Searching the Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
Copy number variation (CNV) is a common chromosomal alteration that can occur during in vitro cultivation of human cells and can be accompanied by the accumulation of mutations in coding region sequences. We describe here a systematic application of current molecular technologies to provide a detailed understanding of genomic and sequence profiles of human embryonic stem cell (hESC) lines that were derived under GMP-compliant conditions. We first examined the overall chromosomal integrity using cytogenetic techniques to determine chromosome count, and to detect the presence of cytogenetically aberrant cells in the culture (mosaicism). Assays of copy number variation, using both microarray and sequence-based analyses, provide a detailed view genomic variation in these lines and shows that in early passage cultures of these lines, the size range and distribution of CNVs are entirely consistent with those seen in the genomes of normal individuals. Similarly, genome sequencing shows variation within these lines that is completely within the range seen in normal genomes. Important gene classes, such as tumor suppressors and genetic disease genes, do not display overtly disruptive mutations that could affect the overall safety of cell-based therapeutics. Complete sequence also allows the analysis of important transplantation antigens, such as ABO and HLA types. The combined application of cytogenetic and molecular technologies provides a detailed understanding of genomic and sequence profiles of GMP produced ES lines for potential use as therapeutic agents.
Pubmed ID: 22265736
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.
View all literature mentionsA database of oncogenes and tumor suppressor genes. Users can search by genes, chromosomes, and keywords. The coAnsensus domain analysis tool functions to identify conserved protein domains and GO terms among selected TAG genes, while the “oncogenic domain analysis” can analyze oncogenic potential of any user-provided protein based on a weighed term frequency table calculated from the TAG proteins. The completion of human genome sequences allows one to rapidly identify and analyze genes of interest through the use of computational approach. The available annotations including physical characterization and functional domains of known tumor-related genes thus can be used to study the role of genes involved in carcinogenesis. The tumor-associated gene (TAG) database was designed to utilize information from well-characterized oncogenes and tumor suppressor genes to facilitate cancer research. All target genes were identified through text-mining approach from the PubMed database. A semi-automatic information retrieving engine was built to collect specific information of these target genes from various resources and store in the TAG database. At current stage, 519 TAGs including 198 oncogenes, 170 tumor suppressor genes, and 151 genes related to oncogenesis were collected. Information collected in TAG database can be browsed through user-friendly web interfaces that provide searching genes by chromosome or by keywords. The “consensus domain analysis” tool functions to identify conserved protein domains and GO terms among selected TAG genes. In addition, the “oncogenic domain analysis” can analyze oncogenic potential of any user-provided protein based on a weighed term frequency table calculated from the TAG proteins. This study was supported by grant from National research program for genomic medicine (NRPGM) and personnel from Bioinformatics Center of Center for Biotechnology and Biosciences in the National Cheng Kung University, Taiwan.
View all literature mentions2100 Bioanalyzer system is an established automated electrophoresis tool for the sample quality control of biomolecules. The 2100 Bioanalyzer instrument, together with the 2100 Expert Software and Bioanalyzer assays, provide highly precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene editing research. Digital data is provided in a timely manner and delivers objective assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for an accurate result, and the data may be exported in a many different formats for ease-of-use.
View all literature mentions