Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 50, 2014, Pages 17947-17952

  Gawad, Charles ^a,b   Koh, Winston ^b   Quake, Stephen R ^b  

^a STANFORD UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Acute lymphoblastic leukemia; Clonal evolution; Cytosine mutagenesis; Intratumor heterogeneity; Single cell genomics

Indexed keywords

ACUTE LYMPHOBLASTIC LEUKEMIA; ALLELE; ARTICLE; AUTOMATION; CHILDHOOD LEUKEMIA; CLINICAL ARTICLE; CODOMINANCE; CYTOLYSIS; CYTOSINE MUTAGENESIS; EXOME; GENE AMPLIFICATION; GENE FREQUENCY; GENE MUTATION; GENOMICS; GENOTYPE; HETEROZYGOSITY LOSS; HUMAN; KARYOTYPE; LEUKEMOGENESIS; MICROFLUIDICS; MISSENSE MUTATION; MOLECULAR CLONING; MUTAGENESIS; MUTATION RATE; NONSENSE MUTATION; ONCOGENE K RAS; PHYLOGENETIC TREE; POINT MUTATION; SINGLE CELL GENOMICS; WILD TYPE; CELL CLONE; CHILD; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MICROFLUIDIC ANALYSIS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROCEDURES; SINGLE CELL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; CHILD; CLONE CELLS; DNA MUTATIONAL ANALYSIS; EXOME; GENETIC VARIATION; GENOMICS; HUMANS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS;

EID: 84919372228     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1420822111     Document Type: Article

References (28)

1. Kandoth C, et al. (2013) Mutational landscape and significance across 12 major cancer types. Nature 502(7471):333-339.
2. Mullighan CG, et al. (2008) Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 322(5906):1377-1380.
3. Welch JS, et al. (2012) The origin and evolution of mutations in acute myeloid leukemia. Cell 150(2):264-278.
4. Walter MJ, et al. (2012) Clonal architecture of secondary acute myeloid leukemia. N Engl J Med 366(12):1090-1098.
5. Ding L, et al. (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481(7382):506-510.
6. Golub TR, et al. (1995) Fusion of the TEL gene on 12p13 to the AML1 gene on 21q22 in acute lymphoblastic leukemia. Proc Natl Acad Sci USA 92(11):4917-4921.
7. Greaves M (2003) Pre-natal origins of childhood leukemia. Rev Clin Exp Hematol 7(3): 233-245.
8. Papaemmanuil E, et al. (2014) RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet 46(2):116-125.
9. Zong C, Lu S, Chapman AR, Xie XS (2012) Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338(6114):1622-1626.
10. Fan HC, Wang J, Potanina A, Quake SR (2011) Whole-genome molecular haplotyping of single cells. Nat Biotechnol 29(1):51-57.
11. Abecasis GR, et al.; 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65.
12. Hou Y, et al. (2012) Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148(5):873-885.
13. Xu X, et al. (2012) Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell 148(5):886-895.
14. Navin N, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472(7341):90-94.
15. Hughes AE, et al. (2014) Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLoS Genet 10(7):e1004462.
16. Myllykangas S, Tikka J, Böhling T, Knuutila S, Hollmén J (2008) Classification of human cancers based on DNA copy number amplification modeling. BMC Med Genomics 1:15.
17. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm(with discussion). J R Stat Soc [Ser A] 39:1-38.
18. Wolfe JW (1970) Pattern clustering by multivariate mixture analysis. Multivariate Behav Res 5:329-350.
19. Begg CB, Eng KH, Hummer AJ (2007) Statistical tests for clonality. Biometrics 63(2): 522-530.
20. Mullighan CG, et al. (2007) Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446(7137):758-764.
21. Schubbert S, Shannon K, Bollag G (2007) Hyperactive Ras in developmental disorders and cancer. Nat Rev Cancer 7(4):295-308.
22. Futreal PA, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4(3):177-183.
23. Gawad C, et al. (2012) Massive evolution of the immunoglobulin heavy chain locus in children with B precursor acute lymphoblastic leukemia. Blood 120(22):4407-4417.
24. Longerich S, Basu U, Alt F, Storb U (2006) AID in somatic hypermutation and class switch recombination. Curr Opin Immunol 18(2):164-174.
25. Wang J, Fan HC, Behr B, Quake SR (2012) Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150(2):402-412.
26. Jan M, et al. (2012) Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Transl Med 4(149):149ra118.
27. Potter NE, et al. (2013) Single-cell mutational profiling and clonal phylogeny in cancer. Genome Res 23(12):2115-2125.
28. Wang Y, et al. (2014) Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512(7513):155-160.