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Shin, Saeam,Hwang, In Sik,Kim, Jieun,Lee, Kyung-A,Lee, Seung-Tae,Choi, Jong Rak The Korean Society for Laboratory Medicine 2017 Annals of Laboratory Medicine Vol.37 No.4
<P>Minimal residual disease (MRD) following B-lymphoblastic leukemia (B-ALL) treatment has gained prognostic importance. Clonal immunoglobulin heavy chain (<I>IGH</I>) gene rearrangement is a useful follow-up marker in B-ALL owing to its high positivity rate. We evaluated the performance and clinical applicability of a next-generation sequencing (NGS) assay for <I>IGH</I> rearrangement in B-ALL MRD monitoring. <I>IGH</I> rearrangement was tested by using fluorescence PCR-fragment analysis and the NGS assay in eight B-ALL patients. The NGS assay was run on two platforms: the Ion Torrent PGM (Thermo Fisher Scientific, USA) (18 samples from 1st to 7th patients) and the MiSeq system (Illumina, USA) (four samples from 8th patient). All initial diagnostic samples and four follow-up samples were positive for clonal <I>IGH</I> rearrangement with fluorescence PCR-fragment analysis and the NGS assay, and six follow-up samples were positive only with NGS. In one case with <I>BCR-ABL1</I> translocation, <I>BCR-ABL1</I> quantitative PCR was negative but the NGS <I>IGH</I> assay was positive just prior to full-blown relapse, suggesting the high sensitivity and clinical utility of the NGS assay. The NGS assay is proposed for MRD monitoring in B-ALL Additional studies are needed to confirm the clinical implications of cases showing positive results only in NGS.</P>
Saeam Shin,Minkyung Kim,Myungsook Kim,김희정,Heejung Kim,이경원,Yunsop Chong 대한진단검사의학회 2012 Annals of Laboratory Medicine Vol.32 No.5
Infection with Clostridium difficile is a growing concern because of the increasing prevalence and spread of nosocomial infections. Emergence of the hypervirulent 027/NAP1/BI strain is also notable. Existing diagnostic methods have low sensitivity or are time-consuming. Therefore, establishing a rapid and accurate microbiological diagnostic assay is needed. We evaluated the Xpert C. difficile assay (Xpert CD assay; Cepheid, USA) to detect toxigenic C. difficile. This assay is a real-time multiplex PCR assay that can be used to detect toxigenic C. difficile strains and differentiate the C. difficile presumptive 027/NAP1/BI strain. A total of 253 loose stool specimens were collected and toxigenic cultures, VIDAS C. difficile A & B assays (VIDAS CDAB assay; bioMérieux, France), and the Xpert CD assay were performed. In comparison to toxigenic cultures, the sensitivity, specificity, and positive and negative predictive values were 100%, 94.6%, 83.1%, and 100%, respectively, for the Xpert CD assay and 40.8%, 98.0%, 100%, and 88.9%, respectively, for VIDAS CDAB assay. Because of the low prevalence of the PCR ribotype 027 in Korea, the evaluation of the usefulness of the Xpert CD assay for screening for the 027 strain was limited. The Xpert CD assay provides great sensitivity in diagnosing toxigenic C. difficile infection. In addition, this method has excellent usability because it is simple and fast.
Shin Saeam,Woo Hye In,Kim Jong-Won,M.D. Yoonjung Kim,Lee Kyung-A 대한진단검사의학회 2022 Annals of Laboratory Medicine Vol.42 No.2
Standardization of cell-free DNA (cfDNA) testing processes is necessary to obtain clinically reliable results. The pre-analytical phase of cfDNA testing greatly influences the results because of the low proportion and stability of circulating tumor DNA (ctDNA). In this review, we provide evidence-based clinical practice guidelines for pre-analytical phase procedures of plasma epidermal growth factor receptor gene (EGFR) variant testing. Specific recommendations for pre-analytical procedures were proposed based on evidence from the literature and our experimental data. Standardization of pre-analytical procedures can improve the analytical performance of cfDNA testing.
Performance of HemosIL ReadiPlasTin, a Liquid Reagent for Prothrombin Time Measurement
Saeam Shin,Yunjung Jung,Wonkeun Song,Min-Jeong Park 대한임상검사정도관리협회 2019 Journal of Laboratory Medicine And Quality Assuran Vol.41 No.1
Background: Prothrombin time (PT) measurement is an important test for screening blood coagulation disorders and monitoring anticoagulant therapy. In this study, we evaluated the analytical performance of HemosIL ReadiPlasTin (Instrumentation Laboratory, USA), a liquid reagent for PT measurement. Methods: The precision of HemosIL ReadiPlasTin was evaluated according to the Clinical and Laboratory Standards Institute (CLSI) EP5-A3 guidelines. Further, comparison with HemosIL RecombiPlasTin 2G (Instrumentation Laboratory, USA) was made according to the CLSI EP9-A3 guidelines. The reference intervals were established according to the CLSI C28-A3 guidelines. Results: The coefficient of variation values for repeatability and total imprecision at two levels of control materials were lower than 1.1% and 3.4%, respectively. The performance of HemosIL ReadiPlasTin was comparable to that of HemosIL RecombiPlasTin 2G, with a high correlation (r =0.996). The reference interval for normal subjects was 10.4–13.3 seconds. Conclusions: HemosIL ReadiPlasTin showed an acceptable degree of imprecision and its performance showed high correlation with that of a conventional reagent. Therefore, it is expected to be useful for PT measurement in clinical laboratories.
Kim, Yoonjung,Shin, Saeam,Lee, Kyung-A Hindawi 2018 BioMed research international Vol.2018 No.-
<P>Liquid biopsies to genotype the epidermal growth factor receptor<I> (EGFR)</I> for targeted therapy have been implemented in clinical decision-making in the field of lung cancer, but harmonization of detection methods is still scarce among clinical laboratories. We performed a pilot external quality assurance (EQA) scheme to harmonize circulating tumor DNA testing among laboratories. For EQA, we created materials containing different levels of spiked cell-free DNA (cfDNA) in normal plasma. The limit of detection (LOD) of the cobas®<I> EGFR</I> Mutation Test v2 (Roche Molecular Systems) was also evaluated. From November 2016 to June 2017, seven clinical diagnostic laboratories participated in the EQA program. The majority (98.94%) of results obtained using the cobas assay and next-generation sequencing (NGS) were acceptable. Quantitative results from the cobas assay were positively correlated with allele frequencies derived from digital droplet PCR measurements and showed good reproducibility among laboratories. The LOD of the cobas assay was 5~27 copies/mL for p.E746_A750del (exon 19 deletion), 35~70 copies/mL for p.L858R, 18~36 copies/mL for p.T790M, and 15~31 copies/mL for p.A767_V769dup (exon 20 insertion). Deep sequencing of materials (>100,000X depth of coverage) resulted in detection of low-level targets present at frequencies of 0.06~0.13%. Our results indicate that the cobas assay is a reliable and rapid method for detecting<I> EGFR</I> mutations in plasma cfDNA. Careful interpretation is particularly important for p.T790M detection in the setting of relapse. Individual laboratories should optimize NGS performance to maximize clinical utility.</P>
Kim, Borahm,Lee, Hyeonah,Shin, Saeam,Lee, Seung-Tae,Choi, Jong Rak Elsevier 2019 The Journal of Molecular Diagnostics Vol.21 No.1
<P>The application of next-generation sequencing (NGS) technology in clinical diagnostics should proceed with care. We have evaluated the clinical validity of two commercially available RNA fusion panels, the TruSight RNA fusion panel (Illumina) and FusionPlex Pan-Heme Kit (ArcherDx), to detect recurrent translocations in hematologic malignancies. Twenty-four bone marrow samples taken at the initial diagnosis of patients with acute leukemia and chronic myeloid leukemia were included. To assess the limit of detection, serial dilutions of <I>BCR-ABL1</I> (e1a2)–positive RNAs were prepared using a commercial reference material. Both NGS panels detected 19 cases with recurrent translocations identified with RT-PCR, as well as a case with <I>KMT2A-AFF1</I> with false-negative results on RT-PCR. Two rare translocations, <I>DDX3X-MLLT10</I> and <I>NUP98-HOXC13</I>, were additionally identified using NGS panels. The detection limit ranged from 10<SUP>−1</SUP> to 10<SUP>−2</SUP>, which was not satisfactory for samples with low tumor burden. To conclude, RNA fusion panels were suitable for the initial diagnosis; however, for follow-up samples, conventional RT-PCR should be selected.</P>
Cho, Sun-Mi,Shin, Saeam,Lee, Kyung-A The Korean Society for Laboratory Medicine 2016 Annals of Laboratory Medicine Vol.36 No.6
<P><B>Background</B></P><P>This study aimed to identify pathogenic variants of <I>PRSS1</I>, <I>SPINK1</I>, <I>CFTR</I>, and <I>CTRC</I> genes in Korean patients with idiopathic pancreatitis.</P><P><B>Methods</B></P><P>The study population consisted of 116 Korean subjects (65 males, 51 females; mean age, 30.4 yr, range, 1-88 yr) diagnosed with idiopathic chronic pancreatitis (ICP), idiopathic recurrent acute pancreatitis (IRAP), or idiopathic acute pancreatitis (IAP). We analyzed sequences of targeted regions in the <I>PRSS1</I>, <I>SPINK1</I>, <I>CFTR</I>, and <I>CTRC</I> genes, copy numbers of <I>PRSS1</I> and <I>SPINK1</I>, and clinical data from medical records.</P><P><B>Results</B></P><P>We identified three types of pathogenic <I>PRSS1</I> variants in 11 patients, including p.N29I (n=1), p.R122H (n=1), and p.G208A (n=9). Sixteen patients exhibited heterozygous pathogenic variants of <I>SPINK1</I>, including c.194+2T>C (n=12), p.N34S (n=3), and a novel pathogenic splicing variation c.194+1G>A. A heterozygous <I>CFTR</I> p.Q1352H pathogenic variant was detected in eight patients. One patient carried a heterozygous <I>CTRC</I> p.P249L pathogenic variant, which is a known high-risk variant for pancreatitis. All patients had normal <I>PRSS1</I> and <I>SPINK1</I> gene copy numbers. Weight loss occurred more frequently in patients carrying the p.G208A pathogenic variant, while pancreatic duct stones occurred more frequently in patients with the c.194+2T>C pathogenic variant.</P><P><B>Conclusions</B></P><P>Pathogenic variants of <I>PRSS1</I>, <I>SPINK1</I>, and <I>CFTR</I> were associated with idiopathic pancreatitis, while pathogenic variants of <I>CTRC</I> were not. Copy number variations of <I>PRSS1</I> and <I>SPINK1</I> were not detected.</P>