Genomic profile of chronic lymphocytic leukemia in Korea identified by targeted sequencing

Jung Ah Kim, Byungjin Hwang, Si Nae Park, Sunghoon Huh, Kyongok Im, Sungbin Choi, Hye Yoon Chung, Joo Ryung Huh, Eul Ju Seo, Je Hwan Lee, Duhee Bang, Dong Soon Lee

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Abstract

Chronic lymphocytic leukemia (CLL) is extremely rare in Asian countries and there has been one report on genetic changes for 5 genes (TP53, SF3B1, NOTCH1, MYD88, and BIRC3) by Sanger sequencing in Chinese CLL. Yet studies of CLL in Asian countries using Next generation sequencing have not been reported. We aimed to characterize the genomic profiles of Korean CLL and to find out ethnic differences in somatic mutations with prognostic implications. We performed targeted sequencing for 87 gene panel using next-generation sequencing along with G-banding and fluorescent in situ hybridization (FISH) for chromosome 12,13q14.3 deletion, 17p13 deletion, and 11q22 deletion. Overall, 36 out of 48 patients (75%) harbored at least one mutation and mean number of mutation per patient was 1.6 (range 0-6). Aberrant karyotypes were observed in 30.4% by G-banding and 66.7% by FISH. Most recurrent mutation (>10% frequency) was ATM (20.8%) followed by TP53 (14.6%), SF3B1 (10.4%), KLHL6 (8.3%), and BCOR (6.25%). Mutations of MYD88 was associated with moderate adverse prognosis by multiple comparisons (P= 0.055). Mutation frequencies of MYD88, SAMHD1, EGR2, DDX3X, ZMYM3, and MED12 showed similar incidence with Caucasians, while mutation frequencies of ATM, TP53, KLHL6, BCOR and CDKN2Atend to be higher in Koreans than in Caucasians. Especially, ATM mutation showed 1.5 fold higher incidence than Caucasians, while mutation frequencies of SF3B1, NOTCH1, CHD2and POT1 tend to be lower in Koreans than in Caucasians. However, mutation frequencies between Caucasians and Koreans were not significantly different statistically, probably due to low number of patients. Collectively, mutational profile and adverse prognostic genes in Korean CLL were different from those of Caucasians, suggesting an ethnic difference, while profile of cytogenetic aberrations was similar to those of Caucasians.

Original languageEnglish
Article numbere0167641
JournalPloS one
Volume11
Issue number12
DOIs
Publication statusPublished - 2016 Dec

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Kim, J. A., Hwang, B., Park, S. N., Huh, S., Im, K., Choi, S., Chung, H. Y., Huh, J. R., Seo, E. J., Lee, J. H., Bang, D., & Lee, D. S. (2016). Genomic profile of chronic lymphocytic leukemia in Korea identified by targeted sequencing. PloS one, 11(12), [e0167641]. https://doi.org/10.1371/journal.pone.0167641