In recent decades, advances in sequencing technologies have led to an explosion of discoveries in cancer. While observing large chromosomal abnormalities under the microscope has demonstrated genome rearrangements can drive cancer progression, more recent technologies enabled discoveries of mutations private to single cancer patients and uncovered a broader mutation diversity. My dissertation introduces novel connections between computational methods and sequencing techniques to solve open problems in genome rearrangement research. To improve non-invasive cancer monitoring, genome rearrangements can serve as the ideal cancer biomarker for accurately monitoring tumor burden and catching relapse earlier. My approach, AmBre (Amplication of Breakpoints), characterizes a target genome rearrangement's breakpoints for use as a quantitative marker in measuring amounts of tumor DNA. For a target genome rearrangement such as CDKN2A deletion, AmBre accounts for diverse deletion breakpoints and amplies any DNA harboring the CDKN2A deletion. Since only the tumor DNA is amplied, breakpoints can be detected in tissues or blood with little tumor DNA in high background of unmutated DNA. Furthermore, AmBre relies on sequencing technologies to read the enriched DNA. For parallel detection of breakpoints across numerous samples, a geometry based rearrangement caller was developed to handle long reads generated by Pacific Biosciences sequencing instruments. In addition, I will discuss the limitations of sequencing technologies in inferring mechanisms for rearranging genomes. Specifically, sequencing data alone cannot infer a complex cancer chromosome was formed by a single shattering and repair mechanism (chromothripsis) or a series of progressive rearrangements. Lastly, genomes are diploid and genome rearrangements can appear on one or both homologous chromosomes. Detecting genome rearrangements is challenging and inferring which chromosome is affected by the rearrangement is even more difficult. Having already called genome rearrangements such as deletions, I will show how proximity-ligation sequencing can be repurposed to assign deletions to a chromosome by phasing deletions with variants. In effect, my endeavors in genome rearrangement research show the field is constantly evolving with advances being made by complementing sequencing strategies and computational methods.

This volume collates world experts’ insights into the molecular biology of cancer chromosomes, their abnormalities and the subsequent cellular consequences. Exploring themes involving oncogenes, such as by chromosomal translocations, other genome rearrangements and somatic mutations, this book is a review of the field of cancer genetics that presages a new era, as whole genome sequencing becomes more accessible. The work begins with a look at historical themes, such as the analysis of metaphase chromosomes using microscopy and staining techniques, advances in which provided our first broad glimpse into the genetic anatomy of a malignant cell. Readers will learn about the application of DNA molecular cloning techniques in the 1980s, that led to the identification of the genes involved in the Philadelphia and Burkitt's lymphoma chromosomal translocations, solidifying the role of oncogenes and tumour suppressor genes in cancer aetiology via chromosomal alterations and which launched a field in cancer genetics. Subsequent chapters bring the reader up to date by reviewing recent developments in the field, with dedicated sections on leukaemia/lymphoma, sarcomas and epithelial tumours. Contributions feature numerous colour tables and illustrations and this volume will provide a basis for understanding cancer chromosomes for many years to come.

This volume collates world experts' insights into the molecular biology of cancer chromosomes, their abnormalities and the subsequent cellular consequences. Exploring themes involving oncogenes, such as by chromosomal translocations, other genome rearrangements and somatic mutations, this book is a review of the field of cancer genetics that presages a new era, as whole genome sequencing becomes more accessible. The work begins with a look at historical themes, such as the analysis of metaphase chromosomes using microscopy and staining techniques, advances in which provided our first broad glimpse into the genetic anatomy of a malignant cell. Readers will learn about the application of DNA molecular cloning techniques in the 1980s, that led to the identification of the genes involved in the Philadelphia and Burkitt's lymphoma chromosomal translocations, solidifying the role of oncogenes and tumour suppressor genes in cancer aetiology via chromosomal alterations, and which launched a field in cancer genetics. Subsequent chapters bring the reader up to date by reviewing recent developments in the field, with dedicated sections on leukaemia/lymphoma, sarcomas and epithelial tumours. Contributions feature numerous colour tables and illustrations and this volume will provide a basis for understanding cancer chromosomes for many years to come.

Genome Chaos: Rethinking Genetics, Evolution, and Molecular Medicine transports readers from Mendelian Genetics to 4D-genomics, building a case for genes and genomes as distinct biological entities, and positing that the genome, rather than individual genes, defines system inheritance and represents a clear unit of selection for macro-evolution. In authoring this thought-provoking text, Dr. Heng invigorates fresh discussions in genome theory and helps readers reevaluate their current understanding of human genetics, evolution, and new pathways for advancing molecular and precision medicine. Bridges basic research and clinical application and provides a foundation for re-examining the results of large-scale omics studies and advancing molecular medicine Gathers the most pressing questions in genomic and cytogenomic research Offers alternative explanations to timely puzzles in the field Contains eight evidence-based chapters that discuss 4d-genomics, genes and genomes as distinct biological entities, genome chaos and macro-cellular evolution, evolutionary cytogenetics and cancer, chromosomal coding and fuzzy inheritance, and more

Research over the past decades has firmly established the genetic basis of cancer. In particular, studies on animal tumour viruses and chromosome rearrangements in human tumours have concurred to identify so-called ‘proto-oncogenes’ and ‘tumour suppressor genes’, whose deregulation promotes carcinogenesis. These important findings not only explain the occurrence of certain hereditary tumours, but they also set the stage for the development of anti-cancer drugs that specifically target activated oncogenes. However, in spite of tremendous progress towards the elucidation of key signalling pathways involved in carcinogenesis, most cancers continue to elude currently available therapies. This stands as a reminder that “cancer” is an extraordinarily complex disease: although some cancers of the haematopoietic system show only a limited number of characteristic chromosomal aberrations, most solid tumours display a myriad of genetic changes and considerable genetic heterogeneity. This is thought to reflect a trait commonly referred to as ‘genome instability’, so that no two cancers are ever likely to display the exact same genetic alterations. Numerical and structural chromosome aberrations were recognised as a hallmark of human tumours for more than a century. Yet, the causes and consequences of these aberrations still remain to be fully understood. In particular, the question of how genome instability impacts on the development of human cancers continues to evoke intense debate.

Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.

A grand summary and synthesis of the tremendous amount of data now available in the post genomic era on the structural features, architecture, and evolution of the human genome. The authors demonstrate how such architectural features may be important to both evolution and to explaining the susceptibility to those DNA rearrangements associated with disease. Technologies to assay for such structural variation of the human genome and to model genomic disorders in mice are also presented. Two appendices detail the genomic disorders, providing genomic features at the locus undergoing rearrangement, their clinical features, and frequency of detection.