Clinical Validity of Next-Generation Sequencing Multi-Gene Panel Testing for Detecting Pathogenic Variants in Patients With Hereditary Breast-Ovarian Cancer Syndrome

BACKGROUND: Hereditary breast and ovarian cancer syndrome (HBOC) is caused by pathogenic variants in BRCA and other cancer-related genes. We analyzed variants in BRCA gene and other cancer-related genes in HBOC patients to evaluate the clinical validity of next-generation sequencing (NGS) multi-gene panel testing. METHODS: The BRCA1/2 NGS testing was conducted for 262 HBOC patients. Multiplex ligation-dependent probe amplification and direct Sanger sequencing were performed for confirmation. Multi-gene panel testing was conducted for 120 patients who did not possess BRCA1/2 pathogenic variants but met the National Comprehensive Cancer Network criteria. RESULTS: Pathogenic variants in BRCA1/2 were detected in 30 HBOC patients (11.5%). Additionally, four out of the 120 patients possessed pathogenic variants by multi-gene panel testing (3.3%): MSH2 (c.256G>T, p.Glu86*), PMS2 (c.1687C>T, p.Arg563*), CHEK2 (c.546C>A, p.Tyr182*), and PALB2 (c.3351-1G>C). All the four patients had a family history of cancer. CONCLUSIONS: Multi-gene panel testing could be a significant screening tool for HBOC patients, especially for those with a family history of cancer.

Five Korean Cases of Respiratory Tract Infection by Filamentous Basidiomycetes

No abstract available.

Usefulness of Reference Change Values for Delta Check Limits in Clinical Laboratory Testing

Background@#In this study, the usefulness of within-subject biological coefficient of variation (CVI) and reference change values (RCVs) for delta check limits were investigated by comparing the population distributionbased delta check limits. @*Methods@#For six tests, including aspartate aminotransferase, alanine aminotransferase, γ-glutamyl transferase, glucose, creatinine, and hemoglobin, the RCV95%, RCV99%, and RCV99.9% delta limits were obtained. The nonparametric 95% and 99% delta limits were obtained from the population distribution of the delta percentage difference of the health examination group (January 2014 to December 2018) and the outpatient and inpatient groups (January to December 2018). Delta check alerts (%) in total and all three subgroups were examined according to the five different delta check limits. Additionally, we analyzed the correlation of the median CVIF estimates with population-delta check limits for the six tests. @*Results@#The delta percentage difference of the six tests showed a nonnormal distribution, and median value significantly differed among the health examination, outpatient, and inpatient groups (all, P <0.001). The overall delta check alerts of six tests decreased in the order of RCV95%, RCV99%, and RCV99.9%, population distribution -95%, and -99% delta limits; the proportion of the health examination group gradually decreased and that of inpatients increased. A good correlation was observed between median CVI (range, 2.7% to 10.1%) and population distribution delta limits (r =0.96 to 0.99). @*Conclusions@#The RCV delta check limits should be applied differently depending on the health and disease group. CVI can be useful for estimating the delta check limits of the population.

Performance Evaluations of the Abbott Alinity m Assay in Comparison with the Abbott m2000Assay for Hepatitis B and Hepatitis C Viruses

Methods@#The precision, linearity, limit of detection (LOD), correlation with the Abbott m2000 assay, and interference were evaluated. @*Results@#The within-laboratory standard deviation ranged from 0.106 to 0.137 log IU/mL for HBV and from 0.073 to 0.097 log IU/mL for HCV, which was lower than the manufacturer’s specification of 0.25 log IU/mL, indicating good precision. Linearity was observed from 1.14 to 8.14 log IU/mL for the HBV assay and from 1.09 to 7.09 log IU/mL for the HCV assay. The LODs of HBV and HCV were 10 and 6.39 IU/mL, respectively, which were equivalent to or better than those claimed by the manufacturer. For comparative evaluation between Alinity m and m2000 assays, 142 HBV and 70 HCV samples were tested. The correlation test revealed a strong correlation for both markers, and the Passing–Bablok regression analysis did not reveal any significant deviation. @*Conclusions@#The Alinity m assay demonstrated excellent performance for HBV and HCV quantifications with reduced hands-on time and a randomaccess format.

KRAS, NRAS, and BRAF mutations in plasma cell myeloma at a single Korean institute

Background@#Plasma cell myeloma (PCM) is a genetically heterogeneous disease. The genetic spectrum of PCM has been expanded to mutations such as KRAS, NRAS, and BRAF genes in the RAS-RAF-MAPK pathway. In this study, we have evaluated the frequency of these mutations and their significance, including baseline characteristics and clinical outcomes. @*Methods@#We explored 50 patients who were newly diagnosed with PCM between 2009 and 2012 at a single Korean institute. Clinical and laboratory parameters were gathered through careful review of medical records. Mutation analysis was carried out using DNA from the bone marrow at the time of diagnosis. Pyrosequencing was performed to detect KRAS G12V,KRASG13D, and NRAS G61R. BRAF V600E was analyzed by allele-specific real-time PCR. Comparison of clinical and laboratory parameters was carried out according to those mutations. @*Results@#We identified 14 patients (28%) with activating mutations in the RAS-RAF-MAPK pathway (RAS/RAF mutations):KRAS (N=3), KRAS (N=4),BRAF (N=7), and both KRAS and BRAF (N=1). RAS/RAF mutations were more frequently observed in patients with complex karyotypes and showed poorer progression free survival (PFS). Specifically, the BRAF V600E mutation had a significantly negative impact on median PFS. @*Conclusion@#We first showed the frequency of RAS/RAF mutations in Korean patients with PCM.Screening of these mutations could be considered as a routine clinical test at the time of diagnosis and follow-up due to their influence on clinical outcome, as well as its potential as a therapeutic target.

Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea

BACKGROUND: To validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA). METHODS: We performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results. RESULTS: A total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively. CONCLUSIONS: Clinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.

Reclassification of Acute Myeloid Leukemia According to the 2016 WHO Classification

We reviewed our leukemia database to reclassify 610 patients previously diagnosed as having acute myeloid leukemia (AML) according to the updated 2016 WHO classification. Nine patients were categorized as having myelodysplastic syndrome and myeloid neoplasms with germline predisposition. AML with recurrent genetic abnormalities accounted for 57.4% (345/601) of the patients under the 2016 WHO classification. AML with mutated NPM1 was the most common form (16.5%), with the majority associated with monocytic differentiation (63.6%). AML with double CEBPA mutations accounted for 8.3% of these cases, and the majority were previously diagnosed as AML with/without maturation (78.0%). These newly classified mutations were mutually exclusive without overlapping with other forms of AML with recurrent genetic abnormalities. AML with mutated NPM1 and AML with myelodysplasia-related changes comprised the oldest patients, whereas AML with RUNX1-RUNX1T1 included the youngest patients. The leukocyte count was highest in AML with mutated NPM1, and the percentage of peripheral blood blasts was the highest in AML with double CEBPA mutations. Our results indicate that implementation of the 2016 WHO classification of AML would not pose major difficulties in clinical practice. Hematopathologists should review and prepare genetic tests for the new classification, according to their clinical laboratory conditions.

PCM1-JAK2 Fusion in a Patient With Acute Myeloid Leukemia

No abstract available.

A Case of Pseudohypoparathyroidism Type Ib Caused by Aberrant Methylation in the GNAS Complex Locus

Pseudohypoparathyroidism (PHP) is a rare disorder caused by genetic and epigenetic aberrations in the GNAS complex locus resulting in impaired expression of stimulatory G protein (Gsα). PHP type Ib (PHP-Ib) is characterized by hypocalcemia and hyperphosphatemia due to renal resistance to the parathyroid hormone, and is distinguished from PHP-Ia by the absence of osteodystrophic features. An 11-yr-old boy presented with poor oral intake and cramping lower limb pain after physical activity. Laboratory studies revealed hypocalcemia, hyperphosphatemia, and increased parathyroid hormone levels. The GNAS complex locus was evaluated using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay. Gain of methylation in the NESP55 domain and loss of methylation in the antisense (AS) transcript, XL, and A/B domains in the maternal allele were observed. Consequently, we present a case of PHP-Ib diagnosed using MS-MLPA.

Characteristics of hematologic malignancies with coexisting t(9;22) and inv(16) chromosomal abnormalities

BACKGROUND: The coexistence of t(9;22)(q34;q11.2) and inv(16)(p13q22) chromosomal abnormalities is extremely uncommon, and only a small number of such cases have been reported. Here, we characterized 7 cases of hematologic malignancy exhibiting t(9;22) and inv(16) coexistence. METHODS: We reviewed the cytogenetic data for hematologic malignancies treated at the Catholic Blood and Marrow Transplantation Center between January 2004 and June 2013. We identified 7 cases exhibiting t(9;22) and inv(16) coexistence. In addition, we analyzed mutations in the IKZF1, NPM1, FLT3, N-RAS, K-RAS, c-KIT, and TP53 genes. RESULTS: Four cases of chronic myelogenous leukemia (CML; 1 chronic phase, 2 accelerated phase, and 1 blast phase) and 3 cases of acute myeloid leukemia (AML; 1 de novo and 2 therapy-related) were identified. The percentages of circulating blasts and bone marrow eosinophils were higher in AML cases than in CML cases (53% vs. 5% and 30% vs. 5.5%, respectively). The proportions of each chromosomal abnormality were used along with follow-up karyotyping results to identify secondary changes. In BCR/ABL, a p210 fusion transcript was associated with CML, whereas a p190 fusion transcript was associated with AML. One patient with AML harbored 2 mutations: c-KIT D816V and TP53 E11Q. All patients except 1 with CML blast phase sustained clinical remission after treatment, which included an imatinib mesylate regimen. CONCLUSION: This study shows that observations of bone marrow morphology, initial and follow-up cytogenetic studies, and karyotyping of BCR/ABL1 and CBFB/MYH11 provide valuable information for characterizing hematologic malignancies exhibiting t(9;22) and inv(16) coexistence.

Spectrin Tunis (Sp alpha I/78) in a Korean Family with Hereditary Elliptocytosis

No abstract available.