{"id":1069,"date":"2019-11-21T04:34:09","date_gmt":"2019-11-21T04:34:09","guid":{"rendered":"https:\/\/www.idtdna.com\/page\/targeted-sequencing-hybridization-capture-or-amplicon-sequencing"},"modified":"2025-08-22T16:15:08","modified_gmt":"2025-08-22T16:15:08","slug":"targeted-sequencing-hybridization-capture-or-amplicon-sequencing","status":"publish","type":"post","link":"https:\/\/www.idtdna.com\/page\/support-and-education\/decoded-plus\/targeted-sequencing-hybridization-capture-or-amplicon-sequencing\/","title":{"rendered":"Targeted sequencing: Hybridization capture or amplicon sequencing?"},"content":{"rendered":"

What is targeted sequencing?<\/strong><\/strong> <\/h2>\n

Next generation sequencing<\/a> (NGS) is a revolutionary technique that has found wide applicability, including determining and characterizing unknown sequences, assessing changes and variability in known sequences, and quantifying gene expression. High-throughput sequencing enables sequence profiling of DNA and RNA and can run samples in parallel, resulting in massive time savings. The ability to generate large amounts of sequencing data in a relatively short amount of time supports a wide range of genetic analysis applications and accelerates advances in fundamental and applied research. <\/p>\n

To even further decrease time and cost associated with sequencing, targeted NGS<\/a> gives users the opportunity to sequence only specific areas of interest of the genome while omitting regions irrelevant to the user for more in-depth analyses, instead of sequencing the whole genome (WGS)<\/a>. Targeted sequencing can identify known and novel variants<\/a> within your region of interest. The method generally requires less sample input, produces only relevant data as opposed to WGS that covers the entire genome, and makes downstream analyses more manageable. <\/p>\n

Hybridization capture vs amplicon sequencing<\/h2>\n

There are several types of targeted sequencing<\/a>, each appropriate for specific applications. The most popular methods are hybridization capture<\/a> and amplicon sequencing<\/a>. The technologies behind these methods are all different and come with their own benefits and challenges (Table 1). <\/p>\n

Table 1. Comparison of hybridization capture and amplicon sequencing.<\/strong><\/p>\n\n\n\n\n\n\n\n\n
Feature<\/th>\nHybridization capture<\/a><\/th>\nAmplicon sequencing<\/a><\/th>\n<\/tr>\n<\/thead>\n
Number of steps<\/td>\nMore steps<\/td>\nFewer steps<\/td>\n<\/tr>\n
Number of targets per panel<\/td>\nVirtually unlimited by panel size<\/td>\nFlexible, usually fewer than 10,000 amplicons<\/td>\n<\/tr>\n
Total time<\/td>\nMore time<\/td>\nLess time<\/td>\n<\/tr>\n
Cost per sample<\/td>\nVaries <\/td>\nGenerally lower cost per sample<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Considerations when choosing a targeted sequencing method<\/h2>\n

The method chosen for performing targeted sequencing can be determined by considering several factors:<\/p>\n