Intro
Contents
1: Basic Hematopoiesis and Leukemia Stem Cells
1.1 Introduction
1.2 Hematopoietic Stem and Progenitor Cells
1.2.1 Hematopoietic Stem and Progenitor Cell Heterogeneity
1.2.2 Lineage Commitment from the Hematopoietic Stem and Progenitor Cell
1.3 Hematopoietic Stem and Progenitor Cell Assays
1.3.1 Phenotypic Characterization
1.3.2 Colony Forming Unit (CFU) and Long-Term Culture-Initiating Cell (LT-CIC) Assays
1.3.3 Xenotransplantation Studies
1.4 Hematopoietic Stem and Progenitor Cell Expansion

1.5 Aging Hematopoiesis, Including Telomeres
1.5.1 Influence of Aging on Hematopoiesis
1.5.2 Telomeres in Hematopoiesis
1.6 Leukemic Stem Cells
References
2: Modern Classification of Acute and Chronic Leukemias: Integrating Biology, Clinicopathologic Features, and Genomics
2.1 Introduction
2.2 Myeloproliferative Neoplasms (MPN)
2.3 Myeloid/Lymphoid Neoplasms with Eosinophilia and Tyrosine Kinase Gene Fusions (MLN-TK)
2.4 Mastocytosis
2.5 Myelodysplastic/Myeloproliferative Neoplasms
2.6 Myelodysplastic Syndromes or Myelodysplastic Neoplasms (MDS)

2.7 Acute Myeloid Leukemia
References
3: Molecular Techniques in the Diagnosis and Monitoring of Acute and Chronic Leukaemias
3.1 Introduction
3.2 Short-Read NGS
3.3 General Principles of NGS
3.4 DNA Sequencing
3.4.1 Principles of NGS Assay Design
3.4.1.1 Panel Selection
3.4.1.2 Gene Selection in Panel Sequencing
3.4.1.3 Considerations of Variant Types During Panel Design
3.4.2 Bioinformatic Analysis for Variant Detection
3.4.2.1 Pre-processing Procedures
3.4.2.2 Variant Calling for SNVs and Short Indels
3.4.2.3 Variant Annotation

3.4.2.4 Variant Calling for Long Indels
3.4.2.5 Detection of CNVs at the Gene Level
3.4.3 Specific Applications of DNA Sequencing Strategies in Leukaemias
3.4.3.1 Molecular Consensus Sequencing for Detection of Subclonal or Rare Variants
3.4.3.2 Evaluation of Immunoglobulin/T-Cell Receptor Genes
3.5 RNA Sequencing
3.5.1 Principles of Assay Design
3.5.2 Bioinformatic Considerations for RNA Sequencing
3.6 Molecular Monitoring of Measurable Residual Disease
3.7 Real-Time Quantitative PCR
3.7.1 Principles
3.7.2 MRD Monitoring in CML

3.7.3 RQ-PCR Monitoring in Other Leukaemias
3.8 Digital PCR
3.8.1 Principles
3.8.2 Considerations on Analytical Sensitivity in DPCR
3.9 Gene Expression Profiling
3.10 Brief Review of GEP Platforms
3.11 Clinical Applications of GEP in Leukaemias
3.12 Newer Techniques
3.12.1 Long-Read Sequencing
3.12.2 Single-Cell Sequencing
3.12.3 Optical Mapping
3.12.4 Circulating Tumour DNA Testing in Leukaemia
3.13 Conclusion
References
4: Flow Cytometric Techniques in the Diagnosis and Monitoring of Acute Leukaemias
4.1 Introduction