Lab Med Qual Assur.  2022 Jun;44(2):76-81. 10.15263/jlmqa.2022.44.2.76.

Detection of ASXL1 Codon 646 Variant Using Amplicon-Based Next-Generation Sequencing

• Kim M
• Kim NY
• Hong S
• Lee J
• Cho Y
• Kim HS
• Kang HJ
• Lee YK

• KMID: 2531122
• DOI: http://doi.org/10.15263/jlmqa.2022.44.2.76

Abstract

Background
The ASXL1 codon 646 variant is the most common ASXL1 variant that negatively impacts the prognoses of patients with myeloid malignancies, particularly those with myelodysplastic syndromes and acute myeloid leukemia. However, it has been suggested that this mutation is not somatic but rather an artifact of next-generation sequencing (NGS) owing to its location in an 8 bp guanine mononucleotide repeat. In this study, we evaluated the performance of amplicon-based NGS in discriminating the ASXL1 codon 646 variant.
Methods
Amplicon-based NGS was performed on the Myeloid DNA Reference Standard HD829 in varying reference material dilution ratios using the TruSight Myeloid panel and a MiSeqDx system.
Results
The expected and measured variant allele frequencies (VAFs) of the ASXL1 codon 646 mutation in the reference material were 40.00% and 18.65%, respectively. The measured VAFs in reference materials serially diluted at 1:1, 1:2, 1:4, and 1:8 were 9.09%, 5.82%, 1.92%, and 2.87%, respectively (y=0.4391x+0.8642; r² =0.9846). Most of the other variants showed VAFs comparable to expected VAFs.
Conclusions
The measured allele frequencies of the ASXL1 codon 646 variant in the serially diluted reference materials were approximately half their expected values, suggesting difficulties in the correct detection of the variant using amplicon-based NGS.

Keyword

ASXL1; Amplicon; Variant allele frequency; Next-generation sequencing