Targeted Next-Generation Sequencing of Plasma Cell-Free DNA in Korean Patients with Hepatocellular Carcinoma

Chae Hyojin,Sung Pil Soo,Choi Hayoung,Kwon Ahlm,Kang Dain,Kim Yonggoo,Kim Myungshin,Yoon Seung Kew 대한진단검사의학회 2021 Annals of Laboratory Medicine Vol.41 No.2

Background: Hepatocellular carcinoma (HCC) is the second-most-common cause of cancer-related deaths worldwide, and an accurate and non-invasive biomarker for the early detection and monitoring of HCC is required. We assessed pathogenic variants of HCC driver genes in cell-free DNA (cfDNA) from HCC patients who had not undergone systemic therapy. Methods: Plasma cfDNA was collected from 20 HCC patients, and deep sequencing was performed using a customized cfDNA next-generation sequencing panel, targeting the major HCC driver genes (TP53, CTNNB1, TERT) that incorporates molecular barcoding. Results: In 13/20 (65%) patients, we identified at least one pathogenic variant of two major HCC driver genes (TP53 and CTNNB1), including 16 variants of TP53 and nine variants of CTNNB1. The TP53 and CTNNB1 variants showed low allele frequencies, with median values of 0.17% (range: 0.06%-6.99%) and 0.07% (range: 0.05%–0.96%), respectively. However, the molecular coverage of variants was sufficient, with median values of 5,543 (range: 2,317–9,088) and 7,568 (range: 2,400–9,633) for TP53 and CTNNB1 variants, respectively. Conclusions: Our targeted DNA sequencing successfully identified low-frequency pathogenic variants in the cfDNA from HCC patients by achieving high coverage of unique molecular families. Our results support the utility of cfDNA analysis to identify somatic gene variants in HCC patients.

Heavy/light chain assay as a biomarker for diagnosis and follow-up of multiple myeloma

Chae, Hyojin,Han, Eunhee,Yoo, Jaeeun,Lee, Jaewoong,Lee, Jeong Joong,Cha, Kyoungho,Kim, Myungshin,Kim, Yonggoo,Lee, Sung-Eun,Min, Chang-Ki Elsevier 2018 Clinica chimica acta Vol.479 No.-

<P><B>Abstract</B></P> <P><B>Background</B></P> <P>The heavy-light chain (HLC) assay enables the accurate measurement of each isotype-specific heavy and light chain (i.e., IgGĸ, IgGλ, IgAĸ, and IgAλ) and the derivation of an HLC-pair ratio. However, to date, only limited data have validated the usefulness of serial HLC measurements in the routine follow-up of intact immunoglobulin multiple myeloma (MM) patients.</P> <P><B>Methods</B></P> <P>A total of 36 diagnostic and 671 post-treatment sera from 115 IgG and 61 IgA MM patients were assessed with capillary zone electrophoresis, immunosubtraction electrophoresis, total immunoglobulin measurement, free light chain, and HLC assay. The correlations between M-protein levels and the HLC and FLC assay-derived parameters were examined and the clinical significance of the biomarkers was evaluated according to patients' status.</P> <P><B>Results</B></P> <P>Involved HLC (iHLC) was the best biomarker correlating with M-protein concentration in both IgG and IgA MM, and could provide a surrogate marker substituting M-protein levels to follow the course of the disease, especially in β-migrating IgA M-proteins. The distribution of iHLC values as well as HLC-pair ratios (rHLC) yielded significantly different results among the various response categories in both IgG and IgA MM. In addition, we detected 2 cases in which an abnormal rHLC in a stringent complete remission (sCR) sample was a marker of early non-symptomatic relapse.</P> <P><B>Conclusion</B></P> <P>In this study of a cohort of 176 patients in a routine clinical setting, we have provided evidence of the clinical utility of real world HLC assays for the identification of M-proteins and to monitor M-proteins with an emphasis on IgA monoclonal gammopathies.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Involved HLC concentration is a superior correlate with M-protein concentration. </LI> <LI> Involved HLC is a superior marker substituting M-protein levels in IgA MM patients. </LI> </UL> </P>

Ribosomal protein mutations in Korean patients with Diamond-Blackfan anemia

Chae, Hyojin,Park, Joonhong,Lee, Seungok,Kim, Myungshin,Kim, Yonggoo,Lee, Jae-Wook,Chung, Nack-Gyun,Cho, Bin,Chul Jeong, Dae,Kim, Jiyeon,Kim, Jung Rok,Park, Geon Nature Publishing Group 2014 Experimental and molecular medicine Vol.46 No.3

<P>Diamond-Blackfan anemia (DBA) is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, associated physical malformations and a predisposition to cancer. DBA has been associated with mutations and deletions in the large and small ribosomal protein genes, and genetic aberrations have been detected in ∼50–60% of patients. In this study, nine Korean DBA patients were screened for mutations in eight known DBA genes (<I>RPS19, RPS24, RPS17, RPS10, RPS26, RPL35A, RPL</I>5 and <I>RPL11</I>) using the direct sequencing method. Mutations in <I>RPS19, RPS26</I> and <I>RPS17</I> were detected in four, two and one patient, respectively. Among the mutations detected in <I>RPS19</I>, two mutations were novel (c.26T>A, c.357-2A>G). For the mutation-negative cases, array-CGH analysis was performed to identify copy-number variations, and no deletions involving the known DBA gene regions were identified. The relative mRNA expression of <I>RPS19</I> estimated using real-time quantitative PCR analysis revealed two- to fourfold reductions in <I>RPS19</I> mRNA expression in three patients with <I>RPS19</I> mutations, and p53 protein expression analysis by immunohistochemistry showed variable but significant nuclear staining in the DBA patients. In conclusion, heterozygous mutations in the known DBA genes <I>RPS19</I>, <I>RPS26</I> and <I>RPS17</I> were detected in seven out of nine Korean DBA patients. Among these patients, <I>RPS19</I> was the most frequently mutated gene. In addition, decreased <I>RPS19</I> mRNA expression and p53 overexpression were observed in the Korean DBA patients, which supports the hypothesis that haploinsufficiency and p53 hyperactivation represent a central pathway underlying the pathogenesis of DBA.</P>

Considerations when using next-generation sequencing for genetic diagnosis of long-QT syndrome in the clinical testing laboratory

Chae, Hyojin,Kim, Jiyeon,Lee, Gun Dong,Jang, Woori,Park, Joonhong,Jekarl, Dong Wook,Oh, Yong Seog,Kim, Myungshin,Kim, Yonggoo Elsevier 2017 Clinica chimica acta Vol.464 No.-

<P><B>Abstract</B></P> <P><B>Background</B></P> <P>Congenital long-QT syndrome (LQTS) is a potentially lethal cardiac electrophysiologic disorder characterized by QT interval prolongation and T-wave abnormalities. At least 13 LQTS-associated genes have been reported, but the high cost and low throughput of conventional Sanger sequencing has hampered the multi-gene-based LQTS diagnosis in clinical laboratories.</P> <P><B>Methods</B></P> <P>We developed an NGS (next-generation sequencing)-based targeted gene panel for 13 LQTS genes using the Ion PGM platform, and a cohort of 36 LQTS patients were studied for characterization of analytical performance specifications.</P> <P><B>Results</B></P> <P>This panel efficiently explored 212 of all 221 coding exons in 13 LQTS-associated genes. And for those genomic regions covered by the design of the NGS panel, the analytical sensitivity and analytical specificity for all potentially pathogenic variants were both 100% and showed 100% concordance with clinically validated Sanger sequencing results in five major LQTS genes (<I>KCNQ1</I>, <I>KCNH2</I>, <I>SCN5A</I>, <I>KCNE1</I>, and <I>KCNE2</I>).</P> <P><B>Conclusion</B></P> <P>This is the first description of an NGS panel targeting a multi-gene panel of 13 LQTS-associated genes. We developed and validated this robust, high-throughput NGS test and informatics pipeline for LQTS diagnosis suitable for the clinical testing laboratory.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We developed an NGS-based targeted gene panel for 13 LQTS genes using the Ion PGM platform. </LI> <LI> The NGS panel showed 100% concordance with Sanger sequencing in the genomic regions covered by the design of the panel. </LI> <LI> This robust and high-throughput NGS panel and informatics pipeline is suitable for LQTS diagnosis in the clinical testing laboratory. </LI> </UL> </P>

Phenotypic and genetic characterization of adult T-cell acute lymphoblastic leukemia with del(9)(q34);SET-NUP214 rearrangement.

Chae, Hyojin,Lim, Jihyang,Kim, Myungshin,Park, Joonhong,Kim, Yonggoo,Han, Kyungja,Lee, Seok,Min, Woo Sung Springer International 2012 Annals of hematology Vol.91 No.2

<P>SET-NUP214 rearrangement is a recently recognized recurrent chromosomal translocation mostly observed in T-ALL. In order to characterize this rare entity, we performed phenotypic and genetic characterization of SET-NUP214 rearrangement through an investigation of a series of 40 consecutive samples of adult T-ALL that was selected among 229 adult ALL cases during 4?years in a single institution. Four cases (10%) of SET-NUP214 translocation were identified in our study. In all cases, diagnosis of T-ALL was established according to the World Health Organization (WHO) classification, and clonal TCR rearrangements were found. The immunophenotypic markers were indicative of the precursor nature of T lymphoblasts, and they expressed one or both of the myeloid-associated antigens (CD13, CD33). Conventional cytogenetic analysis revealed complex chromosomal aberrations in all four SET-NUP214 rearranged cases and del(12)(p13)/ETV6 was frequently involved. Array-CGH demonstrated additional genomic imbalances in addition to deletion 9q34. The genomic breakpoint sequencing identified breakpoints at SET intron 7 and NUP214 intron 17, and random nucleotide addition was found in two cases at the site of rearrangement. Our independently derived data set from a single institution confirms previous findings of SET-NUP214 rearrangement, indicates the relatively high incidence of SET-NUP214 rearrangement in adult T-ALLs, and also demonstrates comprehensive clinical, phenotypic, and genetic characteristics of this entity. Also, our report on genomic breakpoints demonstrates the homogeneity in the localization of the genomic breakpoints at 9q34. Concurrent chromosomal aberrations identified in this study should provide further areas of interest in investigation of SET-NUP214-mediated leukemogenesis.</P>

Elevated Pleural Adenosine Deaminase Levels in IgG4-related Disease With Pleural Effusion: A Case Series

Chae Seungwan,Lee JeongJoong,Cho Hanwool,Chae Hyojin,Oh Eun-Jee 대한진단검사의학회 2023 Annals of Laboratory Medicine Vol.43 No.1

Detection of Low Frequency Variants with Customized Cell-Free DNA Panel in Blood Samples of Hepatocellular Carcinoma Patients Undergoing Sorafenib Treatment

( Hyojin Chae ),( Pil Soo Sung ),( Yonggoo Kim ),( Myungshin Kim ),( Seung Kew Yoon ) 대한간학회 2021 춘·추계 학술대회 (KASL) Vol.2021 No.1

Feasibility of a Microarray-Based Point-of-Care <i>CYP2C19</i> Genotyping Test for Predicting Clopidogrel On-Treatment Platelet Reactivity

Chae, Hyojin,Kim, Myungshin,Koh, Yoon-Seok,Hwang, Byung-Hee,Kang, Min-Kyu,Kim, Yonggoo,Park, Hae-il,Chang, Kiyuk Hindawi Publishing Corporation 2013 BioMed research international Vol.2013 No.-

<P>Clopidogrel is a prodrug which is converted into active metabolite by cytochrome P450 isoenzyme, <I>CYP2C19</I>. Numerous polymorphisms of <I>CYP2C19</I> are reported, and a strong link exists between loss-of-function (LOF) or gain-of-function polymorphisms, clopidogrel metabolism, and clinical outcome. Hence, a fully automated point-of-care CYP2C19 genotyping assay is more likely to bring personalized antiplatelet therapy into real practice. We assessed the feasibility of the Verigene 2C19/CBS Nucleic Acid Test, a fully automated microarray-based assay, compared to bidirectional sequencing, and performed VerifyNow P2Y12 assay to evaluate the effect of <I>CYP2C19</I> polymorphisms on on-treatment platelet reactivity in 57 Korean patients treated with clopidogrel after percutaneous coronary intervention. The Verigene 2C19/CBS assay identified ∗2, ∗3, and ∗17 polymorphisms with 100% concordance to bidirectional sequencing in 180 minutes with little hands-on time. Patients were classified into 4 groups: extensive (∗1/∗1; <I>n</I> = 12, 21.1%), intermediate (∗1/∗2, ∗1/∗3; <I>n</I> = 33, 57.9%), poor (∗2/∗2, ∗2/∗3, and ∗3/∗3; <I>n</I> = 11, 19.3%), and ultrarapid metabolizers (∗1/∗17; <I>n</I> = 1, 1.8%). The prevalence of the <I>CYP2C19</I> ∗2, ∗3, and ∗17 alleles was 36.0%, 12.3%, and 0.9%. Platelet reactivity showed gene dose response according to the number of <I>CYP2C19</I> LOF allele. In conclusion, the Verigene 2C19/CBS assay gave accurate <I>CYP2C19</I> genotype results which were in well match with the differing on-treatment platelet reactivity.</P>

국내 정수장 먹는 물 중 폼알데히드 함유실태 조사 및 위해성 평가 연구

채효진(Hyojin Chae),김현구(Hyun Ku Kim),김승기(Seungki Kim),표희수(Heesoo Pyo),홍종기(Jongki Hong) 한국분석과학회 2009 분석과학 Vol.22 No.5

Fluorescent determination of zinc by a quinoline-based chemosensor in aqueous media and zebrafish

Chae, Ju Byeong,Yun, Dongju,Kim, Sehoon,Lee, Hyojin,Kim, Mingeun,Lim, Mi Hee,Kim, Ki-Tae,Kim, Cheal Elsevier 2019 Spectrochimica acta. Part A, Molecular and biomole Vol.219 No.-

<P><B>Abstract</B></P> <P>A quinoline-based fluorescence sensor <B>QDTD</B> was developed for Zn<SUP>2+</SUP>. <B>QDTD</B> can detect Zn<SUP>2+</SUP> by fluorescence turn-on. Detecting limit (0.27 μM) of <B>QDTD</B> for Zn<SUP>2+</SUP> was far below WHO standard (76.0 μM). For the practical application, compound <B>QDTD</B> could be used to determine Zn<SUP>2+</SUP> in real samples and applied to the test kit. More importantly, <B>QDTD</B> was expertly applied for Zn<SUP>2+</SUP> imaging in HeLa cells and zebrafish with good membrane-permeability. Detection mechanism of Zn<SUP>2+</SUP> ion by compound <B>QDTD</B> was suggested through the analytical tools like <SUP>1</SUP>H NMR titration, ESI-MS, Job plot, fluorescent and UV–vis titration, and theoretical calculations, and through the synthesis and applications of a model compound <B>AAQA</B>.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A highly selective fluorescent chemosensor <B>QDTD</B> for Zn<SUP>2+</SUP> was designed and synthesized. </LI> <LI> <B>QDTD</B> could detect Zn<SUP>2+</SUP> by fluorescence turn-on with the low detection limit (0.27 μM). </LI> <LI> Sensor <B>QDTD</B> was applied to the real water samples and test strip. </LI> <LI> Sensor <B>QDTD</B> could successfully quantify Zn<SUP>2+</SUP> in HeLa cells and zebrafish. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>