DSpace Community:

Targeted Sequencing of Human Aorta Tissue Reveals Undiagnosed Heritable Thoracic Aortic Disease

Fri, 01 May 2026 00:00:00 GMT

Title: Targeted Sequencing of Human Aorta Tissue Reveals Undiagnosed Heritable Thoracic Aortic Disease Authors: Lee, Ha; Kim, Yoonjung; Kim, Myeong Su; Lee, Kyung-A; Song, Suk-Won Abstract: Objectives To diagnose undiagnosed heritable thoracic aortic disease (HTAD) using targeted next-generation sequencing technology on human aorta tissue obtained from a single-centre biobank.Methods From May 2016 to November 2021, 622 patients undergoing surgical repair for thoracic aortic aneurysm or acute aortic syndrome donated blood or tissue samples to the research biobank. A total of 134 aortic tissue samples were retrieved from patients suspected of HTAD. The inclusion criteria were (1) family history, (2) age <= 45, (3) annuloaortic ectasia, (4) bicuspid aortic valve, (5) patent ductus arteriosus, (6) polycystic kidney disease, or (7) patients previously classified as variant of uncertain significance by germline sequencing (n = 17). Exclusion criteria included patients previously classified as likely pathogenic or pathogenic by germline sequencing. The targeted panel included 96 genes.Results A total of 29 variants were identified including FBN1, MYH11, COL11A1, SMAD3, SMAD6, ACTA2, COL3A1, FLNA, PKD2, THSD4, ACVRL1, and FBN2. A total of 27 patients (20.1%) had variants with 2 patients having digenic variants. Clinical data were combined with genetic data, and finally, 17 patients (12.7%) were additionally diagnosed with HTAD.Conclusions Genomic data analysis of human aortic tissue allowed for additional diagnoses of undiagnosed HTAD, contributing to resolving discrepancies between clinical and genomic data. Considering the surgical treatment of HTAD, human aortic tissue can be a valuable resource for genomic analysis. Thoracic aortic aneurysm (TAA), characterized by progressive dilatation of the thoracic aorta, may culminate in acute aortic syndrome (AAS), including dissection or rupture.

Comparative evaluation of two NGS-based assays for somatic hypermutation analysis of IGHV genes in chronic lymphocytic leukemia

Wed, 01 Apr 2026 00:00:00 GMT

Title: Comparative evaluation of two NGS-based assays for somatic hypermutation analysis of IGHV genes in chronic lymphocytic leukemia Authors: Kang, Yehyun; Lee, Hyeonah; Park, Yu Jin; Lee, Seung-Tae; Choi, Jong Rak; Shin, Saeam Abstract: PurposeSomatic hypermutation (SHM) of the immunoglobulin heavy chain variable (IGHV) region is a key prognostic marker in chronic lymphocytic leukemia (CLL). Traditionally, SHM status has been determined using Sanger sequencing (SS); however, next-generation sequencing (NGS) provides an alternative method for assessing both SHM status and clonal rearrangements. This study aimed to compare the performance of two commercially available NGS assays for evaluating IGH clonality and SHM status in CLL.MethodsIn this retrospective study, 42 samples from patients diagnosed with CLL were analyzed. Genomic DNA extracted from peripheral blood or bone marrow aspirates was analyzed using two commercial NGS assays: the LymphoTrack (R) IGHV Leader (Leader) and IGH FR1 (FR1) assays (Invivoscribe, CA, USA). SS was performed as the reference method for SHM assessment.ResultsThe Leader assay identified clonality in 95.2% of cases, whereas the FR1 assay detected clonality in 88.1%. Conclusive SHM status was determined in 90.5% of samples using the Leader assay and in 76.2% using the FR1 assay; when results from both assays were combined, the rate increased to 92.9%. Among samples with conclusive results by both SS and each NGS assay, the Leader assay demonstrated higher concordance with SS (97.1%, 34/35) than the FR1 assay (86.2%, 25/29). Greater variability in clonal detection was observed with the FR1 assay.ConclusionThese findings indicate that the Leader assay provides a more reliable assessment of SHM status, with higher concordance with SS. Although the FR1 assay may offer additional information regarding clonal patterns, its results should be interpreted cautiously. Given the limited sample size, further studies are warranted to validate these findings. Overall, the Leader assay appears to be more suitable as a primary tool for SHM evaluation, with FR1 results serving a complementary role when interpreted in clinical context.

Application of Long-Read Whole-Genome Sequencing to Clarify Genotypic-Phenotypic Discrepancies in Methicillin-Resistant Staphylococcus aureus

Wed, 01 Apr 2026 00:00:00 GMT

Title: Application of Long-Read Whole-Genome Sequencing to Clarify Genotypic-Phenotypic Discrepancies in Methicillin-Resistant Staphylococcus aureus Authors: Jhang, Jin Ho; Ahn, Kwangjin; Kim, Dokyun; Jeong, Seok Hoon; Kim, Hyun Soo; Kim, Young Ree; Kim, Young Ah; Shin, Kyeong Seob; Shin, Jeong Hwan; Park, Jeong Su; Park, Kyoung Un; Kwon, Yong Jun; Kim, Soo Hyun; Shin, Jong Hee; Ahn, Soon Young; Lee, Sung Young; Bae, Song-mee; Yoo, Jung Sik; Uh, Young Abstract: Background/Objectives: The Korean Global Antimicrobial Resistance Surveillance System monitors bloodstream Staphylococcus aureus infections by combining antimicrobial susceptibility testing (AST) with conventional polymerase chain reaction (PCR). Considering the clinical significance of methicillin-resistant S. aureus (MRSA), we performed an in-depth analysis of isolates showing genotypic-phenotypic discrepancies. Methods: Isolates were collected from designated collection centers in the Republic of Korea between 2017 and 2024. The 30 mu g cefoxitin disk diffusion method was used to define the phenotypes. PCR targeting mecA and the staphylococcal cassette chromosome mec (SCCmec) was used to identify genotypes through gel electrophoresis. Long-read whole-genome sequencing (WGS) was performed using the Revio system (Pacific Biosciences) for isolates exhibiting discrepancies between phenotypes and genotypes. Results: In total, 5808 isolates were screened, and seven cases of genotypic-phenotypic discrepancies were identified, including one infant and six elderly patients with chromosomal SCCmec type IV. Although WGS confirmed intact PCR primer-binding sites, structural alterations were observed: three isolates had normal-length mecA and mecR1, two had partial deletions in mecA, and two featured either mecA or mecR1 split into two proteins. Notably, although the six isolates with intact mecR1 genes matched the nucleotide length of SCCmec type IV, their sequences exhibited high homology with SCCmec type II. Conclusions: Despite the presence of mecA, the non-standard configuration of regulatory genes within the SCCmec elements suppressed actual resistance expression. Because conventional PCR focusing on partial gene segments could overlook such phenotypic traits, the meticulous observation and implementation of WGS are crucial for the accurate characterization of genotypic-phenotypic discrepancies.

Germline Mutations Related to Complete Remission After Neoadjuvant Chemotherapy in Patients With Triple-negative Breast Cancer

Wed, 01 Apr 2026 00:00:00 GMT

Title: Germline Mutations Related to Complete Remission After Neoadjuvant Chemotherapy in Patients With Triple-negative Breast Cancer Authors: Ahn, Jee Hyun; Park, Ji Soo; Won, Dongju; Lee, Seung-Tae; Lee, Suk Jun; Yang, Seung Hye; Kim, Jee Ye; Park, Seho; Kim, Seung Il; Park, Byeong-Woo; Kim, Min Hwan; Kim, Gun Min; Sohn, Joohyuk; Park, Hyung Seok; 박지수 Abstract: Purpose: Triple-negative breast cancer (TNBC) is a frequent phenotype of BRCA-mutant tumors. Tumors with BRCAness may show characteristics of BRCA-mutant tumors and respond to similar treatments. Next-generation sequencing is an efficient and cost-effective method for simultaneously sequencing multiple cancer susceptibility genes, surpassing conventional Sanger testing. Methods: A total of 148 women with TNBC were recruited from December 2015 to November 2018, as part of a sub-analysis based on the PEARLY trial data. Of them, 103 patients received neoadjuvant chemotherapy (NCT). The targeted genes related to hereditary cancers were sequenced using the 65-gene germline next-generation sequencing (gNGS) panel pathogenic and likely pathogenic variants (P&LPs) were determined by Sanger sequencing. We examined the occurrence of pathologic complete remission (ypCR) in patients with P&LPs. Results: The patients' median age was 47 years (range, 27-69 years). Twenty (13.7%) of 148 patients had P&LP in six genes, including BARD1 (n = 2), BRCA1 (n = 9), BRCA2 (n = 5), CHEK2 (n = 1), RAD51C (n = 1), and RAD51D (n = 2). Among the 103 patients with NCT, 43 (41.7%) achieved ypCR (P & LPs; 9 individuals vs. non-variants; 34 individuals). Among the 103 patients with NCT, 14 (9.3%) had P&LPs. Nine of 14 patients with P&LPs, including BARD1 (n = 2), BRCA1 (n = 4), BRCA2 (n = 1), RAD51C (n = 1), and RAD51D (n = 1), achieved ypCR, showing a trend toward statistical significance (p = 0.066). Conclusion: Germline P&LP mutations in TNBC patients can be detected by gNGS. This panel test can identify BRCA and BRCAness mutations that may predict ypCR in TNBC.