum. Genet. 2015 16 79 102 10.1146/annurev-genom-090413-025352 26077818 · DOI
  26. [26]Handyside A.H. Robinson M.D. Simpson R.J. Omar M.B. Shaw M.A. Grudzinskas J.G. Rutherford A. Isothermal whole genome amplification from single and small numbers of cells: A new era for preimplantation genetic diagnosis of inherited disease Mol. Hum. Reprod. 2004 10 767 772 10.1093/molehr/gah101 15322224 · DOI
  27. [27]Hellani A. Coskun S. Tbakhi A. Al-Hassan S. Clinical application of multiple displacement amplification in preimplantation genetic diagnosis Reprod. Biomed. Online 2005 10 376 380 10.1016/S1472-6483(10)61799-3 15820046 · DOI
  28. [28]Handyside A.H. Harton G.L. Mariani B. Thornhill A.R. Affara N. Shaw M.A. Griffin D.K. A universal method for genome wide analysis of genetic disease based on mapping crossovers between parental haplotypes J. Med. Genet. 2010 47 651 658 10.1136/jmg.2009.069971 19858130 · DOI
  29. [29]Zong C. Lu S. Chapman A.R. Xie X.S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell Science 2012 338 1622 1626 10.1126/science.1229164 23258894 PMC3600412 · DOI · Paper page
  30. [30]Li N. Wang L. Wang H. Ma M. Wang X. Li Y. Zhang W. Zhang J. Cram D.S. Yao Y. The Performance of Whole Genome Amplification Methods andNext-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities J. Genet. Genom. 2015 42 151 159 10.1016/j.jgg.2015.03.001 25953353 · DOI
  31. [32]Huang J. Yan L. Fan W. Zhao N. Zhang Y. Tang F. Xie X.S. Qiao J. Validation of multiple annealing and looping-based amplification cycle sequencing for 24-chromosome aneuploidy screening of cleavage-stage embryos Fertil. Steril. 2014 102 1685 1691 10.1016/j.fertnstert.2014.08.015 25241375 · DOI
  32. [36]Alfarawati S. Fragouli E. Colls P. Wells D. First births after preimplantation genetic diagnosis of structural chromosome abnormalities using comparative genomic hybridization and microarray analysis Hum. Reprod. 2011 26 1560 1574 10.1093/humrep/der068 21447693 · DOI
  33. [37]Yin X. Tan K. Vajta G. Jiang H. Tan Y. Zhang C. Chen F. Chen S. Zhang C. Pan X. Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts Biol. Reprod. 2013 88 69 10.1095/biolreprod.112.106211 23349234 · DOI
  34. [38]Zhang C. Zhang C. Chen S. Yin X. Pan X. Lin G. Tan Y. Tan K. Xu Z. Hu P. A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing PLoS ONE 2013 8 e54236 10.1371/journal.pone.0054236 23372689 PMC3553135 · DOI
  35. [39]Handyside A.H. Kontogianni E.H. Hardy K. Winston R.M.L. Pregnancies from biopsied human preimplantation embryos sexed by Y-specific DNA amplification Nature 1990 344 768 770 10.1038/344768a0 2330030 · DOI
  36. [40]Hellani A. Abu-Amero K. Azouri J. El-Akoum S. Successful pregnancies after application of array-comparative genomic hy-bridization in PGS-aneuploidy screening Reprod Biomed Online. 2008 17 841 847 10.1016/S1472-6483(10)60413-0 19079969 · DOI
  37. [41]Yang Z. Salem S. S-Lyle S. Bayrak A. Salem R. Trophectoderm Cells Derived From Blastocyst Biopsy Are Suitable For Array CGH Analysis of 24 Chromosomes Fertil. Steril. 2011 95 S23 10.1016/j.fertnstert.2011.01.096 · DOI
  38. [42]Sabina J. Leamon J.H. Bias in whole genome amplification: Causes and considerations Methods in Molecular Biology Springer Berlin/Heidelberg, Germany 2015 26374307
  39. [43]Karrer E.E. Lincoln J.E. Hogenhout S. Bennett A.B. Bostock R.M. Martineau B. Lucas W.J. Gilchrist D.G. Alexander D. In situ isolation of mRNA from individual plant cells: Creation of cell- specific cDNA libraries Proc. Natl. Acad. Sci. USA 1995 92 3814 3818 10.1073/pnas.92.9.3814 7731989 PMC42052 · DOI
  40. [44]Volozonoka L. Perminov D. Korņejeva L. Alkšere B. Novikova N. Pīmane E.J. Blumberga A. Kempa I. Miskova A. Gailīte L. Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing J. Assist. Reprod. Genet. 2018 35 1457 1472 10.1007/s10815-018-1187-4 29687370 PMC6086788 · DOI
  41. [45]Lledó B. Ten J. Galán F.M. Bernabeu R. Preimplantation genetic diagnosis of Marfan syndrome using multiple displacement amplification Fertil. Steril. 2006 86 949 955 10.1016/j.fertnstert.2006.03.036 17027361 · DOI
  42. [46]Hou Y. Wu K. Shi X. Li F. Song L. Wu H. Dean M. Li G. Tsang S. Jiang R. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing Gigascience 2015 4 37 10.1186/s13742-015-0068-3 26251698 PMC4527218 · DOI
  43. [47]Lasken R.S. Stockwell T.B. Mechanism of chimera formation during the Multiple Displacement Amplification reaction BMC Biotechnol. 2007 7 19 10.1186/1472-6750-7-19 17430586 PMC1855051 · DOI
  44. [48]Tu J. Lu N. Duan M. Huang M. Chen L. Li J. Guo J. Lu Z. Hotspot selective preference of the chimeric sequences formed in multiple displacement amplification Int. J. Mol. Sci. 2017 18 492 10.3390/ijms18030492 28245591 PMC5372508 · DOI
  45. [49]Ribustello L. Escudero T. Margiatto E. Nagy P. Acacio B.M.D. Munne S. Differences between blastomere and blastocyst biopsies for preimplantation genetic diagnosis (PGD) using array comparative genomic hybridization (aCGH) Fertil. Steril. 2013 100 S130 10.1016/j.fertnstert.2013.07.1606 · DOI
  46. [50]Kokkali G. Traeger-Synodinos J. Vrettou C. Stavrou D. Jones G.M. Cram D.S. Makrakis E. Trounson A.O. Kanavakis E. Pantos K. Blastocyst biopsy versus cleavage stage biopsy and blastocyst transfer for preimplantation genetic diagnosis of β-thalassaemia: A pilot study Hum. Reprod. 2007 22 1443 1449 10.1093/humrep/del506 17261575 · DOI
  47. [51]Tzvetkov M.V. Becker C. Kulle B. Nürnberg P. Brockmöller J. Wojnowski L. Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification Electrophoresis 2005 26 710 715 10.1002/elps.200410121 15690424 · DOI
  48. [52]Dimitriadou E. Van Der Aa N. Cheng J. Voet T. Vermeesch J.R. Single cell segmental aneuploidy detection is compromised by S phase Mol. Cytogenet. 2014 7 46 10.1186/1755-8166-7-46 25075223 PMC4114140 · DOI
  49. [53]Wagner A. Blackstone N. Cartwright P. Dick M. Misof B. Snow P. Wagner G.P. Bartels J. Murtha M. Pendleton J. Surveys of Gene Families Using Polymerase Chain Reaction: PCR Selection and PCR Drift Syst. Biol. 1994 43 250 261 10.1093/sysbio/43.2.250 · DOI
  50. [54]De Bourcy C.F.A. De Vlaminck I. Kanbar J.N. Wang J. Gawad C. Quake S.R. A quantitative comparison of single-cell whole genome amplification methods PLoS ONE 2014 9 e105585 10.1371/journal.pone.0105585 25136831 PMC4138190 · DOI
  51. [55]Deleye L. Tilleman L. Van Der Plaetsen A.S. Cornelis S. Deforce D. Van Nieuwerburgh F. Performance of four modern whole genome amplification methods for copy number variant detection in single cells Sci Rep. 2017 7 3422 10.1038/s41598-017-03711-y 28611458 PMC5469777 · DOI
  52. [56]ESHRE PGT-SR/PGT-A Working Group Coonen E. Rubio C. Christopikou D. Dimitriadou E. Gontar J. Goossens V. Maurer M. Spinella F. Vermeulen N. ESHRE PGT Consortium good practice recommendations for the detection of structural and numerical chromosomal aberrations Hum. Reprod. Open 2020 2020 hoaa017 10.1093/hropen/hoaa017 32500102 PMC7257111 · DOI
  53. [57]Dean F.B. Hosono S. Fang L. Wu X. Faruqi A.F. Bray-Ward P. Sun Z. Zong Q. Du Y. Du J. Comprehensive human genome amplification using multiple displacement amplification Proc. Natl. Acad. Sci. USA 2002 99 5261 5266 10.1073/pnas.082089499 11959976 PMC122757 · DOI · Paper page
  54. [58]Ostrowski L.E. Dutcher S.K. Lo C.W. Cilia and Models for Studying Structure and Function Proc. Am. Thorac. Soc. 2011 8 423 429 10.1513/pats.201103-027SD 21926393 PMC3209580 · DOI
  55. [59]Wang Y. Navin N.E. Advances and Applications of Single-Cell Sequencing Technologies Mol. Cell 2015 58 598 609 10.1016/j.molcel.2015.05.005 26000845 PMC4441954 · DOI
  56. [60]Zhou X. Xu Y. Zhu L. Su Z. Han X. Zhang Z. Huang Y. Liu Q. Comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in limited DNA sequencing based on tube and droplet Micromachines 2020 11 645 10.3390/mi11070645 PMC7407204 32610698 · DOI
  57. [61]Peters B.A. Kermani B.G. Sparks A.B. Alferov O. Hong P. Alexeev A. Jiang Y. Dahl F. Tang Y.T. Haas J. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells Nature 2012 487 190 195 10.1038/nature11236 22785314 PMC3397394 · DOI
  58. [62]Esteki M.Z. Dimitriadou E. Mateiu L. Melotte C. Van der Aa N. Kumar P. Das R. Theunis K. Cheng J. Legius E. Concurrent Whole-Genome Haplotyping and Copy-Number Profiling of Single Cells Am. J. Hum. Genet. 2015 96 894 912 25983246 PMC4473724
  59. [63]Paez J.G. Lin M. Beroukhim R. Lee J.C. Zhao X. Richter D.J. Gabriel S. Herman P. Sasaki H. Altshuler D. Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification Nucleic Acids Res. 2004 32 e71 10.1093/nar/gnh069 15150323 PMC419624 · DOI
  60. [64]Spits C. Le Caignec C. De Rycke M. Van Haute L. Van Steirteghem A. Liebaers I. Sermon K. Optimization and evaluation of single-cell whole-genome multiple displacement amplification Hum. Mutat. 2006 27 496 503 10.1002/humu.20324 16619243 · DOI
  61. [65]Fiorentino F. Bono S. Biricik A. Nuccitelli A. Cotroneo E. Cottone G. Kokocinski F. Michel C.E. Minasi M.G. Greco E. Application of next-generation sequencing technology for comprehensive aneuploidy screening of blastocysts in clinical preimplantation genetic screening cycles Hum. Reprod. 2014 29 2802 2813 10.1093/humrep/deu277 25336713 · DOI
  62. [66]Deleye L. Dheedene A. De Coninck D. Sante T. Christodoulou C. Heindryckx B. Van den Abbeel E. De Sutter P. Deforce D. Menten B. Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts Fertil. Steril. 2015 104 1276 1285.e1 10.1016/j.fertnstert.2015.07.1144 26282994 · DOI
  63. [67]Griffin D. Gould R. What is Karyomapping and where does it fit in the world of preimplantation genetic diagnosis (PGD)? Med. Res. Arch. 2017 5 1 18 10.18103/mra.v5i6.1256 · DOI
  64. [68]Masset H. Zamani Esteki M. Dimitriadou E. Dreesen J. Debrock S. Derhaag J. Derks K. Destouni A. Drüsedau M. Meekels J. Multi-centre evaluation of a comprehensive preimplantation genetic test through haplotyping-by-sequencing Hum. Reprod. 2019 34 1608 1619 10.1093/humrep/dez106 31348829 · DOI
  65. [69]Xiong L. Huang L. Tian F. Lu S. Xie X.S. Bayesian model for accurate MARSALA (mutated allele revealed by sequencing with aneuploidy and linkage analyses) J. Assist. Reprod. Genet. 2019 36 1263 1271 10.1007/s10815-019-01451-8 31187331 PMC6602990 · DOI
  66. [70]Yan L. Huang L. Xu L. Huang J. Ma F. Zhu X. Tang Y. Liu M. Lian Y. Liu P. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by nextgeneration sequencing with linkage analyses Proc. Natl. Acad. Sci. USA 2015 112 15964 15969 10.1073/pnas.1523297113 26712022 PMC4702982 · DOI
  67. [71]Mai A.D. Harton G.L. Quang V.N. Van H.N. Thi N.H. Thuy N.P. Le Thi T.H. Minh D.N. Quoc Q.T. Development and clinical application of a preimplantation genetic testing for monogenic disease (PGT-M) for beta thalassemia in Vietnam J. Assist. Reprod. Genet. 2021 38 365 374 10.1007/s10815-020-02006-y 33216308 PMC7884556 · DOI
  68. [72]Xu J. Zhang Z. Niu W. Yang Q. Yao G. Shi S. Jin H. Song W. Chen L. Zhang X. Mapping allele with resolved carrier status of Robertsonian and reciprocal translocation in human preimplantation embryos Proc. Natl. Acad. Sci. USA 2017 114 E8695 E8702 10.1073/pnas.1715053114 28973897 PMC5642733 · DOI
  69. [73]Wu H. Shen X. Huang L. Zeng Y. Gao Y. Shao L. Lu B. Zhong Y. Miao B. Xu Y. Genotyping single-sperm cells by universal MARSALA enables the acquisition of linkage information for combined pre-implantation genetic diagnosis and genome screening J. Assist. Reprod. Genet. 2018 35 1071 1078 10.1007/s10815-018-1158-9 29790070 PMC6030017 · DOI
  70. [74]Backenroth D. Zahdeh F. Kling Y. Peretz A. Rosen T. Kort D. Zeligson S. Dror T. Kirshberg S. Burak E. Haploseek: A 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy Genet. Med. 2019 21 1390 1399 10.1038/s41436-018-0351-7 30449887 · DOI
  71. [75]Zeevi D.A. Backenroth D. Hakam-Spector E. Renbaum P. Mann T. Zahdeh F. Segel R. Zeligson S. Eldar-Geva T. Ben-Ami I. Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing Genet. Med. 2021 23 1334 1340 10.1038/s41436-021-01145-6 33772222 · DOI
  72. [76]Chen S. Yin X. Zhang S. Xia J. Liu P. Xie P. Yan H. Liang X. Zhang J. Chen Y. Comprehensive preimplantation genetic testing by massively parallel sequencing Hum Reprod. 2021 36 236 247 10.1093/humrep/deaa269 33306794 · DOI
  73. [77]Rajan-Babu I.S. Lian M. Cheah F.S. Chen M. Tan A.S. Prasath E.B. Loh S.F. Chong S.S. FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome Expert Rev. Mol. Med. 2017 19 E10 10.1017/erm.2017.10 28720156 PMC5733830 · DOI
  74. [78]Lian M. Lee C.G. Chong S.S. Robust preimplantation genetic testing strategy for myotonic dystrophy type 1 by bidirectional triplet-primed polymerase chain reaction combined with multi-microsatellite haplotyping following whole-genome amplification Front. Genet. 2019 10 598 10.3389/fgene.2019.00589 31316546 PMC6611416 · DOI
  75. [79]Ren Y. Lian Y. Yan Z. Zhai F. Yang M. Zhu X. Wang Y. Nie Y. Guan S. Kuo Y. Clinical application of an NGS-based method in the preimplantation genetic testing for Duchenne muscular dystrophy J. Assist. Reprod. Genet. 2021 38 1979 1986 10.1007/s10815-021-02126-z 33719023 PMC8417207 · DOI
  76. [80]Capalbo A. Romanelli V. Patassini C. Poli M. Girardi L. Giancani A. Stoppa M. Cimadomo D. Ubaldi F.M. Rienzi L. Diagnostic efficacy of blastocoel fluid and spent media as sources of DNA for preimplantation genetic testing in standard clinical conditions Fertil. Steril. 2018 110 870 879.e5 10.1016/j.fertnstert.2018.05.031 30316433 · DOI
  77. [81]Magli M.C. Albanese C. Crippa A. Tabanelli C. Ferraretti A.P. Gianaroli L. Deoxyribonucleic acid detection in blastocoelic fluid: A new predictor of embryo ploidy and viable pregnancy Fertil. Steril. 2019 111 77 85 10.1016/j.fertnstert.2018.09.016 30528055 · DOI
  78. [82]Hanson B.M. Tao X. Hong K.H. Comito C.E. Pangasnan R. Seli E. Jalas C. Scott R.T. Jr. Noninvasive preimplantation genetic testing for aneuploidy exhibits high rates of deoxyribonucleic acid amplification failure and poor correlation with results obtained using trophectoderm biopsy Fertil. Steril. 2021 115 1461 1470 10.1016/j.fertnstert.2021.01.028 33745720 · DOI
  79. [83]Yin B. Zhang H. Xie J. Wei Y. Zhang C. Meng L. Validation of preimplantation genetic tests for aneuploidy (PGT-A) with DNA from spent culture media (SCM): Concordance assessment and implication Reprod. Biol. Endocrinol. 2021 19 41 10.1186/s12958-021-00714-3 33673853 PMC7936457 · DOI
  80. [84]Shamonki M.I. Jin H. Haimowitz Z. Liu L. Proof of concept: Preimplantation genetic screening without embryo biopsy through analysis of cell-free DNA in spent embryo culture media Fertil. Steril. 2016 106 1312 1318 10.1016/j.fertnstert.2016.07.1112 27565258 · DOI
  81. [85]Leaver M. Wells D. Non-invasive preimplantation genetic testing (niPGT): The next revolution in reproductive genetics? Hum. Reprod. Update 2020 26 16 42 10.1093/humupd/dmz033 31774124 · DOI
  82. [86]MM Y.C. Yu Q. Ma M. Wang H. Tian S. Zhang W. MM J.Z. Liu Y. Yang Q. Pan X. Variant haplophasing by long-read sequencing: A new approach to preimplantation genetic testing workups Fertil. Steril. 2021 116 774 783 10.1016/j.fertnstert.2021.04.012 34020778 · DOI
  83. [87]Chow J.F.C. Cheng H.H.Y. Lau E.Y.L. Yeung W.S.B. Ng E.H.Y. Distinguishing between carrier and noncarrier embryos with the use of long-read sequencing in preimplantation genetic testing for reciprocal translocations Genomics 2020 112 494 500 10.1016/j.ygeno.2019.04.001 30946890 · DOI
  84. [88]Peters B.A. Kermani B.G. Alferov O. Agarwal M.R. McElwain M.A. Gulbahce N. Hayden D.M. Tang Y.T. Zhang R.Y. Tearle R. Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing Genome Res. 2015 25 426 434 10.1101/gr.181255.114 25672852 PMC4352880 · DOI
  85. [90]Verdyck P. Berckmoes V. Van Laere S. Keymolen K. Olsen C. De Rycke M. Analysis of parental contribution for aneuploidy detection (APCAD): A novel method to detect aneuploidy and mosaicism in preimplantation embryos Reprod. Biomed. Online 2021 44 459 468 10.1016/j.rbmo.2021.10.023 34930679 · DOI
  86. [91]Picher A.J. Budeus B. Wafzig O. Krüger C. García-Gómez S. Martínez-Jiménez M.I. Díaz-Talavera A. Weber D. Blanco L. Schneider A. TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol Nat. Commun. 2016 7 13296 10.1038/ncomms13296 27897270 PMC5141293 · DOI
  87. [92]Deleye L. De Coninck D. Dheedene A. De Sutter P. Menten B. Deforce D. Van Nieuwerburgh F. Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing Sci Rep. 2016 6 31825 10.1038/srep31825 27546482 PMC4992833 · DOI
  88. [93]Smith G.D. Takayama S. Application of microfluidic technologies to human assisted reproduction Mol. Hum. Reprod. 2017 23 257 268 10.1093/molehr/gaw076 28130394 PMC5387843 · DOI
  89. [94]Sidore A.M. Lan F. Lim S.W. Abate A.R. Enhanced sequencing coverage with digital droplet multiple displacement amplification Nucleic Acids Res. 2015 44 e66 10.1093/nar/gkv1493 26704978 PMC4838355 · DOI
  90. [95]Tian H.C. Benitez J.J. Craighead H.G. Single cell on-chip whole genome amplification via micropillar arrays for reduced amplification bias PLoS ONE 2018 13 e0191520 10.1371/journal.pone.0191520 29432426 PMC5809021 · DOI
  91. [96]Nishikawa Y. Hosokawa M. Maruyama T. Yamagishi K. Mori T. Takeyama H. Monodisperse picoliter droplets for low-bias and contamination-free reactions in single-cell whole genome amplification PLoS ONE 2015 10 e0138733 10.1371/journal.pone.0138733 26389587 PMC4577099 · DOI
  92. [97]Yu Z. Lu S. Huang Y. Microfluidic whole genome amplification device for single cell sequencing Anal. Chem. 2014 86 9386 9390 10.1021/ac5032176 25233049 · DOI
  93. [98]Liu Y. Jeraldo P. Mendes-Soares H. Masters T. Asangba A.E. Nelson H. Patel R. Chia N. Walther-Antonio M. Amplification of Femtograms of Bacterial DNA within 3 h Using a Digital Microfluidics Platform for MinION Sequencing ACS Omega 2021 6 25642 25651 10.1021/acsomega.1c03683 34632220 PMC8495859 · DOI

Cited by

Sorted by citations

Authors
Volozonoka, L., Miskova, A., & Gailite, L.
Affiliations
  • Scientific Laboratory of Molecular Genetics, Riga Stradins University, LV-1007 Riga, Latvia
  • Riga Stradiņš University (LV)
ORCID
Venue
International Journal of Molecular Sciences
Publisher
MDPI AG
Published
2022-04-27
Volume
23
Issue
9
Pages
4819
ISSN
1422-0067 (ISSN-L)
DOI
10.3390/ijms23094819
PMC
PMC9102663
OpenAlex
W4280558381
Cited by
52
References
2
Citations by year
2026: 14 · 2025: 13 · 2024: 13 · 2023: 9 · 2022: 3
FWCI
2.33
Type
journal article
Language
en
Open access
Licence
Locations
  • International Journal of Molecular Sciences (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Health Sciences › Medicine › Pediatrics, Perinatology and Child Health › Prenatal Screening and Diagnostics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
whole genome amplification, preimplantation genetic testing, next-generation sequencing, multiple displacement amplification, MALBAC, copy number variation, bioinformatics pipeline
MeSH terms
Genetic Testing, Nucleotides, Genomics, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing

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