Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.

Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.

Community Integration and Quality of Life in Aphasia after Stroke

PURPOSE: To examine community integration and contributing factors in people with aphasia (PWA) following stroke and to investigate the relationship between community integration and quality of life (QOL). MATERIALS AND METHODS: Thirty PWA and 42 age-and education-matched control subjects were involved. Main variables were as follows: socioeconomic status, mobility, and activity of daily living (ADL) (Modified Barthel Index), language function [Frenchay Aphasia Screening Test (FAST)], depression [Geriatric Depression Scale (GDS)], Community Integration Questionnaire (CIQ) and Stroke and Aphasia Quality of Life Scale-39 (SAQOL-39). Differences between aphasia and control groups and factors affecting community integration and QOL were analyzed. RESULTS: Home and social integration and productive activity were significantly decreased in the aphasia group compared to the control group; 8.5 and 18.3 points in total CIQ score, respectively. Amount of time spent outside the home and frequency of social contact were also significantly reduced in the aphasia group. Total mean score on the SAQOL-39 was 2.75+/-0.80 points and was significantly correlated with economic status, gait performance, ADL, depressive mood, and social domain score on the CIQ. Depression score measured by GDS was the single most important factor for the prediction of QOL, but the FAST score was significantly correlated only with the communication domain of the SAQOL-39. CONCLUSION: Community activities of PWA were very limited, and depression was highly associated with decreased community integration and QOL. Enhancing social participation and reducing emotional distress should be emphasized for rehabilitation of PWA.

Localized Cutaneous Infection due to Stenotrophomonas maltophilia in Immunocompetent Patient / 대한피부과학회지

No abstract available.

Comments to "Two Cases of Toenail Onychomycosis Treated by 1,064 nm Nd:YAG Laser" / 대한피부과학회지

No abstract available.

Instructional Analysis of Lecture Video Recordings and Its Application for Quality Improvement of Medical Lectures / 한국의학교육

PURPOSE: The lecture is a technique for delivering knowledge and information cost-effectively to large medical classes in medical education. The aim of this study was to analyze teaching quality, based on triangle analysis of video recordings of medical lectures, to strengthen teaching competency in medical school. METHODS: The subjects of this study were 13 medical professors who taught 1st- and 2nd-year medical students and agreed to a triangle analysis of video recordings of their lectures. We first performed triangle analysis, which consisted of a professional analysis of video recordings, self-assessment by teaching professors, and feedback from students, and the data were crosschecked by five school consultants for reliability and consistency. RESULTS: Most of the distress that teachers experienced during the lecture occurred in uniform teaching environments, such as larger lecture classes. Larger lectures that primarily used PowerPoint as a medium to deliver information effected poor interaction with students. Other distressing factors in the lecture were personal characteristics and lack of strategic faculty development. CONCLUSION: Triangle analysis of video recordings of medical lectures gives teachers an opportunity and motive to improve teaching quality. Faculty development and various improvement strategies, based on this analysis, are expected to help teachers succeed as effective, efficient, and attractive lecturers while improving the quality of larger lecture classes.

Epstein-Barr Virus-Positivity in Tumor has no Correlation with the Clinical Outcomes of Patients with Angioimmunoblastic T-cell Lymphoma

BACKGROUND/AIMS: Epstein-Barr virus (EBV) is involved in the pathogenesis of angioimmunoblastic T-cell lymphoma (AILT), but its precise role and prognostic impact are not clear. This study aimed to evaluate the incidence of EBV-postitivity in the tumor and bone marrow (BM) samples from AILT patients, and their correlations with the clinical variables and patient survival. METHODS: Seventy AILT cases were identified over a period of 8 years. Twenty seven cases were investigated for their EBV tumor status, and 10 BM samples of these patients were investigated for their EBV status with using in situ hybridization (ISH). EBV PCR was performed for the BM mononuclear cells in 8 cases. RESULTS: Among the 27 tumor specimens, ten (37%) were EBV-positive. Only CD20-negativity in tumor correlated with the EBV-positivity (p=0.035). In 13 (48%) patients, gross tumor involvement was recognized by hematoxylin-eosin staining at the time of diagnosis. Among the 10 patients who had additional BM slides available, there were 3 with BM involvement, and none showed EBV positive results on ISH. EBV PCR of the BM mononuclear cells revealed one-positive case among 8 patients. This patient was negative for both BM involvement and EBV ISH. The median overall survival of the 25 treated patients was 48.9 months (95% CI: 18.6~79.2 months). Neither overall survival nor progression-free survival was related with EBV-positivity of the tumor. CONCLUSIONS: EBV-positivity of tumor had no impact on the prognosis of AILT patients.

A phase II study of etoposide (VP-16), ifosfamide, and carboplatin combination chemotherapy plus concurrent thoracic irradiation for limited stage small cell lung cancer / 대한내과학회지

BACKGROUND: Small cell lung cancer (SCLC) is very sensitive to both chemotherapy and radiation therapy. In limited disease of SCLC, the addition of radiation therapy to chemotherapy improves survival and decrease local relapse over chemotherapy alone. This study evaluated the response rate, duration of response, overall survival and toxicity for the combination of etoposide, ifosfamide, carboplatin given concurrently with thoracic irradiation in limited SCLC. METHODS: Twenty eight patients with histologically proven SCLC who have a measurable disease and previously untreated, were enrolled in this study. Each cycle consisted of VP-16 100 mg/m2 IV days 1~3, ifosfamide 1,200 mg/m2 IV days 1~3 with mesna, carboplatin AUC 6 IV day 1. Cycles were repeated every 21days. Patients received a total of median 6,000 cGy thoracic radiation therapy (180~200 cGy/day) starting on the first day of chemotherapy. Prophylactic cranial irradiation was given to complete remission after chemoradiotherapy. RESULTS: The overall response rate in 27 evaluable patients was 93% (41% of complete response, 52% of partial response). The median time to progression was 10.3 months. The median disease free survival was 18.4 months in patients with complete response. The median overall survival was 16.7 months in all evaluable patients. Hematologic toxicities (> or = Grade3) of 129 cycles of chemotherapy were leukopenia in 38% and fever with infection in 26%. Nonhematologic toxicities (> or = Grade2) of evaluable 27 patients included alopecia in 11%, post-irradiation esophagitis in 44% and pneumonitis in 11%. CONCLUSIONS: VIC combination chemotherapy with concurrent thoracic irradiation is effective in limited SCLC. It's maior toxicity is myelosuppression.

Two Cases of Interstitial Pneumonitis Caused by Rituximab Therapy

Rituximab, a chimeric monoclonal antibody directed against CD20, has become a part of the standard therapy for patients with non-Hodgkin's lymphoma either in combination with other drugs or as a single agent. The CD20 antigen is expressed on 95% of B-cell lymphoma cells and normal B-cells but, is not found on precursor B-cells or stem cells. Rituximab is now approved for patients with diffuse large B-cell lymphoma when combined with standard CHOP chemotherapy (cyclophosphamide, doxorubicin, vincristine and prednisone) or patients with follicular lymphoma who have failed first line chemotherapy. The monoclonal antibody is generally well tolerated. Most of the adverse events are infusion-associated, mild to moderate non-hematological toxicities. Severe respiratory adverse events have been infrequent. Here, we report two patients with non-Hodgkin's lymphoma in whom interstitial pneumonitis developed with rituximab therapy.