Title Page -- Copyright Page -- Contents -- Contributors -- Preface to the Fourth Edition -- Chapter 1 How it all began: cancer cytogenetics before sequencing -- References -- Chapter 2 Cytogenetic methods -- Sampling for cytogenetic analysis -- Chromosome banding -- In situ hybridization -- Genomic arrays -- Large-scale sequencing -- Interpretation of cytogenetic data -- References -- Chapter 3 Cytogenetic nomenclature -- Designation of regions and bands -- Karyotypic nomenclature -- Nomenclature of tumor cell populations -- In situ hybridization nomenclature -- References -- Chapter 4 Nonrandom chromosome abnormalities in cancer: an overview -- Primary and secondary neoplasia-associated chromosome abnormalities -- Why and how do chromosome aberrations arise? -- When do chromosome aberrations arise? -- In which cells do chromosome aberrations arise? -- Are acquired chromosome aberrations sufficient for neoplastic proliferation? -- Do all tumors have chromosome abnormalities, and are such changes present only in neoplastic cells? -- General effects of structural and numerical chromosome abnormalities -- Net loss of chromosomal material -- Net gain of chromosomal material -- Relocation of sequences with no gain or loss of genetic material -- At what resolution level are neoplasia-associated mutations best studied? -- Pathogenetic versus phenotypic tumor classification -- References -- Chapter 5 From chromosomes to genes: searching for pathogenetic fusions in cancer -- Types of fusion genes -- Fusion genes involving regulatory elements of the immunoglobulin and T-cell receptor genes -- Promoter swapping -- Fusion genes coding for fusion proteins -- "Out-of-frame" fusion transcripts -- Generation of fusion genes -- Methods to identify fusion genes -- Methodologies based on cytogenetics -- "Omics" and gene expression-based methodologies.

Comparative genomic hybridization-based methodology -- Protein-based methodologies -- DNA-mediated transformation methodology -- Clinic-based methodology -- Next-generation sequencing-based methodologies -- Conclusion -- References -- Chapter 6 Acute myeloid leukemia -- Most AML harbor clonal chromosomal abnormalities -- Impact of age -- Impact of previous treatment/genotoxic exposure -- Impact of gender -- Impact of geographic/ethnic origin -- Impact of constitutional genetics -- Characteristic chromosomal abnormalities in AML -- t(1 -- 3)(p36 -- q21) [RPN1-PRDM16] -- t(1 -- 21)(p36 -- q22) [RUNX1-PRDM16] -- t(1 -- 16)(p31 -- q24) [NFIA-CBFA2T3] -- t(1 -- 11)(p32 -- q23) [MLL-EPS15] -- t(1 -- 22)(p13 -- q13) [RBM15-MKL1] -- der(1 -- 7)(q10 -- p10) -- t(1 -- 11)(q21 -- q23) [MLL-MLLT11] -- t(2 -- 3)(p11 ~ 23 -- q23 ~ 28) [MECOM deregulation] -- t(2 -- 11)(p21 -- q23) [MLL rearrangement (?)] -- t(2 -- 11)(q31 -- p15) [NUP98-HOXD11(13)] -- t(2 -- 11)(q37 -- q23) [MLL-SEPT2] -- inv(3)(q21q26)/t(3 -- 3)(q21 -- q26) [RPN1-MECOM] -- t(3 -- 5)(q25 -- q35) [NPM1-MLF1] -- t(3 -- 12)(q26 -- p13) [ETV6-MECOM] -- t(3 -- 21)(q26 -- q22) [RUNX1-MECOM] -- Trisomy 4 -- t(4 -- 12)(q12 -- p13) [CHIC2-ETV6] -- t(4 -- 11)(q21 -- q23) [MLL-AFF1] -- Monosomy 5/del(5q) -- t(5 -- 11)(q31 -- q23) [MLL-ARHGAP26] -- t(5 -- 11)(q35 -- p15) [NUP98-NSD1] -- t(5 -- 17)(q35 -- q21) [NPM1-RARA] -- t(6 -- 9)(p22 -- q34) [DEK-NUP214] -- t(6 -- 11)(q27 -- q23) [MLL-MLLT4] -- Monosomy 7/del(7q) -- t(7 -- 21)(p22 -- q22) [RUNX1-USP42] -- t(7 -- 11)(p15 -- p15) [NUP98-HOXA9(11,13)] -- t(7 -- 12)(q36 -- p13) [MNX1-ETV6] -- Trisomy 8 -- inv(8)(p11q13) [KAT6A-NCOA2] -- t(8 -- 16)(p11 -- p13) [KAT6A-CREBBP] -- t(8 -- 22)(p11 -- q13) [KAT6A-EP300] -- t(8 -- 21)(q22 -- q22) [RUNX1-RUNX1T1] -- t(9 -- 11)(p22 -- p15) [NUP98-PSIP1] -- t(9 -- 11)(p21 -- q23) [MLL-MLLT3] -- del(9q) -- t(9 -- 22)(q34.

q11) [BCR-ABL1] -- Trisomy 10 -- t(10 -- 11)(p12 -- q14) [PICALM-MLLT10] -- 10p11.2-p12/11q23 rearrangements [MLL-ABI1 or MLL-MLLT10] -- t(10 -- 11)(q21 -- q23) [MLL-TET1] -- t(10 -- 16)(q22 -- p13) [KAT6B-CREBBP] -- Trisomy 11 -- inv(11)(p15q22) [NUP98-DDX10] -- t(11 -- 12)(p15 -- p13) [NUP98-KDM5A] -- t(11 -- 12)(p15 -- q13) [NUP98-HOXC11(C13)] -- t(11 -- 20)(p15 -- q12) [NUP98-TOP1] -- 11q gain [MLL amplification] -- t(11 -- 16)(q23 -- p13) [MLL-CREBBP] -- t(11 -- 17)(q23 -- q12) [MLL-MLLT6] -- t(11 -- 17)(q23 -- q21) [ZBTB16-RARA] -- t(11 -- 17)(q23 -- q25) [MLL-SEPT9] -- t(11 -- 19)(q23 -- p13.1) [MLL-ELL] -- t(11 -- 19)(q23 -- p13.3) [MLL-MLLT1] -- t(11 -- 22)(q23 -- q11) [MLL-SEPT5] -- del(12p) -- t(12 -- 22)(p13 -- q12) [MN1-ETV6] -- Trisomy 13 -- t(15 -- 17)(q22 -- q21) [PML-RARA] -- inv(16)(p13q22)/t(16 -- 16)(p13 -- q22) [CBFB-MYH11] -- inv(16)(p13q24) [CBFA2T3-GLIS2] -- t(16 -- 21)(p11 -- q22) [FUS-ERG] -- t(16 -- 21)(q24 -- q22) [RUNX1-CBFA2T3] -- del(17p) -- i(17q) -- del(20q) -- Trisomy 21 -- Trisomy 22 -- t(X -- 6)(p11 -- q23) [MYB-GATA1] -- Xq24/11q23 rearrangements [MLL-SEPT6] -- Loss of the Y chromosome -- Characteristic karyotypic patterns in AML -- Complex Karyotype (CK) -- Monosomal Karyotype (MK) -- Normal Karyotype (NK) -- Acknowledgments -- References -- Chapter 7 Myelodysplastic syndromes -- Diagnosis -- Clinical correlations -- Cytogenetic analysis -- Cytogenetic findings in MDS -- Normal karyotype -- −Y -- +8 -- Rearrangements of chromosome 5 or del(5q) -- MDS with an isolated del(5q) (the 5q- syndrome) -- Molecular analysis of the del(5q) -- Loss of chromosome 7 or del(7q) -- Loss of 17p -- del(20q) -- Complex karyotypes -- Rare recurring translocations -- Translocations of 11q23.3 -- t(11 -- 16) -- PDGFRB translocations -- Abnormalities of 3q -- Evolution of the karyotype -- Molecular pathogenesis of MDS.

Cytogenetic abnormalities in MDS/MPD -- Other technologies -- Emerging paradigms -- Summary -- References -- Chapter 8 Chronic myeloid leukemia -- The discovery and characterization of the Philadelphia chromosome -- Cytogenetic abnormalities in CML CP -- Molecular pathology of the t(9 -- 22)(q34 -- q11) in CML -- Treatment of CML -- Disease monitoring of CML during treatment -- Cytogenetic evolution in Ph-positive CML -- Molecular genetic evolution in Ph-positive CML -- Summary -- Acknowledgments -- References -- Chapter 9 Chronic myeloproliferative neoplasms -- The classic BCR-ABL1-negative MPN: PV, ET, and PMF -- Polycythemia vera (PV) -- Essential thrombocythemia (ET) -- Primary myelofibrosis (PMF) -- Molecular changes in classic MPN -- "Nonclassic" BCR-ABL1-negative MPN -- Chronic neutrophilic leukemia (CNL) -- Chronic eosinophilic leukemia/idiopathic hypereosinophilic syndrome (CEL/iHES) -- Mastocytosis -- Myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB, and FGFR1 -- PDGFRA (4q12) rearrangements and mutations -- Translocations involving PDGFRB (5q33) -- Translocations involving FGFR1 (8p11) -- Translocations involving 9p24 (JAK2) -- Concluding remarks -- Acknowledgments -- References -- Chapter 10 Acute lymphoblastic leukemia -- Morphologic, immunophenotypic, and cytogenetic characteristics -- B-ALL -- T-ALL -- Morphologic and immunophenotypic features -- Early T-cell precursor ALL -- Most patients with ALL have characteristic, acquired karyotypic abnormalities in their leukemic cells -- Established ploidy groups in ALL -- High hyperdiploidy -- Hypodiploid and near-haploid ALL -- Clinical features of the different hypodiploid groups -- Near triploidy -- Near tetraploidy -- Trisomy 5 -- Structural rearrangements -- t(1 -- 5)(q21 -- q33) -- t(1 -- 7)(p34 -- q34) -- t(1 -- 7)(p32 -- q34) -- t(1 -- 11)(p32.

q23) -- t(1 -- 14)(p32 -- q11)/TAL1 deletion -- dup(1)(q12~21 or q31~32) -- t(1 -- 19)(q23 -- p13.3) -- t(2 -- 8)(p11 -- q24) -- t(4 -- 11)(q21 -- q23) -- del(5)(q32q33.3) -- t(5 -- 9)(q22 -- q34) -- t(5 -- 14)(q31 -- q32) -- t(5 -- 14)(q35 -- q32) -- del(6q) -- t(6 -- 7)(q23 -- q34) and MYB duplication -- t(6 -- 11)(q27 -- q23) -- t(6 -- 14)(p22 -- q32) -- inv(7)(p15q34)/t(7 -- 7)(p15 -- q34)/t(7 -- 14)(p15 -- q11)/t(7 -- 14)(p15 -- q32) -- dic(7 -- 9)(p11~ 13 -- p11 ~13) -- del(7)(p12.2p12.2)/IKZF1 deletion -- i(7)(q10) -- t(7 -- 9)(q34 -- q32) -- t(7 -- 9)(q34 -- q34.3) -- t(7 -- 10)(q34 -- q24) -- t(7 -- 11)(q34 -- p13)/t(7 -- 11)(q34 -- p15) -- t(7 -- 12)(q34 -- p13.3) -- t(7 -- 12)(q36 -- p13) -- t(7 -- 19)(q34 -- p13) -- t(8 -- 14)(q11 -- q32) -- t(8 -- 14)(q24 -- q11) -- t(8 -- 14)(q24 -- q32) -- t(8 -- 22)(q24 -- q11) -- del(9p) -- t(9 -- 12)(p24 -- p13) -- t(9 -- 11)(p21 -- q23) -- dic(9 -- 12)(p11~12 -- p11~13) -- dic(9 -- 20)(p13 -- q11) -- i(9)(q10) -- t(9 -- 9)(q34 -- q34)/del(9)(q34q34) -- t(9 -- 10)(q34 -- q22.3) -- t(9 -- 12)(q34 -- p13) -- t(9 -- 14)(q34 -- q32) -- t(9 -- 22)(q34 -- q11) -- t(10 -- 11)(p12 -- q14) -- Rearrangements between 10p12 and 11q23 -- t(10 -- 14)(q24 -- q11) -- t(11 -- 14)(p13 -- q11)/t(11 -- 14)(p15 -- q11) -- t(11 -- 19)(q23 -- p13) -- t(12 -- 14)(p13 -- q11) -- t(12 -- 17)(p13 -- q12) -- t(12 -- 19)(p13 -- p13) -- t(12 -- 21)(p13 -- q22) -- t(12 -- 22)(p13 -- q12) -- del(13)(q12~14) -- inv(14)(q11q32)/t(14 -- 14)(q11 -- q32) -- t(14 -- 18)(q32 -- q21) -- t(14 -- 19)(q32 -- p13) -- t(14 -- 19)(q32 -- q13) -- t(14 -- 20)(q32 -- q13) -- t(14 -- 21)(q11 -- q22) -- 15q13~15 rearrangements -- i(17)(q10) -- t(17 -- 19)(q22 -- p13) -- Submicroscopic del(21)(q22.2q22.2) -- i(21)(q10) -- Intrachromosomal amplification of chromosome 21 (iAMP21) -- t(X -- 14)(p22 -- q32) or t(Y -- 14)(p11.

q32)/del(X)(p22.33p22.33) or del(Y)(p11.32p11.32).