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Neranjan Perera edited this page Dec 17, 2018 · 8 revisions

Introduction to Variant Detection using Whole Exome Sequencing

Genome-wide sequencing methods have provided a method of deep understanding in the sequence variations between genotype and phenotype. The 1000 genome project (http://www.1000genomes.org) have indeed made inroads into the study of population genetics, including the investigation of causal variants of genes for various human syndromes. Next Generation Sequencing (NGS) technology is evolving at a rapid rate and new sequencing platforms are been developed. Whole Genome Sequencing (WGS) have been used comprehensively to detecting genomic variations such as single nucleotide variants (SNVs), Copy number variants (CNVs), insertions and deletions (InDels) and chromosomal rearrangements. However at low cost, whole exome sequencing (WES) platforms, have performed well in high sequencing coverage and readily interpreting protein coding exons associated compared to WGS platforms. This technique has also led to more samples to be analyzed and can generate targeted DNA sequences and identify substantially more genetic variations.

The exome is the part of the genome composed of exons, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing and contribute to the final protein product encoded by that gene. It consists of all DNA that is transcribed into mature RNA in cells of any type, as distinct from the transcriptome, which is the RNA that has been transcribed only in a specific cell population. The exome of the human genome consists of roughly 180,000 exons constituting about 1% of the total genome. There is two main experimental techniques in use in exome capture; which is solution based and array based method.

Ref:

  1. Ahn, Y. J., Markkandan, K., Baek, I. P., Mun, S., Lee, W., Kim, H. S., & Han, K. (2018). An efficient and tunable parameter to improve variant calling for whole genome and exome sequencing data. Genes and Genomics, 40(1), 39–47. https://doi.org/10.1007/s13258-017-0608-6
  2. Warr, A., Robert, C., Hume, D., Archibald, A., Deeb, N., & Watson, M. (2015). Exome Sequencing: Current and Future Perspectives. G3: Genes|Genomes|Genetics, 5(8), 1543–1550. https://doi.org/10.1534/g3.115.018564
  3. Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., … DePristo, M. A. (2002). Current Protocols in Bioinformatics. Current protocols in bioinformatics (Vol. 43). NIH Public Access. https://doi.org/10.1002/0471250953

We use SRP019719 Illumina Exome Samples

Bioproject https://www.ncbi.nlm.nih.gov/bioproject/PRJNA193293/ 15 biosamples were used

SRR796868 SRR796869 SRR796870 SRR796871 SRR796872 SRR796873 SRR796874 SRR796875 SRR796876 SRR796877 SRR796878 SRR796879 SRR796880 SRR796881 SRX265476

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