Use of the Ion AmpliSeq Cancer Hotspot Panel in clinical molecular pathology laboratories for analysis of solid tumours: With emphasis on validation with relevant single molecular pathology tests and the Oncomine Focus Assay

Lee, Ahwon,Lee, Sung-Hak,Jung, Chan Kwon,Park, Gyungsin,Lee, Kyo Young,Choi, Hyun Joo,Min, Ki Ouk,Kim, Tae Jung,Lee, Eun Jung,Lee, Youn Soo Elsevier 2018 Pathology, research and practice Vol.214 No.5

<P><B>Abstract</B></P> <P>Targeted application of next-generation sequencing (NGS) technology allows detection of specific mutations that can provide treatment opportunities for cancer patients. We evaluated the applicability of the Ion AmpliSeq Cancer Hotspot Panel V2 (CHV2) using formalin-fixed, paraffin-embedded (FFPE) tissue of clinical specimens.</P> <P>Thirty-five FFPE tumour samples with known mutational status were collected from four different hospitals and sequenced with CHV2 using an Ion Chef System and Ion S5 XL system. Out of 35 cases, seven were sequenced with Oncomine focus Assay Panel for comparison. For the limit of detection test, we used an FFPE reference standard, a cell line that included an engineered 50% EGFR T790 M in an RKO cell line background. Coverage analysis results including number of mapped reads, on target percent, mean depth, and uniformity were not different according to hospitals. Sensitivity for mutation detection down to 3% was demonstrated. NGS results showed 100% concordance with the results from single molecular pathology tests Assay in 30 cases with 24 known positive mutations and 14 known negative mutations, and another NGS panel of the Oncomine focus in seven cases.</P> <P>The CHV2 NGS test for solid tumours using Ion chef system and S5 XL system in clinical molecular pathology laboratories for analysis of solid tumours could be routinely used and could replace some single molecular pathology tests after a stringent and thorough validation process.</P>

새만금 유역 유입하천 하상퇴적물의 이화학적 분석

한아원 ( Ahwon Han ),조영권 ( Youngkwon Cho ),이희선 ( Heeseon Lee ),이흥수 ( Heungsoo Lee ),정세웅 ( Sewoong Jeong ),조영철 ( Youngcheol Cho ) 한국농공학회 2009 한국농공학회 학술대회초록집 Vol.2009 No.-

본 연구에서는 새만금호의 상류유역인 만경강과 동진강 유역의 하상 퇴적물이 내부오염원으로서 새만금 수질에 영향을 미칠 수 있는 가능성을 검토하기 위해 이들 지역에 퇴적물 중 유기물과 총질소, 총인을 분석하여 오염정도를 파악하였다. 퇴적물 시료는 2008년 8월부터 11월까지 3회에 걸쳐 두 강의 상류와 중류, 하류에서 각각 채취하였으며, 각 지점에서 좌안, 중앙, 우안으로 구분하여 시료를 채취하였다. 만경강과 동진강의 상류와 중류에서 채취한 퇴적물의 토성은 모두 “sand"로 분류되었다. 하류 일부 지점에서 silt 입자의 비율이 0.78~89%의 범위로 지점 또는 채취시점에 따른 변이가 컸으며, 토성도 “sand", "loamy sand", "sandy loam", "silt loam" 및 ”loam"으로 다양하게 나타났다. 만경강에서 채취된 퇴적물에서 강열감량은 상류와 중류에서 각각 평균 1.39±0.40, 1.30±0.62%로 측정되었으며, 하류에서는 평균 1.73±0.41%로 상류나 중류에 비해 약간 높은 값이 나타났다. 동진강의 경우 상류와 중류에서 일부 변이가 크게 나타나는 지점을 제외하고, 만경강과 거의 유사한 값을 나타내었으며, 하류에서는 평균 4.13±2.09%로, 만경강에 비해 높게 나타났다. 만경강 상류, 중류, 하류 퇴적물 중 COD 평균값은 각각 0.54±0.27, 0.64±0.51, 0.64±0.47 mg/g-sediment이었으며, 동진강의 경우 각각 0.64±0.77, 1.01±1.36, 1.77±1.15 mg/g-sediment로 측정되었다. 두 지역에서 측정된 강열감량과 COD 결과는 한강 하류와 팔당호, 대청호 퇴적물의 준설 기준에 비해 낮은 값을 나타내었다. 만경강 퇴적물에서 측정된 총질소의 양은 1.21~1.94 mg-N/g-sediment로 나타났으며, 중류의 좌안 퇴적물에서 이상적으로 높은 값이 측정되었고, 하류로 내려갈수록 농도가 상승하는 경향을 보였다. 동진강의 경우에는 상류, 중류 및 하류 지점에서 각각 평균 1.25, 1.83, 2.63 mg-N/g-sediment로 나타났다. 이는 팔당호 퇴적물 준설 기준보다 대부분 상회한 것이며, 일부 지점에서는 한강 하류 퇴적물 준설 기준보다 높게 측정되었다. 만경강 퇴적물에서 총인의 농도는 상류, 중류, 하류 지점에서 각각 평균 0.07, 0.11, 0.21mg-P/g-sediment로 하류로 갈수록 총인의 농도가 증가하였다. 동진강의 경우에는 상류, 중류, 하류 지점에서 각각 평균 0.15, 0.20, 0.21 mg-P/g-sediment로 만경강 퇴적물과 큰 차이가 없었다. 두 강의 총인의 농도는 팔당호 및 한강 하류 퇴적물 준설 기준에 비해 매우 낮았다. 만경강과 동진강의 하상 퇴적물의 오염도를 분석한 결과, 현재 오염이 심각하지 않은 것으로 판단되며, 만경강과 동진강의 하상퇴적물이 내부 오염원으로 새만금 수질에 영향을 미치지 않는 것으로 사료된다. 그러나 새만금 방조제 체절로 인한 오염 가능성이 존재하기 때문에, 만경강과 동진강 퇴적물의 지속적인 모니터링이 필요할 것으로 사료된다.

<i>BRCA1/2</i> somatic mutation detection in formalin-fixed paraffin embedded tissue by next-generation sequencing in Korean ovarian cancer patients

Lee, Ahwon,Kang, Jun,Lee, Hyoungnam,Lee, Youn Soo,Choi, Youn Jin,Lee, Keun Ho,Nistala, Goutam J,Scafe, Charles R.,Choi, Jongpill,Yoo, Jaeeun,Han M.D, Eunhee,Kim, Yonggoo,Kim, Myungshin Elsevier 2019 Pathology, research and practice Vol.215 No.11

<P><B>Abstract</B></P> <P><B>Introduction</B></P> <P>The detection of <I>BRCA1/2</I> mutations is important because PARP1 inhibitors are approved for germline and/or somatic <I>BRCA</I>-mutated advanced ovarian cancer. Next-generation sequencing (NGS) is increasingly used in clinical practice for <I>BRCA1</I>/2 mutations. The purpose of this study was to consider several conditions of NGS <I>BRCA1/2</I> assay applicable to clinical laboratory tests, in particular for using formalin fixed paraffin embedded (FFPE) ovarian tissues.</P> <P><B>Materials and methods</B></P> <P>We selected 64 ovarian cancer patients and performed Oncomine™ BRCA assay using FFPE tissue. Effect of FFPE sample quality was analyzed by NGS quality parameters including deamination metric. Somatic variants were selected by removing germline variants of peripheral blood and interpreted as pathogenic, variants of unknown significance, and false positive.</P> <P><B>Results</B></P> <P>We found a positive relationship between the number of variants over the deamination metric and FFPE age (<I>P</I> < 0.001) with a cutoff values of approximately 0.7 and 60 months, respectively. When comparing NGS results with Sanger sequencing, NGS misreported 3 of 15 variants using default parameters which were corrected after changing parameters. We detected somatic variants in eight patients and classified them into pathogenic (n = 3), VUS (n = 3) and false positive (n = 2).</P> <P><B>Conclusions</B></P> <P>This study is important for improving <I>BRCA1/2</I> mutation detection capabilities of NGS analytical pipelines and strategy to overcome their limitations using FFPE tissue in ovarian cancer patients.</P>

읍·면·동 지역사회보장협의체 위원의 복지사각지대 발굴 경험에 대한 영향요인 : P시를 중심으로

정아원 ( Jung Ahwon ),강병덕 ( Kang Byungdeok ),박준혁 ( Park Joonhyeog ),정숙희 ( Jung Sook-hee ) 한국지방행정연구원 2020 地方行政硏究 Vol.34 No.2

본 연구의 목적은 읍·면·동 복지허브화의 기조에 발맞추어 복지사각지대 해소를 위해 구성된 읍·면·동 지역사회보장협의체 위원들의 복지사각지대 발굴 경험에 영향을 미치는 요인을 탐색하는 것이다. 이를 위해 P시 29개 읍·면·동 지역사회보장협의체 위원을 대상으로 조사를 진행하였으며, 최종적으로 358명이 연구대상으로 선정되었다. 독립변수로 개인요인, 전문성요인, 복지인식요인을 투입하여 종속변수인 협의체 위원의 복지사각지대 발굴 경험에의 영향요인을 이항 로지스틱 회귀분석을 통해 살펴보았다. 분석결과, 개인요인에서는 연령, 봉사활동 경험, 복지 서비스 수혜경험이, 전문성요인에서는 협의체 위원의 역할인지와 사회복지 관련 교육경험 변수가 읍·면·동 지역사회보장협의체 위원들의 복지사각지대 발굴 경험을 유의미하게 예측하는 것으로 나타났다. 이를 바탕으로 읍·면·동 지역사회보장협의체가 지역복지의 한 주체로서의 실효성 있는 역할 수행을 위해 필요한 함의를 제시하였다. The study aims at exploring factors that predict the experience of discovering welfare blind spots among members of the Eup·Myeon·Dong Community Social Security Council, whose purpose is to address welfare blind spots in line with the trend of welfare hub development in local areas. To that end, a survey was conducted on Community Social Security Councils in 29 districts of P city, and 358 people were finally selected for research. Individual factors, professional factors, and welfare recognition factors were used as independent variables to examine the predicting factors on the experience of discovering welfare blind spots for members of Community Security Council through a binary logistic regression analysis. According to the analysis, the age, experience in volunteer work, experience in benefiting welfare services, the level of role recognition as a council member, educational experience related to social work significantly predict the experience of discovering welfare blind spots of council members. Based on this, necessary implications were presented for the effective performance of the Eup·Myeon·Dong Community Social Security Council as a main body of local welfare.

Acute unilateral isolated abducens nerve palsy associated with anti-GM1 immunoglobulin M antibody

Hyoshin Son,Ahwon Kim,Sang Bin Hong,Dae Lim Koo 대한임상신경생리학회 2019 Annals of Clinical Neurophysiology Vol.21 No.2

Acute ophthalmoparesis that includes the oculomotor, trochlear, or abducens nerve may occur as an initial presentation of Miller Fisher syndrome (MFS). The symptoms of MFS or variant forms of Guillain-Barre syndrome are pathogenically related to anti-GQ1b antibodies. We report a case of a 36-year-old man with unilateral isolated abducens nerve palsy associated with anti-GM1 antibody. To the best of our knowledge, this is the first report of unilateral isolated abducens nerve palsy with positivity for anti-GM1 immunoglobulin M antibody.

Comprehensive Molecular Genetic Analysis in Glioma Patients by Next Generation Sequencing

( Taeeun Kim ),( Ahwon Lee ),( Stephan Ahn ),( Jae Sung Park ),( Sin Soo Jeun ),( Youn Soo Lee ) 대한뇌종양학회·대한신경종양학회·대한소아뇌종양학회 2024 Brain Tumor Research and Treatment Vol.12 No.1

Background Glioma is caused by multiple genomic alterations. The evolving classification of gliomas emphasizes the significance of molecular testing. Next generation sequencing (NGS) offers the assessment of parallel combinations of multiple genetic alterations and identifying actionable mutations that guide treatment. This study comprehensively analyzed glioma patients using multi-gene NGS panels, providing powerful insights to inform diagnostic classification and targeted therapies. Methods We conducted a targeted panel-based NGS analysis on formalin-fixed and paraffinembedded nucleic acids extracted from a total of 147 glioma patients. These samples underwent amplicon capture-based library preparation and sequenced using the Oncomine Comprehensive Assay platform. The resulting sequencing data were then analyzed using the bioinformatics tools. Results A total of 301 mutations, were found in 132 out of 147 tumors (89.8%). These mutations were in 68 different genes. In 62 tumor samples (42.2%), copy number variations (CNVs) with gene amplifications occurred in 25 genes. Moreover, 25 tumor samples (17.0%) showed gene fusions in 6 genes and intragenic deletion in a gene. Our analysis identified actionable targets in several genes, including 11 with mutations, 8 with CNVs, and 3 with gene fusions and intragenic deletion. These findings could impact FDA-approved therapies, NCCN guideline-based treatments, and clinical trials. Conclusion We analyzed precisely diagnosing the classification of gliomas, detailing the frequency and co-occurrence of genetic alterations and identifying genetic alterations with potential therapeutic targets by NGS-based molecular analysis. The high-throughput NGS analysis is an efficient and powerful tool to comprehensively support molecular testing in neurooncology.

Development and Validation of the Korean Version of the Edinburgh Cognitive and Behavioral Amyotrophic Lateral Sclerosis Screen (ECAS-K)

Jeeun Lee,Ahwon Kim,Seok-Jin Choi,Eric Cho,Jaeyoung Seo,Seong-il Oh,Jinho Jung,Ji-Sun Kim,Jung-Joon Sung,Sharon Abrahams,Yoon-Ho Hong 대한신경과학회 2023 Journal of Clinical Neurology Vol.19 No.5

Background and Purpose Cognitive and behavioral changes are common in amyotrophic lateral sclerosis (ALS), with about 15% of patients presenting with overt frontotemporal dementia and 30%–50% with varying degrees of impairments. We aimed to develop and validate the Korean version of the Edinburgh Cognitive and Behavioral ALS Screen (ECAS-K), a brief multidomain assessment tool developed for ALS patients with physical disability. Methods We developed the ECAS-K according to the translation guidelines, and administered it to 38 patients with ALS and 26 age- and education-level-matched controls. We also administered the Montreal Cognitive Assessment (MoCA) and Frontal Assessment Battery (FAB) to investigate convergent validity, and the Center for Neurologic Study-Liability Scale to assess the association between pseudobulbar affect and cognitive/behavioral changes. Results Internal consistency among the ECAS-K test items was found to be high, with a Cronbach’s alpha of 0.87. Significant differences were found between patients with ALS and the controls in language, fluency, and memory functions (p<0.05). Abnormal performance based on the ECAS total score was noted in 39.4% of patients, and 66.6% presented behavioral changes in at least one domain. Significant correlations were observed between the scores of the ECAS-K and those of other cognitive screening tools (MoCA and FAB, with correlation coefficients of 0.69 and 0.55, respectively; p<0.01). Conclusions We developed and validated the ECAS-K which could be used as an effective tool to screen the cognitive and behavioral impairments in Korean patients with ALS.

E2/E6 ratio and L1 immunoreactivity as biomarkers to determine HPV16-positive high-grade squamous intraepithelial lesions (CIN2 and 3) and cervical squamous cell carcinoma

Choi, Youn-Jin,Lee, Ahwon,Kim, Tae-Jung,Jin, Hyun-Tak,Seo, Yong-Bok,Park, Jong-Sup,Lee, Sung-Jong Asian Society of Gynecologic Oncology; Korean Soci 2018 Journal of Gynecologic Oncology Vol.29 No.3

<P><B>Objective</B></P><P>Human papillomavirus (HPV) 16 is the most carcinogenic HPV genotype. We investigated if HPV16 L1 capsid protein and E2/E6 ratio, evaluated by cervical cytology, may be used as biomarkers of ≥cervical intraepithelial neoplasia (CIN) 2 lesions.</P><P><B>Methods</B></P><P>Cervical specimens were obtained from 226 patients with HPV16 single infection. Using cytology specimen, L1 capsid protein and E2/E6 ratio were detected and the results were compared with those of the conventional histologic analysis of cervical tissues (CIN1–3 and squamous cell carcinoma [SCC]) to evaluate the association.</P><P><B>Results</B></P><P>The L1 positivity of CIN2/3 was significantly lower than that of normal cervical tissue (p<0.001) and SCC demonstrated significantly lower L1 positivity than CIN1 (p<0.001). The mean E2/E6 ratios of specimens graded as SCC (0.356) and CIN2/3 (0.483) were significantly lower than those of specimens graded as CIN1 (0.786) and normal (0.793) (p<0.05). We observed that area under the receiver operating characteristic curve (AUC) for E2/E6 ratio (0.844; 95% confidence interval [CI]=0.793–0.895) was higher than that for L1 immunochemistry (0.636; 95% CI=0.562–0.711). A combination of E2/E6 ratio and L1 immunocytochemistry analyses showed the highest AUC (0.871; 95% CI=0.826–0.917) for the prediction of ≥CIN2 lesions.</P><P><B>Conclusion</B></P><P>To our knowledge, this is the first study to validate HPV L1 capsid protein expression and decreased HPV E2/E6 ratio as valuable predictive markers of ≥CIN2 cervical lesions. Cervical cytology may be analyzed longitudinally on an outpatient basis with noninvasive procedures as against invasive conventional histologic analysis.</P>

The usefulness of QuantiGene 2.0 assay for evaluation of ER and PR in breast cancer.

Byung Joo Chae,Ahwon Lee,Byung Joo Song,Hae Myung Jeon,Sang Seol Jung 대한외과학회 2009 대한외과학회 학술대회 초록집 Vol.2009 No.11

Acute unilateral isolated abducens nerve palsy associated with anti-GM1 immunoglobulin M antibody

Son, Hyoshin,Kim, Ahwon,Hong, Sang Bin,Koo, Dae Lim The Korean Society of Clinical Neurophysiology 2019 Annals of Clinical Neurophysiology Vol.21 No.2

Acute ophthalmoparesis that includes the oculomotor, trochlear, or abducens nerve may occur as an initial presentation of Miller Fisher syndrome (MFS). The symptoms of MFS or variant forms of Guillain-Barre syndrome are pathogenically related to anti-GQ1b antibodies. We report a case of a 36-year-old man with unilateral isolated abducens nerve palsy associated with anti-GM1 antibody. To the best of our knowledge, this is the first report of unilateral isolated abducens nerve palsy with positivity for anti-GM1 immunoglobulin M antibody.