Optimization of a Protocol for Isolating Cell-free DNA From Cerebrospinal Fluid

A standardized protocol for the isolation of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) is lacking. Therefore, we established a cfDNA isolation protocol optimized for clinical CSF specimens, integrating acceptable modifications and using artificial CSF generated from remnant CSF spiked with reference cell-free tumor DNA (ctDNA). We compared the isolation yields of in vitro diagnostic (IVD)-certified column-based (CB) and magnetic bead-based (MB) isolation. Furthermore, we modified both methods, including pre- and post-elution steps. To confirm ctDNA integrity and quantify the variant allele frequency after isolation, we performed droplet digital PCR (ddPCR) targeting IDH1 R132C in the reference ctDNA. MB isolation had a higher yield than CB isolation (P<0.0001), and post-isolation vacuum increased the final concentration in both methods, with little effect on cfDNA integrity. Our study provides a protocol to maximize CSF-ctDNA concentrations in IVD testing and future studies.

Coagulation Testing in Real-World Setting: Insights From a Comprehensive Survey

The objective of this survey was to gain a real-world perspective on coagulation testing by evaluating the availability of various coagulation laboratory tests, assessing specific analytic and postanalytic steps in clinical laboratories in Korea.Participants were surveyed using a 65-question questionnaire specifically focused on their coagulation testing practices related to prothrombin time (PT), activated partial thromboplastin time (aPTT), plasma-mixing studies, lupus anticoagulant (LA) tests, platelet function tests, coagulation factor assays, and the composition of hemostasis and thrombosis test panels. The survey was performed between July and September 2022.The survey achieved a 77.9% (81 of 104) response rate. PT or aPTT tests were performed directly at all participating institutions, followed by D-dimer and fibrinogen tests, platelet function test, and plasma-mixing studies in order of frequency. Variations existed in the performance of mixing test and LA assessment. Patterns of coagulating testing differed depending on the size of the hospital. The survey revealed that most laboratories conducted coagulation tests following the international guidelines such as Clinical Laboratory Standards Institute guidelines and the Korean Laboratory Certification system. However, some coagulation tests, including mixing test and LA tests, are yet to be standardized in Korea.Continuous education on coagulation test methods and internal and external quality control are required to encourage laboratories to enhance the performance of coagulation testing.

Identification of a novel HLA-B allele, HLA-B*54:47, in a Korean individual

B*54:47 allele differs from B*54:01:01:01 in codon 74 in exon 2.

The new HLA-DQA1*03:50Q allele discovered by next-generation sequencing in a Korean family

DQA1*03:50Q differs from DQA1*03:02:01:01 by a three-nucleotide insertion at gDNA position 3968 in exon 2.

Sample size calculation in clinical trial using R

Since the era of evidence-based medicine, it has become a matter of course to use statistics to create objective evidence in clinical research. As an extension of this, it has become essential in clinical research to calculate the correct sample size to demonstrate a clinically significant difference before starting the study. Also, because sample size calculation methods vary from study design to study design, there is no formula for sample size calculation that applies to all designs. It is very important for us to understand this. In this review, each sample size calculation method suitable for various study designs was introduced using the R program (R Foundation for Statistical Computing). In order for clinical researchers to directly utilize it according to future research, we presented practice codes, output results, and interpretation of results for each situation.

Immunogenicity of Third-dose BNT162b2 mRNA Vaccine Following Two Doses of ChAdOx1 in Health Care Workers: A Prospective Longitudinal Study

Following the original severe acute respiratory syndrome coronavirus 2 strain (Wuhan-Hu-1) in December 2019, the Delta variant in May 2021 and the Omicron variant in December 2021 were classified as variants of concern. The pandemic has been ongoing for more than two years, and the three-dose vaccination rate has reached approximately 50% in Korea. We analyzed anti-S antibodies (Abs) and neutralizing Abs (NAbs) in 32 healthcare workers at a university hospital, focusing on the first to third doses of ChAdOx1-ChAdOx1-BNT162b2, which is the most common vaccination regimen in Korea. Antibodies were analyzed at eight time points according to the vaccine regimen. The first to third doses of ChAdOx1-ChAdOx1-BNT162b2 produced high Ab concentrations; NAb concentrations after the third dose were predicted to remain high for a longer period than those after the first and second doses. The effectiveness of a second dose of ChAdOx1 in the real world was demonstrated by analyzing samples collected during an outbreak that occurred in the study period, 4-5 months after the second dose. The relative risk ratio was 88.0%, and the efficacy of the second ChAdOx1 dose was 12.0% (P<0.05). Therefore, maintaining appropriate Ab concentrations through regular vaccination will help protect against coronavirus disease-19.

A novel bi-alleleic DDX41 mutations in B-cell lymphoblastic leukemia: case report

Background

The germline mutations of DDX41, also known as DEAD box RNA helicase 41, have been found in about 1.5% of myeloid neoplasms (MNs). Development of MDS/AML is relatively common in germline DDX41 mutations. However, a variety of hematological malignancies (HMs) have been reported.

Case presentation

We report a novel case of bi-alleleic DDX41 mutations in B-cell lymphoblastic leukemia (B-ALL), with unusual location of DDX41 mutations. The gene expression profile (GEP) of Ph + B-ALL with bi-alleleic DDX41 mutations showed heterogeneously transitional GEP and altered gene expression levels of genes involved in the process essential for red blood cells and myeloid cell differentiation were noted.

Conclusions

We report that DDX41 mutations are unusual but can be an underlying event in Ph + B-ALL and screening DDX41 mutations can be also informative for patients awaiting for haploidentical stem cell transplantation and choosing the therapy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01191-2.

Diagnostic challenges of indolent peripheral T cell lymphoma: A case report and literature review

INTRODUCTION

Peripheral T cell lymphoma, not otherwise specified (PTCL-NOS) is a heterogeneous group of mature T cell lymphomas which do not correspond to any specific subtype of mature T-cell lymphoma in current classifications. Some researchers have suggested that PTCL with low Ki-67 labeling index should be classified as indolent PTCL PATIENT CONCERNS:: A 58-year old man diagnosed with alcoholic fatty liver 3 months prior complained of tenesmus and abdominal distension. Colonoscopy of the small and large intestines revealed multiple polyps, which were histologically diagnosed as lymphoid hyperplasia. One month later, he re-visited with a weight loss of 3 to 4 kg over 2 months. Radiologic examination revealed numerous small, homogenous, hypovascular lymph node enlargement in the para-aortic, mesenteric, and both inguinal areas, suggesting malignant lymphoma.

DIAGNOSIS

Laparoscopic biopsy of an omental lymph node was performed, which was histologically confirmed as PTCL-NOS.

INTERVENTIONS

The patient was administered 3 cycles of cyclophosphamide, doxorubicin, vincristine, and prednisone, but his general condition did not improve. Therefore, treatment was changed to ifosfamide, carboplatin, and etoposide -dexamethasone (4 cycles) followed by allogeneic stem cell transplantation.

OUTCOME

Even after allogeneic stem cell transplantation, fluorodeoxyglucose uptake in his abdominal lymph nodes and small bowel in positron emission tomography- computed tomography persisted at a Deauville score of 4. The patient has been followed-up for 2 years without progression.

CONCLUSION

These indolent PTCLs histologically show diffuse infiltrated small lymphoid cells with low KI-67 labeling index and have a relatively good prognosis, although the epidemiology and pathogenesis are not fully elucidated. We report a case of indolent PTCL with cytogenetic abnormalities and poor response to chemotherapy, along with a brief review of the literature.

Monomicrobial gram-negative necrotizing fasciitis: An uncommon but fatal syndrome

This study aimed to characterize patients with monomicrobial gram-negative necrotizing fasciitis in three university hospitals in Korea. In this study, of the 115 patients with community-acquired necrotizing fasciitis, 67 (58%) had monomicrobial infections: 31 (27%) in the gram-negative group and 36 (31%) in the gram-positive group. The majority of patients in the gram-negative group were infected with Escherichia coli followed by Klebsiella pneumoniae and Vibrio vulnificus. More patients in the gram-negative group showed liver cirrhosis than those in the gram-positive group (39% vs. 14%, P = 0.02). In a multivariable logistic regression analysis, liver cirrhosis (adjusted odds ratio [aOR], 13.7; 95% confidence interval [CI], 2.9-67.0), treatment with antibiotics without surgery (aOR, 10.2; 95% CI, 2.1-48.3), and lower level of albumin (aOR 4.9; 95% CI, 1.6-14.9) were associated with 30-day mortality. Our findings suggest that gram-negative necrotizing fasciitis is more often associated with liver cirrhosis and has poorer outcomes than gram-positive necrotizing fasciitis.

2371. Monomicrobial Gram-Negative Necrotizing Fasciitis: An Uncommon but Fatal Syndrome

Background

Necrotizing fasciitis is a rapid progressive and potentially life-threatening infection. Although the relative emergence of non-synergistic single Gram-negative organisms as pathogen could be a therapeutic issue for clinicians, limited studies so far described the characteristics due to the low incidence.

Methods

We retrospectively reviewed clinical data of necrotizing fasciitis patients who were clinically diagnosed between May 2001 and December 2015 in university hospitals of three different cities of the Republic of Korea. We compared clinical characteristics and outcomes of patients with monomicrobial Gram-negative with those of the Gram-positive counterpart.

Results

A total of 115 patients with community acquired necrotizing fasciitis were identified. Among them, monomicrobial infections were 67 (58%) cases: 31 (27%) in the Gram-negative group and 36 (31%) in the Gram-positive group. The majority of Gram-negative group was E. coli followed by K. pneumonia and V. vulnificus. There were more cases of the Gram-negative group showing liver cirrhosis (39% vs. 14%, P = 0.02) and bacteremia (52% vs. 16%, P = 0.02). A total of 23 (10%) patients died within 30 days, including 15 (19%) in the Gram-negative group and 8 (10%) in the Gram-positive group (P = 0.02). In multivariable logistic regression, liver cirrhosis (adjusted odds ratio [aOR], 13.7; 95% confidence interval [CI], 2.9–67.0), treatment with antibiotics without surgery (aOR, 10.2; 95% CI, 2.1–48.3), and lower level of albumin (aOR 4.9; 95% CI, 1.6–14.9) were significantly associated with 30-day mortality.

Conclusion

Our findings suggest that necrotizing fasciitis caused by Gram-negative pathogen more often associated with liver cirrhosis and has poorer outcomes than the Gram-positive counterpart.

Disclosures

All authors: No reported disclosures.

Evaluation of the Triage TOX Drug Screen Assay for Detection of 11 Drugs of Abuse and Therapeutic Drugs

The demand for rapid and broad clinical toxicology screens is on the rise. Recently, a new rapid toxicology screening test, the Triage TOX Drug Screen (Alere Inc., USA), which can simultaneously detect 11 drugs of abuse and therapeutic drugs with an instrument-read cartridge, was developed. In the present study, we evaluated the efficacy of this new on-site immunoassay using 105 urine specimens; the results were compared with those obtained by using ultra-performance liquid chromatography with tandem mass spectrometry (UPLC-TMS). Precision was evaluated according to the CLSI EP12-A2 for analyte concentrations near the cutoff, including C₅₀ and±30% of C₅₀, for each drug using standard materials. The C₅₀ specimens yielded 35–65% positive results and the ±30% concentration range of all evaluated drugs encompassed the C₅–C₉₅ interval. The overall percent agreement of the Triage TOX Drug Screen was 92.4–100% compared with UPLC-TMS; however, the Triage TOX Drug Screen results showed some discordant cases including acetaminophen, amphetamine, benzodiazepine, opiates, and tricyclic antidepressants. The overall performance of the Triage TOX Drug Screen assay was comparable to that of UPLC-TMS for screening of drug intoxication in hospitals. This assay could constitute a useful screening method for drugs of abuse and therapeutic drugs in urine.

Usefulness of AFP, AFP-L3, and PIVKA-II, and their combinations in diagnosing hepatocellular carcinoma

Alpha-fetoprotein (AFP), Lens culinaris-agglutinin-reactive fraction of AFP (AFP-L3), and protein induced by vitamin K absence or antagonist-II (PIVKA-II) are widely used as tumor markers for the diagnosis of hepatocellular carcinoma (HCC). This study compared the diagnostic values of AFP, AFP-L3, and PIVKA-II individually and in combination to find the best biomarker or biomarker panel.Seventy-nine patients with newly diagnosed HCC and 77 non-HCC control patients with liver cirrhosis were enrolled. AFP, AFP-L3, and PIVKA-II were measured in the same serum samples using microchip capillary electrophoresis and a liquid-phase binding assay on an automatic analyzer. Receiver-operating characteristic curve analyses were also applied to all combinations of the markers.When the 3 biomarkers were analyzed individually, AFP showed the largest area under the receiver-operating characteristic curve (AUC) (0.751). For combinations of the biomarkers, the AUC was highest (0.765) for "PIVKA-II > 40 mAU/mL and AFP > 10 ng/mL." The combination of "PIVKA-II > 40 mAU/mL and AFP > 10 ng/mL and AFP-L3 > 10%" had worse sensitivity and lower AUC (P = 0.001). The highest AUC of a single biomarker was highest for AFP and of a combination was "PIVKA-II > 40 mAU/mL and AFP > 10 ng/mL," with this also being the case when the cut-off value of AFP and AFP-L3 was changed.Alpha-fetoprotein showed the best diagnostic performance as a single biomarker for HCC. The diagnostic value of AFP was improved by combining it with PIVKA-II, but adding AFP-L3 did not contribute to the ability to distinguish between HCC and non-HCC liver cirrhosis. These findings were not altered when the cut-off value of AFP and AFP-L3 was changed.

Efficiency of an automated reception and turnaround time management system for the phlebotomy room

BACKGROUND

Recent advances in laboratory information systems have largely been focused on automation. However, the phlebotomy services have not been completely automated. To address this issue, we introduced an automated reception and turnaround time (TAT) management system, for the first time in Korea, whereby the patient's information is transmitted directly to the actual phlebotomy site and the TAT for each phlebotomy step can be monitored at a glance.

METHODS

The GNT5 system (Energium Co., Ltd., Korea) was installed in June 2013. The automated reception and TAT management system has been in operation since February 2014. Integration of the automated reception machine with the GNT5 allowed for direct transmission of laboratory order information to the GNT5 without involving any manual reception step. We used the mean TAT from reception to actual phlebotomy as the parameter for evaluating the efficiency of our system.

RESULTS

Mean TAT decreased from 5:45 min to 2:42 min after operationalization of the system. The mean number of patients in queue decreased from 2.9 to 1.0. Further, the number of cases taking more than five minutes from reception to phlebotomy, defined as the defect rate, decreased from 20.1% to 9.7%.

CONCLUSIONS

The use of automated reception and TAT management system was associated with a decrease of overall TAT and an improved workflow at the phlebotomy room.

A novel BTK gene mutation, c.82delC (p.Arg28 Alafs*5), in a Korean family with X-linked agammaglobulinemia

X-linked agammaglobulinemia (XLA) is a hereditary humoral immunodeficiency that results from Bruton’s tyrosine kinase (BTK) gene mutations. These mutations cause defects in B-cell development, resulting in the virtual absence of these lymphocytes from the peripheral circulation. Consequently, this absence leads to a profound deficiency of lg all isotypes, and an increased susceptibility to encapsulated bacterial infections. A 15-month-old Korean boy presented with recurrent sinusitis and otitis media after 6 months of age, and had a family history of 2 maternal uncles with XLA. Laboratory tests revealed a profound deficiency of Ig isotypes, and a decreased count of CD19⁺ B cells in the peripheral circulation. Based on his family history and our laboratory test results, he was diagnosed with XLA. We performed BTK gene analysis of peripheral blood samples obtained from family members to confirm the diagnosis. Mutational analysis revealed a novel hemizygous frameshift mutation (c.82delC, p.Arg28Alafs^*5), in the BTK gene. His mother and maternal grandmother were heterozygous carriers of this mutation and his two maternal uncles were hemizygous at the same position. After XLA diagnosis, intravenous immunoglobulin (400 mg/kg, monthly) treatment was initiated; recurrent sinusitis and otitis media were subsequently brought under control. To our knowledge, this is the first reported case of a Korean pedigree with a novel mutation in the BTK gene.

Comparison of total and IgG ABO antibody titers in healthy individuals by using tube and column agglutination techniques

Background

Most immune reactions related to transfusion and transplantation are caused by IgM ABO antibodies. However, IgG also plays an important role in these reactions. Therefore, a method to measure antibodies, including IgG, is necessary. We investigated ABO antibody titers of healthy individuals using a column agglutination technique (CAT) with or without dithiothreitol (DTT) and compared them with titers obtained using a conventional tube method.

Methods

Among healthy adults who underwent a medical examination, 180 individuals (60 with blood group A, 60 with group B, and 60 with group O) were selected. Antibody titrations were performed using the immediate spin (IS) tube, anti-human globulin (AHG) tube, and CAT with or without DTT methods.

Results

Higher median values of anti-B and anti-A titers in groups A and B individuals, respectively, were obtained using the IS method than using the AHG method. Higher values for group O individuals were obtained using the AHG method. Higher median titers of anti-B and anti-A in group O individuals were obtained using CAT without DTT than using the AHG method. Median titers of anti-B and anti-A in all blood groups were higher in CAT without DTT than in CAT with DTT, especially for group O individuals.

Conclusions

We recommend CAT with and without DTT for titration of anti-A and anti-B, especially in group O individuals, to provide more sensitive results that include IgG data. Adjustment of insurance coverage of fees associated with antibody titration might be necessary, considering the actual cost of reagents and personnel.

Two novel FAH gene mutations in a patient with hereditary tyrosinemia type I

BACKGROUND

Hereditary tyrosinemia type I (HT I) is a severe inborn metabolic disorder affecting the tyrosine degradation pathway. Most untreated patients die within the first two years of life. HT I results from fumarylacetoacetate hydrolase (FAH) deficiency caused by mutations in the FAH gene. The diagnosis of HT I is confirmed by measuring FAH enzyme activity in cultured fibroblasts or liver tissue and/or detecting disease-causing mutations in the FAH gene.

METHODS

A female neonate was referred to our hospital for further evaluation of an abnormal newborn screening test that showed elevated tyrosine levels. We analyzed amino acids and organic acids in the patient's blood and urine. To identify the genetic abnormality, all the coding exons and flanking introns of the FAH gene were analyzed via PCR.

RESULTS

A repeat newborn screening test and plasma amino acid analysis revealed increased tyrosine levels in the patient. Urine organic acid analysis showed increased urinary excretion of 4-hydroxyphenyllactate, 4-hydroxyphenylpyruvate, and succinylacetone. Sequence analysis of the FAH gene identified two novel variations (c.536A>G (p.Gln179Arg) and c.913+5G>A) that had not been previously reported and that were not found in 170 healthy controls.

CONCLUSIONS

HT I was confirmed in this patient by molecular genetic analysis of the FAH gene, with highly suggestive biochemical findings. The novel sequence variations detected in the present study should be considered disease-causing mutations by in silico analysis. In the Korean population, this is the first described case of HT I caused by a point mutation in the FAH gene.

[A case of central nervous system myelomatosis with complex chromosome aberrations]

Involvement of the central nervous system is very uncommon in multiple myeloma, observed in approximately 1% of the multiple myeloma patients. We report a case of central nervous system myelomatosis with complex chromosome aberrations in a 62-yr-old female patient, who had previously been diagnosed as multiple myeloma. Fluorescent in situ hybridization revealed 13q deletion, p53 gene deletion and IGH/FGFR3 rearrangement and chromosomal study showed complex chromosome aberrations. After four cycles of chemotherapy, the patient was admitted to the hematology department with severe headache. Plasma cells were found in the cerebrospinal fluid (CSF), and CSF immunoelectrophoresis revealed abnormal precipitin arcs against anti-IgG and anti-lambda antisera. She was given systemic chemotherapy and eight courses of intrathecal chemotherapy, which cleared plasma cells in the CSF. Two months later, she was given autologous stem cell transplantation. Three months after stem cell transplantation, central nervous system myelomatosis progressed to plasma cell leukemia and two months later, the patient expired.