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      Somatic Genome Variations in Health and Disease

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          Abstract

          It is hard to imagine that all the cells of the human organism (about 10 14) share identical genome. Moreover, the number of mitoses (about 10 16) required for the organism’s development and maturation during ontogeny suggests that at least a proportion of them could be abnormal leading, thereby, to large-scale genomic alterations in somatic cells. Experimental data do demonstrate such genomic variations to exist and to be involved in human development and interindividual genetic variability in health and disease. However, since current genomic technologies are mainly based on methods, which analyze genomes from a large pool of cells, intercellular or somatic genome variations are significantly less appreciated in modern bioscience. Here, a review of somatic genome variations occurring at all levels of genome organization (i.e. DNA sequence, subchromosomal and chromosomal) in health and disease is presented. Looking through the available literature, it was possible to show that the somatic cell genome is extremely variable. Additionally, being mainly associated with chromosome or genome instability (most commonly manifesting as aneuploidy), somatic genome variations are involved in pathogenesis of numerous human diseases. The latter mainly concerns diseases of the brain (i.e. autism, schizophrenia, Alzheimer’s disease) and immune system (autoimmune diseases), chromosomal and some monogenic syndromes, cancers, infertility and prenatal mortality. Taking into account data on somatic genome variations and chromosome instability, it becomes possible to show that related processes can underlie non-malignant pathology such as (neuro)degeneration or other local tissue dysfunctions. Together, we suggest that detection and characterization of somatic genome behavior and variations can provide new opportunities for human genome research and genetics.

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          The DNA-damage response in human biology and disease.

           Jiri Bartek,  Stephen P. Jackson (2009)
          The prime objective for every life form is to deliver its genetic material, intact and unchanged, to the next generation. This must be achieved despite constant assaults by endogenous and environmental agents on the DNA. To counter this threat, life has evolved several systems to detect DNA damage, signal its presence and mediate its repair. Such responses, which have an impact on a wide range of cellular events, are biologically significant because they prevent diverse human diseases. Our improving understanding of DNA-damage responses is providing new avenues for disease management.
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            Global variation in copy number in the human genome.

             Mandy H. Perry,  Daisuke Komura,  Fengtang Yang … (2006)
            Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
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              A comprehensive catalogue of somatic mutations from a human cancer genome.

               David H. Williamson,  Julie Gormley,  Lynda Chin … (2010)
              All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.
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                Author and article information

                Affiliations
                [1 ]National Research Center of Mental Health, Russian Academy of Medical Sciences
                [2 ]Institute of Pediatrics and Children Surgery, Rosmedtechnologii
                [3 ]Moscow City University of Psychology and Education, Moscow, Russia
                Author notes
                [* ]Address correspondence to this author at the National Research Center of Mental Health, Russian Academy of Medical Sciences, Zagorodnoe sh. 2, Moscow 119152, Russia; Tel: 7 495 952 89 90; Fax: 7 495 952 89 40; E-mail: ivan_iourov@ 123456yahoo.com
                Journal
                Journal ID (nlm-ta): Curr Genomics
                Journal ID (publisher-id): CG
                Title: Current Genomics
                Publisher: Bentham Science Publishers Ltd.
                ISSN (Print): 1389-2029
                ISSN (Electronic): 1875-5488
                Publication date (Print): September 2010
                Volume: 11
                Issue: 6
                Pages: 387-396
                PMC ID: 3018718
                PubMed ID: 21358982
                Publisher ID: CG-11-387
                DOI: 10.2174/138920210793176065
                Copyright statement: ©2010 Bentham Science Publishers Ltd.

                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.5/), which permits unrestrictive use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Subject: Article

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                ScienceOpen disciplines: Genetics

                Keywords: disease., aneuploidy, somatic genome variations, genomic instability, chromosome instability

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