Some current problems of cancer cytogenetics

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

Mechanisms and impacts of chromosomal translocations in cancers

Chromosomal aberrations have been associated with cancer development since their discovery more than a hundred years ago. Chromosomal translocations, a type of particular structural changes involving heterologous chromosomes, have made a critical impact on diagnosis, prognosis and treatment of cancers. For example, the discovery of translocation between chromosomes 9 and 22 and the subsequent success of targeting the fusion product BCR-ABL transformed the therapy for chronic myelogenous leukemia. In the past few decades, tremendous progress has been achieved towards elucidating the mechanism causing chromosomal translocations. This review focuses on the basic mechanisms underlying the generation of chromosomal translocations. In particular, the contribution of frequency of DNA double strand breaks and spatial proximity of translocating loci is discussed.

Chromosome translocations: dangerous liaisons revisited

Although it has been clear for more than a century that the chromosomes in human tumour cells are often wildly abnormal, there has been controversy as to whether these changes are primary events or are merely secondary epiphenomena that reflect the genomic instability of these cells. The prevailing view for most of this period was that chromosome changes were secondary events. What happened to change this view?

A breakpoint map of recurrent chromosomal rearrangements in human neoplasia

Cytogenetic studies over the past few decades have revealed clonal chromosomal aberrations in almost 27,000 human neoplasms. Many of these neoplasia-associated chromosomal abnormalities have been characterised at the molecular level, revealing previously unknown genes that are closely associated with the tumorigenic process. Information on chromosome changes in neoplasia is growing rapidly, making it difficult to identify all recurrent chromosomal aberrations. We have developed a computer program to ascertain, for the first time, all recurrent structural abnormalities in all haematological malignancies and solid tumours published up to June 1996. Out of 26,523 cases, a total of 215 balanced and 1,588 unbalanced recurrent aberrations were identified among 75 different neoplastic disorders. Our compilation of all recurrent balanced and unbalanced neoplasia-associated rearrangements should help in directing future efforts aimed at identifying the molecular mechanisms involved in tumorigenesis.

[Chromosome abnormalities, tumours and developmental disorders (author's transl)]

Clonal chromosome disorders occurring or acquired at any postnatal age are often closely related with the origin of tumours. In man the Ph1-chromosome (9; 22) anomaly in CML or the 8; 14 translocation in the African malignant Burkitt Non-Hodgkin lymphoma are, among other cases, prominent examples. On the other hand, constitutive, inherited or novel chromosome anomalies conveyed from the zygote to all tissues of the organism may cause a higher risk for the origin of tumours. Rarely, inheritable minor structural chromosome mutations are known to determine the occurrence of dysontogenetic tumours, as e.g., nephroblastoma, but it is assumed that more such cases will become elucidated in the future. As a special phenomenon, true hydatiform mole is a tumour of the placental tissue due to a disorder of intragenome regulation. Constitutive or numerical structural chromosome anomalies of man are a frequent cause of early or late abortion or of abnormal development and malformation. Despite the predominating principle of selective fetal elimination, a few anomalies such as Down's syndrome, may escape to longer survival due to the relatively mild effects of chromosome 21 triplication. Trisomies which represent in man the most frequent type of chromosome disorders, can be induced, and systematically studied in an experimental model of the mouse. This allows the elaboration of the developmental profiles of all trisomies (and monosomies) of the mouse. Also, the above mentioned principle of selective elimination of abnormal implants can be analysed experimentally. Although the developmental span of a trisomic zygote is limited, there is evidence that cells and tissues isolated from the chromosomally abnormal organism can survive much longer. Thus, haemopoietic stem cells, at least in Ts 12 and 19 of the mouse, can be rescued from trisomic fetuses by transferring them to lethally irradiated adult mice, whose blood forming organs may eventually become permanently repopulated by the trisomic cell lineage. This type of experiments is suited for closer analyses of potential functions vs. defects of chromosomally abnormal cellular systems, e.g., with regard to growth and development.

Cytogenetic studies of preinvasive lesions and invasive carcinomas' of the cervix uteri. III. Survey and interpretation of the results reported in the literature

Summary. Cytogenetic studies were performed of 54 preinvasive carcinomas and invasive squamous cervix carcinomas altogether. The chromosome number could be determined in 9 dysplasias, 25 carcinomas in situ, 4 carcinomas in situ with micro-invasion and 16 invasive squamous carcinomas (at least clinical stage Ib). It was shown that carcinomas in situ, carcinomas in situ with microinvasion and invasive squamous carcinomas could not be differentiated from each other in principle as groups with regard to numerical chromosome deviations...

Certain patterns of karyotype evolution in chronic myelogeneous leukaemia. Chromosome abnormalities in CML

The study of chromosome banding pattern of leukaemic cells in 15 patients with CML revealed t(9;22) in all cases. Similar additional chromosome abnormalities were observed in the terminal stage of the disease in 5 of 9 patients with aneuploid cell lines. The most frequent abnormalities were i(17q) and trisomy 8. The regularities of karyotype evolution in the terminal stage of CML are discussed.