Targeted Reseq/Exome Sequencing Data Analysis

Targeted Reseq/Exome Sequencing Data Analysis Introduction
Workflow
Turn-around Time
Publications
FAQ

Introduction

Due to high sequencing and data management costs associated with Whole Genome Resequencing, Targeted Resequencing provides a time- and cost-effective alternative. Before subject to next-generation sequencing, genome regions are selectively enriched by PCR amplification, Molecular Inversion Probes (MIP), or hybridization capture.

One of the most popular approaches in Targeted Resequencing is Exome Sequencing. It focuses on sequencing the coding regions in a genome, plus untranslated regions (UTR) and microRNA.

Targeted Resequencing, including Exome Sequencing, primarily focuses on detecting SNP and small Indels.

Workflow

Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Alignment to a reference with mapping statistics
4) Local realignment
5) SNP and small indel calling
6) SNP/small indel characterization
7) Written project report with analysis methods, publication-ready graphics, and references

Turn-around Time

Upon data receipt, we usually finish a typical Targeted Resequencing/Exome Sequencing analysis project in 2-3 days. The actual turn-around time, however, is highly dependent on sample number, data amount, and project complexity.

Publications

Publications below are representative research or review papers that will help you understand how Targeted Resequencing/Exome Sequencing is employed in biomedical research.

  • Clark MJ. et al. (2011) Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 29(10):908-14.
  • Mamanova, L. et al. (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods. 7(2):111-8.

FAQ

What kind of reads should I use for my Targeted Resequencing or Exome Sequencing experiment?
100-bp pair-end reads are quite standard for Targeted Resequencing or Exome Sequencing project. But any pair-end reads should work.
How many folds of coverage do I need for my Targeted Resequencing or Exome Sequencing experiment?
In general 30– 50x coverage is needed for a Targeted Resequencing or Exome Resequencing experiment. For certain biomarker discovery projects, 5-10x coverage may be sufficient. For tumor-related project, 100x or more is needed. We encourage you to Contact one of our expert bioinformaticians to discuss an optimal coverage for your Targeted Resequencing or Exome Sequencing project.