Recent Update in Pathologic Diagnosis for Pancreatic Cystic Neoplasm / 대한췌담도학회지

Pancreas cystic neoplasm is a relatively common disease. However, its' pathologic diagnosis is not easy. The most frequent problem is low cellularity when compared to another organ cytology or biopsy material. Considering the procedure and anatomic difficulty, it is not uncommon to observe a low cellular smear or scanty volume of cells in the biopsy specimen. In this case, the molecular pathology test, including next-generation sequencing, may be helpful. If pathologist can identify some mutation in cells or cystic fluid, differential diagnosis of cystic neoplasm may be possible. These are KRAS and GNAS, VHL, and CTNNB1 mutation in mucinous cystic neoplasm, intraductal papillary-mucinous neoplasm, serous cystic neoplasm, and solid pseudopapillary neoplasm, respectively. The next-generation sequencing is an emerging molecular test that can detect multiple biomarkers for diagnosis, including pancreas cystic neoplasm. It has been reported that next-generation sequencing test can be applied for differential diagnosis of pancreas cystic neoplasm. However, these molecular pathology tests were not all-around; it needs to be properly managed with pathologist's quality control. It should be remembered that even if it goes through quality control, it may show a failure rate of around 30%. Despite the advances in molecular methods of high techniques, it should be remembered that the most important thing in pathologic diagnosis of pancreas cystic neoplasm is an endoscopist's skill and pathologist's expertise those provide adequate specimen and accurate diagnosis.

Sampling and storage methods of fecal samples in human intestinal microbiome study / 国际儿科学杂志

With the rapid development of high-throughput sequencing ( NGS) technique, intestinal microbiome could be studied more deeply. Intestinal contents and fecal samples have the characteristics of con-venient sampling and strong representation, so they are often used as the main research objects in the study of intestinal microbiota. The method of collecting and storage of samples are very important to affect the internal flora structure and diversity, which determines the accuracy of subsequent sequencing analysis. This review summarizes the sampling and storage methods of fecal samples in the study of intestinal microbiome.

Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) 3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

Whole Exome Sequencing of a Patient with Duchenne Muscular Dystrophy / 대한소아신경학회지

Duchenne muscular dystrophy (DMD) is the most common and lethal dystrophy in childhood, caused by mutations in the dystrophin (DMD) gene. Multiplex ligation dependent probe amplification (MLPA) or array comparative genome hybridization (aCGH) is widely used as an initial molecular diagnostic tool. If no deletions or duplications are found in MLPA or aCGH, the samples must be subjected to a second test of direct sequencing. Direct sequencing of the DMD gene, however, is time-consuming, high-cost, and can be inconclusive. Here, we performed whole exome sequencing on a patient with progressive muscle weakness whose MLPA result was negative; the result revealed a rare frame shift mutation. Direct sequencing on the patient's mother showed the same mutation. Whole exome sequencing can be a new diagnostic routine for DMD patients with negative MLPA3.

A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data

High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.