A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Zhang, Chunlei ^a   Zhang, Chunsheng ^a   Chen, Shengpei ^a,e   Yin, Xuyang ^a   Pan, Xiaoyu ^a,f   Lin, Ge ^b,d   Tan, Yueqiu ^b,d   Tan, Ke ^b   Xu, Zhengfeng ^c   Hu, Ping ^c   Li, Xuchao ^a   Chen, Fang ^a,g   Xu, Xun ^a   Li, Yingrui ^a   Zhang, Xiuqing ^a   Jiang, Hui ^a,g   Wang, Wei ^a  

^a BGI SHENZHEN   (China)

^b CENTRAL SOUTH UNIVERSITY   (China)

^c NANJING MEDICAL UNIVERSITY   (China)

^d BEIJING HOSPITAL   (China)

^e SOUTHEAST UNIVERSITY   (China)

^f SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^g UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; GUANINE;

ALGORITHM; ARTICLE; BIOINFORMATICS; BLASTOCYST; BLOOD; COPY NUMBER VARIATION; EMBRYO; FEMALE; GENE AMPLIFICATION; GENE SEQUENCE; HUMAN; HUMAN CELL; KARYOTYPE; LOW COVERAGE MASSIVELY PARALLEL SEQUENCING; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SINGLE CELL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BASE COMPOSITION; BLASTOCYST; CHROMOSOME MAPPING; DNA COPY NUMBER VARIATIONS; GENE DOSAGE; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KARYOTYPING; LEUKOCYTES, MONONUCLEAR; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS; SOFTWARE;

EID: 84872766258     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054236     Document Type: Article

References (30)

1. Carlson C, Sirotkin H, Pandita R, Goldberg R, McKie J, et al. (1997) Molecular definition of 22q11 deletions in 151 velo-cardio-facial syndrome patients. Am J Hum Genet 61: 620-629.
2. Ben-Shachar S, Ou Z, Shaw CA, Belmont JW, Patel MS, et al. (2008) 22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome. Am J Hum Genet 82: 214-221.
3. Edelmann L, Pandita RK, Spiteri E, Funke B, Goldberg R, et al. (1999) A common molecular basis for rearrangement disorders on chromosome 22q11. Hum Mol Genet 8: 1157-1167.
4. Lejeune J, Lafourcade J, Berger R, Vialatte J, Boeswillwald M, et al. (1963) [3 Cases of Partial Deletion of the Short Arm of a 5 Chromosome]. C R Hebd Seances Acad Sci 257: 3098-3102.
5. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, et al. (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463: 899-905.
6. Xu X, Hou Y, Yin X, Bao L, Tang A, et al. (2012) Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell 148: 886-895.
7. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94.
8. Hou Y, Song L, Zhu P, Zhang B, Tao Y, et al. (2012) Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148: 873-885.
9. Dokras A, Sargent IL, Ross C, Gardner RL, Barlow DH, (1990) Trophectoderm biopsy in human blastocysts. Hum Reprod 5: 821-825.
10. Strom CM, Verlinsky Y, Milayeva S, Evsikov S, Cieslak J, et al. (1990) Preconception genetic diagnosis of cystic fibrosis. Lancet 336: 306-307.
11. Griffin DK, Handyside AH, Penketh RJ, Winston RM, Delhanty JD, (1991) Fluorescent in-situ hybridization to interphase nuclei of human preimplantation embryos with X and Y chromosome specific probes. Hum Reprod 6: 101-105.
12. Bianchi DW, Flint AF, Pizzimenti MF, Knoll JH, Latt SA, (1990) Isolation of fetal DNA from nucleated erythrocytes in maternal blood. Proc Natl Acad Sci U S A 87: 3279-3283.
13. Huang R, Barber TA, Schmidt MA, Tompkins RG, Toner M, et al. (2008) A microfluidics approach for the isolation of nucleated red blood cells (NRBCs) from the peripheral blood of pregnant women. Prenat Diagn 28: 892-899.
14. Gutierrez-Mateo C, Colls P, Sanchez-Garcia J, Escudero T, Prates R, et al. (2011) Validation of microarray comparative genomic hybridization for comprehensive chromosome analysis of embryos. Fertil Steril 95: 953-958.
15. Bi W, Breman A, Shaw CA, Stankiewicz P, Gambin T, et al. (2012) Detection of >/ = 1 Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays. Prenat Diagn 32: 10-20.
16. Corneveaux JJ, Kruer MC, Hu-Lince D, Ramsey KE, Zismann VL, et al. (2007) SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplification. Biotechniques 42: 77-83.
17. Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, et al. (2004) Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res 32: e71.
18. Arriola E, Lambros MB, Jones C, Dexter T, Mackay A, et al. (2007) Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation. Lab Invest 87: 75-83.
19. Lage JM, Leamon JH, Pejovic T, Hamann S, Lacey M, et al. (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 13: 294-307.
20. Bredel M, Bredel C, Juric D, Kim Y, Vogel H, et al. (2005) Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J Mol Diagn 7: 171-182.
21. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
22. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, et al. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6: 99-103.
23. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41: 1061-1067.
24. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
25. Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
26. Dan S, Chen F, Choy KW, Jiang F, Lin J, et al. (2012) Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing. PLoS One 7: e27835.
27. Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, et al. (2012) Copy number variation detection and genotyping from exome sequence data. Genome Res.
28. Yu M, Stott S, Toner M, Maheswaran S, Haber DA, (2011) Circulating tumor cells: approaches to isolation and characterization. J Cell Biol 192: 373-382.
29. Uum van CMJ, Stevens SJC, Dreesen JCFM, Drusedau M, Smeets HJM, et al. (2010) Session 42: Preimplantation Genetic Diagnosis. Human Reproduction 25: i61-i63.
30. Oliver JL, Carpena P, Roman-Roldan R, Mata-Balaguer T, Mejias-Romero A, et al. (2002) Isochore chromosome maps of the human genome. Gene 300: 117-127.