...study (GWAS) is now becoming a routine analysis when there are large-scale genotype data and phenotypes data available from a population. However, conventional statistical techniques used in GWAS have yielded very little information considering the amount of data available. Low statistical power due to weak genetic effects is a possible explanation for this but applying simplistic tests for association could be another reason. For instance, currently there is no established method for detecting pleiotropy, that is when a single genetic variant influences multiple outcomes, from genome-wide scans, and generally phenotypes, which are often strongly biologically related, are rarely modelled together. Therefore, a new method that can identify pleiotropic genetic loci and model related phenotypes from genome-wide association study is needed. Method In this project, a novel method for the detection of pleiotropic genetic effects based on the genome-wide association study approach is developed. The method models multiple phenotypes simultaneously and in doing so may improve the power to detect genetic variants effecting phenotypes as well as identifying pleiotropic effects. The Usual way of association testing between genetic variants and phenotypes of interest, where a single phenotype or trait is the response variable and a single nucleotide polymorphisms (SNP) is the predictor, is reversed such that SNP is the outcome and multiple phenotypes are modelled simultaneously as predictors...
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...Outline Overview • Every day we observe heritable variations (such as brown, green, or blue eyes) among individuals in a population. • These traits are transmitted from parents to offspring. • One possible explanation for heredity is a “blending” hypothesis. ° This hypothesis proposes that genetic material contributed by each parent mixes in a manner analogous to the way blue and yellow paints blend to make green. ° With blending inheritance, a freely mating population will eventually give rise to a uniform population of individuals. ° Everyday observations and the results of breeding experiments tell us that heritable traits do not blend to become uniform. • An alternative model, “particulate” inheritance, proposes that parents pass on discrete heritable units, genes, that retain their separate identities in offspring. ° Genes can be sorted and passed on, generation after generation, in undiluted form. • Modern genetics began in an abbey garden, where a monk named Gregor Mendel documented a particulate mechanism of inheritance. A. Gregor Mendel’s Discoveries 1. Mendel brought an experimental and quantitative approach to genetics. • Mendel discovered the basic principles of heredity by breeding garden peas in carefully planned experiments. • Mendel grew up on a small farm in what is today the Czech Republic. • In 1843, Mendel entered an Augustinian monastery. • He studied at the University of Vienna from 1851 to...
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...A Review: Genetics as a Predictor for Success for Elite Athletes Performing in Power vs. Endurance Sports Common wisdom tells us that a sprinter is highly unlikely to excel in a marathon, and vice versa. It is easy to conceive that genetic variation is a major source of such differences in athletic ability. Actually identifying these genetic causes requires classification of athletic traits and in depth data analysis. Every year the number of polymorphisms that are candidates to clarify individual variations in sports performance increases. The growth of complexity and disproportion between studies parallels with advances in sports genetics. Additionally, there are numerous factors that play a part in these studies of elite athletes. These factors include gender, size of population, ethnic origin or level of competition of candidates, and the statistical approaches all make correlations between studies difficult. Recent studies support the possibility of developing polygenic profiles that could be used as a method to determine an athlete’s genetic predisposition to certain sports and events. A recent study conducted by Buxens et al., investigated the correlation between genetic polymorphisms and world-class endurance vs power athletes. Their research was published in an academic journal and was titled; “Can we predict top-level sports performance in power vs endurance events? A genetic approach”. The goal of their study was to discriminate potential genetic differences...
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...INTRODUCTION The fruit fly, Drosophila melanogaster, was used as a model organism to study the law of segregation and the law of independent assortment in Mendelian genetics. Drosophila was chosen as our model organism not only because of its short life cycle and fast breeding time but also because they are easy to maintain and handle in the laboratory. In this experiment a monohybrid cross and a dihybrid cross were performed. The law of segregation establishes the concept of dominance. The law of segregation states that an individual organism possesses two alleles that can encode a trait and that these alleles separate when gametes are formed and one of the two alleles go into each gamete. The concept of dominance states that when two alleles that encode for a trait are present in an individual only the “dominant” trait will be observed. For a dihybrid cross these statements still hold true but the law of independent assortment can also be observed. This law states that alleles at different loci on a chromosome that encode for different things separate independently of one another. METHOD Before beginning the experiment it was important to determine the sexes of the flies using a dissecting microscope and then to predict which phenotypes would be expressed. To distinguish between the sexes it was helpful to observe size, shape, and color of the flies, and to also check for the existence of sex combs. Only male flies have sex combs. Female flies are usually somewhat larger...
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...sychologyHow depression affects people Kim Branim Psychology 326 Sonja Bethune October 16, 2012 Introduction This study was design to find loci major depression via linkage analysis of a large sibling pair sample. Depressions in twins and families have been shown moderate high. “However the gene that caused depression had not been detected says” Lewis Cathryn but Gerome Breen “says that Chromosome3 it a link to severe depression. Breen study took 417 families with 479 concordant sibling pairs to perform genome-wide linkage analysis. Breen used the first wave of families, suggestive and modest suggestive and modest evidence for linkage was found on chromosomes 1p36, 12q, 13q, and 15q. The peaks on chromosomes 12q and 15q also showed evidence for linkage in other samples (8-10). In the present study, we report linkage analysis results using an expanded sample that includes 325 additional families contributing 474 sibling pairs, resulting in a total of 971 concordant sibling pairs with recurrent depression. The total sample also consisted of 118 discordant sibling pairs and 12 unaffected sibling pairs. Linkage can be detected when heterogeneity and error in phenotype are decreased. Also for depression, reliability is improved by focusing on severe cause ad indexed by symptom count or impairment. (Breen,2011) . Literature review The article name is Genome-Wide Association Study of Major Recurrent Depression in the U.K. Population. The Studies of major depression...
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...monohybrid rations of 3 taster: 1 non-taster phenotypes respectively. This supported the hypothesis that the traits were controlled by one gene with two alleles, where T is dominant to t. INTRODUCTION Mendel’s Law of Segregation – that two copies of a character (gene) segregate from each other during the formation of gametes, is apparent in the inheritance of PTC tasting in humans (Begg, 1959). The PTC sensory variation was first discovered in the early 1930s by A.L. Fox, which subsequently led to much research. It was reported not long after that PTC tasting is controlled by one gene with two alleles, and that inheritance of these traits is that of Mendel’s monohybrid ration of 3:1. However, there is evidence to suggest transmission of PTC tasting is more complex than this (Kim & Drayna, 2005). The presence of the dominant allele T determines wether or not an individual can taste PTC. A monohybrid cross of two heterozygotes results in three possible genotypes – TT, Tt, and tt, the only non-taster phenotype being tt (Schull, 1948). This study investigated inheritance of PTC tasting in humans to determine wether or not taster and non-taster phenotypes fell into the expected Mendelian ration. It was hypothesised that there would be a ratio of 3 taster: 1 non-taster phenotypes, and that the traits are controlled by one gene with two alleles, where T is dominant to t. MATERIALS AND METHODS Data was collected by 3rd year Genetics students. Blank paper and paper containing...
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...self-fertilizing hermaphrodite (XX) and a male (XO) there is no separate female sex. When a male mates with a hermaphrodite there is up to a 50% chance that the offspring will be male. But when a hermaphrodite self-fertilizes there’s about a 0.1% chance that a male will arise. Hermaphroditic self-mating allows efficient generation of recessive mutants and a single hermaphrodite has about 300 progeny. Ethyl Methanesulfonate (EMS) is a chemical that adds an alkyl groups to nucleotides, it is considered a chemical mutagen. Using this mutagen on the P0 generation of C.elegans and examining F2 generations, the mutation VAB-1 is of interest for this lab. This mutation expresses a phenotype of a notched head (Figure-1). By examining the F2 generation for this particular phenotype, isolation and replication of that phenotype will be goal of this lab. The VAB_1 mutation is most similar (59% identical, 72% similarity) to that of human EphA3/Hek [4]. The EphA3 is associated with protein-tyrosine kinases that show to be silenced in leukemia. Also EphA3 numbers and expression levels were decreased in lung cancers...
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...G×M×E adaptation or fitness landscape. Here we consider design of an integrated systems approach to crop improvement that incorporates advanced technologies in molecular markers, statistics, bio-informatics, and crop physiology and modelling. We suggest that such an approach can enhance the efficiency of crop improvement relative to conventional phenotypic selection by changing the focus from the paradigm of identifying superior varieties to a focus on identifying superior combinations of genetic regions and management systems. A comprehensive information system to support decisions on identifying target combinations is the critical core of the approach. We discuss the role of ecophysiology and modelling in this integrated systems approach by reviewing (i) applications in environmental characterization to underpin weighted selection; (ii) complex-trait physiology and genetics to enhance the stability of QTL models by linking the vector of coefficients defining the dynamic model to the genetic regions generating variability; and (iii) phenotypic prediction in the target population of environments to assess the value of putative combinations of traits and management...
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...Genetic Analysis in Plants Abbey Emmanuel and Danielle Peterson Life 120—Lab Section 136 October 29, 2014 Introduction Every living organism is made up of a series of genes. Each characteristic, such as color and texture, rely on the genetic coding of the organism. These genes can be passed along, mixed with other genes, or removed throughout the generations. The process of traits being passed from parent to offspring is called gene transmission. (Bailey, 2014) In the 1860’s a monk, Gregor Mendel set basic principles for heredity. His first law was Mendel’s law of segregation. He discovered this law while studying pea plants. He studied a series of seven different traits. (Bailey, 2014) He first observed and confirmed through experimentation that one pea plant of a certain color could self fertilize and produce another pea plant of the same color. He referred to the process of these self-fertilizing pea plants as true-breeding. (Urry et. Al, 2014) Mendel continued his studies of pea plants by testing that outcome of cross-pollination between two true-breeding plants. He took the two parent plants, one green and one yellow, and found the offspring to be all green. He continued experimenting by crossing two of the offspring from the first generation plants. Mendel found that in the second generation, an offspring color appeared from the parents that were lost in the first generation. His law of segregation explains that allele pairs segregate during...
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...Research, University of Chicago, Chicago, Illinois, United States of America Summary: Recent cancer studies emphasize that genetic and heritable epigenetic changes drive the evolutionary rate of cancer progression and drug resistance. We discuss the ways in which nonheritable aspects of cellular variability may significantly increase evolutionary rate. Nonheritable variability arises by stochastic fluctuations in cells and by physiological responses of cells to the environment. New approaches to drug design may be required to control nonheritable variability and the evolution of resistance to chemotherapy. Cancer progression is a series of evolutionary changes. Those changes include enhanced cellular proliferation, reduced cellular death by abrogating normal apoptotic mechanisms, greater invasiveness by increased expression of proteases, and improved colonizing ability to achieve metastasis [1]. In response to drug treatment, cancer cells often evolve resistance and continue to spread. Each evolutionary step typically proceeds by acquisition of genetic or heritable epigenetic changes in cells. When does the novel genetic change arise in an evolutionary step? By the current view, rare genetic variants arise before widespread phenotypic change. The idea is that a novel phenotype always comes from a novel genotype [2,3]. For example, rare resistant genetic variants may exist before drug treatment [4]. The drug selects those rare resistant variants, killing the other cancer...
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...DISORDER AND ADULT ONSET PANIC ATTACKS SHARE A COMMON GENETIC DIATHESIS Roxann Roberson-Nay, Ph.D.,1 ∗ Lindon J. Eaves, Ph.D.,1,2 John M. Hettema, M.D.,1 Kenneth S. Kendler, M.D.,1,2 and Judy L. Silberg, Ph.D.1,2 Background: Childhood separation anxiety disorder (SAD) is hypothesized to share etiologic roots with panic disorder. The aim of this study was to estimate the genetic and environmental sources of covariance between childhood SAD and adult onset panic attacks (AOPA), with the primary goal to determine whether these two phenotypes share a common genetic diathesis. Methods: Participants included parents and their monozygotic or dizygotic twins (n = 1,437 twin pairs) participating in the Virginia Twin Study of Adolescent Behavioral Development and those twins who later completed the Young Adult Follow-Up (YAFU). The Child and Adolescent Psychiatric Assessment was completed at three waves during childhood/adolescence followed by the Structured Clinical Interview for DSM-IIIR at the YAFU. Two separate, bivariate Cholesky models were fit to childhood diagnoses of SAD and overanxious disorder (OAD), respectively, and their relation with AOPA; a trivariate Cholesky model also examined the collective influence of childhood SAD and OAD on AOPA. Results: In the best-fitting bivariate model, the covariation between SAD and AOPA was accounted for by genetic and unique environmental factors only, with the genetic factor associated with childhood SAD explaining significant...
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...APPLICATION OF STATISTICS IN MEDICAL GENETICS INTRODUCTION "Significance" has a very particular meaning in biology thanks to statistics. How does this term prove an experiment's results are worth special attention? Once one has performed an experiment, how can one tell if the results are significant? For example, say if we are performing a genetic cross in which we know the genotypes of the parents. In this situation, we might hypothesize that the cross will result in a certain ratio of phenotypes in the offspring. But what if our observed results do not exactly match our expectations? How can we tell whether this deviation was due to chance? The key to answering these questions is the use of statistics, which allows us, geneticists, to determine whether our data are consistent with our hypothesis. Statistics and Human Genetics are twin subjects, having grown with the century together, and there are many connections between the two. Some fundamental aspects in particular the concept of Analysis of Variance, first arose in Human Genetics, while statistical and probabilistic methods are now central to many aspects of analysis of questions is human genetics. The most common areas where one can find an extensive applications of statistical methods in human genetics is * Human Genome Project * Linkage Analysis * Sequencing STATISTICAL GENETICS Statistical Genetics involves the identification of genetic variation to help us understand why certain people are...
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...Clinical Connection 1.1 Exome Sequencing Saves a Boy’s Life Bioethics: Choices for the Future Genetic Testing and Privacy CHAPTER OVERVIEW Chapter 1 provides a glimpse of the basic concepts of genetics and genomics, and offers examples of DNA information impacting daily life. In this new era of genomics, individuals have access to their own genetic information, and health care providers are learning how to incorporate DNA data into diagnostic and therapeutic medicine. Bioethics deals with issues of privacy, discrimination, and justice that arise from use and misuse of genetic information. DNA, genes, chromosomes, and genomes are the levels of genetic information, and they impact biology at the cell, tissue, organ, individual, family, and population levels. Genes encode proteins, and the exome is the small part of the genome that does so. Most traits arise from interactions of genes and environmental factors. Genetic information is in health care to identify individuals, in investigating the environment, and in understanding evolution. CHAPTER OUTLINE 1.1 Introducing Genes and Genomes 1. Genetics is a branch of biology concerned with inherited traits and their variation, and how these traits are passed from one generation to the next (heredity). 2. With continuing analysis of human genome sequences, human genetics has grown from a largely academic science to touch many areas of medicine, with practical and societal implications...
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...Ch 5:Cancer types Carcinoma - epithelial tissue, - metastasize Leukemia - bone marrow stem cells that produce white blood cells Sarcoma - connective tissue, muscle, bone, cartilage Lymphoma - lymph tissue, Hodgkins Adenocarcinoma - glandular epithelia, liver, salivary, breast Cancer Is Uncontrolled Cell Division What Is Cancer? Cell division is the process through which a cell copies itself Cancer begins when the a cell divides although it should not Unregulated cell division leads to a tumor, a mass of cells with no apparent function in the body Benign tumors do not affect surrounding structures Malignant tumors invade surrounding structures and are cancerous Malignant tumors can break away and start new cancers elsewhere through the process of metastasis What Is Cancer? Cancer cells differ from normal cells: Divide when they should not Invade surrounding tissue Move to other locations in the body What Is Cancer? All tissues that undergo cell division, such as ovarian tissue, are susceptible to cancer Cancer Risk Factors Known risk factors are linked to particular cancers… Not all exposures to chemicals and radiation causes cancers Cell Division Overview Cell division produces new cells in order to: Heal wounds Replace damaged cells For growth Also for reproduction Cell Division Overview DNA is organized into structures called chromosomes which can carry hundreds of genes along their length The number of in each cell depends...
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...The genetics of S. cerevisiae Biology 2 Genetics of Saccharomyces cerevisiae Part 1: Introduction & Determination of Phenotypes Overview You will be given three strains of Saccharomyces cerevisiae (named A, B, and C), each with a different genotype. The hypotheses for this study are (1) identify the phenotypes and genotypes of the three strains in regards to their ability to synthesize leucine, and uracil; and (2) determine whether these genes follow Mendel’s Second Law and assort independently. Goals and objectives of this project: • • • • • Learn how to work with S. cerevisiae, a model organism that is powerful for genetic research Experimentally explore genetic concepts (auxotroph vs. prototroph, genes vs. alleles, diploid vs. haploid, complementation, segregation and independent assortment, meiosis vs. mitosis, genotype vs. phenotype) Develop and test scientific hypotheses Learn to work with a microscope, micropipettor, microcentrifuge and hemacytometer Learn about the genetics of metabolism How this project will be graded: 1. Your scores for Question Sets 1, 2, and 3 will be combined into a single grade. That grade will be included in your Lab Average for the course. Your Lab Average will be included in your final semester average as described in the syllabus for this course. (the deadline for the question submission will be determined in class depending on the progress of the lab) 2. Your scores for Question Sets 4, 5, and 6 will...
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