Abstract Background Although meningioma is the most common primary brain tumor, treatments rely on surgery and radiotherapy, recurrent meningiomas have no standard therapeutic options due to a lack of clinically relevant research models. Current cell lines or organoids cannot reflect biological features patient tumors since they undergo transformation along culture consist only tumor cells without microenvironment. We aim establish patient-derived (MNOs) preserving diverse types...

Vulvar squamous cell carcinoma (SCC) consists of two different etiologic categories: human papilloma virus (HPV)-associated (HPV (+)) and HPV-non-associated (−)). There have been no genome-wide studies on the genetic alterations vulvar SCCs or differences between HPV (+) (−) SCCs. In this study, we performed whole-exome sequencing copy number profiling 6 9 found known mutations (TP53, CDKN2A HRAS) (CNAs) (7p 8q gains 2q loss) in (+), novel PIK3CA, BRCA2 FBXW7 that had not reported exhibited...

// Sung Hak Lee 1, * , Seung Hyun Jung 4, 6, Tae-Min Kim 2 Je-Keun Rhee Hyeon-Chun Park 3, 4 Min 5, 6 Soo 7 Chang Hyeok An 8 Sug Hyung Yeun-Jun Chung 5 1 Departments of Hospital Pathology, The Catholic University Korea, Seoul, Korea Medical Informatics, 3 Microbiology, Integrated Research Center for Genome Polymorphism, Cancer Evolution Center, Department Internal Medicine, General Surgery These two authors contributed equally to this work Correspondence to: Chung, email:...

Abstract Little is known about genomic alterations of gestational choriocarcinoma (GC), unique cancer that originates in pregnant tissues, and the progression mechanisms from nonmalignant complete hydatidiform mole (CHM) to GC. Whole-exome sequencing (20 GCs) and/or single-nucleotide polymorphism microarray (29 were performed. We analyzed copy-neutral loss-of-heterozygosity (CN-LOH) 29 GCs exhibited androgenetic CN-LOHs monospermic, 8 dispermic) no CN-LOH (one with NLRP7 mutation). Most...

// Shinn Young Kim 1, 4, 5, 6 , Seung-Hyun Jung 2 Min Sung 2, 3 Mi-Ryung Han 4 Hyeon-Chun Park Eun Sun 7 Hak Lee Sug Hyung and Yeun-Jun Chung 5 1 Department of Precision Medicine Research Center, College Medicine, The Catholic University Korea, Seoul, South Korea Cancer Evolution Pathology, Integrated Center for Genome Polymorphism, Microbiology, Surgery, Hospital Correspondence to: Chung, email: yejun@catholic.ac.kr Lee, suhulee@catholic.ac.kr Keywords: hepatoblastoma, uniparental disomy,...

Purpose: Gastric adenoma (GA) is a premalignant lesion that precedes intestinal-type gastric carcinoma (GC). However, genetic progression mechanisms from GA to GC have not been clarified.Experimental Design: We performed whole-exome sequencing-based mutational analyses for 15 synchronous pairs of attached GAs and GCs.Results: There was no significant difference in the number driver mutations or copy-number alterations between GCs. Well-known TP53, APC, RNF43, RPL22 were recurrently detected...

To develop a genotype-based ankylosing spondylitis (AS) risk prediction model that is more sensitive and specific than HLA-B27 typing.To the AS genetic scoring (AS-GRS) model, 648 individuals (285 cases 363 controls) were examined for 5 copy number variants (CNV), 7 single-nucleotide polymorphisms (SNP), an marker by TaqMan assays. The AS-GRS was developed using logistic regression validated with larger independent set (576 680 controls).Through regression, we built consisting of components:...

Despite growing evidence of the relevance alternative splicing (AS) to cancer development and progression, biological implications AS for tumor behaviors, including papillary thyroid (PTC), remain elusive. With aim further understanding molecular histological subtypes PTC, we in this study explored whether events might act as new determinants. For purpose, profiles were analyzed RNA-sequencing data from The Cancer Genome Atlas (TCGA) a Korean patient dataset. A total 23 distinct...

Germ cell tumors (GCTs) originate during the histogenesis of primordial germ cells to mature gametes. Previous studies identified five histogenic mechanisms in ovarian teratomas (type I: failure meiosis I; type II: II; III: duplication genome a gamete; IV: no meiosis; and V: fusion two different ova), but those other GCTs remain elusive. In this study, we analyzed 84 various pathologic types identify using single-nucleotide polymorphism array by analyzing copy-neutral loss heterozygosity...

<title>Abstract</title> Background Housekeeping genes (HKGs), essential for cellular differentiation, are traditionally thought to be uniformly expressed. However, recent analyses revealed variable expression of most across tissues, challenging this view. Identifying HKGs based on stable necessitates precise, repeated experiments. The limited number transcription factors during differentiation implies that stabilise phenotypes through compensatory gene regulation. Methods We investigated the...

<title>Abstract</title> Housekeeping genes (HKGs), essential for cellular differentiation, are traditionally thought to be uniformly expressed. However, recent analyses show variable expression across tissues, challenging this view. Identifying HKGs based on stable necessitates precise, repeated experiments. The limited number of transcription factors during differentiation suggests stabilise phenotypes via compensatory gene regulation. We examined retroelements, comprising approximately 40%...

Highly pathogenic avian influenza (HPAI) viruses have caused severe respiratory disease and death in poultry human beings. Although most of the (AIVs) are low pathogenicity cause mild infections birds, some subtypes including hemagglutinin H5 H7 subtype HPAI. Therefore, sensitive accurate subtyping AIV is important to prepare prevent for spread Next-generation sequencing (NGS) can analyze full-length sequence information entire genome at once, so this technology becoming a more common...

&lt;p&gt;Supplementary Fig. S1. Histology of synchronous GAs and GCs. Microscopic features STC GA01-15 GC01-15 are shown. Black boxes indicate GA or GC lesion. Supplementary S2. Immunohistochemical staining MLH1 in STC15. S3. Mutation rate genomes. S4. Genomic similarities MSS GC. S5. MSI S6. Multi-region targeted deep sequencing collision tumors (STC04 STC07). S7. High-level amplifications homozygous deletions. S8. Chromothripsis STC. S9. Copy-neutral LOH on chromosome 8 S10. ClonEvol...

&lt;p&gt;Supplementary Table S1. The description of whole-exome sequencing data Supplementary S2. Somatic point mutations and indels identified across 15 synchronous gastric adenoma carcinom genomes S3. Copy number alterations S4. targeted panel S5. Recurrent regions copy alterations&lt;/p&gt;

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Gastric adenoma (GA) is a premalignant lesion that precedes intestinal-type gastric carcinoma (GC). However, genetic progression mechanisms from GA to GC have not been clarified.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We performed whole-exome sequencing–based mutational analyses for 15 synchronous pairs of attached GAs and GCs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; There was no significant difference in the...

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Gastric adenoma (GA) is a premalignant lesion that precedes intestinal-type gastric carcinoma (GC). However, genetic progression mechanisms from GA to GC have not been clarified.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We performed whole-exome sequencing–based mutational analyses for 15 synchronous pairs of attached GAs and GCs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; There was no significant difference in the...

&lt;p&gt;Supplementary Fig. S1. Histology of synchronous GAs and GCs. Microscopic features STC GA01-15 GC01-15 are shown. Black boxes indicate GA or GC lesion. Supplementary S2. Immunohistochemical staining MLH1 in STC15. S3. Mutation rate genomes. S4. Genomic similarities MSS GC. S5. MSI S6. Multi-region targeted deep sequencing collision tumors (STC04 STC07). S7. High-level amplifications homozygous deletions. S8. Chromothripsis STC. S9. Copy-neutral LOH on chromosome 8 S10. ClonEvol...

&lt;p&gt;Supplementary Table S1. The description of whole-exome sequencing data Supplementary S2. Somatic point mutations and indels identified across 15 synchronous gastric adenoma carcinom genomes S3. Copy number alterations S4. targeted panel S5. Recurrent regions copy alterations&lt;/p&gt;

Abstract Background: Recent advancements in next-generation sequencing (NGS) technologies allow the simultaneous identification of targeted copy number alterations (CNAs) as well somatic mutations using same panel-based NGS data. We investigated whether CNAs detected by data provided additional clinical implications, over mutations, myelodysplastic syndrome (MDS). Methods: Targeted deep 28 well-known MDS-related genes was performed for 266 patients with MDS. Results: Overall, 215 (80.8%)...