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Can Target Amplicon-Based Sequencing Capture Translocations In NGS-Based Disease Panels?

Translocation Mutation and Translocation Mutation Diseases

Chromosomal translocation is a type of mutation wherein a potion on one chromosome breaks off and attaches to another chromosome which results in the fusion of two supposedly separated genes. This mutation has been linked to several genetic disorders such as human leukemias, lymphomas, and cancers such as prostate cancer which is an epithelial tumor. Some of the specific examples of human translocation mutation diseases are the following: (1) Burkitt’s lymphoma, (2) Mantle cell lymphoma, (3) Follicular lymphoma, (4) Papillary thyroid cancer, (5) Acute myeloblastic leukemia with maturation, (6) Schizophrenia, (7) Down syndrome, and (8) XX male syndrome. The linking is possible through comprehensive sequencing studies of the genomes, especially in cancer research.

Next-Generation Sequencing (NGS) Based Amplicon Target Enrichment

Next-generation sequencing is a method that can provide significant insight into cancer treatment and prevention. In cancer research, targeted next-generation sequencing can focus on specific areas of the genome relevant to the genome such as protein-coding genes which is especially important when evaluating mutation load. Amplicon sequencing is one of the most common NGS-based methods used in target enrichment which has many applications in clinical and industrial fields. It relies on PCR-amplification of the targeted regions of the genome using sequence-specific primers and probes. It is considered a more suitable option for efficient gene panel testing, as well as in production-scale applications such as industrial genomic screening and clinical diagnostics. Some of its applications in the clinical area are cancer research, tumor profiling, cancer liquid biopsy, circulating tumor cell analysis, and inherited disease testing.

Next Generation-Targeted Amplicon Sequencing (NG-TAS) in Cancer Research

Next generation-targeted Amplicon Sequencing has been used and described in several studies as a method for profiling cell-free DNA (cfDNA) in the plasma of cancer patients. cfDNA was first analyzed in cancer patients approximately half a decade ago. Since the design of NG-TAS is flexible in terms of the genome region of interest, it is applicable in cancer research applications. It particularly has four important unique characteristics. First, this method can be optimized for low input cfDNA. Second, it has a high level of multiplexing which enables analyses of multiple gene targets. Third, it is considered as a bespoke computational pipeline for data analysis. Lastly, it is a cost-effective method.

Many researchers have been successfully identified genetic alterations behind cancer progression and oncogenesis using NG-TAS. Some of the significant advances in cancer genomics include cancer development in breast, ovary, colon, and rectal areas, lung, liver, kidney (renal cell carcinoma), head and neck, as well as research in melanoma and acute myeloid leukemia.

Limitations of NG-TAS in Cancer Research

Although NG-TAS is used in several studies involving cancer, characterizing mutations using this method is prone to sequencing error. This is according to a genomic study of lung cancer which involves compound mutation or the co-exiting of epidermal growth factor receptor tyrosine kinase inhibitor sensitizing mutations and rare minor epidermal growth factor receptor mutations. Based on several cancer studies, hybrid capture-based sequencing is better than amplicon sequencing according to the following characteristics: (1) more homogenous coverage across genetic regions, (2) sensitivity of the assay, and lastly, (3) has fewer library-induced artifacts.

References:

  1. Gao M, Callari M, Beddowes E, et al. Next generation-targeted amplicon sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA. Genome medicine. 2019, 11(1):1-4.
  2. Hung SS, Meissner B, Chavez EA, et al. Assessment of capture and amplicon-based approaches for the development of a targeted next-generation sequencing pipeline to personalize lymphoma management. The Journal of Molecular Diagnostics. 2018, 20(2):203-14.
  3. Chang F, Li MM. Clinical application of amplicon-based next-generation sequencing in cancer. Cancer genetics. 2013, 206(12):413-9.
  4. Forshew T, Murtaza M, Parkinson C, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Science translational medicine. 2012.
* For Research Use Only. Not for use in diagnostic procedures.

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