**1. Introduction**

Bone marrow transplantation is widely used for many different kinds of haematological malignancies such as leukaemias/lymphomas and immunodeficiency which are rare diseases. Over the past decades, allogeneic haematopoietic stem cell transplantation (allo-hSCT) has gained increasing importance as a treatment

option for patients with both malignant and non-malignant life-threatening disorders in adult as well as paediatric patients. High risk leukaemias that are indicated for allo-hSCT are acute myeloid leukaemia (AML) [1], acute lymphoblastic leukaemia (ALL) and chronic myeloid leukaemia (CML) resistant to tyrosinekinase inhibitor targeted treatment [2]. Also, myelodysplastic syndrome (MDS) and many other non-malignant disorders (bone marrow failure syndromes, haemoglobinopathies, immunodeficiencies and osteopetrosis) can profit from allo-hSCT [3].

Considerable progress has been made in the analysis of haematopoietic chimerism afterwards, and the molecular monitoring of the genotypic origin of engrafted cells has become a routine diagnostic tool to document engraftment and to detect graft rejection or impending relapse, at most centres performing allogeneic hSCT [4]. The term 'chimerism' was introduced in the field of medicine by Anderson et al. [5] to describe organisms whose cells derive from two or more zygote lineages. Close surveillance of chimerism within total peripheral blood leukocytes after an allogeneic hSCT seems an indispensable tool for the clinical management of transplant recipients [6]. In order to identify donor cells and even small amounts of residual host cells, many genetic methods have been established for this purpose. Cytogenetics and fluorescence in situ hybridization (FISH) analysis are the older ones and are applicable only in sex-mismatched transplantations where the proportion of X and Y chromosomes are detected [7]. The variability between individuals can be found both on the phenotype and on the genotype levels, especially in non-coding areas of the DNA. The later can be used not only in the population genetics, evolutionary studies and forensic and paternity proofs but also in the medicine as appropriate DNA informative markers to identify the donor and the recipient (host; patient) on the molecular level and monitor chimerism after allo-hSCT. For sex-independent patient chimerism monitoring, the PCR-based analyses of highly polymorphic short tandem repeats (STR; PCR-STR) DNA markers with subsequent fragment analysis ('FA') on Genetic Analyser are frequently used [8, 9]. Single-nucleotide polymorphism (SNP) or nucleotide polymorphisms (NPs) assessment by relative quantification SYBR Green-based real-time PCR, ('RQ PCR') Real-time PCR and semi-nested real-time PCR are used less [10–12], but due to increased interest in diallelic insertion/deletion polymorphisms 'DIPs' [13, 14], many new commercially kits for chimerism monitoring are available. In spite of the different analytical approaches to detect post-transplant chimerism, it seems to be useful to explain some common features. The term 'complete chimerism' (CC) expresses the status, where only the donor genotype is detected in the patient blood sample after allo-hSCT by the certain method. The term 'mixed chimerism' (MC) expresses the status, where both donor and recipient (host) genotypes are detected in the patient blood sample after allo-hSCT by the certain method. However, the post-transplant chimerism is a dynamic process. Several days, weeks, or months after allo-hSCT, the mixed chimerism is usually slowly changed to complete donor chimerism named 'decreasing mixed chimerism'. Vice versa in the case of a relapse when autologous haematopoiesis is appeared often the complete chimerism becomes to the status of mixed chimerism named 'increasing chimerism'. The coexistence of donor and recipient haematopoiesis for months or a longer period (especially in non-malignant disorders) is named 'stable mixed chimerism' [3].

In following chapters, we would like to describe not only two different DNA molecular methods ('FA' and 'RQ PCR'), which have been used in chimerism monitoring after allo-hSCT in our laboratories, but also its comparison from our results.

*Monitoring of Chimerism in Rare Haematological Malignant Diseases after Allogeneic… DOI: http://dx.doi.org/10.5772/intechopen.89845*
