Genomic and gene expression profiling in malignant hematology
... At any given moment, each of our cells has some combination of genes turned on, while others are turned off. The combined expression of this magnitude of genes is affected by acquired chromosomal aberrations (e.g. translocations, inversions, deletions and amplifications) and by various mutations at ...
... At any given moment, each of our cells has some combination of genes turned on, while others are turned off. The combined expression of this magnitude of genes is affected by acquired chromosomal aberrations (e.g. translocations, inversions, deletions and amplifications) and by various mutations at ...
DNA Extraction, PCR Amplification and Sequencing: the IGS
... Because of the length of the IGS region, and the potential for secondary structures, a PCR enhancer (Ralser et al., 2006) containing a final concentration of 0.54 M betaine, 1.34 mM DL-Dithiothreitol (DTT), 1.34% Dimethyl Sulfoxide (DMSO), and 11 ug/ml Bovine Serum Albumin (BSA) was used in each rea ...
... Because of the length of the IGS region, and the potential for secondary structures, a PCR enhancer (Ralser et al., 2006) containing a final concentration of 0.54 M betaine, 1.34 mM DL-Dithiothreitol (DTT), 1.34% Dimethyl Sulfoxide (DMSO), and 11 ug/ml Bovine Serum Albumin (BSA) was used in each rea ...
Acute Lymphocytic Leukemia (ALL) Panel by FISH, Adult
... • Preferred test for fresh specimens at time of diagnosis for detecting prognostically important genomic abnormalities in leukemias/lymphomas and solid tumors involving o Loss/gain of DNA o Loss of heterozygosity (LOH) o Monitor disease progression and response to therapy Chromosome FISH, Interphase ...
... • Preferred test for fresh specimens at time of diagnosis for detecting prognostically important genomic abnormalities in leukemias/lymphomas and solid tumors involving o Loss/gain of DNA o Loss of heterozygosity (LOH) o Monitor disease progression and response to therapy Chromosome FISH, Interphase ...
Document
... Microsatellites (variable # of short repeats) CGCGCG vs. CGCGCGCGCG vs. CGCG Restriction Fragment Length Polymorphism (RFLP) SNP leading to a loss/gain of a restriction cut site ...
... Microsatellites (variable # of short repeats) CGCGCG vs. CGCGCGCGCG vs. CGCG Restriction Fragment Length Polymorphism (RFLP) SNP leading to a loss/gain of a restriction cut site ...
In Silico Mapping of Complex Disease
... three mouse strains are shown. The blue and purple strains exhibit a similar phenotype, while the green strain has a different phenotype. SNP alleles at a chromosomal region are represented as orange or yellow ovals. Black boxes indicate genomic regions with a high probability for regulating a trait ...
... three mouse strains are shown. The blue and purple strains exhibit a similar phenotype, while the green strain has a different phenotype. SNP alleles at a chromosomal region are represented as orange or yellow ovals. Black boxes indicate genomic regions with a high probability for regulating a trait ...
Genomic Library cDNA Library
... cut in the middle of genes, otherwise those genes will be “lost” from the library. ...
... cut in the middle of genes, otherwise those genes will be “lost” from the library. ...
Supplementary Tables and Figures (doc 5938K)
... has a local amplification, amounting to approximately four copies, whereas lung cell line NCI-H226 and melanoma SK-MEL-2 show diffuse hypodiploidy in the genomic area surrounding CHEK2 locus. C: Table of copy number variations in cancer cell lines from the NCI-60. Data obtained using Nimblegen 385k ...
... has a local amplification, amounting to approximately four copies, whereas lung cell line NCI-H226 and melanoma SK-MEL-2 show diffuse hypodiploidy in the genomic area surrounding CHEK2 locus. C: Table of copy number variations in cancer cell lines from the NCI-60. Data obtained using Nimblegen 385k ...
Molecular Methods for Evolutionary Genetics
... through when conducting an evolutionary genetic analysis of a new genome. The first two sections “Characterizing the Genome” and “Targeting Regions of the Genome” contain chapters detailing molecular biology techniques that can be employed to characterize unexplored genomes, such as determining geno ...
... through when conducting an evolutionary genetic analysis of a new genome. The first two sections “Characterizing the Genome” and “Targeting Regions of the Genome” contain chapters detailing molecular biology techniques that can be employed to characterize unexplored genomes, such as determining geno ...
Restriction Mapping Restriction Fragment Length Polymorphism
... These are 1 to 5 kb in length consisting of repeats 15 to 100 nucleotides in length and are identified by Southern analysis. 2. Microsatellite DNA ...
... These are 1 to 5 kb in length consisting of repeats 15 to 100 nucleotides in length and are identified by Southern analysis. 2. Microsatellite DNA ...
file
... performed using 49-bp paired reads on the Illumina HiSeq2000 to an average depth of 843X, and evaluated for genomic aberrations including base substitutions, deletions, insertions, copy number alterations (CNA; amplifications and homozygous deletions), and several gene fusions/rearrangements. The fa ...
... performed using 49-bp paired reads on the Illumina HiSeq2000 to an average depth of 843X, and evaluated for genomic aberrations including base substitutions, deletions, insertions, copy number alterations (CNA; amplifications and homozygous deletions), and several gene fusions/rearrangements. The fa ...
Wadsworth Center
... of 10 ng to 1.5 ug) per sample is required to perform the assay. Step 1 - Multiplex PCR Reaction will make multiple copies of multiple DNA targets within the CFTR gene. Step 2 - Amplicon Treatment Enzymatic treatment of amplified PCR products cleaves unused reagents (primers and dNTPs) left over aft ...
... of 10 ng to 1.5 ug) per sample is required to perform the assay. Step 1 - Multiplex PCR Reaction will make multiple copies of multiple DNA targets within the CFTR gene. Step 2 - Amplicon Treatment Enzymatic treatment of amplified PCR products cleaves unused reagents (primers and dNTPs) left over aft ...
MGG330 L1-2007
... Probe sets are designed to 3’ end of gene as labelling of probe starts at “end” of gene ...
... Probe sets are designed to 3’ end of gene as labelling of probe starts at “end” of gene ...
ppt - Department of Plant Sciences
... Example: EcoRI • What is the probability of a sequence of DNA in a plant genome having the sequence of bases corresponding to an EcoRI cut site? • Each site can be 4 possible bases (A, T, C, or G), and the EcoRI enzyme requires 6 sites (GAATTC) • The probability of finding a random site in a genome ...
... Example: EcoRI • What is the probability of a sequence of DNA in a plant genome having the sequence of bases corresponding to an EcoRI cut site? • Each site can be 4 possible bases (A, T, C, or G), and the EcoRI enzyme requires 6 sites (GAATTC) • The probability of finding a random site in a genome ...
Lecture 2: Biology Review II
... PCR with short probes that bind randomly to sites in the genome. Good for genomes where little sequence information is available. Band-present is dominant. Expected number of products = 2fN/16b ...
... PCR with short probes that bind randomly to sites in the genome. Good for genomes where little sequence information is available. Band-present is dominant. Expected number of products = 2fN/16b ...
Enzyme POGIL-PCR
... 2. How do you think the graph you drew for amylase would compare to a graph for other enzymes from the same organism? EXPLAIN YOUR ANSWER. ...
... 2. How do you think the graph you drew for amylase would compare to a graph for other enzymes from the same organism? EXPLAIN YOUR ANSWER. ...
My Dinosaur
... • The smart scientist were able to gather a source of DNA from a couple of extinct dinosaurs. • Don’t forget the surrogate mother! • With birds being the closet relative to a dinosaur our team of researches were able to use a Hawk as the surrogate mother for the cloning. ...
... • The smart scientist were able to gather a source of DNA from a couple of extinct dinosaurs. • Don’t forget the surrogate mother! • With birds being the closet relative to a dinosaur our team of researches were able to use a Hawk as the surrogate mother for the cloning. ...
DNA methylation signature of activated human natural killer cells
... few gene loci met the criteria for Class I. When the same criteria were applied to the replication set, 21 Class I loci (within 9 genes; all hypomethylated) were found in common between the two datasets. These loci/genes were given top priority for further investigation. Additionally, there were 44 ...
... few gene loci met the criteria for Class I. When the same criteria were applied to the replication set, 21 Class I loci (within 9 genes; all hypomethylated) were found in common between the two datasets. These loci/genes were given top priority for further investigation. Additionally, there were 44 ...
CSC598BIL675-2016
... Evolving SNV analysis needs • Single SNP • Millions of SNPs How to structure the analysis is based on the same theories… It’s a question of scale and heuristics • Finding SNPs in single gene sequence • Finding SNPs in GWAS studies, other exome sequencing etc… ...
... Evolving SNV analysis needs • Single SNP • Millions of SNPs How to structure the analysis is based on the same theories… It’s a question of scale and heuristics • Finding SNPs in single gene sequence • Finding SNPs in GWAS studies, other exome sequencing etc… ...
Annexure `CD – 01` FORMAT FOR COURSE CURRICULUM L T P/S
... Introduction, Sources and types of funding, Types of proposals, Necessary ingredients in an application, Fatal flaws and common problems, Budgets, Resources, Collaborators, Reviewing and Acceptance proposal, Responsible conduct, confidentiality and conflicts of interest. Role of search engines and l ...
... Introduction, Sources and types of funding, Types of proposals, Necessary ingredients in an application, Fatal flaws and common problems, Budgets, Resources, Collaborators, Reviewing and Acceptance proposal, Responsible conduct, confidentiality and conflicts of interest. Role of search engines and l ...
GENETICS EXAM 3 FALL 2004 Student Name
... 13. Which of the following may be a useful feature of some cloning vectors, but is not a necessary feature of all cloning vectors? a) Means of selection (i.e., identifying bacteria that contain recombinant DNA molecules) b) Origin of replication c) lac z gene d) Cloning sites 14. Assume you have id ...
... 13. Which of the following may be a useful feature of some cloning vectors, but is not a necessary feature of all cloning vectors? a) Means of selection (i.e., identifying bacteria that contain recombinant DNA molecules) b) Origin of replication c) lac z gene d) Cloning sites 14. Assume you have id ...
Visualization of Gene Expression Patterns by in situ
... Expression of Ube3a in the Head of a 15.5 day mouse fetus ...
... Expression of Ube3a in the Head of a 15.5 day mouse fetus ...
BCR3169-S4 (Microsoft Word, 72Kb)
... analyses if they failed any of these criteria. Studies included per SNP in our analysis are shown in Supplementary Table 2. Details of the statistical analysis methods for evaluating the associations between SNP genotypes and breast cancer risk have been published previously (13). In short, the phen ...
... analyses if they failed any of these criteria. Studies included per SNP in our analysis are shown in Supplementary Table 2. Details of the statistical analysis methods for evaluating the associations between SNP genotypes and breast cancer risk have been published previously (13). In short, the phen ...
Exercise 5
... which terminate at a given nucleotide (A, C, G and T). By sizing these chains we can infer the normal positions of each of the four residues in the sequence. (insert circular DNA sketch here) The products of the reaction are analysed on 5% polyacrylamide urea gels which allow resolution of chains 1– ...
... which terminate at a given nucleotide (A, C, G and T). By sizing these chains we can infer the normal positions of each of the four residues in the sequence. (insert circular DNA sketch here) The products of the reaction are analysed on 5% polyacrylamide urea gels which allow resolution of chains 1– ...
SNP Discovery Services - Sanger Sequencing
... It is crucial that the guidelines mentioned in the User Guide be carefully followed so that unnecessary delays can be avoided. ...
... It is crucial that the guidelines mentioned in the User Guide be carefully followed so that unnecessary delays can be avoided. ...
Molecular Inversion Probe
Molecular Inversion Probe (MIP) belongs to the class of Capture by Circularization molecular techniques for performing genomic partitioning, a process through which one captures and enriches specific regions of the genome. Probes used in this technique are single stranded DNA molecules and, similar to other genomic partitioning techniques, contain sequences that are complementary to the target in the genome; these probes hybridize to and capture the genomic target. MIP stands unique from other genomic partitioning strategies in that MIP probes share the common design of two genomic target complementary segments separated by a linker region. With this design, when the probe hybridizes to the target, it undergoes an inversion in configuration (as suggested by the name of the technique) and circularizes. Specifically, the two target complementary regions at the 5’ and 3’ ends of the probe become adjacent to one another while the internal linker region forms a free hanging loop. The technology has been used extensively in the HapMap project for large-scale SNP genotyping as well as for studying gene copy alterationsand characteristics of specific genomic loci to identify biomarkers for different diseases such as cancer. Key strengths of the MIP technology include its high specificity to the target and its scalability for high-throughput, multiplexed analyses where tens of thousands of genomic loci are assayed simultaneously.