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Amplicon sequencing is typically used for variant detection and single-base characterization of complex samples. This approach can detect rare somatic mutations, hot-spot mutations, insertions, deletions, copy number variations, gene fusions, and single-nucleotide polymorphisms (SNPs). Because of the sensitivity and versatility of the approach, amplicon sequencing has reached and established itself in a range of disciplines, including oncology, nutrition, public health (like the recent SARS-CoV-2 pandemic), microbial genomics, etc.

In amplicon sequencing, amplicons are generated by PCR or multiplex PCR, pooled, and later sequenced. This highly targeted approach enables thousands of regions in the genome to be determined and amplified simultaneously. Furthermore, amplicons originating from different samples can be combined and sequenced together by adding a unique barcode or index to each individual sample, which is later used as leverage to demultiplex for downstream analysis, simplifying subsequent data interpretation and processing.

DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of these four bases: A, T, G, and C. In the DNA double helix, the four chemical bases always bond with the same partner to form “base pairs” A always pairs with T; C always pairs with G.

In recent decades there have been significant advancements in the technology available for DNA sequencing. Broadly, there are two types of DNA sequencing:
shotgun and high-throughput. Shotgun (Sanger) sequencing is the more traditional approach, which is designed for sequencing entire chromosomes or long DNA strands with more than 1000 base pairs. It involves a rapidly expanding firing pattern to read the DNA in short fragments of 100 to 1000 base pairs, which are then overlapped with a computed analysis system.

High-throughput is the next-generation sequencing (NGS) method of DNA sequencing, which has led to the rapid acceleration of DNA sequencing and broadened knowledge in the field. It is able to produce thousands of sequences simultaneously, which lowers the cost of the technique significantly.

New methods are still under development, including some that utilize nanopores to sequence the DNA. This would work by threading single strands of DNA through nanopores in the cell membrane, which would then be read by the technology in a single file.

DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions, full chromosomes, or entire genomes of any organism. This information is useful for researchers in understanding the type of genetic information that is carried in the DNA, which may affect its function in the body. The human genome contains about 3 billion base pairs that spell out the instructions for making and maintaining a human being. Applications such as whole genome sequencing or WGS allows complete coverage of the entire genomic material. This is in contrast to targeted sequencing where only specific regions of interest are sequenced.

Sequencing is the procedure of determining the order of nucleotides in a DNA section comprising a gene. Next-generation sequencing is a technology for determining the sequence of DNA or RNA to study genetic variation associated with diseases or other biological phenomena.

This method was initially called “massively parallel sequencing”, because it enabled the sequencing of many DNA strands at the same time, instead of one at a time as with traditional Sanger sequencing by capillary electrophoresis.