Jihoon G. Yoon

Comparison of Six Automated Treponema-Specific Antibody Assays

ABSTRACT Six different Treponema (TP)-specific immunoassays were compared to the fluorescent treponemal antibody absorption (FTA-ABS) test. A total of 615 samples were tested. The overall percent agreement, analytical sensitivity, and analytical specificity of each assay compared to the FTA-ABS test were as follows: Architect Syphilis TP, 99.2%, 96.8%, and 100%; Cobas Syphilis, 99.8%, 99.4%, and 100%; ADVIA Centaur Syphilis, 99.8%, 99.4%, and 100%; HISCL Anti-TP assay kit, 99.7%, 98.7%, and 100%; Immunoticles Auto3 TP, 99.0%, 97.5%, and 99.6%; Mediace TPLA, 98.0%, 98.1%, and 98.0%. All results that were discrepant between the TP-specific assays were associated with samples from noninfectious cases (11 immunoassay false positives and 7 from previous syphilis cases). Our study demonstrated that TP-specific immunoassays generally showed high sensitivities, specificities, and percentages of agreement compared to FTA-ABS, with rare cases of false-positive or false-negative results. Therefore, most TP-specific immunoassays are acceptable for use in screening for syphilis. However, it is important to perform a thorough review of a patients clinical and treatment history for interpreting the results of syphilis serology.

Comparison of MALDI-TOF MS, Housekeeping Gene Sequencing, and 16S rRNA Gene Sequencing for Identification of Aeromonas Clinical Isolates

Purpose The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB). Materials and Methods We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS. Results The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level. Conclusion The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.

Machine learning-based diagnosis for disseminated intravascular coagulation (DIC): Development, external validation, and comparison to scoring systems

The major challenge in the diagnosis of disseminated intravascular coagulation (DIC) comes from the lack of specific biomarkers, leading to developing composite scoring systems. DIC scores are simple and rapidly applicable. However, optimal fibrin-related markers and their cut-off values remain to be defined, requiring optimization for use. The aim of this study is to optimize the use of DIC-related parameters through machine learning (ML)-approach. Further, we evaluated whether this approach could provide a diagnostic value in DIC diagnosis. For this, 46 DIC-related parameters were investigated for both clinical findings and laboratory results. We retrospectively reviewed 656 DIC-suspected cases at an initial order for full DIC profile and labeled their evaluation results (Set 1; DIC, n = 228; non-DIC, n = 428). Several ML algorithms were tested, and an artificial neural network (ANN) model was established via independent training and testing using 32 selected parameters. This model was externally validated from a different hospital with 217 DIC-suspected cases (Set 2; DIC, n = 80; non-DIC, n = 137). The ANN model represented higher AUC values than the three scoring systems in both set 1 (ANN 0.981; ISTH 0.945; JMHW 0.943; and JAAM 0.928) and set 2 (AUC ANN 0.968; ISTH 0.946). Additionally, the relative importance of the 32 parameters was evaluated. Most parameters had contextual importance, however, their importance in ML-approach was different from the traditional scoring system. Our study demonstrates that ML could optimize the use of clinical parameters with robustness for DIC diagnosis. We believe that this approach could play a supportive role in physicians’ medical decision by integrated into electrical health record system. Further prospective validation is required to assess the clinical consequence of ML-approach and their clinical benefit.

An 18.3-Mb Duplication on Chromosome 14q With Multiple Cardiac Anomalies and Clubfoot Was Identified by Microarray Analysis

Dear Editor, Abnormalities involving the proximal segment of the long arm of chromosome 14 (14q) are rare. Clinical phenotypes of duplications on 14q vary, with autistic disorder, mental retardation, delayed development, and dysmorphic features being the common phenotypes [1,2,3]. Several studies have attempted to elucidate the correlation between these clinical phenotypes and candidate genes. However, because of insufficient reports and genetic studies, establishing a correlation between genotype and the corresponding phenotype has been difficult. In this study, we report a newborn with an 18.3 Mb large duplication in the 14q11.2q21.1 that was identified by a chromosomal microarray. Our case was a 1-month-old newborn girl born at 41 weeks of gestation through vaginal delivery. She was the third child, and her parents were both 33 yr old. Her mother had an obstetric history of gravida 4, para 3, and abortus 1. The first and second children did not have developmental problems or intellectual disabilities, and there was no family history. The birth weight, height, and head circumference of the patient were within normal ranges (2,940 g [3rd-10th percentile], 47.5 cm [10th-25th percentile], and 32.5 cm [10th-25th percentile], respectively). Cardiac murmur was detected, and hypoxemia (SpO2, 68-85%) was observed after birth. Echocardiography indicated a ventricular septal defect, pulmonary stenosis, and an overriding aorta, correlating to tetralogy of Fallot (TOF). The patient had bilateral clubfoot. However, other dysmorphic features in the extremities and face were unnoticeable. G-banding chromosome analysis of phytohemagglutinin (PHA) stimulation on cultured lymphocytes from peripheral blood showed an insertion in the proximal segment of 14q in all 25 metaphase cells (Fig. 1). At the level of 550-band resolution, the breakpoint and origin of the inserted fragment could not be clearly identified. We further investigated copy number alterations using Cytoscan 750K array (Affymetrix, Santa Clara, CA, USA). An approximately 18.3-Mb gain from 14q11.2 to 14q21.1 (chr14:20,516,277-38,826,881) was identified (Fig. 2). The karyotype was 46,XX,dup(14)(q11.2q21).arr 14q11.2q21.1 (20,516,277-38,826,881)x3 according to the International System for Human Cytogenetic Nomenclature (2013). Chromosome analyses in both parents showed normal karyotypes, indicating a de novo duplication mechanism. Fig. 1 G-banding chromosome analysis showed a duplication in the proximal segment of the long arm of chromosome 14 (indicated by red brackets). Fig. 2 Microarray analysis of chromosome 14 showed an 18.3-Mb duplication in the 14q11.2q21.1 (20,516,277-38,826,881) region (indicated by the blue bar). Compared with other patients with 14q duplications, our patient showed multiple cardiac anomalies. We found 47 duplication cases in the 14q11.2q21.1 region from DECIPHER (DatabasE of Chromosomal Imbalance and Phenotype in Human using Ensemble Resources, http://www.decipher.sanger.ac.uk). The most frequent phenotypes were intellectual disability (34.0%) and autism (19.1%); only two patients showed cardiac anomalies. One patient (DECIPHER ID: 283016) with a 0.39-Mb duplication in 14q12 (chr14:29,829,325-30,220,298) had autistic spectrum disorder, malformation of the heart and great vessels, nystagmus, and TOF. The other patient (DECIPHER ID: 287854) with a 0.37-Mb duplication in 14q11.2 (chr14:20,424, 580-20,796,696) had a hypoplastic right heart and malformation in the heart and great vessels. The 18.3-Mb duplication observed in our patient was large enough to be detected by chromosomal analysis. This region contains 446 genes and is associated with 32 phenotypes (NCBI database: http://www.ncbi.nlm.nih.gov/mapview/maps.cgi? [Build 35]). The only cardiac anomaly-associated gene in this region is myosin heavy chain 6 (MYH6) [4]. However, a missense mutation in MYH6, not a duplication, is known to be associated with cardiac anomalies. Most congenital heart defects arise from abnormal heart development in embryogenesis. During heart development, the dose of a gene product available at a specific time and location is important for normal cardiogenesis [5]. Hence, the cardiac anomalies observed in our patient may have resulted from dosage imbalances during cardiac development. Monfort et al. [2] reported that quantitative trait loci (QTLs) in 14q11.2 controlled stature. Similarly, we propose that the duplication observed in our patient supported the presence of a putative QTL in 14q that controlled heart development. The current results indicated that a duplication in chromosome 14 could lead to congenital heart defects. Clubfoot can be associated with chromosomal abnormalities [6,7]. Six patients from DECIPHER (ID: 1366, 248559, 249644, 249887, 277167, and 279247) have anomalies of the extremities and overlapping duplicated regions with our case. The critical region for anomalies of extremities is still uncertain, because there was no common region among these cases. Two patients (nssv578665, nssv578667) with 19-Mb duplications overlapping with the 14q11.2q21.1 region have been reported in the International Standards for Cytogenomic Arrays database (http://www.ncbi.nlm.nih.gov/dbvar/). Both had facial dysmorphism, hypertonia, intellectual disability, and developmental delay. Because of the young age of our patient, intellectual disability and delayed development could not be evaluated. Follow-up examinations for expected phenotypes are necessary. Thus, we confirmed an insertion of unknown origin in a congenital heart defect case using chromosomal microarray analysis. Chromosomal microarray is useful for determining the size and precise breakpoints of abnormalities, regardless of whether they could be detected by G-banding analysis.

Magnetic bead-based nucleic acid purification kit: Clinical application and performance evaluation in stool specimens

Two different methods - the semi-automated magnetic bead-based kit (SK, Stool DNA/RNA Purification kit®) and the manual membrane column-based kit (QS, QIAamp® DNA Stool Mini kit) - for purifying nucleic acids from clinical stool samples were compared and evaluated. The SK kit was more user-friendly than QS due to the reduced manual processing, partial automation, and short turnaround time with half cost. Furthermore, SK produced high yields in both DNA and RNA extractions but poor purity in RNA extraction. In the assessment of rotavirus and Clostridium difficile infection, both kits had equivalent or more sensitive performance compared with the standard method. Although SK showed some interference and inhibition in nucleic acid extraction, the performance, including the repeatability, linearity, analytical sensitivity, and matrix effect, was sufficient for routine clinical use.

Automated CH50 liposome-based immunoassay: consideration in dilution and validation of reference interval.

*Corresponding author: Hyon-Suk Kim, Department of Laboratory Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea, Phone: +82-2-2228-2443, Fax: +82-2-364-1583, E-mail: kimhs54@yuhs.ac Jihoon G. Yoon, Borae G. Park, Soon Sung Kwon and Jaewoo Song: Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea. http://orcid.org/0000-0001-9710-9253 (B.G. Park) Letter to the Editor