A Flexible Gene-Based Test for Genome-Wide Association Studies Essay example

A Flexible Gene-Based Test for Genome-Wide Association Studies Essay example

Length: 2003 words (5.7 double-spaced pages)

Rating: Powerful Essays

Open Document

Essay Preview

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 a...


... middle of paper ...


...lated using the Cholesky decomposition method implemented in the R mvtnorm package [19]. The number of simulations per gene is determined adaptively. In the first stage, 103 simulations will be performed. If the resulting empirical p-value is less than 0.1, an additional 104 will be performed. If the empirical p-value from 104 simulations is 0, the program will perform 106 simulations. For computational reasons, if the empirical p-value is still 0, then no more simulations will be performed. An empirical p-value of 0 from 106 simulations can be interpreted as p < 10-6, which exceeds a Bonferroni corrected threshold of p < 2.85×10-6 (this threshold is likely to be conservative given the overlap between genes). The user may select whether to perform the gene-based test on either the full set of SNPs within a gene or a specified percentage of the most significant SNPs.

Need Writing Help?

Get feedback on grammar, clarity, concision and logic instantly.

Check your paper »

Problems Associated With Genetic Diseases Essay

- Though there is no single definition of rare diseases, the term is most often used as an umbrella encompassing life threatening or chronically debilitating diseases, which affect less than 1 in every 2000 people in Europe or 1 in every 1250 in USA (Remuzzi and Garattini 2008; Department of Health Western Australia 2015). While these limits are widely recognised, the majority of rare diseases have a much lower prevalence (Remuzzi and Garattini 2008). Although individually uncommon, collectively, rare diseases are estimated to affect up to 8% of the population or approximately 1.2 million Australians (Aymé and Rodwell 2011; Department of Health Western Australia 2015)....   [tags: Genetics, DNA, Human genome, Molecular biology]

Powerful Essays
1153 words (3.3 pages)

Essay on A New Non-Invasive test for Food Based Allergies

- 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 guidelines for diagnosis and management of food allergies in the United States....   [tags: Food Based Allergies]

Powerful Essays
1479 words (4.2 pages)

The Human Genome Project ( Hgp ) Essay

- The Human Genome Project (HGP) is a Multinational, collaborative research program whose goal was to complete mapping and understanding of all the genes present in the human being. The commencement of Human Genome Project began in 1988, with the support of the National Institute of Health (NIH) and Department of Energy (DOE). The Initial phase of the Human Genome Project (1990’s) relied on the findings and techniques such as Site-specific Restriction enzymes, positional cloning, Polymerase chain reaction, Fluorescence In-Situ Hybridization (FISH ) and STS ( sequence Tagged site )determination, used in early 1970-1980’s, to study and sequence genes....   [tags: DNA, Genetics, Human Genome Project, Human genome]

Powerful Essays
1091 words (3.1 pages)

The Ability to Map a Human Genome Essay

- Science is a field of study that is always evolving and changing with time and new discoveries. New studies in medicine are constantly improving, such as the flu shot, which changes every year to protect America’s population against influenza. With all the adventure into the unknown comes the worry of taking science too far. Also, not letting people’s bodies and life take its natural course is a fear of genetic testing. While others believe the improvements to using genetic tests will benefit society drastically....   [tags: genome, genetics, genetic testing]

Powerful Essays
2574 words (7.4 pages)

Essay about A Student 's Ability Should Not Be Based On A Single Test Score

- A student’s ability should not be based on a single test score, but rather on the student’s growth through the year. Some of the wisest and most influential minds in history understood the importance of this belief. William Butler Yeats once said “Education is not the filling of a pail, but the lighting of a fire.” Creating a system that focuses on student’s scores is not only harmful to the children in America but to the Country as a whole. In an effort to remain competitive with other Countries around the World, the United Sates has significantly increased the number of tests that students are required to take....   [tags: Education, United States, Test, Standardized test]

Powerful Essays
1790 words (5.1 pages)

Wide Range Achievement Test 4th Edition Essay

- Darrell Sabers and Amy Olson reviewed the Wide Rage Achievement Test 4th edition (WRAT-4) in the Mental Measurements Yearbook eighteen edition. In their review Sabers and Olson mentioned differences and similarities between the WRAT-4 and the previous three editions of the WRAT. The WRAT was created to assess “basic academic skills necessary for effective learning, communication and thinking” in addition it evaluates people age 5 to 94 years old that have learning, behavioral, and vocational struggles....   [tags: mental measurements]

Powerful Essays
1493 words (4.3 pages)

The Human Genome Project Commenced Essay example

- The Human Genome Project commenced in 1990, with the goal of sequencing the entire human genome within 25 years. This was successfully completed in the early 2000s due to widespread research efforts and advancements in computing technology (4). With this knowledge, researchers shifted their focus to individual genes; particularly, the function of the proteins they coded for. “Gene knockout” is the general term used for synthetically inactivating a gene of interest. There are three basic approaches for gene-inactivation: [i] take a normal (wild type) gene and replace it with a nonfunctional sequence (which will be discussed below), [ii] express another allele that codes for an inhibitory prot...   [tags: DNA, Gene, Genetics, Genome]

Powerful Essays
919 words (2.6 pages)

The Debate For Modifying The Human Genome Essay

- Perhaps one of the most controversial topics to be addressed in the modern age concerns the ethicality of being able to “edit” our species. The debate for modifying the human genome asks us to consider the very core of our nature and the morality behind deliberately changing our written genetic code to produce “superior” offspring. For example, what kinds of consequences could result from altering the precise code of our DNA. Some scientists ask whether altering the genome of fetuses or adults will produce unwanted results that could end up being passed down through generations, causing more harm than good....   [tags: DNA, Genetics, Gene, Human genome]

Powerful Essays
2449 words (7 pages)

Essay about Morality And The Human Genome Project

- Morality and the Human Genome Project      Does the Human Genome Project affect the moral standards of society. Can the information produced by it become a beneficial asset or a moral evil. For example, in a genetic race or class distinction the use of the X chromosome markers can be used for the identification of a persons ethnicity or class (Murphy,34). A seemingly harmless collection of information from the advancement of the Human Genome Project. But, lets assume this information is used to explore ways to deny entry into countries, determine social class, or even who gets preferential treatment....   [tags: Science Human Genome Ethics Essays]

Powerful Essays
1359 words (3.9 pages)

The Human Genome Project Essay

- The Human Genome Project Now more than ever it is not uncommon to hear of scientific barriers being crossed. This is seen through, "a scientific research effort . . . currently under way which is unlike anything ever before attempted. International in its scope, it is enormously expensive and, if successful, could lead to our ultimate control of human disease, aging, and death. It is nothing short of a revolution against the way science has traditionally progressed"1 . This statement of Thomas Lee refers to a massive scientific undertaking known as the human genome project, an endeavor that aims to discover each and every intricacy of human genetics....   [tags: Genome Science biology Essays]

Powerful Essays
2348 words (6.7 pages)