A Flexible Gene Based Test For Genome Wide Association Studies

1883 words - 8 pages

Gene-based tests for association are increasingly being seen as a useful complement to genome-wide association studies (GWAS) [1]. A gene-based approach considers association between a trait and all markers (usually SNPs) within a gene rather than each marker individually. Depending on the underlying genetic architecture, gene-based approaches can be more powerful than traditional individual-SNP based GWAS. For example, if a gene contains more than one causative variant, then several SNPs within that gene may show marginal levels of significance that are often indistinguishable from random noise in the initial GWAS results. By making use of prior biological information and combining the effects of all SNPs in a gene into a test-statistic and p-value, the gene-based test may be able to detect these effects. Gene-based tests are also ideally suited for network (or pathway) approaches for interpreting the findings from GWAS [2,3]. These approaches are necessarily gene-centric and require a measure of the relative importance of each gene to the phenotype of interest. The gene-based approach also alleviates the multiple-testing problem faced by GWAS by only considering statistical tests for ~20,000 genes per genome as opposed to testing more than half a million SNPs in a typical GWAS.
Computing a gene-based test for basic GWAS designs using permutations is conceptually simple and is currently implemented as the ‘set-based test’ in the PLINK software package [4]; however heavy computational requirements have restricted this method from being adopted on a genome-wide scale. Other gene-based tests such as those based on genetic distances [5] or entropy [6] are often also restricted to situations where individual genotype information is available, or to specific GWAS designs (usually case-control). There are several important situations in which permutation or existing methods cannot be used; these include family-based GWAS, meta-analysis GWAS based on summary data, and DNA pooling based GWAS. To address these situations, our approach only requires individual marker p-values in order to compute a gene-based p-value. The test summarises the evidence for association on a per gene basis by summarizing either the full set of markers (typically SNPs) in the gene or a subset of the most significant makers (for example, the top 10% most significant SNPs). Under some genetic models, an approach considering all the markers in a gene may be most powerful; under other genetic models, focusing on just the most associated within a gene may be apt. The correct genetic model is of course not known in advance. The default, in our implementation and for the rest of this paper, was all markers in the gene. Our approach accounts for linkage disequilibrium (LD) between markers in a gene by using simulation from the multivariate normal distribution based on the LD structure of a set of reference individuals (HapMap CEU, YRI or CHB/JPT at ~2.1million autosomal SNPs), or a...

Find Another Essay On A Flexible Gene-Based Test for Genome-Wide Association Studies

Origins and misuse of the human genome project for a for profit basis only

521 words - 2 pages all of the scientists involved would share, freely, their information with each other. Some of the scientists involved in this project are perverting this goal to include a for profit only section. The sad part is that the only scientists that are making huge monetary gains are those that hold the patents to the genes sequences they discover. At this point in time the United States is the only country involved in the Human Genome Project that

A Massive Project for the Benefit of Mankind. A Look at the Human Genome Project

1440 words - 6 pages data of a normal or healthy gene. The entire research project is entitled 'The Human Genome Project.''The Human Genome Project' is a large scale project being conducted by more than 200 laboratories, with even more researchers and labs having joined in. Most of the labs and researchers are located in France and the United States. The project started in 1990 and was slated to take 15 years and cost $3 billion in U.S. money for the entire project

Sendai School of Design: Project Driven Design Education Based on a Wide Range of Highly Adaptive Collaboration

1660 words - 7 pages individuals with the ability to adapt to a wide range of professional situations in this constantly fluctuating era. And finally, change also emerges from Sendai. In the interurban competition that marks this phase of globalism, the SSD, while drawing out the potential of Sendai’s creative industries, strives to create a firm foundation for design, a hub for a network of creators, and a base for dispatching information to the world. Graduates of the SSD

Marketing Strategy For a Service-based Organization

2650 words - 11 pages directing a total system of marketing action to achieve predetermined objectives. The systems approach is essential for effective decision making, for the utilization of models in marketing, and for the application of computer technology. Systems analysis is a managerial breakthrough, somewhat akin to breakthroughs in various sciences, and has given rise to powerful concepts and tools of analysis. The systems approach is based on the work of Von

A Conceptual Model for Metadata-based Frameworks

2657 words - 11 pages Abstract. Recent frameworks employ the strategy to define a specific metadata schema for applications to use in their classes and programming elements, enabling framework behavior customization. Despite this technique is being widely used, there are not models, design patterns or development guidelines that aim to help in the creation of this kind of framework. This thesis proposes a conceptual model for metadata-based frameworks that has the

RSA-based Undeniable Signature for a Group

1071 words - 5 pages 3. Proposed Approach In this paper, a new RSA-based undeniable signatures approach for a group is proposed. A group member can sign a document on behalf of the group without revealing the identity of the actual signer. The group secret key is split into two parts by Group Manager, one part is provided, as his group membership secret, to the group member; and the other part is provided to a trusted security mediator, SM. In our scheme, it is

A Perfect Score: Effective Ways to Study for a Test

983 words - 4 pages Most college students are piled with difficult work each week. Collection of assignments, are stack carefully on the students desk ready to be completed. Let alone, a history professor later mentions that a test will be assigned in less than two days. The test makes a college student drown in caffeine;therefore, canceling all his plans due to planning a long marathon of studying. But luck has come along and studies of straight A’s students have

A Novel Path Selection Method for Small Delay Defects Test

746 words - 3 pages Aggressive technology scaling has resulted in increasing process variations and statistical diversity in manufacturing. Process variations result in varying in path lengths, and thus a possibly different set of critical paths for different process corners, necessitating consideration of process variation in delay test methods. Also, process variation adds some of near-critical paths to the critical/longest paths set [4]. Therefore, to maintain

How to Pass a Drug Test for Marijuana: The Ultimate Guide for How to Beat a Drug Test

3641 words - 15 pages , how, and why a drug testing should be put to order. One is that employers must do drug screenings to test for drugs - the law forbids the testing of other illnesses or medical situations during drug tests. This seem to shed light to the importance of knowing how long substances included in drug testing remain in one's body which is tackled later in this book. Drug testing may consist of the following types: hair testing, alcohol, oral fluid

Role-Play: A Strategy for Teaching Social Studies

1779 words - 7 pages Role-Play: A Strategy for Teaching Social Studies One of the reasons social studies is viewed as a tough academic discipline is the result of force-fed historical dates and data. It is also one of the reasons that students think history is boring and irrelevant. Furthermore, their inability to relate to the culture and people of the past creates a what-does-this-have-to-do-with-me attitude early on in their education that directly

A Knowledge -based Approach to Innovation An Application for Project- based Firms

1055 words - 4 pages knowledge depend on networks of relationships in a PBO. Knowledge-based perspective concentrates on building up capabilities during the implementation of projects. Networks are formed by knowledge flows through collaboration, sub contract and strategic alliances.#Knowledge, Networks and InnovationAccording to the Knowledge-based View (KBV), knowledge is of strategic importance and firm's competitive advantage lies in its ability to integrate the

Similar Essays

A New Non Invasive Test For Food Based Allergies

1590 words - 6 pages Table of Contents Prevalence/Problem 3 What is currently being done? 3 Types of invasive tests 4 Noninvasive tests 5 My solution 5 What’s next 5 References 6   A New Non-Invasive test for Food Based Allergies Prevalence/Problem Food allergy and intolerance is described as a wide range of adverse reactions to foods and in 2010 an expert panel, sponsored by the National Institute of Allergy and Infectious Diseases, published

A Gene For Alcoholism Essay

893 words - 4 pages relative of ours has suffered from alcoholism, it is likely that we have the gene that causes the development of the disease (Horvath). But what we sometimes ignore, is that if we have a gene for alcoholism, it is not certain that we will develop the disease. It means we could be an alcoholic, but for that to happen, and external factor must trigger it. Among these factors, media exposure is a strong one because it changes our perspective, which

The Problematic Hunt For A Gay Gene

1369 words - 5 pages A genetic study that has concerned many people is the search for the ‘gay gene’. The finding of this gene began in the 90’s and is still in question to whether the gene exists and if it truly influences sexual orientation. Several studies have been completed that look into sexual orientation through behavioral and molecular genetics. Most of these studies, however, have failed to be replicated and they bring about ethical issues. Simon LeVay, a

Cystic Fibrosis: A Case For Gene Therapy

752 words - 3 pages one in four chance of getting the disease. Another problem with the test is that the mutation it pinpoints is responsible for only about 75 per cent of cases of the disease. Consequently, testing individuals would detect only 75 per cent of the carriers. In addition to that, the test itself charges $173 per person making it accessible only to those who are able to afford it.The cystic fibrosis gene was eventually isolated in 1989. As a result to