Performance of four modern whole genome amplification methods for copy number variant detection in single cells

被引:40
|
作者
Deleye, Lieselot [1 ]
Tilleman, Laurentijn [1 ]
Vander Plaetsen, Ann-Sophie [1 ]
Cornelis, Senne [1 ]
Deforce, Dieter [1 ]
Van Nieuwerburgh, Filip [1 ]
机构
[1] Univ Ghent, Lab Pharmaceut Biotechnol, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
来源
SCIENTIFIC REPORTS | 2017年 / 7卷
关键词
CIRCULATING TUMOR-CELLS; SOMATIC MUTATIONS; ANEUPLOIDY; DIAGNOSIS; CATALOG; CANCER;
D O I
10.1038/s41598-017-03711-y
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Whole genome amplification (WGA) has become an invaluable tool to perform copy number variation (CNV) detection in single, or a limited number of cells. Unfortunately, current WGA methods introduce representation bias that limits the detection of small CNVs. New WGA methods have been introduced that might have the potential to reduce this bias. We compared the performance of PicoPLEX DNA-Seq (Picoseq), DOPlify, REPLI-g and Ampli-1 WGA for aneuploidy screening and copy number analysis using shallow whole genome massively parallel sequencing (MPS), starting from single or a limited number of cells. Although the four WGA methods perform differently, they are all suited for this application.
引用
收藏
页数:9
相关论文
共 50 条
  • [41] Cost effective DNA copy number profiling of singlecells without upfront whole-genome amplification
    Theunis, K.
    Kumar, P.
    Haan, J.
    Van der Aa, N.
    Sifrim, A.
    Vanuytven, S.
    Desmedt, C.
    Rothe, F.
    Ignatiadis, M.
    Sotiriou, C.
    EUROPEAN JOURNAL OF HUMAN GENETICS, 2018, 26 : 726 - 727
  • [42] Detection of copy number variants in African goats using whole genome sequence data
    Wilson Nandolo
    Gábor Mészáros
    Maria Wurzinger
    Liveness J. Banda
    Timothy N. Gondwe
    Henry A. Mulindwa
    Helen N. Nakimbugwe
    Emily L. Clark
    M. Jennifer Woodward-Greene
    Mei Liu
    George E. Liu
    Curtis P. Van Tassell
    Benjamin D. Rosen
    Johann Sölkner
    BMC Genomics, 22
  • [43] Detection of copy number variants in African goats using whole genome sequence data
    Nandolo, Wilson
    Meszaros, Gabor
    Wurzinger, Maria
    Banda, Liveness J.
    Gondwe, Timothy N.
    Mulindwa, Henry A.
    Nakimbugwe, Helen N.
    Clark, Emily L.
    Woodward-Greene, M. Jennifer
    Liu, Mei
    Liu, George E.
    Van Tassell, Curtis P.
    Rosen, Benjamin D.
    Solkner, Johann
    BMC GENOMICS, 2021, 22 (01)
  • [44] Clinical experience with shallow whole genome sequencing as a detection method for Copy Number Variations
    Menten, B.
    De Smet, M.
    Raman, L.
    Sante, T.
    Van Roy, N.
    Dheedene, A.
    EUROPEAN JOURNAL OF HUMAN GENETICS, 2019, 27 : 846 - 847
  • [45] Comparison of whole genome amplification methods on single and pooled cells for comparative genomic hybridization array analysis
    Needham, Rachel H. . V.
    Ramirez, Arturo B.
    Kishawi, Iman
    Stilwell, Jackie L.
    Kaldjian, Eric P.
    CANCER RESEARCH, 2016, 76
  • [46] WisecondorX: improved copy number detection for routine shallow whole-genome sequencing
    Raman, Lennart
    Dheedene, Annelies
    De Smet, Matthias
    Van Dorpe, Jo
    Menten, Bjorn
    NUCLEIC ACIDS RESEARCH, 2019, 47 (04) : 1605 - 1614
  • [47] A validation study of copy number variant (CNVs) detection to replace constitutional microarray from low resolution whole genome sequencing data
    Chaubey, Alka
    Valencia, C. Alexander
    Zeqiang, Ma
    Irzyk, Gerard
    Szekeres, Edward, Jr.
    Markovic, Zdenek
    Wang, Yang
    Tanner, Alice
    Collins, Christin
    Hegde, Madhuri
    CANCER GENETICS, 2018, 224 : 56 - 56
  • [48] Improved methods for in situ enzymatic amplification and detection of low copy number genes in bacteria
    Jacobs, D
    Angles, ML
    Goodman, AE
    Neilan, BA
    FEMS MICROBIOLOGY LETTERS, 1997, 152 (01) : 65 - 73
  • [49] A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products
    Ferrarini, Alberto
    Forcato, Claudio
    Buson, Genny
    Tononi, Paola
    del Monaco, Valentina
    Terracciano, Mario
    Bolognesi, Chiara
    Fontana, Francesca
    Medoro, Gianni
    Neves, Rui
    Moehlendick, Birte
    Rihawi, Karim
    Ardizzoni, Andrea
    Sumanasuriya, Semini
    Flohr, Penny
    Lambros, Maryou
    de Bono, Johann
    Stoecklein, Nikolas H.
    Manaresi, Nicolo
    PLOS ONE, 2018, 13 (03):
  • [50] Whole exome sequencing-based copy number variant detection in inherited retinal disease
    Coppieters, Frauke
    Van de Sompele, Stijn
    Van Schil, Kristof
    Van Laethem, Thalia
    Six, Rani
    De Jaegere, Sarah
    Meire, Francoise
    De Vries, Meindert
    Balikova, Irina
    De Zaeytijd, Julie
    Leroy, Bart P.
    Rosseel, Toon
    De Baere, Elfride
    INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 2019, 60 (09)