암 유전체에서의 체세포 Intron Loss: Targeted NGS 기반 분석 파이프라인 개발과 대규모 분석을 통한 발견 = Somatic Intron Loss in the Cancer Genome : Development of a targeted NGS Pipeline and insights form Large-Scale Analysis

다국어 초록 (Multilingual Abstract)

Intron Loss, a well-known event in species evolution, has not previously been described as a somatic alteration in human cancer. This study presents the first systematic characterization of somatic intron loss using targeted next-generation sequencing (NGS) data. A total or 6,784 tumor samples across 30 cancer types were analyzed, encompassing 188 shared genes. The dataset consisted of three independent cohorts. To detect intron loss events, a novel computational pipeline was developed, leveraging split- read signatures as the key indicator of intronic deletions.
Somatic intron loss was identified in 173 samples (2.6%), with nearly one-third of analyzed genes affected. Among them, TOP2A and GNAS together accounted for almost half of all detected events. Most intron loss regions were located the 3’-end of genes or within central protein kinase domains, suggesting potential biological selection. In lung cancer, intron loss was notably enriched in tumors lacking canonical driver mutations, indicating a possible alternative oncogenic biomarker. ‘
The analytical pipeline was validated using two independent cohorts: a colorectal cancer dataset and a circulating tumor DNA (ctDNA) corhot from patients with metastatic non-small cell lung cancer. In the ctDNA dataset, intron loss was detected even in cases previously classified as mutation-negative, highlighting its diagnostic potential as a complementary biomarker.
Collectively, these findings establish somatic intron loss as a new class of structural alteration in human cancer. This work not only expands the current framework of structural variant interpretation but also provides new insight into genomic plasticity of driver-negative tumors, suggesting that intron loss may act as a functional and clinically relevant oncogenic event.

목차 (Table of Contents)

• Abstract i
• Contents ii
• Chapter 1. Study Background 1
• 1.1 Genetic and Molecular Basis of Cancer 1
• 1.1.1 Genetic Alterations 1
• 1.1.2 RNA Splicing and the Role of Introns in Gene Regulation 1
• 1.2 Splicing Dysregulation and the Current Focus of Cancer Genomics 2
• 1.2.1 Splicing Aberrations and Their Functional Consequences 2
• 1.2.2 Limitations of Conventional NGS and the Need for New Approaches 2
• 1.3 Study Aims, Hypothesis, and Scientific Significance 3
• 1.3.1 Aims and Central Questions 3
• 1.3.2 Hypotheses and Scientific Significance 4
• Chapter 2. Intron Loss in Cancer Genomics 5
• 2.1 Introduction 5
• 2.2 Methods 7
• 2.2.1 Patient Cohorts 7
• 2.2.2 Establishment of the Intron Loss Training Set 11
• 2.3.3 Principle of Split-Read Alignment 11
• 2.2.4 Development of the Intron Loss Detection Pipeline 14
• 2.2.5 Experimental Validation of Intron Loss by PCR 17
• 2.2.6 Somatic Mutational Profiling 17
• 2.2.7 Correlation Analysis 18
• 2.3 Results 20
• 2.3.1 Exploring intron loss characteristics in the training set 20
• 2.3.2 Experimental validation of intron loss 20
• 2.3.3 Incidence Rate of intron loss within the AMC cohort 27
• 2.3.4 Mutational profiling and association with intron loss 34
• 2.3.5 Correlation between intron loss and tumorigenesis 34
• 2.3.6 Validation of intron loss identification using an external colorectal dataset 38
• 2.3.7 Identification of intron loss in ctDNA (ctDNA cohort) 38
• 2.4 Discussion 41
• Reference 44
• 국문요약 47