The Discordance between G-Banding Karyotyping and Microarray in Structural Abnormality.

BACKGROUND: Cytomolecular genetic laboratory techniques have developed from conventional G-banding karyotyping to whole genome sequencing. Although resolution has greatly increased, various cytogenetic techniques have their advantages and limitations in detecting genomic variations. METHODS: We compared the chromosomal abnormalities detected by G-banding karyotyping and SNP-based microarray testing in 62 patients from July 2020 to December 2022. We analyzed their difference according to chromosomal abnormalities, including numerical and structural and others. RESULTS: Of the 62 patients, 28 patients showed chromosomal aberration detected in one or more of the two test methods. Aneuploidy was detected in both methods, while gain and loss less than 3 Mb were only detectable by the microarray. G-banding karyotyping is fundamental to detect structural chromosome rearrangement such as inversions, ring chromosomes, and translocations, but additional breakpoint or unknown origin materials informa-tion obtained from microarray. Loss of heterozygosity was only detectable in microarray, and mosaicism had limitations in both G-banding karyotyping and microarray. CONCLUSIONS: Various disease cause genomic structural variants, it is very important to detect this. We showed discordance between G-banding karyotyping and SNP based microarray in clinical laboratory. It can be helpful to clinical physicians to decide which diagnostic tool to use.

Evaluation of LabType-SSO HLA Typing for HLA-A, -B, -C, -DRB1, and -DQB1 loci.

BACKGROUND: For HLA genotyping, PCR sequence-specific oligonucleotide (SSO) methods using the Luminex platform are widely used. We evaluated the performance of LabType-SSO (One Lambda, USA) in Koreans. METHODS: LabType-SSO were performed on 50 residual DNA samples analyzed by sequence-based typing (SBT) for all HLA-A, -B, -C, -DRB1, and -DQB1 alleles with gene frequency > 0.1% in Koreans. RESULTS: The LabType-SSO results were in complete agreement with SBT at the 2-digit level. For 4-digit level, 9 HLA-A alleles, 1 HLA-B allele, 3 HLA-C alleles, neither HLA-DRB1 nor -DQB1 allele showed ambiguous results for assignment of most probable types considering HLA gene frequency in Koreans. In addition, two cases of DQB1*04:01 allele were incorrectly assigned to DQB1*04:02. CONCLUSIONS: LabType-SSO tests showed accurate assignment of 2-digit level and LabType-SSO HLA-DRB1 test showed correct 4-digit most probable HLA type. The tests can be useful as intermediate resolution typing for solid organ transplantation.

Performance evaluation of three automated quantitative immunoassays and their correlation with a surrogate virus neutralization test in coronavirus disease 19 patients and pre-pandemic controls.

BACKGROUND: SARS-CoV-2 pandemic is currently ongoing, meanwhile vaccinations are rapidly underway in some countries. The quantitative immunoassays detecting antibodies against spike antigen of SARS-CoV-2 have been developed based on the findings that they have a better correlation with the neutralizing antibody. METHODS: The performances of the Abbott Architect SARS-CoV-2 IgG II Quant, DiaSorin LIAISON SARS-CoV-2 TrimericS IgG, and Roche Elecsys anti-SARS-CoV-2 S were evaluated on 173 sera from 126 SARS-CoV-2 patients and 151 pre-pandemic sera. Their correlations with GenScript cPass SARS-CoV-2 Neutralization Antibody Detection Kit were also analyzed on 173 sera from 126 SARS-CoV-2 patients. RESULTS: Architect SARS-CoV-2 IgG II Quant and Elecsys anti-SARS-CoV-2 S showed the highest overall sensitivity (96.0%), followed by LIAISON SARS-CoV-2 TrimericS IgG (93.6%). The specificities of Elecsys anti-SARS-CoV-2 S and LIAISON SARS-CoV-2 TrimericS IgG were 100.0%, followed by Architect SARS-CoV-2 IgG II Quant (99.3%). Regarding the correlation with cPass neutralization antibody assay, LIAISON SARS-CoV-2 TrimericS IgG showed the best correlation (Spearman rho = 0.88), followed by Architect SARS-CoV-2 IgG II Quant and Elecsys anti-SARS-CoV-2 S (all rho = 0.87). CONCLUSIONS: The three automated quantitative immunoassays showed good diagnostic performance and strong correlations with neutralization antibodies. These assays will be useful in diagnostic assistance, evaluating the response to vaccination, and the assessment of herd immunity in the future.

An Analysis of Technologies and Standards for Designing Smart Manufacturing Systems.

Smart manufacturing is defined by high degrees of automation. Automation, in turn, is defined by clearly defined processes. The use of standards in this environment is not just commonplace, but essential to creating repeatable processes and reliable systems. As with the rest of society, manufacturing systems are becoming more tightly connected through advances in information and communication technologies (ICT). As a result, manufacturers are able to receive information from their business partners and operational units much more quickly and are expected to respond quickly as well. Quick responses to changes in a manufacturing system are much more challenging than the responses that we have come to expect in other aspects of our lives. Manufacturing revolves around heavy capital investments to rapidly produce large amounts of product in anticipation of steady streams of commerce. Changes under these conditions not only disrupt the operations, slowing the production of goods, but also create difficulties with managing the capital investments. These are challenges manufacturers face daily. A large part of these challenges is understanding how best to refit manufacturing facilities to respond to variability, and how to plan new production facilities. By analyzing the information that is available in a manufacturing system, manufacturers can make more informed decisions as to how to respond to change. Advances in the technological infrastructure underlying manufacturing systems are enabling more reliable and timely flow of information across all levels of the manufacturing operation. We propose that effective utilization of such operational information will enable more automated, agile responses to the changing conditions, i.e. Smart Manufacturing. In this paper, we analyze the sources and the standards supporting the flow of that information throughout the enterprise. The analysis is based an intersection of two reference models: the Factory Design and Improvement (FDI) process and the ISA88 hierarchical model of manufacturing operations. The FDI process consists of a set of high-level activities for designing and improving manufacturing operations. The ISA88 hierarchical model specifies seven levels of control within a manufacturing enterprise.

Using formal methods to scope performance challenges for Smart Manufacturing Systems: focus on agility.

Smart Manufacturing Systems (SMS) need to be agile to adapt to new situations by using detailed, precise, and appropriate data for intelligent decision-making. The intricacy of the relationship of strategic goals to operational performance across the many levels of a manufacturing system inhibits the realization of SMS. This paper proposes a method for identifying what aspects of a manufacturing system should be addressed to respond to changing strategic goals. The method uses standard modeling techniques in specifying a manufacturing system and the relationship between strategic goals and operational performance metrics. Two existing reference models related to manufacturing operations are represented formally and harmonized to support the proposed method. The method is illustrated for a single scenario using agility as a strategic goal. By replicating the proposed method for other strategic goals and with multiple scenarios, a comprehensive set of performance challenges can be identified.

Allele and haplotype frequencies of 11 HLA loci in Koreans by next-generation sequencing.

Data on HLA genotype distribution, including DQA1 and DPA1, in the Korean population are limited. We aimed to investigate the allele and haplotype frequencies of 11 HLA loci in 339 Korean subjects using next-generation sequencing (NGS)-based HLA typing. A total of 339 samples from unrelated healthy subjects were genotyped for HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1, -DQA1, -DPB1, and -DPA1 using two different NGS-based HLA typing kits (166 tested using the NGSgo-MX11-3 kit [GenDx, Netherlands] and 173 by the AllType NGS 11 Loci Amplification kit [One Lambda, USA]). PyPop software was used to estimate allele and haplotype frequencies and linkage disequilibrium between the loci. Additionally, a principal component analysis was performed to compare the allele distribution of Koreans with that of other populations. A total of 214 HLA alleles (97 class I and 117 class II alleles) were assigned. The most frequent alleles for each locus were A*24:02:01 (24.78%), B*15:01:01 (10.18%), C*01:02:01 (18.44%), DRB1*04:05:01 (9.59%), DRB3*02:02:01 (13.72%), DRB4*01:03:01 (25.81%), DRB5*01:01:01 (9.0%), DQA1*01:02:01 (16.96%), DQB1*03:01:01 (14.31%), DPA1*01:03:01 (44.4%), and DPB1*05:01:01 (35.1%), respectively. The most frequent haplotypes were A*33:03:01-C*03:02:02-B*58:01:01 for HLA class I (5.01%) and DRB1*04:05:01-DQA1*03:03:01-DQB1*04:01:01-DPA1*02:02:02-DPB1*05:01:01 for HLA class II (6.23%). The total allelic ambiguities by NGS were estimated to be minimal and considerably decreased compared with those by Sanger sequencing. The Japanese population had the most similar allele distribution to Koreans, followed by the Chinese population. Frequency data of 11 HLA loci in Koreans can provide essential data for population genetics and disease association studies.

RNF213 vasculopathy manifested in various forms within a family: A case report.

RATIONALE: The ring finger protein 213 (RNF213) p.R4810K variant has been identified as being associated with Moyamoya disease (MMD), a condition that is more prevalent in East Asians. This association extends beyond cerebral vessels and has been implicated in coronary artery disease. PATIENT CONCERNS: A 36-year-old female was admitted to the emergency room with chest pain. Although the patient had no known underlying conditions or risk factors for atherosclerosis, she was diagnosed with unstable angina and underwent percutaneous coronary intervention. Given her older sister's ongoing treatment for MMD, it was suspected that the patient's coronary artery disease might be linked to the MMD-associated gene mutation. DIAGNOSES: Coronary angiography revealed 80% narrowing of the proximal left anterior descending artery. Based on clinical symptoms and coronary angiography, we diagnosed it as unstable angina. INTERVENTION: Due to the family history of MMD and detection of the RNF213 p.R4810K heterozygous variant in the patient's older sister, genetic counseling was recommended. Next-generation sequencing for vascular diseases was performed. OUTCOMES: Genetic testing confirmed the presence of an RNF213 p.R4810K heterozygous variant in the patient, mirroring that in her sister. An RNF213 p.C4397R heterozygous variant was identified concomitantly, although it was categorized as a variant of uncertain significance. Coronary artery disease has been attributed to the RNF213 p.R4810K variant. LESSONS: Although MMD is rare in Western populations, it is more common in East Asian populations. Traditionally, MMD diagnoses have focused solely on the cerebral vessels without guidelines for the assessment of other vascular involvements. This familial case underscores the fact that a single genetic mutation can manifest in diverse ways in different diseases. Hence, the need and regularity of systemic vessel screening should be thoughtfully considered in such a context.

Association of HLA-DRB1 and -DQB1 Alleles with Susceptibility to IgA Nephropathy in Korean Patients.

BACKGROUND: Associations between IgA nephropathy (IgAN) and HLA-DRB1 and -DQB1 alleles have been reported in several ethnic groups. We investigated the association of HLA-DRB1 and -DQB1 alleles with the predisposition for IgAN and disease progression to end-stage kidney disease (ESKD) in Korean patients. METHODS: We analyzed HLA-DRB1 and -DQB1 genotypes in 399 IgAN patients between January 2000 and January 2019 using a LIFECODES sequence-specific oligonucleotide (SSO) typing kit (Immucor, Stamford, CT, USA) or a LABType SSO Typing Test (One Lambda, Canoga Park, CA, USA). Alleles with a significant difference in two-digit resolution were further analyzed using in-house sequence-based typing and sequence-specific primer PCR. As controls, 613 healthy hematopoietic stem cell donors were included. Kidney survival was analyzed in 281 IgAN patients with available clinical and laboratory data using Cox regression analysis. Where needed, P-values were adjusted using Bonferroni correction. RESULTS: The allele frequencies of HLA-DRB1*04:05 (corrected P [Pc]<0.001), -DQB1 *04:01 (Pc=0.048), and -DQB1*03:02 (Pc=0.021) were significantly higher in IgAN patients than in controls, whereas those of HLA-DRB1*07:01, -DRB1*15:01, -DQB1*02:02, and -DQB1*06:02 (Pc<0.001 for all) were significantly lower in IgAN patients than in controls. The allele frequency of HLA-DQB1*05:03 (Pc=0.016) was significantly lower in the ESKD group than in the non-ESKD group; however, there was no significant difference for ESKD progression between these groups. CONCLUSIONS: We report novel associations of HLA-DRB1*15:01, DQB1*02:02, -DQB1*03:02, and -DQB1*04:01 with IgAN. Further studies of HLA alleles associated with IgAN progression in a larger cohort and in various ethnic groups are needed.

SnackNTM: An Open-Source Software for Sanger Sequencing-based Identification of Nontuberculous Mycobacterial Species.

BACKGROUND: Sequence-based identification is one of the most effective methods for species-level identification of nontuberculous mycobacteria (NTM). However, it is time-consuming because of the bioinformatics processes involved, including sequence trimming, consensus sequence generation, and public database searches. We developed a simple and fully automated software that enabled species-level identification of NTM from trace files, SnackNTM (https://github.com/Young-gonKim/SnackNTM). METHODS: JAVA programing language was used for software development. The SnackNTM diagnostic algorithm utilized 16S rRNA gene sequences, according to the Clinical & Laboratory Standards Institute guidelines, and an rpoB gene region was adjunctively utilized to narrow down the species. The software performance was validated using trace files of 234 clinical cases, comprising 217 consecutive cases and 17 additionally selected cases of unique species. RESULTS: SnackNTM could analyze multiple cases at once, and all the bioinformatics processes required for sequence-based NTM identification were automatically performed with a single mouse click. SnackNTM successfully identified 95.9% (208/217) of consecutive clinical cases, and the results showed 99.0% (206/208) agreement with manual classification results. SnackNTM successfully identified all 17 cases of unique species. In a processing time comparison test, the analysis and reporting of 30 cases, which took 150 minutes manually, took only 40 minutes with SnackNTM. CONCLUSIONS: SnackNTM is expected to reduce the workload for NTM identification, especially in clinical laboratories that process large numbers of cases.

Removal of Non-specific Reactions of LABScreen Single Antigen Class II Assay by Fetal Bovine Serum Treatment.

Recently, the removal of false reaction from beads 10 (DRB1 *04:04), 30 (DRB1 *16:01), and 31 (DRB1 *16:02) by fetal bovine serum (FBS) treatment in LABScreen Single Antigen Class II Assay was reported. We aimed to confirm the reaction in many cases. Fifty-nine sera showed positivity on at least two among beads 10, 30 and 31 from Nov 2017 to Oct 2018 in Seoul National University Hospital were included. FBS treatment was performed on 59 sera, and Single Antigen Class II Assay was repeated. Among 59 cases, the negative conversion rates of DR16 (57/59, 96.6%), DR4 (37/39, 94.9%), and accompanied other antibodies, e.g.) DP19 (39/45, 86.7%) were very high. The prior use of intravenous immunoglobulin in a non-specific binding group was significantly higher than the sex, age-matched control group (P=0.005).

An Investigation to Manufacturing Analytical Services Composition using the Analytical Target Cascading Method.

As cloud computing is increasingly adopted, the trend is to offer software functions as modular services and compose them into larger, more meaningful ones. The trend is attractive to analytical problems in the manufacturing system design and performance improvement domain because 1) finding a global optimization for the system is a complex problem; and 2) sub-problems are typically compartmentalized by the organizational structure. However, solving sub-problems by independent services can result in a sub-optimal solution at the system level. This paper investigates the technique called Analytical Target Cascading (ATC) to coordinate the optimization of loosely-coupled sub-problems, each may be modularly formulated by differing departments and be solved by modular analytical services. The result demonstrates that ATC is a promising method in that it offers system-level optimal solutions that can scale up by exploiting distributed and modular executions while allowing easier management of the problem formulation.

An Overview of a Smart Manufacturing System Readiness Assessment.

Smart manufacturing, today, is the ability to continuously maintain and improve performance, with intensive use of information, in response to the changing environments. Technologies for creating smart manufacturing systems or factories are becoming increasingly abundant. Consequently, manufacturers, large and small, need to correctly select and prioritize these technologies correctly. In addition, other improvements may be necessary to receive the greatest benefit from the selected technology. This paper proposes a method for assessing a factory for its readiness to implement those technologies. The proposed readiness levels provide users with an indication of their current factory state when compared against a reference model. Knowing this state, users can develop a plan to increase their readiness. Through validation analysis, we show that the assessment has a positive correlation with the operational performance.

IDENTIFYING PERFORMANCE ASSURANCE CHALLENGES FOR SMART MANUFACTURING.

Smart manufacturing has the potential to address many of the challenges faced by industry. However, the manufacturing community often needs assistance to leverage available technologies to improve their systems. To assure the performance of these technologies, this paper proposes a shared knowledge base that collects problem areas, solutions, and best practices for manufacturing technology. An Implementation Risk Assessment Framework (IRAF) is also described to identify the primary weaknesses of technologies in specific manufacturing contexts. Such approaches have the potential to stimulate new ideas and drive standardization activities critical to scale up and deploy smart manufacturing technologies successfully and quickly.