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  • Review Article2022-05-01 Diagnostic Genetics

    Current Issues, Challenges, and Future Perspectives of Genetic Counseling in Korea

    Namhee Kim , M.D., Sun-Young Kong , M.D., Ph.D., Jongha Yoo , M.D., Ph.D., Do-Hoon Kim , M.D., Ph.D., Soo Hyun Seo , M.D., and Jieun Kim , M.D., Ph.D.

    Ann Lab Med 2022; 42(3): 314-320

    Abstract : Genetic testing has become increasingly integrated into all areas of healthcare, and complex genetic testing usage continues to grow; thus, the demand for genetic counseling (GC) is likely to increase. However, it is unclear whether the current clinical GC capacity is sufficient for meeting the existing demand. This review describes the current issues, challenges, and future perspectives of GC in Korea based on a professional survey conducted among laboratory physicians. In view of the growing GC demand in the clinical setting, participants expressed a concern about the lack of support from the national healthcare insurance policy and legal requirements, such as certification, for GC practice. The implementation of genetic testing in the overall healthcare system in Korea is in an early phase. Proper implementation can be achieved through education and training of specialists, collaboration among healthcare personnel, proper regulatory oversight, genomic policies, and public awareness. Understanding the current GC capacity, issues, and challenges is a prerequisite for effective strategic planning by healthcare systems considering the expected growth in the demand for clinical genetic services over the next few decades.

  • Original Article2023-01-01 Diagnostic Genetics

    Comparison of Homologous Recombination Repair Gene Next-Generation Sequencing Analysis in Patients With Metastatic Castration-Resistant Prostate Cancer Between Local and Central Laboratories in Korea

    Yoonjung Kim , M.D., Ph.D., Inho Park , Ph.D., Boyeon Kim , M.D., Ph.D., Yu Jeong Choi , M.D., Seoung Chul Oh , M.T., M.S., and Kyung-A Lee , M.D., Ph.D.

    Ann Lab Med 2023; 43(1): 64-72

    Abstract : Background: Following success of the phase III PROfound trial, the poly (ADP-ribose) polymerase (PARP) inhibitor olaparib was approved by the US Food and Drug Administration in May 2020 for adult patients with deleterious homologous recombination repair (HRR) gene-mutated metastatic castration-resistant prostate cancer (mCRPC). As locally adopted multigene panel next-generation sequencing (NGS) assays for selecting PARP inhibitor candidates have not been thoroughly evaluated, we compared the analytical performance of the FoundationOne CDx (Foundation Medicine, Inc., Cambridge, MA, USA) (central laboratory) and other NGS assays (local laboratory) with samples from the PROfound trial in Korea. Methods: One hundred PROfound samples (60 HRR mutation [HRRm] cases and 40 non-HRRm cases) were analyzed. The results of HRR gene mutation analysis were compared between the FoundationOne CDx and two other NGS assays [SureSelect Custom Design assay (Agilent Technologies, Inc., Santa Clara, CA, USA) and Oncomine Comprehensive assay (Thermo Fisher Scientific, Inc., Waltham, MA, USA)]. Results: The positive percent agreement for single nucleotide variants (SNVs) and insertion/deletions (indels) between the central laboratory and local laboratory was 98.7%–100.0%. The negative percent agreement and overall percent agreement (OPA) for SNVs and indels between central and local laboratories were both 100%. Compared with that of the FoundationOne CDx assay, the OPA for copy number variations of the Oncomine Comprehensive and SureSelect Custom assays reached 99.8%–100%. Most mCRPC patients harboring a deleterious genetic variant were successfully identified with both local laboratory assays. Conclusions: The NGS approach at a local laboratory showed comparable analytical performance for identifying HRRm status to the FoundationOne CDx assay used at the central laboratory.

  • Original Article2023-01-01 Diagnostic Genetics

    Cost-Effectiveness Analysis of Germline and Somatic BRCA Testing in Patients With Advanced Ovarian Cancer

    Jaehyeok Jang , M.D., Yoonjung Kim , M.D., Ph.D., Jae-Hoon Kim , M.D., Ph.D., Sun-Mi Cho , M.D., and Kyung-A Lee , M.D., Ph.D.

    Ann Lab Med 2023; 43(1): 73-81

    Abstract : Background: BRCA testing is necessary for establishing a management strategy for ovarian cancer. Several BRCA testing strategies, including germline and somatic testing, are implemented in clinical practice in Korea. We aimed to comparatively evaluate their cost-effectiveness from patients’ perspective. Methods: We developed a decision model comprising five BRCA testing strategies implemented in Korea: (1) germline testing first, followed by somatic tumor testing for patients without a germline variant; (2) somatic testing first, followed by germline testing for patients with a variant detected by somatic testing; (3) both germline and somatic testing; (4) germline testing alone; and (5) somatic testing alone, with no testing as the comparator. One-way sensitivity analysis was conducted to test the uncertainty of key parameters. Results: Assuming a willingness-to-pay of $20,000 per progression-free life-year gain (PF-LYG), all five strategies were considered cost-effective. Strategy 4 was the most cost-effective option, with an incremental cost-effectiveness ratio (ICER) of $2,547.7 per PF-LYG, followed by strategy 1, with an ICER of $3,978.4 per PF-LYG. Even when the parameter values were varied within the possible range, the ICERs of all strategies did not exceed the willingness-to-pay threshold. Conclusions: Considering the importance of knowing a patient’s BRCA gene status, germline testing first, followed by somatic testing, may be a reasonable option.

  • Letter to the Editor2023-03-01 Diagnostic Genetics

    The First Korean Case of VEXAS Syndrome Caused by a UBA1 Somatic Variant

    Jihoon G. Yoon , M.D., Ph.D., Seungbok Lee , M.D., Ph.D., Sheehyun Kim , M.D., Man Jin Kim , M.D., Ph.D., Yoon Hwan Chang , M.D., Ph.D., Jin Kyun Park , M.D., Ph.D., Dong-Yeop Shin , M.D., Ph.D., and Jangsup Moon , M.D., Ph.D.

    Ann Lab Med 2023; 43(2): 217-220
  • Original Article2022-05-01 Diagnostic Genetics

    Genetic Counseling and Long-Term Surveillance Using a Multidisciplinary Approach in von Hippel–Lindau Disease

    Sun Joo Yoon , M.D. , Won Kyung Kwon , M.D., Ph.D., Geehay Hong , M.D., Ja-Hyun Jang , M.D., Ph.D., Byong Chang Jeong , M.D., Ph.D., Jae Hyeon Kim , M.D., Ph.D., and Jong-Won Kim , M.D., Ph.D.

    Ann Lab Med 2022; 42(3): 352-357

    Abstract : Background: von Hippel–Lindau (VHL) disease is an autosomal dominant disorder caused by variants of the VHL tumor suppressor gene (VHL). Early detection and treatment are essential to prevent morbidity and mortality. We evaluated the effectiveness of surveillance strategies and the utility of a VHL clinic with a multidisciplinary team for the first time in Korea. Methods: The VHL clinic was organized at the Samsung Medical Center in 2011 and consisted of a multidisciplinary team, including an endocrinologist, urologist, general surgeon, neurosurgeon, ophthalmologist, otolaryngologist, and radiologist. Biochemical and imaging surveillance and personalized genetic counseling were conducted at the VHL clinic and patients were referred to the necessary departments upon detection of disease manifestation. We divided the patients in three groups (I–III) based on their compliance to VHL clinic attendance. Results: Between 2011 and 2018, 50 VHL patients were identified by VHL molecular analysis and referred to the VHL clinic. Most patients regularly participated in imaging of the central nervous system (43/50, 86.0%) and of the abdomen (46/50, 92.0%). However, there were differences in compliance to determination of the catecholamine level, audiometry, and ophthalmic examination among the three groups. Conclusions: We present the results of using a multidisciplinary team approach and showed that the VHL clinic strategy is useful for the comprehensive surveillance and management of VHL disease. We hope that VHL clinics will be widely set up in hospitals to improve prognosis in patients with VHL.

  • Original Article2023-05-01 Diagnostic Genetics

    Rapid Targeted Sequencing Using Dried Blood Spot Samples for Patients With Suspected Actionable Genetic Diseases

    Man Jin Kim , M.D., Soo Yeon Kim , M.D., Jin Sook Lee , M.D., Sanggoo Kang , M.B.A., Lae-Jeong Park , Ph.D., Wooyong Choi , B.S., Ju Yeol Jung , M.S., Taehyung Kim , M.S., Sung Sup Park , M.D., Jung Min Ko , M.D., Moon-Woo Seong , M.D., Ph.D., and Jong Hee Chae , M.D., Ph.D.

    Ann Lab Med 2023; 43(3): 280-289

    Abstract : Background: New genome sequencing technologies with enhanced diagnostic efficiency have emerged. Rapid and timely diagnosis of treatable rare genetic diseases can alter their medical management and clinical course. However, multiple factors, including ethical issues, must be considered. We designed a targeted sequencing platform to avoid ethical issues and reduce the turnaround time. Methods: We designed an automated sequencing platform using dried blood spot samples and a NEOseq_ACTION panel comprising 254 genes associated with Mendelian diseases having curable or manageable treatment options. Retrospective validation was performed using data from 24 genetically and biochemically confirmed patients. Prospective validation was performed using data from 111 patients with suspected actionable genetic diseases. Results: In prospective clinical validation, 13.5% patients presented with medically actionable diseases, including short- or medium-chain acyl-CoA dehydrogenase deficiencies (N=6), hyperphenylalaninemia (N=2), mucopolysaccharidosis type IVA (N=1), alpha thalassemia (N=1), 3-methylcrotonyl-CoA carboxylase 2 deficiency (N=1), propionic acidemia (N=1), glycogen storage disease, type IX(a) (N=1), congenital myasthenic syndrome (N=1), and citrullinemia, type II (N=1). Using the automated analytic pipeline, the turnaround time from blood collection to result reporting was

  • Original Article2022-11-01 Diagnostic Genetics

    Deciphering Epigenetic Backgrounds in a Korean Cohort with Beckwith–Wiedemann Syndrome

    Hwa Young Kim , M.D., Ph.D., Choong Ho Shin , M.D., Ph.D., Young Ah Lee , M.D., Ph.D., Chang Ho Shin , M.D., Gu-Hwan Kim , Ph.D., and Jung Min Ko , M.D., Ph.D.

    Ann Lab Med 2022; 42(6): 668-677

    Abstract : Background: Beckwith–Wiedemann syndrome (BWS) is a congenital overgrowth disorder caused by genetic or epigenetic alterations at two imprinting centers (ICs) in the 11p15.5 region. Delineation of the molecular defects is important for prognosis and predicting familial recurrence. We evaluated epigenetic alterations and potential epigenotype–phenotype correlations in Korean children with BWS. Methods: Forty children with BWS with proven genetic or epigenetic defects in the 11p15.5 region were included. The phenotype was scored using the BWS consensus scoring system. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), bisulfite pyrosequencing, a single-nucleotide polymorphism microarray, and CDKN1C sequencing were used for confirmative diagnosis. Results: Patients met the criteria for genetic testing, with a mean clinical score of 5.4±2.0. Methylation alterations were consistent between MS-MLPA and bisulfite pyrosequencing in all patients. Twenty-six patients (65.0%) had IC2 loss of methylation (IC2-LoM), 11 (27.5%) had paternal uniparental disomy (patUPD), and one (2.5%) had IC1 gain of methylation. Macroglossia and external ear anomalies were more common in IC2-LoM than in patUPD, and lateralized overgrowth was more common in patUPD than in IC2-LoM (all P

  • Original Article2024-03-01 Diagnostic Genetics

    Identification of Potential Genomic Alterations Using Pan-Cancer Cell-Free DNA Next-Generation Sequencing in Patients With Gastric Cancer

    Boyeon Kim , M.D., Ph.D., Yoonjung Kim , M.D., Ph.D., Jae Yong Cho , M.D., Ph.D., and Kyung-A Lee , M.D., Ph.D.

    Ann Lab Med 2024; 44(2): 164-173

    Abstract : Background: Molecular cancer profiling may lead to appropriate trials for molecularly targeted therapies. Cell-free DNA (cfDNA) is a promising diagnostic and/or prognostic biomarker in gastric cancer (GC). We characterized somatic genomic alterations in cfDNA of patients with GC. Methods: Medical records and cfDNA data of 81 patients diagnosed as having GC were reviewed. Forty-nine and 32 patients were tested using the Oncomine Pan-Cancer Cell-Free Assay on the Ion Torrent platform and AlphaLiquid 100 kit on the Illumina platform, respectively. Results: Tier I or II alterations were detected in 64.2% (52/81) of patients. Biomarkers for potential targeted therapy were detected in 55.6% of patients (45/81), and clinical trials are underway. ERBB2 amplification is actionable and was detected in 4.9% of patients (4/81). Among biomarkers showing potential for possible targeted therapy, TP53 mutation (38.3%, 35 variants in 31 patients, 31/81) and FGFR2 amplification (6.2%, 5/81) were detected the most. Conclusions: Next-generation sequencing of cfDNA is a promising technique for the molecular profiling of GC. Evidence suggests that cfDNA analysis can provide accurate and reliable information on somatic genomic alterations in patients with GC, potentially replacing tissue biopsy as a diagnostic and prognostic tool. Through cfDNA analysis for molecular profiling, it may be possible to translate the molecular classification into therapeutic targets and predictive biomarkers, leading to personalized treatment options for patients with GC in the future.

  • Letter to the Editor2022-05-01 Diagnostic Genetics

    The First Korean Case of Griscelli Syndrome Type 2 With Hemophagocytic Lymphohistiocytosis and Partial Albinism

    Youngeun Lee , M.D., Hyun Jin Park , M.D., Hyoung Jin Kang , M.D., Ph.D., Jung Min Ko , M.D., Ph.D., Boram Kim , M.D., Yoon Hwan Chang , M.D., Ph.D., Hyun Kyung Kim , M.D., Ph.D., Jee-Soo Lee , M.D., Man Jin Kim , M.D., Sung Sup Park , M.D., Ph.D., and Moon-Woo Seong , M.D., Ph.D.

    Ann Lab Med 2022; 42(3): 384-388
  • Letter to the Editor2022-07-01 Diagnostic Genetics

    Whole-genome Sequencing Reveals a Novel Structural Variant of CCDC39 in a Term Neonate with Primary Ciliary Dyskinesia

    Jun Hee Shin , M.D., Sae-Mi Lee , M.D., Hyun Ho Kim , M.D., Ph.D., and Jin Kyu Kim , M.D., Ph.D.

    Ann Lab Med 2022; 42(4): 500-503
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Annals of Laboratory Medicine
Journal Information May, 2024
Vol.44 No.3
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