Did You Know There Are (At Least) 20 Applications of Next-generation DNA Sequencing?
November 25, 2012 by ·
Did you know there are at least 20 different applications for next-generation DNA sequencing. In a review paper titled “The expanding scope of DNA sequencing” (this month’s Nature Biotechnology issue), Shendure and Aiden lists 20 applications of next-gen sequencing.
Granted that many of the applications are not main stream yet, but it drives the point that next-gen sequencing is just a means to an end and they represent the meaning of “next” in next-gen sequencing.
Here is the 20 different applications of Next-Gen Sequencing with references from the paper.
- DNA-Seq
- Targeted DNA-Seq
- Methyl-Seq
- Targeted methyl-Seq
- DNase-Seq, Sono-Seq and FAIrE-Seq
- MAINE-Seq (MNase-mediated purification of mononucleosomes to extract histone-bound DNA (MAINE))
- ChIP-Seq
- RIP-Seq, CLIP-Seq, HITS-CLIP
- RNA-Seq
- FRT-Seq
- NET-Seq (Native Elongating Transcript Sequencing)
- Hi-C
- ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag sequencing)
- Ribo-Seq
- TRAP
- PARS (Parallel Analysis of RNA Structure)
- Synthetic saturation mutagenesis
- Immuno-Seq
- Deep protein mutagenesis
- PhIT-Seq
What is Your Favorite Application of Next-Gen Sequencing That is Missing?
A common problem in RNA-Seq is that each tissue has a few genes (at least one) that are highly expressed. Often, they can account for over 10-20% of the sequenced reads. Many RNA-Seq applications can afford to miss the “crazily” expressed genes and gain a view on lowly expressed genes. Just like one throws out ribosomal RNA in the standard RNA-Seq library prep, one can possibly exclude these highly expressed genes and then sequence the left-over sample.
Another related application that is not listed here is microRNA-seq. Do you think the list can be expanded? Please feel free to chime in to add any of your favorite applications of next-gen DNA sequencing.
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