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Personalized identification of altered pathways in cancer using accumulated normal tissue data
Ahn, TaeJin,Lee, Eunjin,Huh, Nam,Park, Taesung Oxford University Press 2014 Bioinformatics Vol.30 No.17
<P><B>Motivation:</B> Identifying altered pathways in an individual is important for understanding disease mechanisms and for the future application of custom therapeutic decisions. Existing pathway analysis techniques are mainly focused on discovering altered pathways between normal and cancer groups and are not suitable for identifying the pathway aberrance that may occur in an individual sample. A simple way to identify individual’s pathway aberrance is to compare normal and tumor data from the same individual. However, the matched normal data from the same individual are often unavailable in clinical situation. Therefore, we suggest a new approach for the personalized identification of altered pathways, making special use of accumulated normal data in cases when a patient’s matched normal data are unavailable. The philosophy behind our method is to quantify the aberrance of an individual sample's pathway by comparing it with accumulated normal samples. We propose and examine personalized extensions of pathway statistics, overrepresentation analysis and functional class scoring, to generate individualized pathway aberrance score.</P><P><B>Results:</B> Collected microarray data of normal tissue of lung and colon mucosa are served as reference to investigate a number of cancer individuals of lung adenocarcinoma (LUAD) and colon cancer, respectively. Our method concurrently captures known facts of cancer survival pathways and identifies the pathway aberrances that represent cancer differentiation status and survival. It also provides more improved validation rate of survival-related pathways than when a single cancer sample is interpreted in the context of cancer-only cohort. In addition, our method is useful in classifying unknown samples into cancer or normal groups. Particularly, we identified ‘amino acid synthesis and interconversion’ pathway is a good indicator of LUAD (Area Under the Curve (AUC) 0.982 at independent validation). Clinical importance of the method is providing pathway interpretation of single cancer, even though its matched normal data are unavailable.</P><P><B>Availability and implementation:</B> The method was implemented using the R software, available at our Web site: http://bibs.snu.ac.kr/ipas.</P><P><B>Contact:</B>tspark@stat.snu.ac.kr or namhuh@samsung.com</P><P><B>Supplementary information:</B>Supplementary data are available at <I>Bioinformatics</I> online.</P>
Storing Digital Information in Long-Read DNA
Ahn, TaeJin,Ban, Hamin,Park, Hyunsoo Korea Genome Organization 2018 Genomics & informatics Vol.16 No.4
There is urgent need for effective and cost-efficient data storage, as the worldwide requirement for data storage is rapidly growing. DNA has introduced a new tool for storing digital information. Recent studies have successfully stored digital information, such as text and gif animation. Previous studies tackled technical hurdles due to errors from DNA synthesis and sequencing. Studies also have focused on a strategy that makes use of 100-150-bp read sizes in both synthesis and sequencing. In this paper, we a suggest novel data encoding/decoding scheme that makes use of long-read DNA (~1,000 bp). This enables accurate recovery of stored digital information with a smaller number of reads than the previous approach. Also, this approach reduces sequencing time.
A Case of Pulmonary Fibrosis with Lung Lobe Torsion in a Pekinese Dog
Byeongwoo Ahn, Du-Min Go, Taejin Lee, Tae-Wang Kim, So Young Youm, Sang-Kyung Shin 충북대학교 동물의학연구소 2012 Journal of Biomedical and Translational Research Vol.13 No.1
Pulmonary fibrosis (PF) is defined as a gradual, interstitial fibrous disease of the lung parenchyma. PF causes collapse of the lung lobe, which can lead to lung lobe torsion of the other side. A 14-year-old male Pekinese dog was referred to the Veterinary Medical Center, Chungbuk National University. The chief complaint was acute dyspnea. The dog had a history of chronic cough, which lasted for 18 months, and the cough had recently deteriorated. Tachypnea was observed on physical examination. As a result of thoracic radiographs, ultrasonography, and computed tomography, lung lobe torsion and collapse were diagnosed. A postmortem examination revealed lung lobe torsion of the left cranial lobe and carnification of the right cranial lobe. Histologically, severe and diffuse interstitial fibrosis with distortion of alveolar architecture and severe congestion and/or hemorrhage were observed in the right cranial lobe and left cranial lobe, respectively. Although the cause of pulmonary fibrosis was undetermined, this case showed a typical lung lobe torsion caused by pulmonary fibrosis.
Pathologic Features of a Systemic Dirofilariasis in a Dog
Byeongwoo Ahn , Taejin Lee, Du-Min Go, Tae-Wang Kim, So Young Youm, Sang-Kyung Shin, Dongwoo Chang 충북대학교 동물의학연구소 2011 Journal of Biomedical and Translational Research Vol.12 No.1
Canine heartworm disease is typically characterized by the presence of heartworms in the pulmonary artery and, to a lesser degree, the right ventricle. Systemic arterial dirofilariasis is an unusual manifestation of heartworm disease of dogs that results from aberrant migration of Dirofilaria immitis into the peripheral arterial circulation. A three-year-old Jindo dog was referred to the Veterinary Medical Center because of hindlimb lameness, paresthesia of hindlimbs, and interdigital ischemic necrosis. Angiography and ultrasonography were performed, resulting in diagnosis of heartworm infestation. In necropsy, entangled heartworms were present throughout the body, including lungs, kidney, small intestinal lumen, and arteries, in addition to the right ventricle and pulmonary artery. Histologically, lung showed adult heart worms in vessels, organized thrombotic vessels, and interstitial pneumonia featuring type II pneumocyte hyperplasia, thickened alveolar wall, and compressed alveolar spaces. Chronic parenchymal lesions, such as focal or diffuse necrosis, fibrosis, and dystrophic calcification were remarkable in liver and kidney. The current case showed a typical canine systemic heartworm disease caused by aberrant migration of Dirofilaria immitis.