Conventional karyotyping is one of standard chromosomal analyses that have been widely used in diagnosis of myeloid leukemias as well as lymphoid neoplasms. Discovery of the recurrent cytogenetic abnormality in Burkitt lymphoma with t(8; 14) and chronic myelogenous leukemia with t(9;22) in early 1960s. [13, 14], is followed by many chromosomal abnormalities described in lymphomas and leukemias. Up to date, certain precursor B lymphoid neoplasms, vast majority of the Burkitt lymphoma, mantle cell lymphoma, follicular lymphoma and a subset of marginal zone lymphomas are associated with recurrent translocations (Table 17.1) [1–3, 15, 16]. Diffuse large B cell lymphomas (DLBCL), can associate with single or multiple breakpoints and translocations, namely BCL6 at 3q and BCl-2 at 18q, “double or triple” hit lymphomas commonly involving MYC and BCL2 and less frequently BCL6 genes [17–20]. Nevertheless, only a minority of T cell lymphomas exhibit recurrent chromosomal translocations. Anaplastic large T cell lymphoma is a good example, often associated with t(2;5) involving NPM1-ALK gene fusion [21], though the other ALK partner genes also encountered.

Most cytogenetic abnormalities seen in lymphomas and leukemias are often detectable by conventional karyotyping by G-banding. Although it is considered to be the “gold standard” technique, some limitations prevent a wide use of this test, including the need to obtain a large volume of fresh tissue and rapid processing. Another problem encountered in cytogenetic testing is that the analysis requires high level of technical skills in culturing tissue, preparing the metaphase cells and analyzing complex karyograms which makes the method labor-intensive, expensive and time consuming [15].

Fluorescence in situ hybridization (FISH) is widely used as an ancillary method in diagnosis of lymphomas and leukemias. It is applicable to cytospin preparations from fresh harvested tissue as well as formalin-fixed and paraffin-embedded (FFPE) tissue without requiring tissue culturing. Thus, FISH is a less complex and rapid molecular technique with shorter turnaround time. The main limitation of FISH is the probe specific testing only for specific abnormalities with no genome-wide analysis.

PCR tests are widely used in lymphomas and lymphoblastic leukemias for clonality analysis of the immunoglobulin genes and T cell receptors (TCR). The testing can be performed on either fresh tissues or FFPE materials. DNA or RNA materials are extracted from submitted specimen according to the study design. Quantitative RT-PCR is also very useful in detecting of the chromosomal translocations that lead to the production of fusion mRNA transcripts. A good example of this fusion transcript and protein generation is cyclin D1-IgH resulting in mantle cell lymphoma [22]. An advantage of PCR in lymphoma and leukemias is that it enables to amplify the fusion transcript; therefore it is superior in detection of minimal residual disease (MRD). PCR analysis for clonality is particularly advantageous in certain circumstances; (1) if the tissue is limited (e.g. small needle biopsies or fine needle aspirations) for immunohistochemical analysis and/or flow cytometry cannot be performed (e.g. FFPE tissue); (2) some B cell lymphoma cells may lack surface light chain antigens so that clonality may be equivalent by flow cytometry. (3) Phenotypic clonality evaluation has not been established for T cell neoplasms, therefore, gene rearrangement studies are helpful determining T cell clonality; (4) differentiation of reactive hematogone response vs. residual/recurrent precursor lymphoid neoplasms with increased immature lymphoblasts [23–26]. On the other hand, there are some limitations when using PCR for diagnostic purposes. False positive gene rearrangement results can be observed especially when testing a small biopsy with small number of lymphocytes as well as various reactive and inflammatory conditions [27, 28]. Furthermore, some T cell lymphomas may have false immunoglobulin (IG) gene re-arrangement [28]. False negative results can also be seen mostly due to technical or biologic factors [29].

SNP array is the most recently introduced molecular method that can analyze the whole genome with higher resolution than the other techniques. An important advantage of SNP array is the ability to detect not only copy number changes but also the regions with loss of heterozygosity without DNA loss or gain. This indicates that the both alleles are homozygous and derived from one parent, “uniparental disomy” (UDP), which is important in certain lymphomas [30–32]. Regions of UDP may harbor one or more genes with inactivating mutations (classical tumor suppressor genes) and since both alleles will have the mutation, the Knudson two-hit rule is fulfilled [15]. The main problem with SNP array is the difficulty in distinguishing acquired abnormalities from polymorphism which may be resolved by comparing to the germline DNA from the same patient [33]. SNP is so far not the replacement of cytogenetics and FISH laboratory, however, it is usually ordered for those patients with normal karyotyping or FISH results when seeking a possible disease related genetic findings.

This is a group of disease characterized by recurrent genetic abnormalities including chromosomal abnormalities and balanced translocations. The distinction of this B-ALL from other types is especially important as they have specific clinical and phenotypic features leading to important prognostic implications.

T lymphoblastic leukemia/lymphoma is a neoplasm of precursor T cells which are typically medium to large sized blasts with dispersed chromatin, inconspicuous nucleoli and scant cytoplasm. It involves bone marrow and blood (T-ALL) or lymphoid organs or extranodal sites (T-LBL). Both forms are more common in children than adults. The blasts usually express TdT with often T cell antigens CD2, cytoplasmic CD3, CD4, CD5, CD7, and CD8 and CD1a. Aberrant expression of myeloid markers (CD13 and CD33) can be seen in up to 30 % of the cases [70]. Coexpression of CD117 occurs less frequently but often associated with FLT3 mutation [71]. Multiple genetic aberrations encounter in T-ALL, but none of them is T-ALL specific. Translocations involving TCR loci are the most common cytogenetic anomalies observed in T-ALL/LBL. t(7;10)(q34;q24) and t(10;14)(q24;q11) are most common in adults involving HOX11(TLX1) gene whereas t(5;14)(q35;q32) involving HOX11L2 (TLX3) gene is commonly found in children [6]. As reported, dysregulation of HOX-type transcription factors is found in 30–40 % of cases of T-ALL [72]. Characteristically, HOX-type T-ALLs often accompany with activating NOTCH1 mutations and CDKN2A loss of function, NUP214-ABL amplifications, C-MYB tandem duplications, PHF6 mutations, PTPN2 deletions, and WT1 mutations [6, 72–78], which are not present in non-HOX-type T-ALL. However, the role of these genetic changes in leukemogenesis is not well understood. The unique genetic features are not only helpful in view of diagnosis but also guide future clinical therapy. An in vitro study has demonstrated that a blockade of both TLX1/HOX and NOTCH could inhibit cell cycle progression in TLX1 T-ALL cell line 9,490 cells (Lesley A. 2011). Mutations that may occur in T-ALL/LBL are important. Mutation of NOTCH oncogene is the most common mutation and is seen about 60 % of cases. NOTCH proteins are transmembrane receptors and are important regulators of T cell differentiation and activation. Recent studies showed that MYC is upregulated by activated NOTCH1 in T-ALL which stimulates the growth of T-ALL cells [46, 79]. N-RAS and FLT3 are other mutation seen in T-ALL [80, 81]. Another common rearrangement is the formation of fusion genes, mostly in children. SIL/TAL1 fusion gene results from a cryptic deletion of chromosome 1 and is seen in up to 30 % of childhood T-ALL. Important translocations resulting in fusion gene formation includes t(10;11) involving CALM/AF10 genes in 10 % of all cases and less frequently t(11;19) involving MLL gene. Other MLL gene translocations {t(6;11), t(10;11), t(X;11) and t(4;11)} seen in some T-ALL cases [6]. Philadelphia chromosome has also been reported in rare cases [82]. Deletions may be detected in as many as 30 % cases. 9p21 involving p16 gene and del(6q) are the important ones. Almost all cases show clonality in T cell receptors with up to 20 % accompanying IGH@ gene rearrangement [83].

Mature B cell lymphomas comprise over 90 % of lymphoid neoplasms worldwide. They are common in Western world and account for 4 % of new cancers each year [1]. The most common types are diffuse large B cell lymphoma and follicular lymphoma. The majority of the B cell lymphomas recapitulate the stages of normal B cell proliferation, except for some types, e.g. hairy cell leukemia, that do not correspond to any maturation stage (Table17.2). Diagnosis of B cell lymphomas, like other mature lymphoid neoplasms, is usually based on histomorphologic and phenotypic features in conjunction with genetic and molecular profiles.