Question

Why would someone choose to do deep sequencing as compared to PCR amplification and sequencing of short sequences?  What are some of the technology platforms used for deep sequencing?

Answer 1

Deep sequencing (also known as next generation sequence/NGS or second generation sequence) is the sequencing of a genomic region multiple times, sometimes hundreds or even thousands of times to detect rare clonal types, cells, or microbes and also useful for studies in oncology, microbial genomics, and other research

PCR amplification is the selective amplification of DNA or RNA targets using the polymerase chain reaction. Here , short single-stranded synthetic oligonucleotides are extended on a target template using repeated cycles of heat denaturation, primer annealing, and primer extension.

By PCR can makes many copies of a small portion of a microorganism’s genetic information. It can be inexpensive and sensitive, but is extremely limited to less than a dozen in one test for identification. PCR creates many copies of small genetic pieces, it is heavily biased and cannot be used to assess abundance of microbial populations.

By the way, deep sequencing creates a genetic fingerprint of everything in the sample. It is more comprehensive approach, and it can be capable of identifying tens of thousands of microorganisms in one sample, only limited by the availability of sequence data.