User:Albentley 99/Exome sequencing

Exome Sequencing
Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons—humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.

The goal of this approach is to identify genetic variants that alter protein sequences, and to do this at a much lower cost than whole-genome sequencing. However, since the introns surrounding exons can modify gene activity, whole-exome sequencing may be less adept at associating diseases and disorders with variations in the exome than whole-genome sequencing. Nevertheless, variants in the exons can be responsible for both Mendelian and common polygenic diseases, such as Alzheimer's disease, resulting in whole exome sequencing being used for academic research and as a clinical diagnostic.

Motivation and comparison to other approaches
Exome sequencing is especially effective in the study of rare Mendelian diseases, because it is an efficient way to identify the genetic variants in all of an individual's genes. These diseases are most often caused by very rare genetic variants that are only present in a tiny number of individuals; by contrast, techniques such as SNP arrays can only detect shared genetic variants that are common to many individuals in the wider population. Furthermore, because significantly impactful errors are much more likely (but by no means exclusively) to be in the protein coding sequence, focusing on this 1% costs far less than whole genome sequencing but still detects a high yield of relevant variants.

In the past, clinical genetic tests were chosen based on the clinical presentation of the patient (i.e. focused on one gene or a small number known to be associated with a particular syndrome), or surveyed only certain types of variation (e.g. comparative genomic hybridization) but provided definitive genetic diagnoses in fewer than half of all patients. Exome sequencing is now increasingly used to complement these other tests: both to find mutations in genes already known to cause disease as well as to identify novel genes by comparing exomes from patients with similar features.

Comparison with other technologies
There are multiple technologies available that identify exome-based variants. Each technology has advantages and disadvantages in terms of technical and financial factors.

Microarray-based genotyping
Microarrays use hybridization probes to test the prevalence of known DNA sequences, and as such cannot be used to identify unexpected genetic changes. In contrast, the high-throughput sequencing technologies used in exome sequencing directly provide the nucleotide sequences of DNA at the thousands of exonic loci tested. Hence, WES addresses some of the present limitations of hybridization genotyping arrays.

Although exome sequencing is more expensive than hybridization-based technologies on a per-sample basis, its cost has been decreasing due to the falling cost and increased throughput of whole genome sequencing.[citation needed]

Whole-genome sequencing
Exome sequencing is only able to identify those variants found in the coding region of genes which affect protein function. It is not able to identify the structural and non-coding variants associated with the disease, which can be found using other methods such as whole genome sequencing. There remains 99% of the human genome that is not covered using exome sequencing, and exome sequencing allows sequencing of portions of the genome over at least 20 times as many samples compared to whole genome sequencing. For translation of identified rare variants into the clinic, sample size and the ability to interpret the results to provide a clinical diagnosis indicates that with the current knowledge in genetics, there are reports of exome sequencing being used for assisting diagnosis. The cost of exome sequencing is typically lower than whole genome sequencing.

=== RNA Sequencing === The basic procedure of RNA Sequencing consists of RNA extraction from a sample followed by isolating mRNA either through Poly(A)-selection or rRNA depletion followed by high throughput sequencing and mapping to a reference. Overlapping reads are used as a proxy for the level of gene expression. DISCUSS HOW RNA-SEQ COMPARES TO WES (HOW ARE THEY SIMILAR/DIFFERENT?)

Diagnoses and Diagnostic Research of Genetic Diseases
Exome sequencing can be used to discover correlations between exomic mutations and genetic diseases. Finding these correlations can lead to the development of new therapies and ways of diagnosing genetic conditions, like Crohn's Disease. Recently, humanity has made massive leaps in exomics progress, especially in sequencing technology. It's now possible to trace exomic code to complex traits, and several studies have already done that. When designing a study and expecting to use WES, it's important to consider what is being sampled for- in other words, whether a study is referencing traits that create a predisposition to a disease such as myocardial infarction, or a quantitative measurement (such as insulin or hormone levels). After performing the study, performing associative analysis is the final step to reveal these linkages. It is recommended to use single-variant tests, such as a Chi-Squared Test.

Researching New Therapies based on Exomic Data
There have been studies that show exomic data can be used to improve cancer treatment. Since cancer evolves and modifies its genome over time, repeatedly sequencing the exome of a patient's tumor has been shown to improve their treatment significantly. That study also identified several genes that corresponded to drug resistance, and reported a better prognosis in the patients whose treatment was modified using their genetic information. There are great implications from this study, especially given that there are more studies of this type that have yielded similar results. The possibilities for new treatments could yield a massive breakthrough in the near future. While the technology for other diseases hasn't been discovered yet, this new form of treatment is a massive discovery in and of itself and could be used to develop other therapeutic protocols for different diseases.

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