Progress of Strategy, Technique and Methodology in Medical GeneticsCONTENTSn nLandmarks in genetics and genomicsLandmarks in genetics and genomicsn nEducating health-care professionals about Educating health-care professionals about genetics and genomicsgenetics and genomicsn nBasic knowledge of medical geneticsBasic knowledge of medical geneticsn nTheoreticalTheoretical、techniques and data basetechniques and data basen nFrom chromosomes to genesFrom chromosomes to genes、 genomesgenomes、transcriptomestranscriptomes、proteomesproteomes、metabonomicsmetabonomicsn nEpigenetics/epigenomicsEpigenetics/epigenomicsn nCancer genetics and genomics as an exampleCancer genetics and genomics as an examplen n Personalized medicine Personalized medicine Educating health-care professionals about genetics and genomicsTo biomedical researchers, this is the genome era. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics have already transformed basic and translational biomedical research. However, for most clinicians, the genome era has not yet arrived. For genomics to have an effect on clinical practice that is comparable to its impact on research will require advances in the genomic literacy of health-care providers A sampling of resources for genetics education for health-care professionalsFrom the US-based National Coalition for Health Professional Education in Genetics(NCHPEG): Core Competencies in Genetics Essential for All Health Care Professionals (2007) Core Principles in Genetics (2004) Genetics and Common Disorders: Implications for Primary Care and Public Health Providers(2005) Genetics, Race, and Health Care: What We Know and What It Means for Your Practice (2006) Psychiatric Genetics: A Program for Genetic Counselors (2002) Family history newsletter (ongoing) Genetics Resources On the Web (GROW) a targeted search engine Genetics in Dentistry (2004) Genetics for Speech-Language Therapists and Audiologists (2006) From other sources: Genetics in Clinical Practice: A Team Approach (developed by the US Centers for Disease Control and Prevention and Dartmouth College of Medicine) Gene Tests and Gene Clinics National Genetics Education and Development Centre (UK National Health Service)BASELINE COMPETENCIES At a minimum, each health-care professional should be able to: a. examine ones competence of practice on a regular basis, identifying areas of strength and areas where professional development related to genetics and genomics would be beneficial. b. understand that health-related genetic information can have important social and psychological implications for individuals and families. c. know how and when to make a referral to a genetics professional. 1 KNOWLEDGE All health professionals should understand: 1.1 basic human genetics terminology. 1.2 the basic patterns of biological inheritance and variation, both within families and within populations. 1.3 how identification of disease-associated genetic variations facilitates development of prevention, diagnosis, and treatment options. 1.4 the importance of family history (minimum three generations) in assessing predisposition to disease. 1. 5 the interaction of genetic, environmental, and behavioral factors in predisposition to disease, onset of disease, response to treatment, and maintenance of health. 1.6 the difference between clinical diagnosis of disease and identification of genetic predisposition to disease (genetic variation is not strictly correlated with disease manifestation). 1 KNOWLEDGE All health professionals should understand: 1.7 the various factors that influence the clients ability to use genetic information and services, for example, ethnicity, culture, related health beliefs, ability to pay, and health literacy. 1.8 the potential physical and/or psychosocial benefits, limitations, and risks of genetic information for individuals, family members, and communities. 1.9 the resources available to assist clients seeking genetic information or services, including the types of genetics professionals available and their diverse responsibilities. 1.10 the ethical, legal and social issues related to genetic testing and recording of genetic information (e.g., privacy, the potential for genetic discrimination in health insurance and employment). 1.11 ones professional role in the referral to or provision of genetics services, and in follow-up for those services. 2 SKILLS All health professionals should be able to: 2.1 gather genetic family history information, including at minimum a three-generation history. 2.2 identify and refer clients who might benefit from genetic services or from consultation with other professionals for management of issues related to a genetic diagnosis. 2.3 explain effectively the reasons for and benefits of genetic services. 2.4 use information technology to obtain credible, current information about genetics. 2.5 assure that the informed-consent process for genetic testing includes appropriate information about the potential risks, benefits, and limitations of the test in question. 3 ATTITUDES All health professionals should: 3.1 appreciate the sensitivity of genetic information and the need for privacy and confidentiality. 3.2 seek coordination and collaboration with an interdisciplinary team of health professionals. A. Principles related to biological variation1. Genetics is the study of heritable biological variation.2. Genetics in the health-care setting concerns heritable variation that is related to health and disease.3. Molecular biology is the study of the structures and functions of macromolecules such as nucleic acids and proteins.4. Genomics is the study of the constitution of entire genomes, that is, all of the genetic material in an organism.5. Proteomics is the study of the structure and functions of the protein products of the genes in the genome.6. Individual genetic variation that leads to biochemical and molecular individuality results in part from the variable sequences of the four bases that are central components of the DNA molecule. A. Principles related to biological variation7. Mutations introduce additional variation, but not all mutations have biological significance. Some can be deleterious in varying degrees; others, fewer in number, may provide selective advantages that are useful to evolution. There would be no differential selection, and therefore no evolution, without mutation and variation. This principle helps to explain phenomena such as the emergence of bacterial strains that are resistant to antibiotics, as well as the obvious human differences we recognize in everyday life.8. Human variation results from the interactions among variable gene products and environmental factors that vary from person to person in kind, duration, and intensity. Variation is expressed at the molecular level in differences in sequences of amino acids and therefore in the structure and function of proteins that maintain physiological systems. It also is expressed in disease, which is a result of some incompatibility between homeostatic variation and the individuals experience with the environment. Because that is the case, genetics and genomics are the most basic sciences for health care and for education of health professionals. A. Principles related to biological variation9. There is no fixed typeno archetypical individualin a species, including Homo sapiens. A species comprises a population of unique individuals that may vary in each of their traits, including metabolism, immune responses, morphology, and behavior, and, therefore, in expression of disease.10. There are no sharp genetic boundaries between populations of human beings around the globe, and there is more genetic variation within populations than between them. These facts make the designation of biological races scientifically untenable and make the grouping of people by phenotypes such as skin color a poor predictor of other traits.11. The genotype for a given trait is the gene(s) associated with that trait. The phenotype is the expression of the genotype. That expression is mediated by protein gene products that work in the context of experiences with the environment, through development, maturation, and aging. A. Principles related to biological variation12. Some human traits, including diseases, result primarily from the action of the product of one gene. Other human traits, including most common diseases, result from the products of more than one gene acting in concert with the influence of environmental variables, which vary in kind, duration, and intensity through time.13. The development of disease reflects three time frames: a) the evolutionary history biological and cultural of our species, which has produced the genome common to all of us; b) the individual developmental history of each person, which interacts with the products of his or her genes, and c) the more immediate factors that results in the expression of disease at a particular moment. A. Principles related to biological variation14. The phrase “the gene for,” as in “the gene for phenylketonuria,” can be misleading. It can imply erroneously that only genetic influences are responsible for a given trait or disease, discounting the influence of the environment. The phrase also can suggest that only one gene is associated with a given trait when there may be genetic heterogeneity, of alleles and modifiers, as well as multiple loci. The blood-group substances and hemoglobin variants demonstrate such heterogeneity.15. Genetically based health care, which now embraces genomics, is uniquely positioned to provide insights into prevention because it acknowledges the individuality of each patient and the biological and environmental influences that produce that individuality. Genetically based care focuses primarily on the person who has the disease, not on the disease itself. It asks, “Why does this person have this disease at this point in his or her life?” and it recognizes that individual variation in genes, development, and experiences means that each person has his or her own version of each disease. B. Principles related to cell biology1. Classic cell theory holds that all life is made of cells and that all cells come from pre-existing cells.2. Cells pass through a series of structural and functional stages known as the cell cycle. The cell cycle, which includes processes leading to cell division, is under genetic control. Cancer results from one or more disruptions in that cell cycle. Because most of these disruptions occur in somatic cells (as opposed to germ cells) all cancer is genetic, but not all of it is inherited.3. Cell division produces new cells.4. Mitosis, one aspect of cell division, helps to ensure genetic continuity from one generation of somatic cells to the next. Human somatic cells contain 46 chromosomes (the diploid number): 22 pairs of autosomes and one pair of sex chromosomes (X and Y). B. Principles related to cell biology5. Human germ cells, sperm and ova, contain 23 chromosomes (the haploid number). A special process of cell divisionmeiosisoccurs in the precursors to germ cells. Meiosis has two major biological effects: it reduces the number of chromosomes from 46 to 23 and it increases genetic variation through independent assortment and through the exchange of genetic material between maternal and paternal chromosomes (crossing over). Meiotic variations can result in abnormalities of chromosome number or structure.6. In Homo sapiens and in other animals, the fungi, and plants, cells contain a nucleus that includes the chromosomes, the carriers of most of the genetic material (DNA).7. Human cells also contain mitochondria. Because mitochondria were free-living organisms early in the evolution of life, they carry their own DNA, which now specifies proteins that are useful to us. Mutations in mitochondrial DNA can cause health problems. C. Principles related to classical (Mendelian) genetics 1. Our understanding of the behavior of chromosomes during meiosis allows us to make predictions about genotype from one generation to the next.2. Some traits are inherited through an autosomal dominant pattern of inheritance, others through an autosomal recessive pattern. Still others, those traits associated with genes on the X chromosome, follow somewhat different patterns of transmission because the male has only one X chromosome.3. Traits, not genes, are dominant or recessive. It is convenient, even traditional, to refer to genes as dominant or recessive, but today it is anachronistic, because of our new knowledge of how protein gene products influence phenotype.4. Aberrations in the behavior of chromosomes during meiosis can result in structural or numerical alterations that have serious consequences for growth and development. Some of these aberrations occur more frequently in the offspring of older mothers. C. Principles related to classical (Mendelian) genetics Others arise more frequently during the formation of sperm. We can detect many chromosomal aberrations prenatally. They account for a significant proportion of fetal death, and to a lesser extent, death in infancy.5. Our understanding of genes in populations allows us to make predictions about the presence of genes in individuals and in given populations and, therefore, about the variable frequencies of disease phenotypes.6. During the last two decades, research has uncovered genetic mechanisms that extend our understanding of non-mendelian inheritance and that provide biological explanations for heretofore-unexplained observations. These mechanisms, such as imprinting, trinucleotide repeats, and epigenesis, however, do not alter our fundamental understanding of the rules that govern genetic and molecular processes. D. Principles related to molecular genetics1. DNA and RNA are information molecules; they store biological information in digital form in a well-defined code.2. DNA is the primary information molecule for virtually all life on earth; this is but one piece of evidence for the relatedness of all life through evolution.3. DNA does very little by itself. It is a stable storehouse of genetic information, but it takes proteins to put the information to use. DNAs transcription and the translation of its information into protein are accomplished by protein-mediated mechanisms. Similarly, the functions of the organs and body are carried out by sets of proteins whose properties and actions are not likely to be understood or predictable by our current knowledge of single genes or proteins.4. The structure of DNA lends itself to replication. DNA replicates with great accuracy, which is critical to the proper transmission of genetic information from one generation of cells to the next and from one generation of organisms to the next. D. Principles related to molecular genetics5. Sometimes errors arise during DNA replication, and evolution has produced mechanisms that repair such mistakes. In fact, some of those mechanisms present in Homo sapiens are conserved evolutionarily all the way back to the bacterium E. coli. When repair mechanisms fail, mutations may remain. Some may become the basis for evolutionary change.6. In most biological systems, the flow of information is: DNA-RNA-protein. The processes by which this occurs are replication of the DNA, transcription of the DNA into messenger RNA, and translation of the messenger RNA into protein.7. DNA is susceptible to damage by environmental insults such as radiation and certain chemicals, and the damage that occurs to our DNA during the course of our lives can contribute to aging and the onset of cancer. Damage that occurs in the DNA of germ cells sperm and ova is not completely repaired. Evolution is a possible result of these new, heritable variations. D. Principles related to molecular genetics8. A gene is a segment of DNA. Some genes code for the production of structural proteins (collagen, for example) or enzymes (lactase, for example). Other genes are regulatory, helping to control such processes as prenatal development and ongoing cellular functions.9. A gene occupies a particular place on a chromosomea locus. A gene can have two or more alternative formsallelesbut only one allele at a time can occupy a given locus on a given chromosome.10. Because proteins direct the operations of cells, such statements as “gene-environment interaction” are inaccurate. The interaction is actually between the environment for example, oxygen, food, drug, or antigen and the protein products of the genes. E. Principles related to development1. The human life span comprises three major phases: development, including embryological development and growth after birth until maturation; maturation; and aging. Progression through the stages is continuous, however, and apart from birth it is difficult to tell where one ends and the next begins.2. Although virtually all human beings proceed through the same developmental stages, there are individual differences in the rate of progression.3. Embryological development begins with the fusion of sperm and ovum. This event restores the diploid number and initiates a complex series of events that involves an increase in the number of cells; differentiation of the zygote into the specialized cells, tissues, and organs that make up a new, individual organism; and growth of the organism itself.4. Embryological development is under genetic control. That is, particular genes must be turned on and off at the correct time to ensure proper development. E. Principles related to development5. Development is not, however, the simple unfolding of a genetic program resulting in a predictable end product. It involves the influence of maternal mitochondrial genes and gene products at the time of fertilization, as well as significant and variable non-genetic factors such as communication between cells, the migration of cells within the developing embryo, the proper spatial orientation of the embryo, and the effects of environmental influences. These factors render the precise outcome of development unpredictable and contribute to the uniqueness of each individual, the hallmark of life on earth.6. Biologists have discovered a set of genes, called homeotic genes, that are central to embryological development of the body plan. These genes are highly conserved throughout evolution, and the genes even appear in the same order on the chromosomes of species as distantly related as round worms, fruit flies, mice, and human beings. Biologists therefore are able to study the genetic and molecular aspects of human development by studying those processes in other species. E. Principles related to development7. The Human Genome Project has provided the complete DNA sequences of all human genes and will allow more detailed analysis of the genetic regulation of development. Likewise, the ability to analyze the protein products of genes involved in development will improve our understanding of the many and varied complex steps that produce a new individual.8. The evolutionary changes that lead to the production of new species undoubtedly result from rare, beneficial changes during embryological development of individual organisms. Most embryological changes will be small, however, because the system will not tolerate major deviations from the basic developmental plan.9. Environmental agents such as radiation or drugs can interfere with embryological development, resulting in birth defects and, more likely, fetal death. Various technologies allow detection of some of these abnormalities in utero. E. Principles related to development10. Unlike development in species whose newborns are juveniles, development in Homo sapiens continues throughout infancy, and there is a long juvenile period. This requires prolonged parental investment and also exposes the still-developing organism to the possibility of environmental insults.11. Change continues throughout the lifespan in the form of maturation and aging, always building upon, and constrained by, what has come before, and providing the substrate for subsequent events.12. Some diseases that have their onset in middle age or old age may actually have had their origins much earlier in the individuals developmental history. F. Principles related to new genetic technology1. Advances in technology allow us to analyze and manipulate the genetic material in ways that were not possible even a few years ago.2. These technologies allow us to identify, isolate, and test for genes associated with disease, and in the future, perhaps for traits that have no clinical significance.3. Like all technologies, genetic technologies are fallible, can have unintended consequences, and may serve the interests of entities apart from the patient.4. The growth of information technology in concert with the expansion of genetic technology is a great boon to genetically based health care and to basic research, but it also raises concerns about the use of genetic information.Genetics is the study of single genes and their effects. Genetics in the health-care setting concerns heritable variation that is related to health and disease（Medical Genetics）Genomics, on the other hand, is a relatively new term describing the study of the function and interaction of all the genes in the genome.Molecular biology is the study of the structures and functions of macromolecules such as nucleic acids and proteins.Chromosomes: the self-replicating genetic structures of cells containing the cellular DNA that carries in its nucleotide sequence the linear array of genes.Gene: specific segments of DNA composed of distinctive sets of nucleotide pairs in discrete region of a chromosome that encodes a particular protein.Transcriptomics: the study of transcriptome which is consist of the complete set of mRNA in any given cell.Proteomics：technology by which systematic surveys are made of the expression of large number of distinct species in a biological sample, such as a cell lysate or a biological fluid. Metabonomics encompasses the comprehensive and simultaneous systematic profiling of multiple metabolite levels and their systematic and temporal changes caused by factors such as diet, lifestyle, environment, genetic effects and pharmaceutical effects both beneficial and adverse, in whole organisms.DNA DNA methylationmethylation DNA methylation occurs predominantly in repetitive genomic regions that contain CpG residues. DNA methylation represses transcription directly by inhibiting the binding of specific transcription factors, and indirectly by recruiting methyl-CpG-binding proteins and their associated repressive chromatin remodelling activities.Epigenetic Refers to mitotically or meiotically heritable changes in gene expression that do not involve a change in DNA sequence.Genomic Genomic imprintingimprinting The epigenetic marking of a locus on the basis of parental origin, which results in monoallelic gene expression.EpigenomeEpigenome The global epigenetic patterns that distinguish or are variable between cell types. These patterns include DNA methylation, histone modifications and chromatin associated proteins.Genetic testing has been described as “the analysis of human DNA, RNA, chromosomes, proteins and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes or karyotypes for clinical purposes”.Cancer genomics malignant phenotype can rarely, if ever, occur as a result of a single genetic defect. As such we should probably now discard the term cancer genetics and talk of cancer genomics among the repertoire of diseases encompassed by genomic medicine Aspects of genomic medicine relevant to cancer as a multifactorial disorder include inherited mutations that confer an increased predisposition, somatic mutations in the process of carcinogenesis and genetic variations that may be pathological or protective in the context of disease expression or management.Categories of human genetic disordersn nUnifactorial disordersn nMultifactorial disordersn nChromosomal disorders n nSomatic cell genetic disordersn nMitochondrial genetic disordersMethodologies of Medical Geneticsn nPopulation Screening n nPedigree Analysisn nKaryotypingn nTwin Analysisn nHuman races comparationn nConstitutive analysisn nLinkage and Association analysisFluorescence in-situ hybridization (FISH) Comparative genomic hybridization (CGH)Multiplex ligation- dependent probe amplificationDenaturing high performance liquid chromatography Temperature gradient capillary electrophoresis Single-strand confirmation polymorphisms (SSCP)Denaturing gradient gel electrophoresis (DGGE)Sequencing HaplotypePCR Southern blot Metabolite analysis 2D-gel electrophoresis MS or MS/MSGC-EI/ToF-MSNMR Spectroscopy TechniquesThe biogenesis of microRNAsMicroRNAs can function as tumour suppressors and oncogenesThe different forms of RNA silencing.RNA-modification strategies for genetic medicineA Depiction of Chromosome 16 Based on the Determination of Its Actual Sequence by the Human Genome Project.50From DNA to proteinFrom DNA to proteinAlternative Splicing. A single gene can produce multiple related proteins, or isoforms, by means of alternative splicing.Examples of Point Mutations.Reciprocal chromosomal translocations in Burkitts lymphoma, a solid tumour of B lymphocytes. The genes for making the heavy chains of antibodies (CH) are located on chromosomes 14, whereas those for making the light chains are on chromosomes 2 and 22. These genes are expressed exclusively in B lymphocytes, because only these cells have the necessary transcription factors to switch on their expression. In most (over 90%) of Burkitts lymphoma cases, a reciprocal translocation moves the proto-oncogene c-myc from its normal position on A.Painting probes stain entire chromosomes. B. Regional painting probes can be generated by chromosome microdissection. C. Centromeric-repeat probes are available for almost all human chromosomes. D. Large insert clones are available for most genomic regions. e | Special probe sets can be designed to facilitate diagnosis of known structural rearrangements. F.Genomic DNA is used as the probe in comparative genomic hybridization (CGH) to establish copy number. G. For high-resolution analysis, DNA fibres can be used as the target for probe hybridization. H. Microarrays can be used as targets for hybridization to provide resolutions down to the single-nucleotide level. A BAC array is shown, to which test DNA and reference DNA are hybridizedComparison of cytogenetic techniques for identifying chromosomal abnormalitiesCombining cytogenetic approaches to understand a complex chromosomal rearrangementStudying genome organization using three-dimensional fluorescence in situ hybridization6061What is a DNA Microarray?What is a DNA Microarray?A A DNA DNA micorarray micorarray allows allows scientists scientists to to perform perform an an experiment experiment on on thousands thousands of of genes genes at at the the same same time. time. Each Each spot spot on on a a microarray microarray contains contains multiple multiple identical identical strands strands of of DNA. DNA. The The DNA DNA sequence sequence on on each each spot spot is is unique. unique. Each Each spot spot represents represents one one gene.Thousands gene.Thousands of of spots spots are are arrayed arrayed in in orderly orderly rows rows and and columns columns on on a a solid solid surface surface (usually (usually glass).The glass).The precise precise location location and and sequence sequence of of each each spot spot is is recorded recorded in in a a computer computer database. database. Microarrays Microarrays can can be be the the size size of of a a microscope slide, or even smaller.microscope slide, or even smaller.Study and reference DNA are labeled with a green (a) and red (b) fluorochrome, respectively, and cohybridized to normal metaphase spreads or tomicroarray. Green and red regions of chromosomes correspond respectively to an overrepresentation (green/red 1.2) and an under representation(green/red 0.8) of the study DNA.How to sequence DNA“Sequencing does put microarrays at risk in someareas of the life-sciences research market.”Individual-cell analysis of signalling. A.Tumour cells that have been isolated from a patient are treated with different environmental cues or therapeutic agents as a way to identify which signalling networks are active. It is possible to study cancer cells from the tumour (Tu), stromal cells (S), cells of the vasculature (V), or immune cells such as T cells (T). B.The same technique can be used to study signalling in subsets ofnormal primary cells, such as T cells (T), B cells (B) or monocytes (M) aftertreatment with various stimuli, such as interleukin (IL)-7 (red circles) or IL-4 (blue circles)Actin fibers (red - stained with rhodamine) and microtubuls (green - stained with fluorescein) in fibroblasts in an in vitro culture. A bottom image - superposition of images of green and red fluorescencePedigree analysisThe scope of proteomicsn n Proteins can be studied in various contexts, including sequence, structure, interactions, expression, localization, and modification.n n Proteomics is divided into several major but overlapping branches, that embrace these different contexts: (a) sequence & structural proteomics, (b) expression proteomics, (c) interaction proteomics, and (d) functional proteomics. Sequence and structural proteomicsn n Three Three primary primary nucleic nucleic acid acid sequence sequence databases: databases: GenbankGenbank, , the the EMBL EMBL nucleotide nucleotide sequence sequence database, database, and and the the DNA DNA database database of of Japan (DDBJ).Japan (DDBJ).n n Protein Protein sequence sequence databases: databases: SWISS-PROT, SWISS-PROT, and and TrEMBLTrEMBLn nProtein Protein structure structure database database : : The The Protein Protein Data Data Bank (Bank (www.rscb.orgwww.rscb.org) ) Expression proteomicsn nThe The analysis analysis of of protein protein abundance abundance and and involves involves the the separation separation of of complex complex protein protein mixtures, mixtures, the the identification identification of of individual individual components components and and their systematic quantitative analysistheir systematic quantitative analysisn nThe The key key technologies technologies in in expression expression proteomics proteomics are are 2D-gel 2D-gel electrophoresis electrophoresis and and multi-multi-dimensional dimensional liquid liquid chromatography chromatography (MDLC) (MDLC) for for protein protein separation, separation, mass mass spectrometry spectrometry for for protein protein identification, identification, and and image image analysis analysis or or mass spectrometry for protein quantification.mass spectrometry for protein quantification.The genome, transcriptome, and proteome Studying the transcriptome using DNA microarraysPM: perfectly matched; MM: mismatched (a single base difference in a central position, compared with PM)Interaction proteomicsn nIt It studies studies the the genetic genetic and and physical physical interactions interactions among among proteins proteins as as well well as as interactions interactions between between proteins proteins and and nucleic acids or small molecules.nucleic acids or small molecules.n nOne One of of its its ambitious ambitious goals goals is is the the creation creation of of proteome proteome linkage linkage maps maps based based on on binary binary interactions interactions between between individual individual proteins proteins and and higher-order higher-order interactions interactions determined determined by by the the systematic systematic analysis analysis of of protein protein complexes.complexes.n nKey Key technologies technologies in in this this area area include include (1) (1) the the yeast yeast two-two-hybrid hybrid system, system, and and mass mass spectrometry spectrometry for for the the analysis analysis of of protein protein complexes, complexes, & & (2) (2) biochemical biochemical assays assays and and structural structural analysis analysis methods methods (e.g., (e.g., X-ray X-ray crystallography, crystallography, NMR) for protein-NMR) for protein-ligandligand interaction study. interaction study.Functional proteomics: The study of protein function on a large scale.The challenges of proteomicsCombination of different protein interaction techniques to increase the level of confidence in the human interactome while minimizing the number of experiments to perform.Steps involved in protein interaction mapping by affinity purification coupled to mass spectrometry. Possible issues are highlighted.Cancer is caused by alterations in oncogenes, tumor-suppressor genes, and microRNA genes. These alterations are usually somatic events, although germ-line mutations can predispose a person to heritable or familial cancer. A single genetic change is rarely sufficient for the development of a malignant tumor. Most evidence points to a multistep process of sequential alterations in several, often many, oncogenes, tumor-suppressor genes, or microRNA genes in cancer cells. Tumors often possess cytogenetically different clones that arise from the initialtransformed cell through secondary or tertiary genetic alterations. This heterogeneity contributes to differences in clinical behavior and responses to treatment of tumors of the same diagnostic type.Functional Properties of Oncogenesn nTranscription Factorsn nChromatin Remodelersn nGrowth Factorsn nGrowth Factor Receptorsn nSignal Transducersn nApoptosis RegulatorsMicroRNA Genes MicroRNA genes, unlike other genes involved in cancer, do not encode proteins. Instead, the products of these genes consist of a single RNA strand of about 21 to 23 nucleotides; their function is to regulate gene expression. A microRNA molecule can anneal to a messenger RNA (mRNA) containing a nucleotide sequence that complementsthe sequence of the microRNAProspects for integrative analysis of comprehensive approaches used to characterize cancer.Cancer pathways and targeted therapy. a, Multiple signalling pathways upregulated in cancer cells owing to specific alterations in oncogenes or tumour suppressors stimulate tumour-cell proliferation, often by promoting G1S cell-cycle progression b, Classical chemotherapy and radiotherapy eliminates cancer cells by inducing DNA damage and subsequent apoptosisComplementary approaches to understanding cancer genetics.Stages of Metastatic ProgressionPressures that Drive Selection for Metastatic TraitsDistinct Fates for Disseminated Cancer CellsPatterns of Metastatic ColonizationA model of the influence of genetic background on metastatic efficiencyComparing the different factors that might influence tumour-gene- and metastasisgene-expression patternsThe deepening of our understanding of normal biology has made it clear that stem cells have a critical role not only in the generation of complex multi-cellular organisms, but also in the development of tumors. Recent findings support the concept that cells with the properties of stem cells are integral to the development and perpetuation of several forms of human cancer. Eradication of the stem-cell compartment of a tumor also may be essential to achieve stable, long-lasting remission, and even a cure, of cancer. Advances in our knowledge of the properties of stem cells have made specific targeting and eradication of cancer stem cells a topic of considerable interest.Embryonic and somatic stem cells as a source of genetic medicinesSummary of LOH studies in ovarian cancerSummary of molecular cytogenetic studies quantifying genomic imbalanceGene Gene Silencing Silencing in in Normal Normal Cells Cells Heritable Heritable gene gene silencing silencing involves, involves, among among other other processes, processes, the the interplay interplay between between DNA DNA methylation, methylation, histone histone covalent covalent modifications, modifications, and and nucleosomal nucleosomal remodeling. remodeling. Some Some of of the the enzymes enzymes that that contribute contribute to to these these modifications modifications include include DNA DNA methyltransferase methyltransferase (DNMTs), (DNMTs), histone histone deacetylases deacetylases (HDACs), (HDACs), histone histone methyltransferases methyltransferases (HMTs), (HMTs), and and complex complex nucleosomal nucleosomal remodeling remodeling factors factors (NURFs). (NURFs). The The interplay interplay between between these these processes processes establishes establishes a a heritable heritable repressive repressive state state at at the the start start site site of of genes genes resulting resulting in in gene gene silencing. silencing. Physiologically, Physiologically, silencing silencing is is critical critical for for development development and and differentiation. differentiation. Pathologically, Pathologically, silencing silencing leads leads to to diseases diseases such such as as cancer. cancer. Recent Recent evidence evidence suggests suggests global global changes changes in in all all three three processes processes in in cancer, perhaps reflecting their interrelationships.cancer, perhaps reflecting their interrelationships.Current methods for high-throughput DNA methylation analysis: sample pretreatmentCurrent methods for high-throughput DNA methylation analysis: readoutMethods for profiling genome-wide DNA-methylation patternsEpigenetic response to extrinsic signals occurs through the transcriptional factors network.Altered DNA-methylation patterns in tumorigenesis. The hypermethylation of CpG islands of tumoursuppressor genes is a common alteration in cancer cells, and leads to the transcriptional inactivation of these genes and the loss of their normal cellular functions. This contributes to many of the hallmarks of cancer cells. At the same time, the genome of the cancer cell undergoes global hypomethylation at repetitive sequences, and tissue-specific and imprinted genes can also show loss of DNA methylation. In some cases, this hypomethylation is known to contribute to cancer cell phenotypes, causing changes such as loss of imprinting, and might also contribute to the genomic instability that characterizes tumours.Techniques for studying epigenetic changes in cancer. Most approaches to detecting DNA methylation start with the purification of DNA from cell samples. Subsequently, the overall DNA 5-methylcytosine content can be determined using high-performance capillary electrophoresis (HPCE) or high-performance liquid chromatography (HPLC), or the DNA methylation of specific candidate genes can be detected with methylation-sensitive methods.The epigenetic progenitor model of cancerThe clonal genetic model of cancerEpigenetic gene-silencing events and tumorigenesisThe role of miRNA hypermethylation in the metastatic behavior of human primary tumors. Methylation-specific PCR analyses for miR-148a, miR-34b/c, miR-9-1, miR-9-2, and miR-9-3 in primary human tumors derived from different tissues. The presence of a band under the U or M lanes indicates unmethylated or methylated sequences, respectively.Gene-transfer vectors that are used to treat hereditary disorders128129Using gene expression to investigate the genetic basis of complex disordersThe identification of complex disease susceptibility loci through genome-wide association studies (GWAS) has recently become possible and is now a method of choice for investigating the genetic basis of complex traits. The number of results from such studies is constantly increasing but the challenge lying forward is to identify the biological context in which these statistically significant candidate variants act. Regulatory variation plays an important role in shaping phenotypic differences among individuals and thus is very likely to also influence disease susceptibility. As such, integrating gene expression data and other disease relevant intermediate phenotypes with GWAS results could potentially help prioritize fine-mapping efforts and provide a shortcut to disease biology. Combining these different levels of information in a meaningful way is however not trivial.Local superimposition of whole-genome disease and expression associations. For any given genomic interval, same SNPs will have been inde- pendently tested for associations with a disease and transcript levels of a set of genes, respectively. (A) No significant eQTLs detected in the interval for Gene A. (B) Significant eQTLs for Gene B do not also display significant disease associations. (C) The association patterns of disease and Gene C expression fit very well, making it the most likely candidate out of the three for a possible regulatory-mediated disease effect.Published Genome-Wide Associations through 6/2010, 904 published GWA at p5x10-8 for 165 traitsNHGRI GWA Catalogwww.genome.gov/GWAStudiesNIH launches Genotype-Tissue Expression projectCorrelations between genotype and tissue-specific gene expression levels will help identify regions of the genome that influence whether and how much a gene is expressed. 2010-10-6Ensembl Genome Browser http:/www.ensembl.org GEN2PHEN Project http:/www.gen2phen.org/ Genetic Association Database http:/geneticassociationdb.nih.gov/ HuGE Navigator (Centers for Disease Control and Prevention) GWAS Integrator http:/hugenavigator.net/HuGENavigator/gWAHitStartPage.do HuGE Literature Finder http:/www.hugenavigator.net/HuGENavigator/startPagePubLit.do Variant Name Mapper http:/www.hugenavigator.net/HuGENavigator/startPageMapper.do Human Gene Coexpression Database http:/www.geneticsofgeneexpression.org/network/ International HapMap Project http:/www.hapmap.org/ National Center for Biotechnology Information (NCBI) Links dbSNP http:/www.ncbi.nlm.nih.gov/projects/SNP/ Entrez Gene http:/www.ncbi.nlm.nih.gov/sites/entrez?db=gene GenBank http:/www.ncbi.nlm.nih.gov/Genbank/ PubMed http:/www.ncbi.nlm.nih.gov/sites/entrez/ UCSC Genome Browser Gateway http:/genome.ucsc.edu/cgi-bin/hgGateway Resources to help clinicians integrate genetics into patient care Thank Thank YouYou