Annovi HRM and Epigenetics
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This document discusses epigenetics and the use of high resolution melting PCR (HRM-PCR) to analyze DNA methylation. It describes how epigenetic mechanisms can produce different phenotypes from a single genotype through histone modifications and DNA methylation. It then explains how HRM-PCR can be used to discriminate between methylated and unmethylated DNA samples based on differences in melting temperatures. The document demonstrates how HRM-PCR can identify methylation levels at specific promoter regions quickly using samples from different sources like tissue or cell culture.
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Single nucleotide polymorphism (sn ps)
Single nucleotide polymorphisms (SNPs) are variations in single nucleotides that occur at specific positions in the genome. For example, the base C may appear in most individuals at a specific position, but in some individuals the position is occupied by base A, representing a SNP. SNPs can be classified as synonymous or nonsynonymous depending on whether they change the amino acid sequence. Common human diseases like sickle cell anemia and cystic fibrosis result from SNPs. SNPs can be identified and analyzed using methods like DNA sequencing, mass spectrometry, and primer extension.
Transcription associated mutation
Transcription-associated mutagenesis (TAM) refers to mutations that occur on the DNA strand being transcribed. The document discusses several causes and mechanisms of TAM, including DNA damage during transcription, cytosine deamination, and R-loop formation. It also covers TAM in yeast and E. coli, noting it increases under stress and affects both genomic and plasmid DNA. The roles of class switch recombination and somatic hypermutation in antibody gene diversification through TAM are also discussed.
L11 dna__polymorphisms__mutations_and_genetic_diseases4
1. DNA polymorphisms, such as single nucleotide polymorphisms (SNPs) and variable number tandem repeats (VNTRs), are natural variations in DNA sequences among individuals.
2. These polymorphisms can be used for indirect DNA diagnosis of genetic diseases through detection of restriction fragment length polymorphisms (RFLPs). DNA from family members is digested with restriction enzymes and analyzed through gel electrophoresis and Southern blotting.
3. If a polymorphism is found near a disease-causing mutation and is linked to it, its inheritance pattern can help determine which family members have inherited the mutation and are at risk for the associated genetic disease.
Dna modifications in the mammalian brain
Bio-Synthesis world’s leading Supplier providing commercial Synthetic DNA, custom DNA synthesis services in US.These are RNA analogues which can be synthesized and spiked with DNA or RNA in order to modify the formation of nucleic acid helices. For more Information visit on- http://www.biosyn.com/dna-oligonucleotide-services.aspx
Seminar presentation on snp (mulualem & janvier)
Single nucleotide polymorphisms (SNPs) are variations in a single DNA nucleotide that occur in over 1% of the population. SNPs are the most common type of genetic variation among humans, as 99.9% of human DNA sequences are identical, while the remaining 0.1% makes each individual unique. Modern techniques can efficiently determine the status of large numbers of SNPs, which promises to advance our understanding and treatment of human disease.
PV92 Scientific Poster
The document describes an experiment analyzing the presence of an Alu sequence in the PV92 locus on chromosome 16 in DNA samples from students. PCR and gel electrophoresis were used to amplify and visualize segments of DNA containing the Alu sequence. Students were found to be homozygous dominant, heterozygous, or homozygous recessive for the sequence. The results demonstrate the potential of using SINEs like the Alu sequence to identify individuals through their DNA profiles.
Snp
This document discusses single nucleotide polymorphisms (SNPs). It defines SNPs as single base changes in DNA sequences that occur in at least 1% of a large population. The document notes that while human genomes are 99.9% identical, there are positions where some people have one nucleotide pair while others have another, which are called SNPs. SNPs are described as the most common form of genetic variation, with over 90% of human genetic variations coming from SNPs. The uses and implications of SNPs are also summarized.
Snp
SNPs are found in
coding and (mostly) noncoding regions.
Occur with a very high frequency
about 1 in 1000 bases to 1 in 100 to 300 bases.
The abundance of SNPs and the ease with which they can be measured make these genetic variations significant.
SNPs close to particular gene acts as a marker for that gene.
SNPs in coding regions may alter the protein structure made by that coding region.
A SNP is defined as a single base change in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a large population. Sequence genomes of a large number of people
Compare the base sequences to discover SNPs.
Generate a single map of the human genome containing all possible SNPs => SNP maps
Recommended
Single nucleotide polymorphism (sn ps)
Single nucleotide polymorphisms (SNPs) are variations in single nucleotides that occur at specific positions in the genome. For example, the base C may appear in most individuals at a specific position, but in some individuals the position is occupied by base A, representing a SNP. SNPs can be classified as synonymous or nonsynonymous depending on whether they change the amino acid sequence. Common human diseases like sickle cell anemia and cystic fibrosis result from SNPs. SNPs can be identified and analyzed using methods like DNA sequencing, mass spectrometry, and primer extension.
Transcription associated mutation
Transcription-associated mutagenesis (TAM) refers to mutations that occur on the DNA strand being transcribed. The document discusses several causes and mechanisms of TAM, including DNA damage during transcription, cytosine deamination, and R-loop formation. It also covers TAM in yeast and E. coli, noting it increases under stress and affects both genomic and plasmid DNA. The roles of class switch recombination and somatic hypermutation in antibody gene diversification through TAM are also discussed.
L11 dna__polymorphisms__mutations_and_genetic_diseases4
1. DNA polymorphisms, such as single nucleotide polymorphisms (SNPs) and variable number tandem repeats (VNTRs), are natural variations in DNA sequences among individuals.
2. These polymorphisms can be used for indirect DNA diagnosis of genetic diseases through detection of restriction fragment length polymorphisms (RFLPs). DNA from family members is digested with restriction enzymes and analyzed through gel electrophoresis and Southern blotting.
3. If a polymorphism is found near a disease-causing mutation and is linked to it, its inheritance pattern can help determine which family members have inherited the mutation and are at risk for the associated genetic disease.
Dna modifications in the mammalian brain
Bio-Synthesis world’s leading Supplier providing commercial Synthetic DNA, custom DNA synthesis services in US.These are RNA analogues which can be synthesized and spiked with DNA or RNA in order to modify the formation of nucleic acid helices. For more Information visit on- http://www.biosyn.com/dna-oligonucleotide-services.aspx
Seminar presentation on snp (mulualem & janvier)
Single nucleotide polymorphisms (SNPs) are variations in a single DNA nucleotide that occur in over 1% of the population. SNPs are the most common type of genetic variation among humans, as 99.9% of human DNA sequences are identical, while the remaining 0.1% makes each individual unique. Modern techniques can efficiently determine the status of large numbers of SNPs, which promises to advance our understanding and treatment of human disease.
PV92 Scientific Poster
The document describes an experiment analyzing the presence of an Alu sequence in the PV92 locus on chromosome 16 in DNA samples from students. PCR and gel electrophoresis were used to amplify and visualize segments of DNA containing the Alu sequence. Students were found to be homozygous dominant, heterozygous, or homozygous recessive for the sequence. The results demonstrate the potential of using SINEs like the Alu sequence to identify individuals through their DNA profiles.
Snp
This document discusses single nucleotide polymorphisms (SNPs). It defines SNPs as single base changes in DNA sequences that occur in at least 1% of a large population. The document notes that while human genomes are 99.9% identical, there are positions where some people have one nucleotide pair while others have another, which are called SNPs. SNPs are described as the most common form of genetic variation, with over 90% of human genetic variations coming from SNPs. The uses and implications of SNPs are also summarized.
Snp
SNPs are found in
coding and (mostly) noncoding regions.
Occur with a very high frequency
about 1 in 1000 bases to 1 in 100 to 300 bases.
The abundance of SNPs and the ease with which they can be measured make these genetic variations significant.
SNPs close to particular gene acts as a marker for that gene.
SNPs in coding regions may alter the protein structure made by that coding region.
A SNP is defined as a single base change in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a large population. Sequence genomes of a large number of people
Compare the base sequences to discover SNPs.
Generate a single map of the human genome containing all possible SNPs => SNP maps
Snp by wajahahat ali
This document discusses single nucleotide polymorphisms (SNPs). It defines SNPs as single base changes in DNA sequences that occur in at least 0.1% of a population. SNPs are usually the result of errors in DNA replication or damage. They can be found in both coding and non-coding regions, and in coding regions they can alter protein structure. Applications of SNP analysis include gene discovery, disease association studies, and drug development. The document also describes several methods for SNP detection and identification, including PCR-based and non gel-based genotyping techniques as well as direct DNA sequencing.
Single nucleotide polymorphism
Single Nucleotide Polymorphism (SNP)
Polymorphism is a generic term that means 'many shapes‘. It is the ability to appsear in different form .
A single nucleotide polymorphism (SNP) is a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome differs between members of a species (or between paired chromosomes in an individual).
For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. For a variation to be considered a SNP, it must occur in at least 1% of the population.
CHARACTERISTICS OF SNP
• In human beings, 99.9 percent bases are same.
• Remaining 0.1 percent makes a person unique.
• Different attributes / characteristics / traits
• How a person looks, diseases he or she develops.
These variations can be:
Harmless (change in phenotype)
Harmful (diabetes, cancer, heart disease, Huntington's disease, and hemophilia )
Latent (variations found in coding and regulatory regions, are not harmful on their own, and the change in each gene only becomes apparent under certain conditions e.g. susceptibility to lung cancer)
TYPES OF SNP
NON-CODING REGION
A segment of DNA that does comprise a gene and thus does not code for a protein .
CODING REGION
Regions of DNA/RNA sequences that code for proteins
Synonymous
A SNP in which both forms lead to the same polypeptide sequence is termed synonymous
(sometimes called a silent mutation).
Non synonymous
If a different polypeptide sequence is produced they are non synonymous . A non synonymous change may either be missense or nonsense, where a missense change results in a different amino acid, while a nonsense change results in a premature stop codon.
SNP Applications
• Gene discovery and mapping
• Association-based candidate polymorphism testing
• Diagnostics/risk profiling
• Response prediction
• Homogeneity testing/study design
• Gene function identification
Single Nucleotide Polymorphism
The change in one nucleotide in a genome is known as single nucleotide polymorphism. There are assorted types of SNPs. SNPs can be detected by several analytical techniques i.e. DNA sequencing, microchip, HPLC and oligonucleotide ligation reaction.
SNP
This document discusses single nucleotide polymorphisms (SNPs). It defines SNPs as variations in DNA sequences that occur when a single nucleotide differs between members of a species. SNPs are the most common type of genetic variation. The document outlines the characteristics of SNPs, how they are used as genetic markers, and various methods for SNP genotyping, including direct sequencing, TaqMan assays, and microchips. It also discusses the advantages and applications of SNPs in areas like gene discovery, disease risk profiling, and genetic variation studies.
Single Nucleotide Polymorphism
This document discusses single nucleotide polymorphisms (SNPs), which are variations in DNA sequences among individuals. SNPs are the most common type of genetic variation, occurring around every 100 to 300 bases. They can be found in coding and non-coding regions, and may alter protein function directly by changing amino acids or indirectly by affecting regulatory sequences. SNPs can influence disease susceptibility and treatment response. Methods for identifying SNPs involve detecting known SNPs using techniques like restriction enzyme analysis or sequencing to find new SNPs. SNPs have many applications including gene mapping, disease association studies, diagnostics, and predicting treatment response.
Single nucleotide polymorphism by kk sahu
Single nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single nucleotide differs between individuals. SNPs are the most common type of genetic variation and can be found in both coding and non-coding regions. They may alter protein function or gene regulation. SNPs can act as biological markers for locating genes associated with diseases like cancer. Studying SNPs helps researchers understand genetic influences on disease susceptibility and drug responses.
Genetic polymorphism and It's Applications
Genetic polymorphism
Genetic polymorphism is the inheritance of a trait controlled by a single genetic locus with two alleles, in which the least common allele has a frequency of about 1% or greater. Genetic polymorphism is a difference in DNA sequence among individuals, groups, or populations.
Types of polymorphisms
Protein/enzyme polymorphisms
In the early days of human genetics, majority of polymorphisms were those associated with proteins and enzymes. To detect the polymorphism and a person’s genotype, one performed assays for the gene product, i.e., the protein or enzyme produced by the genetic blueprint.
DNA polymorphisms
The large class of polymorphisms are those that detect Slight variations at the level of DNA nucleotides.
Single nucleotide polymorphisms
A single nucleotide polymorphism or SNP is a sequence of DNA on which humans vary by one and only one nucleotide . Because humans differ by one nucleotide per every thousand or so nucleotides, there are millions of SNPs scattered throughout the human genome.
Tandem repeat polymorphisms
A tandem repeat polymorphism consists of a series of nucleotides that are repeated in tandem (i.e., one time after another). The polymorphism consists of the number of repeats.
Restriction Fragment Length Polymorphism (RFLP)
Restriction Fragment Length Polymorphism (RFLP) is a type in which organisms may be differentiated by analysis of patterns derived from cleavage of their DNA. If two organisms differ in the distance between sites of cleavage of a particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme.
Applications of Genetic Polymorphism
The study of polymorphism has many uses in medicine, biological research, and law enforcement. Genetic diseases may be caused by a specific polymorphism. Scientists can look for these polymorphisms to determine if a person will develop the disease, or risks passing it on to his or her children.
Genetic polymorphism
The document discusses genetic polymorphisms in Plasmodium falciparum, the parasite that causes malaria. It defines key terms like locus, allele, and genome. It then describes different types of genetic polymorphisms like single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), and short tandem repeats (STRs). The document focuses on polymorphisms related to drug resistance in P. falciparum, discussing genes associated with resistance to chloroquine (pfcrt) and other antimalarial drugs, along with specific mutations in those genes linked to resistance.
Pcr single strand conformation polymorphism
This document discusses PCR-SSCP (single-strand conformation polymorphism) analysis, which is a sensitive technique for detecting mutations. It works by separating double-stranded PCR products into single strands, which take on conformations depending on their sequence. Minor mutations can alter the conformation and cause bands to shift on a gel. The technique is useful for detecting unknown single nucleotide polymorphisms and has various applications in clinical diagnosis, forensics, and studying genetics in animals, plants, and microbes.
Genetic polymorphism
Polymorphisms are genetic variations that occur in at least 1% of a population. They can involve single nucleotide variations or larger differences in DNA sequences. Most polymorphisms do not cause disease, but some can influence traits or increase susceptibility to certain diseases. Common types of polymorphisms include SNPs, indels, repetitive elements, and microsatellites. Polymorphisms are identified through laboratory techniques like DNA sequencing and can be distinguished from mutations, which are rare variations that alter normal DNA sequences.
Presentation1
This document discusses single nucleotide polymorphisms (SNPs). SNPs represent variations in a single DNA nucleotide where one nucleotide differs between members of a species. They are the most common type of genetic variation. SNPs can occur in coding and non-coding regions, and may alter protein function or be silent. Methods to genotype SNPs include direct sequencing, TaqMan assays, and microchips. SNPs are useful as genetic markers and have applications in gene mapping, disease association studies, and personalized medicine.
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The document describes experiments conducted to induce apoptosis in non-invasive retinoblastoma cell lines using tissue-specific promoter guided suicide gene transfection. Key objectives included propagating the suicide gene plasmid, transfecting it into a non-invasive retinoblastoma cell line, validating transfection efficiency through various assays, and studying the apoptotic effects induced. Transfection was confirmed at the mRNA and protein level. Assays showed over 60% of transfected cells undergoing early apoptosis and 35% undergoing late apoptosis, demonstrating the suicide gene successfully induced apoptosis in the targeted retinoblastoma cells.
Genomics in Crop improvement
The document provides a timeline and overview of important developments in genomics from 1871 to present day. It begins with Friedrich Miescher identifying nuclein in cell nuclei in 1871 and continues through modern developments like CRISPR/Cas9 genome editing. Key events include discoveries of DNA structure, the genetic code, DNA sequencing techniques, sequencing the first plant and animal genomes, and launching of major genome projects. The document also outlines types and branches of genomics as well as some applications and limitations of genomics research in crops like rice, chili, wheat, barley, chickpea and maize.
Restriction fragment length polymorphism
RFLP is a genetic variant that can be examined by cleaving DNA with restriction enzymes, revealing inherited differences in restriction fragment patterns. Genomic variations like single nucleotide polymorphisms (SNPs) and variable number tandem repeats (VNTRs) can result in RFLPs. RFLPs are detected by cutting DNA with restriction enzymes, separating fragments by size, and comparing to normal patterns to identify length alterations caused by mutations or polymorphisms. This technique can be used to diagnose genetic diseases like sickle cell anemia where a single base mutation alters a restriction site.
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The distinctive character of modern biology is the study of biology as information. Merging of biology and information sciences is a fundamental drive in biomedicine. Indeed, the post-genomic era is providing a huge of amount of molecular data, pertaining to different levels of evidence, which requires specific expertise in raw data processing, explorative data analysis and systems biology.
Translational genomics relies on our ability to recognize the functional elements of the genome and to disentangle the complexity of their interactions, starting from the sequence and following its implications in transcriptomics, proteomics, metabolomics, epigenomics. The promise of genomic medicine is improved diagnosis and treatment through the application of genomic information and technologies, leading to precision medicine.
This talk will give an overview of computational genomics and its current challenges.
Tools used in molecular biology
This document provides information about genetic polymorphisms and methods used to detect single nucleotide polymorphisms (SNPs), including DNA isolation, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and gel electrophoresis. It defines a polymorphism as a harmless DNA variation between individuals and SNPs as single base mutations that are the most common source of genetic variation. The document outlines the steps of PCR including melting, annealing, and extension cycles to amplify DNA, as well as how restriction enzymes are used to digest PCR products into different fragments depending on sequences, which can then be separated by size via gel electrophoresis to detect SNPs.
Single nucleotide polymorphisms (sn ps), haplotypes,
This document provides an overview of SNPs (single nucleotide polymorphisms), including their biological background, terminology, detection techniques, and applications. It defines SNPs as single base changes that occur in at least 1% of a population. SNPs can be harmless, harmful, or latent, and are found primarily in noncoding regions, occurring around every 100-300 bases. The document discusses techniques for detecting known and unknown SNPs, including hybridization methods like microarrays and PCR, as well as enzyme-based techniques like nucleotide extension, cleavage, and ligation. It notes applications of SNPs in areas like gene discovery, disease association studies, diagnostics, and predicting treatment response.
Oligonucleotide ligation assay presentation
PCR-OLA is a technique that combines polymerase chain reaction with oligonucleotide ligation assay to detect single nucleotide polymorphisms by distinguishing between ligation and non-ligation of oligonucleotides. It involves two phases - a multiplex PCR amplification to amplify the target DNA, followed by a multiplex oligonucleotide ligation assay where detection probes hybridize adjacent to each other and are ligated if complementary, which can identify normal vs. mutant genotypes. Ligation is regulated by the specificity of oligonucleotide hybridization, the need for adjacent hybridization of probes, and perfect complementarity of two bases.
Microsatellite analysis in organelle genomes of chlorophyta（論文討論）
The document analyzes the frequency and distribution of simple sequence repeats (SSRs) in the chloroplast and mitochondrial genomes of chlorophyta algae. It finds that SSRs are more common in non-coding regions than coding regions. The most frequent SSRs are mono-nucleotide repeats, with poly A/T repeats being most common. Dinucleotide repeats are also present but less frequent, with poly AT/TA repeats being the most abundant. The SSR patterns in chlorophyta organellar genomes are similar to those in organelle and nuclear genomes of higher taxa. The study provides insight into SSR patterns in lower plant organellar genomes and their potential use as genetic markers.
Ppt snp detection
This document summarizes methods for detecting single nucleotide polymorphisms (SNPs). It discusses two main approaches: detecting unknown SNPs and detecting known SNPs. For unknown SNPs, global methods like restriction fragment length polymorphisms and targeted methods like denaturing gradient gel electrophoresis are used to scan DNA for new polymorphisms. For known SNPs, techniques like hybridization, primer extension, ligation, and mass spectrometry can be applied to screen individuals. Direct DNA sequencing is also discussed as the gold standard method, though historically it was labor-intensive. The document provides details on the principles and advantages/limitations of various SNP detection techniques.
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Snp by wajahahat ali
This document discusses single nucleotide polymorphisms (SNPs). It defines SNPs as single base changes in DNA sequences that occur in at least 0.1% of a population. SNPs are usually the result of errors in DNA replication or damage. They can be found in both coding and non-coding regions, and in coding regions they can alter protein structure. Applications of SNP analysis include gene discovery, disease association studies, and drug development. The document also describes several methods for SNP detection and identification, including PCR-based and non gel-based genotyping techniques as well as direct DNA sequencing.
Single nucleotide polymorphism
Single Nucleotide Polymorphism (SNP)
Polymorphism is a generic term that means 'many shapes‘. It is the ability to appsear in different form .
A single nucleotide polymorphism (SNP) is a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome differs between members of a species (or between paired chromosomes in an individual).
For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. For a variation to be considered a SNP, it must occur in at least 1% of the population.
CHARACTERISTICS OF SNP
• In human beings, 99.9 percent bases are same.
• Remaining 0.1 percent makes a person unique.
• Different attributes / characteristics / traits
• How a person looks, diseases he or she develops.
These variations can be:
Harmless (change in phenotype)
Harmful (diabetes, cancer, heart disease, Huntington's disease, and hemophilia )
Latent (variations found in coding and regulatory regions, are not harmful on their own, and the change in each gene only becomes apparent under certain conditions e.g. susceptibility to lung cancer)
TYPES OF SNP
NON-CODING REGION
A segment of DNA that does comprise a gene and thus does not code for a protein .
CODING REGION
Regions of DNA/RNA sequences that code for proteins
Synonymous
A SNP in which both forms lead to the same polypeptide sequence is termed synonymous
(sometimes called a silent mutation).
Non synonymous
If a different polypeptide sequence is produced they are non synonymous . A non synonymous change may either be missense or nonsense, where a missense change results in a different amino acid, while a nonsense change results in a premature stop codon.
SNP Applications
• Gene discovery and mapping
• Association-based candidate polymorphism testing
• Diagnostics/risk profiling
• Response prediction
• Homogeneity testing/study design
• Gene function identification
Single Nucleotide Polymorphism
The change in one nucleotide in a genome is known as single nucleotide polymorphism. There are assorted types of SNPs. SNPs can be detected by several analytical techniques i.e. DNA sequencing, microchip, HPLC and oligonucleotide ligation reaction.
SNP
This document discusses single nucleotide polymorphisms (SNPs). It defines SNPs as variations in DNA sequences that occur when a single nucleotide differs between members of a species. SNPs are the most common type of genetic variation. The document outlines the characteristics of SNPs, how they are used as genetic markers, and various methods for SNP genotyping, including direct sequencing, TaqMan assays, and microchips. It also discusses the advantages and applications of SNPs in areas like gene discovery, disease risk profiling, and genetic variation studies.
Single Nucleotide Polymorphism
This document discusses single nucleotide polymorphisms (SNPs), which are variations in DNA sequences among individuals. SNPs are the most common type of genetic variation, occurring around every 100 to 300 bases. They can be found in coding and non-coding regions, and may alter protein function directly by changing amino acids or indirectly by affecting regulatory sequences. SNPs can influence disease susceptibility and treatment response. Methods for identifying SNPs involve detecting known SNPs using techniques like restriction enzyme analysis or sequencing to find new SNPs. SNPs have many applications including gene mapping, disease association studies, diagnostics, and predicting treatment response.
Single nucleotide polymorphism by kk sahu
Single nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single nucleotide differs between individuals. SNPs are the most common type of genetic variation and can be found in both coding and non-coding regions. They may alter protein function or gene regulation. SNPs can act as biological markers for locating genes associated with diseases like cancer. Studying SNPs helps researchers understand genetic influences on disease susceptibility and drug responses.
Genetic polymorphism and It's Applications
Genetic polymorphism
Genetic polymorphism is the inheritance of a trait controlled by a single genetic locus with two alleles, in which the least common allele has a frequency of about 1% or greater. Genetic polymorphism is a difference in DNA sequence among individuals, groups, or populations.
Types of polymorphisms
Protein/enzyme polymorphisms
In the early days of human genetics, majority of polymorphisms were those associated with proteins and enzymes. To detect the polymorphism and a person’s genotype, one performed assays for the gene product, i.e., the protein or enzyme produced by the genetic blueprint.
DNA polymorphisms
The large class of polymorphisms are those that detect Slight variations at the level of DNA nucleotides.
Single nucleotide polymorphisms
A single nucleotide polymorphism or SNP is a sequence of DNA on which humans vary by one and only one nucleotide . Because humans differ by one nucleotide per every thousand or so nucleotides, there are millions of SNPs scattered throughout the human genome.
Tandem repeat polymorphisms
A tandem repeat polymorphism consists of a series of nucleotides that are repeated in tandem (i.e., one time after another). The polymorphism consists of the number of repeats.
Restriction Fragment Length Polymorphism (RFLP)
Restriction Fragment Length Polymorphism (RFLP) is a type in which organisms may be differentiated by analysis of patterns derived from cleavage of their DNA. If two organisms differ in the distance between sites of cleavage of a particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme.
Applications of Genetic Polymorphism
The study of polymorphism has many uses in medicine, biological research, and law enforcement. Genetic diseases may be caused by a specific polymorphism. Scientists can look for these polymorphisms to determine if a person will develop the disease, or risks passing it on to his or her children.
Genetic polymorphism
The document discusses genetic polymorphisms in Plasmodium falciparum, the parasite that causes malaria. It defines key terms like locus, allele, and genome. It then describes different types of genetic polymorphisms like single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), and short tandem repeats (STRs). The document focuses on polymorphisms related to drug resistance in P. falciparum, discussing genes associated with resistance to chloroquine (pfcrt) and other antimalarial drugs, along with specific mutations in those genes linked to resistance.
Pcr single strand conformation polymorphism
This document discusses PCR-SSCP (single-strand conformation polymorphism) analysis, which is a sensitive technique for detecting mutations. It works by separating double-stranded PCR products into single strands, which take on conformations depending on their sequence. Minor mutations can alter the conformation and cause bands to shift on a gel. The technique is useful for detecting unknown single nucleotide polymorphisms and has various applications in clinical diagnosis, forensics, and studying genetics in animals, plants, and microbes.
Genetic polymorphism
Polymorphisms are genetic variations that occur in at least 1% of a population. They can involve single nucleotide variations or larger differences in DNA sequences. Most polymorphisms do not cause disease, but some can influence traits or increase susceptibility to certain diseases. Common types of polymorphisms include SNPs, indels, repetitive elements, and microsatellites. Polymorphisms are identified through laboratory techniques like DNA sequencing and can be distinguished from mutations, which are rare variations that alter normal DNA sequences.
Presentation1
This document discusses single nucleotide polymorphisms (SNPs). SNPs represent variations in a single DNA nucleotide where one nucleotide differs between members of a species. They are the most common type of genetic variation. SNPs can occur in coding and non-coding regions, and may alter protein function or be silent. Methods to genotype SNPs include direct sequencing, TaqMan assays, and microchips. SNPs are useful as genetic markers and have applications in gene mapping, disease association studies, and personalized medicine.
FINAL
The document describes experiments conducted to induce apoptosis in non-invasive retinoblastoma cell lines using tissue-specific promoter guided suicide gene transfection. Key objectives included propagating the suicide gene plasmid, transfecting it into a non-invasive retinoblastoma cell line, validating transfection efficiency through various assays, and studying the apoptotic effects induced. Transfection was confirmed at the mRNA and protein level. Assays showed over 60% of transfected cells undergoing early apoptosis and 35% undergoing late apoptosis, demonstrating the suicide gene successfully induced apoptosis in the targeted retinoblastoma cells.
Genomics in Crop improvement
The document provides a timeline and overview of important developments in genomics from 1871 to present day. It begins with Friedrich Miescher identifying nuclein in cell nuclei in 1871 and continues through modern developments like CRISPR/Cas9 genome editing. Key events include discoveries of DNA structure, the genetic code, DNA sequencing techniques, sequencing the first plant and animal genomes, and launching of major genome projects. The document also outlines types and branches of genomics as well as some applications and limitations of genomics research in crops like rice, chili, wheat, barley, chickpea and maize.
Restriction fragment length polymorphism
RFLP is a genetic variant that can be examined by cleaving DNA with restriction enzymes, revealing inherited differences in restriction fragment patterns. Genomic variations like single nucleotide polymorphisms (SNPs) and variable number tandem repeats (VNTRs) can result in RFLPs. RFLPs are detected by cutting DNA with restriction enzymes, separating fragments by size, and comparing to normal patterns to identify length alterations caused by mutations or polymorphisms. This technique can be used to diagnose genetic diseases like sickle cell anemia where a single base mutation alters a restriction site.
Bioengineering Information for Genomic Medicine
The distinctive character of modern biology is the study of biology as information. Merging of biology and information sciences is a fundamental drive in biomedicine. Indeed, the post-genomic era is providing a huge of amount of molecular data, pertaining to different levels of evidence, which requires specific expertise in raw data processing, explorative data analysis and systems biology.
Translational genomics relies on our ability to recognize the functional elements of the genome and to disentangle the complexity of their interactions, starting from the sequence and following its implications in transcriptomics, proteomics, metabolomics, epigenomics. The promise of genomic medicine is improved diagnosis and treatment through the application of genomic information and technologies, leading to precision medicine.
This talk will give an overview of computational genomics and its current challenges.
Tools used in molecular biology
This document provides information about genetic polymorphisms and methods used to detect single nucleotide polymorphisms (SNPs), including DNA isolation, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and gel electrophoresis. It defines a polymorphism as a harmless DNA variation between individuals and SNPs as single base mutations that are the most common source of genetic variation. The document outlines the steps of PCR including melting, annealing, and extension cycles to amplify DNA, as well as how restriction enzymes are used to digest PCR products into different fragments depending on sequences, which can then be separated by size via gel electrophoresis to detect SNPs.
Single nucleotide polymorphisms (sn ps), haplotypes,
This document provides an overview of SNPs (single nucleotide polymorphisms), including their biological background, terminology, detection techniques, and applications. It defines SNPs as single base changes that occur in at least 1% of a population. SNPs can be harmless, harmful, or latent, and are found primarily in noncoding regions, occurring around every 100-300 bases. The document discusses techniques for detecting known and unknown SNPs, including hybridization methods like microarrays and PCR, as well as enzyme-based techniques like nucleotide extension, cleavage, and ligation. It notes applications of SNPs in areas like gene discovery, disease association studies, diagnostics, and predicting treatment response.
Oligonucleotide ligation assay presentation
PCR-OLA is a technique that combines polymerase chain reaction with oligonucleotide ligation assay to detect single nucleotide polymorphisms by distinguishing between ligation and non-ligation of oligonucleotides. It involves two phases - a multiplex PCR amplification to amplify the target DNA, followed by a multiplex oligonucleotide ligation assay where detection probes hybridize adjacent to each other and are ligated if complementary, which can identify normal vs. mutant genotypes. Ligation is regulated by the specificity of oligonucleotide hybridization, the need for adjacent hybridization of probes, and perfect complementarity of two bases.
Microsatellite analysis in organelle genomes of chlorophyta（論文討論）
The document analyzes the frequency and distribution of simple sequence repeats (SSRs) in the chloroplast and mitochondrial genomes of chlorophyta algae. It finds that SSRs are more common in non-coding regions than coding regions. The most frequent SSRs are mono-nucleotide repeats, with poly A/T repeats being most common. Dinucleotide repeats are also present but less frequent, with poly AT/TA repeats being the most abundant. The SSR patterns in chlorophyta organellar genomes are similar to those in organelle and nuclear genomes of higher taxa. The study provides insight into SSR patterns in lower plant organellar genomes and their potential use as genetic markers.
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Single nucleotide polymorphisms (sn ps), haplotypes,
Single nucleotide polymorphisms (sn ps), haplotypes,
Microsatellite analysis in organelle genomes of chlorophyta（論文討論）
Microsatellite analysis in organelle genomes of chlorophyta（論文討論）
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Types of pcr and fluorimeter (1)
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Types of pcr
PCR is a technique that amplifies a specific DNA sequence. It works by repeated cycles of heating and cooling of the DNA sample to separate, copy, and recombine strands. Each cycle approximately doubles the number of target sequences. This allows a very small initial sample to generate millions of copies of the target sequence. PCR is used in various applications including DNA sequencing, genetic disease diagnosis, cloning, and forensic analysis. It has become essential to many areas of biological research and medical diagnostics.
Molecular Methods for Diagnosis of Genetic Diseases
1. Many molecular methods have evolved for detecting mutations, moving from older techniques like Southern blotting to more rapid high-throughput methods.
2. These include amplification refractory mutation system (ARMS) PCR, single-strand conformational polymorphism (SSCP) analysis, denaturating gradient gel electrophoresis (DGGE), denaturating high performance liquid chromatography (DHPLC), real-time PCR, DNA microarrays, and sequencing.
3. The optimal method depends on the genetic disease, mutation type, and specific laboratory; techniques generally involve amplification, digestion, separation of DNA, labeling, and hybridization.
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qPCR assays using intercalating dyes, such as SYBR® Green dye, are an economical and effective tool for measuring gene expression. To interpret intercalating dye assays, users need to know how to analyze melt curves, and understand the benefits and limitations of melt curve analysis. In this presentation, Nick Downey, PhD, covers melt curve basics and shares examples of multiple peaks due to suboptimal sample prep, primer dimers, and asymmetric GC content of amplicons. He demonstrates troubleshooting strategies. Experienced and novice users will benefit from an overview of uMeltSM software, developed by the Wittwer lab at the University of Utah, that can predict the melt profile of your assay before you run your experiment.Detection of monoclonal immunoglobulin heavy chain gene rearrangement (fr3) i...
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DNA Denaturation
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Epigenetic
Epigenetic mechanism and advance in technique to study histone modification and Diseases associated with epigenetic
TILLING & ECOTILLING
A powerful non-transgenic reverse genetics method that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
EcoTILLING is a molecular technique that is similar to TILLING, except that its objective is to uncover natural genetic variation as opposed to induced mutations.
The answers can be found below as discussedPart 1)The human gen.pdf
The answers can be found below as discussed:
Part 1)
The human genome is highly vast in nature and hence there are some complicating factors in the
study of human genetics:
1: Size and packing: The human genome is enoromously large in linear seqeunce which makes it
highly difficult to be analysed as a whole. Moreover, the DNA is wounded in complex primary,
secondary and tertiary structures which makes is difficult to isolate intact i.e. formation of
nucleosomes over histones, solenoid formation, high writhe and twist etc. The human genome is
highly compact and along with it, chemical modifications such as
acetylation/methylation/sumoylation/phosphorylation of the DNA-associated proteins also occur.
Similarly, post-transcriptional modifications of mRNA also occur only in eukaryotes.
Compensation: These structural features of the human genome have been well exploited for their
analysis. The size cannot be reduced directly but the complexity of packing can be used by
action of relaxation enzymes such as topoisomerases.
Part 2)
The coding sequences: The human genome is not continuously coding in nature, but it has been
differentiated into stretches of coding euchromatin exons and non-coding intervening
heterochromatin intron sequences. This makes the linearity of the coding sequence highly
compromised and a single mechanism of linear transcription or translation cannot take place.
Compensation: The human genome contains the intron sequences only in the DNA. These
sequences are effectively removed out of the DNA after transcription by mRNA splicing and
thus only exons are remained in the mRNA. Thus, this ensures that only exons can reach the
translation process.
3. Polymorphism: The human genome shows very high degree of single nucleotide
polymorphism (SNP) which shows pattern of inheritance and can be transitted form one person
to another genetically. These SNPs are crucial for providing discrete phenotypic features to
individuals which can be difficult to assess and identify due to large size of human genome.
Compensation: Although there occur SNPs in human genome, the modern techniques such as
next-generation seqeuncing have made it possible to effectively, efficiently and quickly screen
the whole genome for such targets.
Answer part 2)
Variations in Mendelian genetics in humans can be described as below:
1. Co-dominance: Unlike Mendelian genetics, the blood group system of humans show co-
dominance between the allele A and allele B and both of these alleles are completely dominant
over the allele O. This makes occurance of various phenotypes in blood groups i.e. A, B, AB and
O.
2. Incomplete dominance: On contrary to Mendel\'s pattern of inheritance, the texture of hair in
human is inherited genetically following a pattern of incomplete dominance. This deciphers that
an offspring of parents having straight and curly hair will have softly curled hair.
3. Quantitative traits: Unlike Mendel\'s patterns of inheritance, some genes show quantitative.
Epigenetic&ms pcr inna
This document discusses epigenetics and methylation-specific PCR (MSP). It defines epigenetics as heritable changes in gene expression that do not involve changes to DNA sequence. Epigenetic mechanisms include DNA methylation, histone modifications, and non-coding RNAs. DNA methylation involves the addition of methyl groups to cytosine bases in CpG islands, influencing gene expression. Methylation-specific PCR is used to detect methylated DNA. Histone modifications like acetylation and methylation also influence chromatin structure and gene transcription. MicroRNAs and small interfering RNAs are types of non-coding RNAs that regulate gene expression post-transcriptionally.
OECD Guidlines By Genotoxicity
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0000ch9.pptaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
This document discusses applications of recombinant DNA technology, including site-specific mutagenesis using PCR and creating mutant mice. It also covers analyzing DNA polymorphisms like single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) using techniques like restriction fragment length polymorphism analysis, allele-specific oligonucleotide hybridization, and DNA microarrays. Finally, it discusses DNA molecular testing for genetic diseases, including purposes like prenatal diagnosis and examples using techniques like restriction fragment length polymorphism analysis for conditions like sickle-cell anemia.
Oncomine Cancer Research Panel (OCP) | ESHG 2015 Poster PS12.131
Treating cancer effectively requires an understanding of the molecular alterations driving each patient’s tumor. Targeted sequencing efforts that characterize prevalent somatic alterations and require limited sample input may provide an effective diagnostic approach. Herein, we describe the design and characterization of the Oncomine™ Cancer Research Panel (OCP) that includes recurrent somatic alterations in solid tumors derived from the Oncomine™ cancer database. Using Ion AmpliSeq™ technology, we designed a DNA panel that includes assays for 73 oncogenes with 1,826 recurrent hotspot mutations, 26 tumor suppressor genes enriched for deleterious mutations, as well as 75 genes subject to recurrent focal copy gain or loss. A complementary RNA panel includes 183 assays for relevant gene fusions involving 22 fusion driver genes. Recommended sample inputs were 10 ng of nucleic acid per pool. Sequencing libraries were analyzed on an Ion Torrent™ Personal Genome Machine™. Initial testing revealed an average read depth of > 1,500X with > 95% uniformity and on target frequency. The panel was shown to reliably detect known hotspots, insertions/deletions, gene copy changes, and gene fusions in molecular standards, cell lines and formalin-fixed paraffin embedded samples. Retrospective analysis of large sample cohorts has been completed and the results of analysis of 100 lung cancer and 100 prostate cancer cases will be summarized. In addition, a prospective cohort of 100 samples from the University of Michigan Molecular Diagnostics laboratory was profiled with OCP. Overall, we achieved >95% sensitivity and specificity for detection of KRAS, EGFR and BRAF mutations and ALK gene fusions.
2014 11 03_bioinformatics_case_studies
The document summarizes a presentation on bioinformatics case studies focusing on epigenetics and personal genomics. It discusses DNA methylation and its role in cancer development. It also describes how next-generation sequencing can be used to identify epigenetic biomarkers for clinical use. Finally, it addresses issues around personal and recreational genomics, including increasing access, educating users, and protecting individual privacy and rights.
Chapt 09
This document discusses cytogenetic techniques used in genetics. It describes (1) cell culture techniques used to grow cells for analysis, (2) harvesting and chromosome spreading to view chromosomes, and (3) karyotyping and analysis to identify chromosomal abnormalities. Modern techniques like fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) allow visualization of specific DNA sequences and identification of DNA copy number changes.
Chapt 09
This document discusses cytogenetic techniques used in biology. It begins by outlining the learning objectives which are to list cytogenetic techniques and understand cell culture, harvesting chromosomes, and karyotyping. It then describes various techniques including cell culture, harvesting and spreading chromosomes, karyotyping, fluorescence in situ hybridization (FISH), and comparative genomic hybridization (CGH). The purpose of these techniques is to examine genetic components of cells including chromosomes to study genetic abnormalities.
Complete Human Genome Sequencing
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Single Nucleotide Polymorphisms And The Causes And Effects...
Single nucleotide polymorphisms (SNPs) can have consequences on gene expression and cause genetic diseases like sickle cell anemia, which results from a single base pair mutation in the beta-globin gene. Researchers have studied SNPs related to sickle cell anemia to better understand genetic causes and establish diagnostic methods through analyzing DNA samples. Analysis of SNPs in populations can also determine if genetic diversity is caused by natural selection or mutation.
Next Generation Sequencing
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1. Operon refers to a cluster of structural genes regulated by a common operator and involved in the same metabolic pathway. Examples include the lac and tryptophan operons.
2. Signal transduction is the process by which extracellular signals are converted into intracellular responses, involving the steps of reception, transduction, and response.
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Annovi HRM and Epigenetics
- 1. Epigenetics and High Resolution Melting-PCR 7th European Elastin Meeting 1st - 4th september 2012 Giulia Annovi, PhD University of Modena and Reggio Emilia, Italy IBCP Lyon, France Moulin L., Cenizo V., André V., Sommer P., Debret R.
- 2. Histone modifications DNA methylation Epigenetic mechanisms are able to produce different phenotypes from a single genotype Effect of DNA methylation: # transcriptional repression # compact chromatine structures # normal embryological development # X chromosome inactivation # imprinting control O NH2 CH3 Cytosine
- 3. MethPrimer analysis of promoters : http://www.urogene.org/methprimer/index1.html NCBI Epigenomics: http://www.ncbi.nlm.nih.gov/epigenomics/view/genome Size (Start - End) Island 1 401 bp (71 - 471) Island 2 261 bp (571 - 831) Predicted CpG islands
- 4. The bisulfite conversion High Resolution Melting (HRM) Tissue samples fixed in paraffin Cell culture ss-DNA DNA extraction
- 5. High Resolution Melting (HRM) - PCR => Melting curves allow discrimination between methylated and unmethylated samples, because melting temperature is nucleotides composition dependent.
- 6. 100% Methylated 0% Methylated 100% Methylated Unconverted Quantitation data for Cycling: - converted ssDNA integrity - inter- and intra-sample comparable amplification 100% Methylated 0% Methylated HRM Data analysis
- 7. ⇒Global Melt Curves analysis can’t give a clear result: cytosines methylation in human samples is unbalanced and depends on environnement. ⇒ We have to analyse each curve independently to identify melting temperature for each sample. 100% Methylated 0% Methylated 100% Methylated
- 8. HRM is a powerful technique to identify methylation at specific promoter very quickly and from different kind of samples. pRloxl1 pRfbn1 pRfbln5 Predicted CpG islands -Moulin L. Romain D.-
- 9. HRM is a powerful technique to identify methylation at specific promoter very quickly and from different kind of samples. 74.95 75.05 75.15 75.25 75.35 75.45 75.55 a-SMA promoter methylation Collagen 5AZA MeltTemp=Methylationlevel 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5 a SMA expression - qPCR Fibro 5AZA mRNAaSMAexpression Fibroblasts Fibroblasts + 5 AZA
- 10. Thank you for your attention!
- 11. DNMT1 DNMT3A, DNMT3B DNA methyl-transferase: transfers a methyl group to DNA
Editor's Notes
- Because it is implicated in the organization of chromatin structure and regulation of gene transcription
- activity of DMNTs, a class of enzimes catalazying the transfer of a methyl moiety to cytosines principally in the CpG dinucleotide.