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1.
Journal of Korean Medical Science ; : e129-2023.
Article in English | WPRIM | ID: wpr-976938

ABSTRACT

Background@#Alpha-toxin (AT), a major virulence factor of Staphylococcus aureus, is an important immunotherapeutic target to prevent or treat invasive S. aureus infections. Previous studies have suggested that anti-AT antibodies (Abs) may have a protective role against S. aureus bacteremia (SAB), but their function remains unclear. Therefore, we aimed to investigate the association between serum anti-AT Ab levels and clinical outcomes of SAB. @*Methods@#Patients from a prospective SAB cohort at a tertiary-care medical center (n = 51) were enrolled in the study from July 2016 to January 2019. Patients without symptoms or signs of infection were enrolled as controls (n = 100). Blood samples were collected before the onset of SAB and at 2- and 4-weeks post-bacteremia. Anti-AT immunoglobin G (IgG) levels were measured using an enzyme-linked immunosorbent assay. All clinical S. aureus isolates were tested for the presence of hla using polymerase chain reaction. @*Results@#Anti-AT IgG levels in patients with SAB before the onset of bacteremia did not differ significantly from those in non-infectious controls. Pre-bacteremic anti-AT IgG levels tended to be lower in patients with worse clinical outcomes (7-day mortality, persistent bacteremia, metastatic infection, septic shock), although the differences were not statistically significant. Patients who needed intensive care unit care had significantly lower anti-AT IgG levels at 2 weeks post-bacteremia (P = 0.020). @*Conclusion@#The study findings suggest that lower anti-AT Ab responses before and during SAB, reflective of immune dysfunction, are associated with more severe clinical presentations of infection.

2.
Cancer Research and Treatment ; : 351-366, 2023.
Article in English | WPRIM | ID: wpr-976723

ABSTRACT

Circulating tumor DNA (ctDNA) is the portion of the cell-free DNA in the blood of cancer patients released from tumor cells via apoptosis, necrosis, or active release. From 10 mL of blood, the 4-5 mL of plasma obtained from a cancer patient contains 5-10 ng/mL of ctDNA. The plasma contains not only ctDNA of tumor origin, but also DNA from normal cells or clonal hematopoiesis. Another characteristic of ctDNA is its rapid clearance from circulation; it has a half-life of 16 minutes to 2.5 hours. Obtaining reliable results from ctDNA requires the application and approval of standardized clinical validation guidelines; however, the status of numerous ctDNA tests currently varies. The clinical use of ctDNA testing should be carefully considered based on the test’s specific needs and characteristics. Here we provide the different characteristics of ctDNA tests and information regarding their validation and approval status.

3.
Journal of Gastric Cancer ; : 264-274, 2023.
Article in English | WPRIM | ID: wpr-1000906

ABSTRACT

Purpose@#In this study, polymerase chain reaction (PCR)-based microsatellite instability (MSI) testing was comprehensively analyzed and compared with immunohistochemistry (IHC) for mismatch repair (MMR) protein expression in patients with gastric cancer (GC). @*Materials and Methods@#In 5,676 GC cases, PCR-based MSI testing using five microsatellites (BAT-26, BAT-25, D5S346, D2S123, and D17S250) and IHC for MLH1 were performed. Reevaluation of MSI testing/MLH1 IHC and additional IHC for MSH2, MSH6, and PMS2 were performed in discordant/indeterminate cases. @*Results@#Of the 5,676 cases, microsatellite stable (MSS)/MSI-low and intact MLH1 were observed in 5,082 cases (89.5%), whereas MSI-high (MSI-H) and loss of MLH1 expression were observed in 502 cases (8.8%). We re-evaluated the remaining 92 cases (1.6%) with a discordant/ indeterminate status. Re-evaluation showed 1) 37 concordant cases (0.7%) (18 and 19 cases of MSI-H/MMR-deficient (dMMR) and MSS/MMR-proficient (pMMR), respectively), 2) 6 discordant cases (0.1%) (3 cases each of MSI-H/pMMR and MSS/dMMR), 3) 14 MSI indeterminate cases (0.2%) (1 case of dMMR and 13 cases of pMMR), and 4) 35 IHC indeterminate cases (0.6%) (22 and 13 cases of MSI-H and MSS, respectively). Finally, MSI-H or dMMR was observed in 549 cases (9.7%), of which 47 (0.8%) were additionally confirmed as MSI-H or dMMR by reevaluation. Sensitivity was 99.3% for MSI testing and 95.4% for MMR IHC. @*Conclusions@#Considering the low incidence of MSI-H or dMMR, discordant/indeterminate results were occasionally identified in GCs, in which case complementary testing is required.These findings could help improve the accuracy of MSI/MMR testing in daily practice.

4.
Infection and Chemotherapy ; : 360-363, 2022.
Article in English | WPRIM | ID: wpr-937672

ABSTRACT

The STANDARD™ M10 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) assay (M10 assay) (SD Biosensor Inc., Suwon, Korea) is a rapid, fully-automated, cartridgetype molecular diagnostic assay that detects SARS-CoV-2 RNA using primers and probes for each target gene (ORF1ab gene, E gene). This study evaluated its performance by assessing its concordance with the approved SARS-CoV-2 real-time PCR assay. Tests were performed on 80 nasopharyngeal samples. The sensitivity and specificity of the M10 assay were 100%.The M10 assay effectively diagnosed SARS-CoV-2 infection, and it was comparable to the approved SARS-CoV-2 real-time PCR assay. It is a viable point-of-care test due to its short turnaround time.

5.
Pediatric Infection & Vaccine ; : 92-100, 2021.
Article in English | WPRIM | ID: wpr-903146

ABSTRACT

Purpose@#Rapid detection of etiologic organisms is crucial for initiating appropriate therapy in patients with central nervous system (CNS) infection. This study aimed to evaluate the diagnostic value of the BioFire® Meningitis/Encephalitis (ME) panel in detecting etiologic organisms in cerebrospinal fluid (CSF) samples from febrile infants. @*Methods@#CSF samples from infants aged <90 days who were evaluated for fever were collected between January 2016 and July 2019 at the Seoul National University Children's Hospital. We performed BioFire® ME panel testing of CSF samples that had been used for CSF analysis and conventional tests (bacterial culture, Xpert® enterovirus assay, and herpes simplex virus-1 and -2 polymerase chain reaction) and stored at −70°C until further use. @*Results@#In total, 72 (24 pathogen-identified and 48 pathogen-unidentified) CSF samples were included. Using BioFire® ME panel testing, 41 (85.4%) of the 48 pathogen-unidentified CSF samples yielded negative results and 22 (91.7%) of the 24 pathogen-identified CSF samples yielded the same results (enterovirus in 19, Streptococcus agalactiae in 2, and Streptococcus pneumoniae in 1) as those obtained using the conventional tests, thereby resulting in an overall agreement of 87.5% (63/72). Six of the 7 pathogen-unidentified samples were positive for human parechovirus (HPeV) via BioFire® ME panel testing. @*Conclusions@#Compared with the currently available etiologic tests for CNS infection, BioFire® ME panel testing demonstrated a high agreement score for pathogen-identified samples and enabled HPeV detection in young infants. The clinical utility and cost-effectiveness of BioFire® ME panel testing in children must be evaluated for its wider application.

6.
Pediatric Infection & Vaccine ; : 92-100, 2021.
Article in English | WPRIM | ID: wpr-895442

ABSTRACT

Purpose@#Rapid detection of etiologic organisms is crucial for initiating appropriate therapy in patients with central nervous system (CNS) infection. This study aimed to evaluate the diagnostic value of the BioFire® Meningitis/Encephalitis (ME) panel in detecting etiologic organisms in cerebrospinal fluid (CSF) samples from febrile infants. @*Methods@#CSF samples from infants aged <90 days who were evaluated for fever were collected between January 2016 and July 2019 at the Seoul National University Children's Hospital. We performed BioFire® ME panel testing of CSF samples that had been used for CSF analysis and conventional tests (bacterial culture, Xpert® enterovirus assay, and herpes simplex virus-1 and -2 polymerase chain reaction) and stored at −70°C until further use. @*Results@#In total, 72 (24 pathogen-identified and 48 pathogen-unidentified) CSF samples were included. Using BioFire® ME panel testing, 41 (85.4%) of the 48 pathogen-unidentified CSF samples yielded negative results and 22 (91.7%) of the 24 pathogen-identified CSF samples yielded the same results (enterovirus in 19, Streptococcus agalactiae in 2, and Streptococcus pneumoniae in 1) as those obtained using the conventional tests, thereby resulting in an overall agreement of 87.5% (63/72). Six of the 7 pathogen-unidentified samples were positive for human parechovirus (HPeV) via BioFire® ME panel testing. @*Conclusions@#Compared with the currently available etiologic tests for CNS infection, BioFire® ME panel testing demonstrated a high agreement score for pathogen-identified samples and enabled HPeV detection in young infants. The clinical utility and cost-effectiveness of BioFire® ME panel testing in children must be evaluated for its wider application.

7.
The Korean Journal of Internal Medicine ; : 11-14, 2021.
Article in English | WPRIM | ID: wpr-875439

ABSTRACT

Recently, the number of patients with coronavirus disease 2019 (COVID-19) who have tested positive for severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), via the reverse transcription polymerase chain reaction (RT-PCR) test, after recovery has increased; this has caused a dilemma regarding the medical measures and policies. We evaluated the dynamics of viral load and anti-SARSCoV-2 antibodies in four patients with positive RT-PCR results after recovery. In all patients, the highest levels of immunoglobulin G (IgG) and IgM antibodies were reached after about a month of the onset of the initial symptoms. Then, the IgG titers plateaued, and the IgM titers decreased, regardless of RT-PCR results.The IgG and IgM levels did not increase after the post-negative positive RT-PCR results in any of the patients. Our results reinforced that the post-negative positive RT-PCR results may be due to the detection of RNA particles rather than reinfection in individuals who have recovered from COVID-19.

8.
The Korean Journal of Internal Medicine ; : 771-781, 2020.
Article | WPRIM | ID: wpr-831784

ABSTRACT

Background/Aims@#Current evidence supports lung ultrasound as a point-ofcare alternative diagnostic tool for various respiratory diseases. We sought to determine the utility of lung ultrasound for early detection of pneumonia and for assessment of respiratory failure among patients with coronavirus disease 2019 (COVID-19). @*Methods@#Six patients with confirmed COVID-19 by reverse transcription-polymerase chain reaction were enrolled. All had undergone chest X-ray and chest computed tomography (CT) on the day of admission and underwent multiple point-of-care lung ultrasound scans over the course of their hospitalization. @*Results@#Lung ultrasound detected early abnormal findings of representative B-lines in a patient with a normal chest X-ray, corresponding to ground-glass opacities on the chest CT scan. The ultrasound findings improved as her clinical condition improved and her viral load decreased. In another minimally symptomatic patient without significant chest X-ray findings, the ultrasound showed B-lines, an early sign of pneumonia before abnormalities were detected on the chest CT scan. In two critically ill patients, ultrasound was performed to assess for evaluation of disease severity. In both patients, the clinicians conducted emergency rapid sequence intubation based on the ultrasound findings without awaiting the laboratory results and radiological reports. In two children, ultrasound was used to assess the improvement in their pneumonia, thus avoiding further imaging tests such as chest CT. @*Conclusions@#Lung ultrasound is feasible and useful as a rapid, sensitive, and affordable point-of-care screening tool to detect pneumonia and assess the severity of respiratory failure in patients hospitalized with COVID-19.

9.
Journal of Korean Medical Science ; : 124-2020.
Article in English | WPRIM | ID: wpr-810936

ABSTRACT

The large outbreak of coronavirus disease 2019 (COVID-19) that started in Wuhan, China has now spread to many countries worldwide. Current epidemiologic knowledge suggests that relatively few cases are seen among children, which limits opportunities to address pediatric specific issues on infection control and the children's contribution to viral spread in the community. Here, we report the first pediatric case of COVID-19 in Korea. The 10-year-old girl was a close contact of her uncle and her mother who were confirmed to have COVID-19. In this report, we present mild clinical course of her pneumonia that did not require antiviral treatment and serial viral test results from multiple specimens. Lastly, we raise concerns on the optimal strategy of self-quarantine and patient care in a negative isolation room for children.

10.
Journal of Korean Medical Science ; : e124-2020.
Article in English | WPRIM | ID: wpr-899809

ABSTRACT

The large outbreak of coronavirus disease 2019 (COVID-19) that started in Wuhan, China has now spread to many countries worldwide. Current epidemiologic knowledge suggests that relatively few cases are seen among children, which limits opportunities to address pediatric specific issues on infection control and the children's contribution to viral spread in the community. Here, we report the first pediatric case of COVID-19 in Korea. The 10-year-old girl was a close contact of her uncle and her mother who were confirmed to have COVID-19. In this report, we present mild clinical course of her pneumonia that did not require antiviral treatment and serial viral test results from multiple specimens. Lastly, we raise concerns on the optimal strategy of self-quarantine and patient care in a negative isolation room for children.

11.
Journal of Korean Medical Science ; : e124-2020.
Article in English | WPRIM | ID: wpr-892105

ABSTRACT

The large outbreak of coronavirus disease 2019 (COVID-19) that started in Wuhan, China has now spread to many countries worldwide. Current epidemiologic knowledge suggests that relatively few cases are seen among children, which limits opportunities to address pediatric specific issues on infection control and the children's contribution to viral spread in the community. Here, we report the first pediatric case of COVID-19 in Korea. The 10-year-old girl was a close contact of her uncle and her mother who were confirmed to have COVID-19. In this report, we present mild clinical course of her pneumonia that did not require antiviral treatment and serial viral test results from multiple specimens. Lastly, we raise concerns on the optimal strategy of self-quarantine and patient care in a negative isolation room for children.

12.
Journal of Korean Medical Science ; : e3-2019.
Article in English | WPRIM | ID: wpr-719497

ABSTRACT

BACKGROUND: Mycobacterium bovis Bacille Calmette-Guérin (BCG) osteitis, a rare complication of BCG vaccination, has not been well investigated in Korea. This study aimed to evaluate the clinical characteristics of BCG osteitis during the recent 10 years in Korea. METHODS: Children diagnosed with BCG osteitis at the Seoul National University Children's Hospital from January 2007 to March 2018 were included. M. bovis BCG was confirmed by multiplex polymerase chain reaction (PCR) in the affected bone. BCG immunization status and clinical information were reviewed retrospectively. RESULTS: Twenty-one patients were diagnosed with BCG osteitis and their median symptom onset from BCG vaccination was 13.8 months (range, 6.0–32.5). Sixteen children (76.2%) received Tokyo-172 vaccine by percutaneous multiple puncture method, while four (19.0%) and one (4.8%) received intradermal Tokyo-172 and Danish strain, respectively. Common presenting symptoms were swelling (76.2%), limited movement of the affected site (63.2%), and pain (61.9%) while fever was only accompanied in 19.0%. Femur (33.3%) and the tarsal bones (23.8%) were the most frequently involved sites; and demarcated osteolytic lesions (63.1%) and cortical breakages (42.1%) were observed on plain radiographs. Surgical drainage was performed in 90.5%, and 33.3% of them required repeated surgical interventions due to persistent symptoms. Antituberculosis medications were administered for a median duration of 12 months (range, 12–31). Most patients recovered without evident sequelae. CONCLUSION: Highly suspecting BCG osteitis based on clinical manifestations is important for prompt management. A comprehensive national surveillance system is needed to understand the exact incidence of serious adverse reactions following BCG vaccination and establish safe vaccination policy in Korea.


Subject(s)
Child , Humans , Drainage , Femur , Fever , Immunization , Incidence , Korea , Methods , Multiplex Polymerase Chain Reaction , Mycobacterium bovis , Mycobacterium , Osteitis , Punctures , Retrospective Studies , Seoul , Tarsal Bones , Vaccination
13.
Laboratory Medicine Online ; : 88-93, 2019.
Article in English | WPRIM | ID: wpr-760485

ABSTRACT

Fungi are a major cause of human infections with diverse clinical manifestations. The incidence of fungal infections has increased over time, particularly in patients who have risk factors such as neutropenia, immune suppression, an intravascular catheter, parenteral nutrition, a prosthetic device, and prior broad spectrum antibiotic therapy. Here, we present an unusual case of co-infection by 2 distinct fungi, Candida parapsilosis and Trichosporon asahii, isolated from a patient who did not have any known risk factors initially, except active pulmonary tuberculosis. Despite the negative conversion of sputum acid-fast bacilli (AFB) culture test after treatment, clinical symptoms were refractory to therapy. The patient developed symptoms suggesting septic shock, and 2 distinct colonies were isolated from a blood specimen, which were identified as C. parapsilosis and T. asahii by MALDI-TOF and rRNA sequencing. Fever and hypotension were relieved after anti-fungal agent injection, and pulmonary lesions identified by imaging also improved.


Subject(s)
Humans , Candida , Catheters , Coinfection , Fever , Fungemia , Fungi , Hypotension , Incidence , Neutropenia , Parenteral Nutrition , Risk Factors , Shock, Septic , Sputum , Trichosporon , Tuberculosis, Pulmonary
14.
Laboratory Medicine Online ; : 107-112, 2019.
Article in English | WPRIM | ID: wpr-760481

ABSTRACT

Iso-oncotic human serum albumin (HSA) is the primary replacement fluid of choice during therapeutic plasma exchange (TPE). Hypersensitivity reactions to HSA are rare, but require proper evaluation and management. In this article, we report two cases of hypersensitivity reactions to 5% HSA during TPE and discuss strategies to address this problem. The first case was a 60-year-old female patient, who was scheduled for TPE for treatment of recurrent focal segmental glomerulosclerosis after ABO-incompatible kidney transplantation. She developed a pruritic rash on her entire body during the first two sessions of TPE using 5% HSA. The third session was conducted using 500 mL normal saline, 1,000 mL 10% pentastarch, and 750 mL 5% HSA, where she eventually developed a pruritic rash when HSA was infused. There were no adverse events during the fourth and fifth session when fresh frozen plasma was used in place of HSA. The second case was a 50-year-old male patient diagnosed with optic neuritis, who was admitted for five sessions of TPE. The patient developed a pruritic rash on his entire body during the first session of TPE using 5% HSA. The patient experienced no adverse events during the following four sessions using fresh frozen plasma. Certain elements contained in HSA, such as albumin aggregates, prekallikrein activator, and caprylate-modified albumin, might be the reason for these hypersensitivity reactions. Careful selection of alternative replacement fluids is important to avoid premature termination of TPE procedures and secure optimal treatment options for patients.


Subject(s)
Female , Humans , Male , Middle Aged , Caprylates , Exanthema , Factor XIIa , Glomerulosclerosis, Focal Segmental , Hydroxyethyl Starch Derivatives , Hypersensitivity , Kidney Transplantation , Optic Neuritis , Plasma Exchange , Plasma , Serum Albumin
15.
Journal of Korean Medical Science ; : e302-2019.
Article in English | WPRIM | ID: wpr-765133

ABSTRACT

BACKGROUND: Nontuberculous mycobacteria (NTM) lymphadenitis is an under-recognized entity, and data of the true burden in children are limited. Without a high index of suspicion, diagnosis may be delayed and microbiological detection is challenging. Here, we report a cluster of NTM lymphadenitis experienced in Korean children. METHODS: Subjects under 19 years of age diagnosed with NTM lymphadenitis during November 2016–April 2017 and April 2018 were included. Electronic medical records were reviewed for clinical, laboratory and pathological findings. Information regarding underlying health conditions and environmental exposure factors was obtained through interview and questionnaires. RESULTS: A total of ten subjects were diagnosed during 18 months. All subjects were 8–15 years of age, previously healthy, male and had unilateral, nontender, cervicofacial lymphadenitis for more than 3 weeks with no significant systemic symptoms and no response to empirical antibiotics. Lymph nodes involved were submandibular (n = 8), preauricular (n = 6) and submental (n = 1). Five patients had two infected nodes and violaceous discoloration was seen in seven subjects. Biopsy specimens revealed chronic granulomatous inflammation and acid-fast bacteria culture identified Mycobacterium haemophilum in two cases and NTM polymerase chain reaction was positive in two cases. Survey revealed various common exposure sources. CONCLUSION: NTM lymphadenitis is rare but increasing in detection and it may occur in children and adolescents. Diagnosis requires high index of suspicion and communication between clinicians and the laboratory is essential for identification of NTM.


Subject(s)
Adolescent , Child , Humans , Male , Anti-Bacterial Agents , Bacteria , Biopsy , Diagnosis , Electronic Health Records , Environmental Exposure , Inflammation , Lymph Nodes , Lymphadenitis , Mycobacterium , Mycobacterium haemophilum , Nontuberculous Mycobacteria , Polymerase Chain Reaction , Tuberculosis, Lymph Node
16.
Annals of Laboratory Medicine ; : 537-544, 2019.
Article in English | WPRIM | ID: wpr-762441

ABSTRACT

BACKGROUND: Several factors contribute to differences in Streptococcus pneumoniae serotype distribution. We investigated the serotype distribution and antimicrobial resistance of S. pneumoniae isolated between 2014 and 2016 in Korea. METHODS: We collected a total of 1,855 S. pneumoniae isolates from 44 hospitals between May 2014 and May 2016, and analyzed the serotypes by sequential multiplex PCR. We investigated the distribution of each serotype by patient age, source of the clinical specimen, and antimicrobial resistance pattern. RESULTS: The most common serotypes were 11A (10.1%), followed by 19A (8.8%), 3 (8.5%), 34 (8.1%), 23A (7.3%), and 35B (6.2%). The major invasive serotypes were 3 (12.6%), 19A (7.8%), 34 (7.8%), 10A (6.8%), and 11A (6.8%). Serotypes 10A, 15B, 19A, and 12F were more common in patients ≤5 years old, while serotype 3 was more common in patients ≥65 years old compared with the other age groups. The coverage rates of pneumococcal conjugate vaccine (PCV)7, PCV10, PCV13, and pneumococcal polysaccharide vaccine 23 were 11.8%, 12.12%, 33.3%, and 53.6%, respectively. Of the 1,855 isolates, 857 (46.2%) were multi-drug resistant (MDR), with serotypes 11A and 19A predominant among the MDR strains. The resistance rates against penicillin, cefotaxime, and levofloxacin were 22.8%, 12.5%, and 9.4%, respectively. CONCLUSIONS: There were significant changes in the major S. pneumoniae serotypes in the community. Non-PCV13 serotypes increased in patients ≤5 years old following the introduction of national immunization programs with the 10- and 13-polyvalent vaccines.


Subject(s)
Humans , Cefotaxime , Immunization Programs , Korea , Levofloxacin , Multiplex Polymerase Chain Reaction , Penicillins , Pneumococcal Vaccines , Pneumonia , Serogroup , Streptococcus pneumoniae , Streptococcus , Vaccines
17.
Korean Journal of Blood Transfusion ; : 159-170, 2018.
Article in Korean | WPRIM | ID: wpr-716146

ABSTRACT

BACKGROUND: Phlebotomy performed for laboratory testing has the potential to cause anemia in newborns and infants. This study investigated the minimum specimen volume required for an automated immunohematology analyzer DAYmate S. METHODS: Three combinations of tubes were evaluated: I. 6 mL EDTA tube, II. 0.5 mL microtainer (on top of 3 mL EDTA tube), and III. 1 mL sample cup (on top of 6 mL EDTA tube). ABO/RhD cell typing was done using centrifuged red cells; unexpected antibody screening was carried out using plasma, and Type & Screening was conducted using whole blood samples. The lowest specimen volume capable of performing 10 repetitive tests without errors was investigated. RESULTS: ABO/RhD cell typing could be performed from I. 30 μL, II. 25 μL, and III. 25 μL. Unexpected antibody screening could be performed from I. 170 μL, II. 150 μL, and III. 140 μL. According to the hematocrit levels, Type & Screening could be performed from 30%, I&III 650 μL, II. 800 μL; 40%, I&III 650 μL, II. 900 μL; and 50%, I&III 1,000 μL, II. Testing using specimen volumes below 1,000 μL was difficult. CONCLUSION: By separating red cells and plasma, pre-transfusion testing of ABO/RhD cell typing and unexpected antibody screening could be conducted with very small specimen volumes using DAYmate S compared to Type & Screening using whole blood. The application of small-sized sample tubes was more competitive and this is expected to be very useful for preventing iatrogenic anemia in neonates and infants less than 4 months old.


Subject(s)
Humans , Infant , Infant, Newborn , Anemia , Edetic Acid , Hematocrit , Mass Screening , Phlebotomy , Plasma
18.
Cancer Research and Treatment ; : 255-264, 2018.
Article in English | WPRIM | ID: wpr-739611

ABSTRACT

PURPOSE: Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2. MATERIALS AND METHODS: The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2. Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. RESULTS: Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. CONCLUSION: Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.


Subject(s)
Humans , DNA , Genome , High-Throughput Nucleotide Sequencing , Statistics as Topic
19.
Annals of Laboratory Medicine ; : 591-598, 2018.
Article in English | WPRIM | ID: wpr-718322

ABSTRACT

BACKGROUND: Forkhead box P3 (FOXP3) is an important marker of regulatory T cells. FOXP3 polymorphisms are associated with autoimmune diseases, cancers, and allograft outcomes. We examined whether single nucleotide polymorphisms (SNPs) at the FOXP3 locus are associated with clinical outcomes after allogenic hematopoietic stem cell transplantation (HSCT). METHODS: Five FOXP3 SNPs (rs5902434, rs3761549, rs3761548, rs2232365, and rs2280883) were analyzed by PCR-sequencing of 172 DNA samples from allogenic HSCT patients. We examined the relationship between each SNP and the occurrence of graft-versus-host disease (GVHD), post-HSCT infection, relapse, and patient survival. RESULTS: Patients with acute GVHD (grades II-IV) showed higher frequencies of the rs3761549 T/T genotype, rs5902434 ATT/ATT genotype, and rs2232365 G/G genotype than did patients without acute GVHD (P=0.017, odds ratio [OR]=5.3; P=0.031, OR=2.4; and P=0.023, OR=2.6, respectively). Multivariate analysis showed that the TT genotype of rs3761549 was an independent risk factor for occurrence of acute GVHD (P=0.032, hazard ratio=5.6). In contrast, the genotype frequencies of rs3761549 T/T, rs5902434 ATT/ATT, and rs2232365 G/G were lower in patients with post-HSCT infection than in patients without infection (P=0.026, P=0.046, and P=0.031, respectively). CONCLUSIONS: rs3761549, rs5902434, and rs2232365 are associated with an increased risk of acute GVHD and decreased risk of post-HSCT infection.


Subject(s)
Humans , Allografts , Autoimmune Diseases , DNA , Genotype , Graft vs Host Disease , Hematopoietic Stem Cell Transplantation , Hematopoietic Stem Cells , Multivariate Analysis , Odds Ratio , Polymorphism, Single Nucleotide , Recurrence , Risk Factors , T-Lymphocytes, Regulatory
20.
Annals of Laboratory Medicine ; : 599-603, 2018.
Article in English | WPRIM | ID: wpr-718321

ABSTRACT

Frequencies of red blood cell (RBC) blood group antigens differ by ethnicity. Since the number of immigrants is increasing in Korea, RBC antigens should be assessed in children/youths with parents of different ethnicities to ensure safe transfusions. We investigated the frequency of RBC antigens, except for ABO and RhD, in 382 children and youths with parents having Korean and non-Korean ethnicities. Subjects were divided into those with ethnically Korean parents (Korean group; N=252) and those with at least one parent of non-Korean ethnicity (non-Korean group; N=130). The 37 RBC antigens were genotyped using the ID CORE XT system (Progenika Biopharma-Grifols, Bizkaia, Spain). The frequencies of the Rh (E, C, e, hr(S), and hr(B)), Duffy (Fy(a)), MNS (Mi(a)), and Cartwright (Yt(b)) antigens differed significantly between the two groups. Eight and 11 subjects in the Korean and non-Korean groups, respectively, exhibited negative expression of high-frequency antigens, whereas 14 subjects in the non-Korean group showed positive expression of low-frequency antigens. The frequency of RBC antigens has altered alongside demographic changes in Korea and might lead to changes in distribution of RBC antibodies that cause acute or delayed hemolytic transfusion reaction.


Subject(s)
Adolescent , Child , Humans , Antibodies , Blood Group Antigens , Emigrants and Immigrants , Erythrocytes , Korea , Molecular Typing , Parents , Transfusion Reaction
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