Key Considerations for Whole Exome Sequencing

exome sequencing and library preparation

Exome, UTR, non-coding regions, CDS

Whole exome sequencing is a powerful technique for sequencing protein coding genes in the genome (known as the exome). It’s a useful tool for applications where detecting variants is important, including population genetics, association and linkage, and oncology studies.

As the main hub for searching and ordering next generation sequencing services, most researchers about to embark on an exome sequencing project start their search on Genohub.com.  It’s our responsibility to make sure the researcher is informed and prepared before placing an order for an exome sequencing service.

Working toward achieving this goal, we’ve established a series of guides for anyone about to start a whole exome sequencing project. We’ve described each of these guides here.

  1. Should I choose Whole Genome Sequencing or Whole Exome Sequencing

This guide describes what you can get with WGS that you won’t with WES and compares pricing on a per sample basis. It also provides an overview of sequence coverage, coverage uniformity, off-target effects and bias due to PCR amplification.

  1. How to choose a Exome Sequencing Kit for capture and sequencing

This guide breaks down each commercial exome capture kit, comparing Agilent SureSelect, Nimblegen SeqCap and Illumina Nextera Rapid Capture. Numbers of probes used for capture, DNA input required, adapter addition strategy, probe length and design, hybridization time and cost per capture are all compared. This comparison is followed by a description of each kit’s protocol.

  1. How to calculate the number of sequencing reads needed for exome sequencing

In the same guide that compares library preparation kits (above), we go through an example on how to determine the amount of sequencing and read length required for your exome study. This is especially important when you start comparing the cost for exome sequencing services (see the next guide).

  1. How to choose an exome sequencing and library preparation service

Are you looking for 100x sequencing coverage, what many in the industry call standard exome sequencing or 200x coverage, considered ‘high depth’?  Or are you interested in a CLIA grade, clinical whole exome sequencing service? This exome guide breaks each down into searches that can be performed on Genohub. The search buttons allow for real time comparison of available exome services, their prices, turnaround times and kits being used. Once you’ve identified a service that looks like a good match, you can send questions to the provider or immediately order the exome-seq service.

  1. Find a service provider to perform exome-seq data analysis only

Do you already have an exome-seq dataset? Do you need a bioinformatician to perform variant calling or SNP ID? Are you interested in studying somatic or germline mutations? Use this guide to identify providers who have experienced bioinformaticians on staff that regularly perform this type of data analysis service. Simply click on a contact button to immediately send a message or question to a provider. If you’re looking for a quote, they will respond within the same or next business day.

If you still need help, feel free to take advantage of Genohub’s complimentary consultation services. We’re happy to help make recommendations for your whole exome sequencing project.

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