Biomedical subjects

Ya-Chien Yang

Publications and source records attributed to Ya-Chien Yang.

5 recordsLinked to original sources

PubMed2026

Graph-KIR: graph-based KIR copy number estimation and allele calling using short-read sequencing data.

MOTIVATION: The Killer-cell Immunoglobulin-like Receptor (KIR) is a highly polymorphic region in the human genome, associated with autoimmune diseases and organ transplantation. The sequences of KIR genes are highly similar among star alleles as well as in between individual genes, with the copy number of each KIR gene typically ranging from 0 to 4. In this study, we introduce Graph-KIR, a tool designed to estimate gene copy numbers and predict full-resolution (7-digit, encompassing both coding and non-coding sequence variations) from a whole genome sequencing (WGS) sample. RESULTS: Graph-KIR is capable of independently typing KIR alleles per sample with no reliance on the distribution of any framework gene in a cohort. In a set of 100 simulated samples, Graph-KIR demonstrated 99.2% accuracy in copy number estimation and high F1-score of allele typing: 91.79% at 7-digit resolution, 97.37% at 5-digit resolution, and 97.11% at 3-digit resolution. Graph-KIR outperforms existing tools such as Geny (96.39% F1-score), PING's WGS version (92.77% F1-score), and T1K (90.44% F1-score) at 5-digit resolution. By analyzing the results on 44 HPRC samples, Graph-KIR achieves better F1-score than Geny and PING at 7-digit resolution. The release of Graph-KIR adds another valuable tool to assist users in accurately estimating copy numbers and calling alleles of KIR genes from WGS samples. AVAILABILITY AND IMPLEMENTATION: The Graph-KIR and paper-related pipeline codes are available at https://github.com/linnil1/KIR_graph.

Receptors, KIR↗

PubMed2003

Obstructive colitis proximal to partially obstructive colonic carcinoma: a case report and review of the literature.

BACKGROUND: Obstructive colitis refers to ulceroinflammatory lesions that occur in the colon proximal to an obstructing lesion. As this condition is not widely appreciated by pathologists or clinicians, we describe herein a case of colonic polyposis and sigmoid colonic carcinoma with obstructive colitis. PATIENT PRESENTATION: A 47-year-old Taiwanese woman presented to Cardinal Tien Hospital with a 3-day history of acute onset of abdominal pain, vomiting, and watery diarrhea. A lower gastrointestinal series using water-soluble contrast medium revealed annular narrowing of the sigmoid colon and showed polyposis at the rectosigmoid colon and regional colitis over the proximal descending colon. She was treated by total colectomy. Microscopic sections showed poorly differentiated adenocarcinoma, tubular adenomas, and a segment of obstructive colitis measuring 25 cm in length 5 cm proximal to the colon tumor. The tumor was also retrieved for simultaneous analyses of replication error and loss of heterozygosity. A total of three instances of loss of heterozygosity were demonstrated at the P53, MET, and D8S254 gene loci. No examples of replication error were detected. CONCLUSION: Obstructive colitis can cause diagnostic and therapeutic problems. Colitis areas may be a source for septicemia or may perforate and lead to peritonitis. The frequently normal appearance at surgery may lead to involved segments of colon being used for anastomoses with consequent complications. Awareness of the features and incidence of obstructive colitis should help physicians avoid these diagnostic and therapeutic problems.

Adenocarcinoma↗

PubMed2003

Loss of heterozygosity and DNA aneuploidy in colorectal adenocarcinoma.

BACKGROUND: This study evaluated the relationship between DNA aneuploidy and loss of heterozygosity (LOH) at different genetic loci in colorectal adenocarcinoma. METHODS: A total of 112 patients with surgically removed colorectal adenocarcinoma in Taipei Veterans General Hospital from January 1999 to July 2001 were included in this study. The pattern of DNA ploidy was determined with DNA flow cytometry, and the LOH of various genetic loci was determined with fluorescence polymerase chain reaction and denaturing gradient gel electrophoresis. The relationship between DNA ploidy, LOH of various genetic loci, and clinicopathologic variables was analyzed with the chi(2) test with Yates' correction as well as by multivariate binary logistic regression analysis. RESULTS: Seventy-one (63.4%) of the 112 carcinomas had DNA aneuploidy. The DNA aneuploidy was not associated with any clinicopathologic variable. Ninety-one tumors (81.3%) exhibited LOH in at least one genetic locus. In the univariate analysis, the DNA aneuploidy was associated with LOH of Tp53-penta, D8S254, D5S346, and high-frequency LOH (P =.001, P =.016, P =.041, and P <.001, respectively). In the multivariate analysis, the most significant factor influencing DNA aneuploidy was D8S254, followed by Tp53-penta, high-frequency LOH, and D5S346. CONCLUSIONS: DNA aneuploidy is strongly associated with LOH at specific genetic loci.

Adenocarcinoma↗

PubMed2002

Resistance to tumor necrosis factor-alpha-induced apoptosis in human T-lymphotropic virus type I-infected T cell lines.

Induction of apoptosis of virus-infected cells is an important host cell defense mechanism. It is well documented that T cells may undergo apoptosis due to interactions between Fas and Fas ligand (FasL). In addition, signals that induce apoptosis in T cells can result from interaction of tumor necrosis factor (TNF)-alpha with TNF receptors (TNFRs). It has been shown that human T cell lines expressing HTLV-I have decreased sensitivity to Fas-mediated apoptosis. The susceptibility of HTLV-I-infected cells to TNF-alpha-induced apoptosis remains to be elucidated. In the present study, we examined the expression of TNFRs on HTLV-I-infected T cell lines that expressed T-cell activation markers and thus phenotypically resemble activated T cells. Different from primary activated T cells that expressed both TNFRs, none of the five HTLV-I-infected T cell lines studied had detectable TNFR1 and only three had TNFR2 on their cell surfaces, although, the RNA transcripts of both TNFR genes could be detected via reverse transcription-polymerase chain reaction in these cell lines. The T cell blasts, which we activated in vitro, were sensitive to apoptosis induced by TNF-alpha and by antibodies to TNFR1 and/or TNFR2. However, all of the HTLV-I-infected cell lines expressing TNFR2 were resistant to TNF-alpha-mediated apoptosis. These findings suggest that HTLV-I infection may interfere with the autonomous suicide programs of T cells, not only Fas/FasL but also TNFRs/TNF-alpha pathways, to prolong the life of the infected cells. This may contribute to viral persistence and favor survival and subsequent expansion of dysregulated infected T cells with the potential to produce HTLV-I-associated autoimmune-like diseases or malignancies.

Antigens, CD↗

PubMedDate not supplied

RER and LOH association with sporadic colorectal cancer in Taiwanese patients.

BACKGROUND/AIMS: This association study was undertaken to determine replication error and loss of heterozygosity in colorectal tumors using a set of 10 microsatellite markers linked to APC, hMSH2, hMLH1, DCC, P53, NM23, HPC1 and MET genes as well as tumor suppressor genes on 8p22. METHODOLOGY: Thirty-nine patients diagnosed and confirmed with sporadic colorectal cancer were biopsied. Their stored frozen tissues were subsequently retrieved for simultaneous analyses of replication error and loss of heterozygosity via an automated fluorescent microsatellite assay. RESULTS: Replication error was observed in 8/39 of the cases (20.5%) and had significantly higher frequency in the patients younger than 60 yr (P = 0.049). More than one third of informative tumors showed loss of heterozygosity at P53, DCC and APC genes (57.9%, 35.3% and 33.3%, respectively). Loss of heterozygosity at TP53-Dint marker was significantly associated with survival status (P = 0.038) in which a higher frequency was observed in the patients who died from colorectal cancer. Of 22 informative tumors, 6 (27.3%) showed loss of heterozygosity at the D8S254 marker that is suspected to be near one or more tumor suppressor genes and was significantly associated with gender (P = 0.046). All 6 cases of loss of heterozygosity at D8S254 were found in male patients. The frequencies of loss of heterozygosity at the NM23, hMSH2, hMLH1 and HPC1 genes were 18.5%, 12.1%, 9.1% and 7.4%, respectively. None of the cases examined displayed loss of heterozygosity at the MET oncogene. CONCLUSIONS: Additional microsatellite markers other than those associated with colorectal cancer were used to conduct the study of genomic instability and alterations in colorectal cancer tumors. The present results for the sporadic occurrence of colorectal cancer in Taiwanese patients further extend the correlation of clinical pathology and prognosis with the analysis of replication error and loss of heterozygosity.

Adenocarcinoma↗