Thursday, 24 April 2014

Exome sequencing

Kemppinen A, Baker A, Liao W, Fiddes B, Jones J, Compston A, Ban M, Sawcer S. Exome sequencing in single cells from the cerebrospinal fluid in multiple sclerosis. Mult Scler. 2014 Apr. [Epub ahead of print]

BACKGROUND Genome-wide association studies (GWAS) have identified over 100 germline variants that influence susceptibility to multiple sclerosis, most of which map within or near to genes with immunological function. However, the role of somatic mutations in multiple sclerosis has not been investigated.

OBJECTIVE:The objective of this paper is to explore the role that somatic mutations might play in the development of multiple sclerosis.

METHODS:We exome-sequenced in total 21 individual CD4+ lymphocytes isolated from cerebrospinal fluid of two patients. In addition we sequenced DNA from the patients' peripheral blood to serve as germline reference.

RESULTS:In comparison with the respective germline sequence, each cell differed at an average of 1784 positions, but as anticipated subsequent analysis confirms that most, if not all, of these potential mutations are likely to represent artefacts generated during the amplification of a single genome and/or by sequencing. Fifty-six of the potential mutations were predicted to have likely functional effects on genes that have previously been implicated by GWAS, including three in the CD6 gene.

CONCLUSION: More robust methods applied to larger numbers of cells will be needed to define the role of somatic mutations.

When DNA is made into a protein the introns (non-coding bits) of DNA are removed to have RNA made up of exons (coding bits) of the DNA, this can be sequenced to see what proteins are likely to be made.

Exome sequencing (also known as targeted exome capture) is an efficient strategy to selectively sequence the coding regions of the genome as a cheaper but still effective alternative to whole genome sequencing. Exons are short, functionally important sequences of DNA which, together, represent only slightly more than the portion of the genome that is actually translated into protein. Exons are flanked by untranslated regions (UTR) that are usually not included in exome studies. In the human genome there are about 180,000 exons. These constitute about 1% of the human genome.

They were looking for mutations (switches of the original DNA sequence) when CD4 T cells made protein but the was loads of mistakes in the technology, so the technology needs improving. The may have found some in CD6. What does it mean I don't know?, but this introduces you to the idea of technology. 

So once every body has been genome-sequenced we can do it again and again for every, cell type at different time points.

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species. Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Examples of human phenotypic traits are skin color, eye color, body height, or specific personality characteristics. Although any phenotype of any organism has a basis in its genotype, phenotypic expression may be influenced by environmental influences, mutation, and genetic variation such as single nucleotide polymorphisms (SNPs), or a combination of these factors.

Phenomics is the study of the phenome and how it is determined, particularly when studied in relation to the set of all genes (genomics) or all proteins (proteomics).

Carroll RJ, Bastarache L, Denny JC. R PheWAS: Data Analysis and Plotting Tools for Phenome Wide Association Studies in the R Environment. Bioinformatics. 2014 Apr . [Epub ahead of print]

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