This document provides an agenda for a lecture on copy number variations (CNV) and their role in cancer development and pharmacogenetics. It begins with an introduction to CNVs, including definitions and mechanisms for their creation. It then discusses how CNVs can contribute to disease susceptibility and notes their role in directly influencing cancer cell genomes. The document outlines how common and rare CNVs may serve as "first hits" to the tumor genome or influence cancer risk. It provides some examples of specific cancers associated with CNVs and discusses how pharmacogenetics focuses on CNV effects in cancer treatment for drugs like tamoxifen and irinotecan. The document concludes by noting the promising potential for further discovery regarding C
This document discusses copy number variation analysis and qBiomarker Copy Number PCR Arrays. It begins with defining copy number variation and describing current methods to analyze copy number, including array CGH, SNP chips, NGS, qPCR and FISH. It then discusses issues with using single gene references and introduces the concept of a multicopy reference assay as a better reference. The remainder focuses on qBiomarker Copy Number PCR Arrays, which allow profiling copy number variation across curated gene sets or custom arrays. The arrays utilize a multicopy reference assay and are compatible with most qPCR instruments. Data analysis is performed using an online portal.
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells
The document discusses genomic concepts including:
- Genomics is the study of genomes including large chromosomal segments containing many genes. Functional genomics aims to deduce information about DNA function.
- The human genome contains 3.2 billion base pairs with about 3% coding for proteins. Genome size is measured in picograms or base pair number and complexity is distinct from length.
- Chromosomal organization differs between prokaryotes and eukaryotes. Eukaryotes possess multiple linear chromosomes packed into complexes while prokaryotes have single circular chromosomes.
- Much non-coding DNA in large genomes includes introns, regulatory elements, repeats and intergenic sequences. Nucleic acid thermodynamics
Single nucleotide polymorphisms (SNPs) are variations in single nucleotides that occur at specific positions in the genome between individuals. There can be 10-30 million SNPs in the human genome, typically found in non-coding DNA between genes. SNPs are important for understanding an individual's response to pathogens, chemicals, drugs, and vaccines as well as realizing personalized medicine. The Human HapMap Project analyzed DNA from different populations to identify haplotypes, sets of SNPs on the same chromosome, that are associated with diseases. The project identified over 50 disease-associated genes and its data has helped find genetic contributors to conditions like diabetes, Crohn's disease, and several cancers.
Whole Exome and Genome sequencing in Neurological disorders. The document discusses the techniques of next generation sequencing (NGS), including whole exome sequencing (WES) and whole genome sequencing (WGS). It provides examples of studies applying WES/WGS to diagnose neurological disorders, finding diagnostic variants in 25-60% of cases of leukoencephalopathy, limb-girdle muscular dystrophy, cerebellar ataxia, and more. The limitations and clinical applications of WES/WGS are also reviewed.
This document provides an overview of exome sequence analysis. It begins with definitions of key terms like genome, genetic variants, and exome sequencing. It then describes the exome sequencing workflow, which involves fragmentation, hybridization to capture exonic regions, sequencing, mapping reads to reference genome, variant calling, and variant annotation. Challenges of finding causal variants are discussed. The document also compares benefits and challenges of exome sequencing versus whole genome sequencing or traditional methods. Finally, it discusses how exome sequencing has helped identify novel disease genes and expand knowledge of known disease genes.
Seminar on dna based diagnosis of genetic diaseaseabhishek mondal
This document discusses methods for diagnosing genetic diseases using DNA analysis. It covers DNA probes, hybridization techniques using radioactive and non-radioactive detection, polymerase chain reaction to amplify DNA samples, DNA microarrays, and examples of genetic diseases that can be diagnosed this way such as cystic fibrosis, sickle cell anemia, and Huntington's disease. The key applications of DNA diagnostics are to detect inherited genetic defects or the presence of pathogenic genes through identification of alterations in genes.
This document discusses copy number variation analysis and qBiomarker Copy Number PCR Arrays. It begins with defining copy number variation and describing current methods to analyze copy number, including array CGH, SNP chips, NGS, qPCR and FISH. It then discusses issues with using single gene references and introduces the concept of a multicopy reference assay as a better reference. The remainder focuses on qBiomarker Copy Number PCR Arrays, which allow profiling copy number variation across curated gene sets or custom arrays. The arrays utilize a multicopy reference assay and are compatible with most qPCR instruments. Data analysis is performed using an online portal.
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells
The document discusses genomic concepts including:
- Genomics is the study of genomes including large chromosomal segments containing many genes. Functional genomics aims to deduce information about DNA function.
- The human genome contains 3.2 billion base pairs with about 3% coding for proteins. Genome size is measured in picograms or base pair number and complexity is distinct from length.
- Chromosomal organization differs between prokaryotes and eukaryotes. Eukaryotes possess multiple linear chromosomes packed into complexes while prokaryotes have single circular chromosomes.
- Much non-coding DNA in large genomes includes introns, regulatory elements, repeats and intergenic sequences. Nucleic acid thermodynamics
Single nucleotide polymorphisms (SNPs) are variations in single nucleotides that occur at specific positions in the genome between individuals. There can be 10-30 million SNPs in the human genome, typically found in non-coding DNA between genes. SNPs are important for understanding an individual's response to pathogens, chemicals, drugs, and vaccines as well as realizing personalized medicine. The Human HapMap Project analyzed DNA from different populations to identify haplotypes, sets of SNPs on the same chromosome, that are associated with diseases. The project identified over 50 disease-associated genes and its data has helped find genetic contributors to conditions like diabetes, Crohn's disease, and several cancers.
Whole Exome and Genome sequencing in Neurological disorders. The document discusses the techniques of next generation sequencing (NGS), including whole exome sequencing (WES) and whole genome sequencing (WGS). It provides examples of studies applying WES/WGS to diagnose neurological disorders, finding diagnostic variants in 25-60% of cases of leukoencephalopathy, limb-girdle muscular dystrophy, cerebellar ataxia, and more. The limitations and clinical applications of WES/WGS are also reviewed.
This document provides an overview of exome sequence analysis. It begins with definitions of key terms like genome, genetic variants, and exome sequencing. It then describes the exome sequencing workflow, which involves fragmentation, hybridization to capture exonic regions, sequencing, mapping reads to reference genome, variant calling, and variant annotation. Challenges of finding causal variants are discussed. The document also compares benefits and challenges of exome sequencing versus whole genome sequencing or traditional methods. Finally, it discusses how exome sequencing has helped identify novel disease genes and expand knowledge of known disease genes.
Seminar on dna based diagnosis of genetic diaseaseabhishek mondal
This document discusses methods for diagnosing genetic diseases using DNA analysis. It covers DNA probes, hybridization techniques using radioactive and non-radioactive detection, polymerase chain reaction to amplify DNA samples, DNA microarrays, and examples of genetic diseases that can be diagnosed this way such as cystic fibrosis, sickle cell anemia, and Huntington's disease. The key applications of DNA diagnostics are to detect inherited genetic defects or the presence of pathogenic genes through identification of alterations in genes.
ChIP-seq is a technique to identify where proteins bind to DNA in the genome. It involves cross-linking proteins to DNA in cells, fragmenting the DNA, immunoprecipitating the protein-DNA complexes using an antibody for the protein of interest, and then sequencing the retrieved DNA. This allows mapping of the genomic binding sites for the protein. The document discusses experimental design considerations for ChIP-seq, such as antibody choice and controls. It also reviews data analysis steps including read mapping, peak calling to identify enriched regions, and downstream analyses like motif finding. Higher resolution techniques like ChIP-exo are also introduced that can identify protein binding sites at base pair level.
This document discusses cancer genomics and tumor sequencing. It explains that tumor genotyping helps clinicians individualize cancer treatments by matching patients to the best treatment based on their tumor's DNA alterations. Next generation sequencing methods have made it possible to sequence entire cancer genomes and identify additional targets for new cancer therapies. Large-scale projects like The Cancer Genome Atlas and the International Cancer Genome Consortium are analyzing hundreds of cancer genomes to better understand the molecular changes driving different cancer types.
This document discusses epigenetics and cancer epigenetics. It defines epigenetics as heritable changes in gene expression that do not involve changes to DNA sequence. There are two forms of information in cells - genetic information encoded in the DNA sequence, and epigenetic information involving modifications like DNA methylation and histone acetylation. These epigenetic changes can contribute to oncogenesis along with genetic variations. The document discusses mechanisms of epigenetic changes like DNA methylation and histone acetylation/deacetylation and how they regulate gene expression. It provides examples of epigenetic changes in tumors and diseases and potential epigenetic therapies using demethylating and HDAC inhibitor drugs.
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
This document summarizes hereditary cancer syndromes and BRCA mutations. It discusses that most cancers are sporadic, but 5-10% are hereditary due to germline mutations passed down from relatives. Hereditary cancers often occur earlier and increase risk for multiple cancer types. Specific cancer susceptibility genes are discussed, including BRCA1 and BRCA2 mutations which increase lifetime risks of breast and ovarian cancers. Diagnostic testing and management strategies for individuals with BRCA mutations are outlined, including increased cancer screening, risk-reducing surgeries, and lifestyle modifications. Genetic counseling plays an important role in assessing cancer risks and managing hereditary cancer syndromes in families.
Gene expression and transcript profiling involves determining the pattern of genes expressed at the transcriptional level under specific circumstances by measuring the expression of thousands of genes simultaneously. This allows one to understand cellular function. Common techniques for profiling include DNA microarrays, RNA sequencing, and EST tags. DNA microarrays involve hybridizing cDNA or cRNA samples to probes on a chip to determine relative abundance of sequences. RNA sequencing uses next-generation sequencing to reveal presence and quantity of RNA in a sample.
Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows detection of copy number variations between a test and reference DNA sample without cell culturing. CGH involves labeling and hybridizing test and reference DNA to normal metaphase chromosomes before visualizing differences in fluorescence to identify regions of gains or losses. While CGH was originally used for cancer research, it can also detect chromosomal abnormalities associated with genetic disorders and has improved resolution over traditional cytogenetic methods. The main limitations of CGH are its inability to detect structural aberrations without copy number changes and resolutions above 5-10 megabases.
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
This document discusses genetic instability. It defines genetic instability as an increased rate of genomic alterations ranging from point mutations to chromosome rearrangements. It describes three main types: nucleotide instability, microsatellite instability, and chromosomal instability. Causes of genetic instability include replication errors, defects in DNA repair pathways, and issues during cell division. Methods for detecting instability include karyotyping, FISH, and array technologies. Genetic instability is a hallmark of cancer and helps accelerate tumor genesis by increasing mutations. Cells use mechanisms like DNA proofreading and cell cycle checkpoints to maintain stability.
CRISPR (clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found within the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacteriophages that have previously infected the prokaryote and are used to detect and destroy DNA from similar phages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes.
Cas9 (CRISPR-associated protein 9) is an enzyme that uses CRISPR sequences as a guide to recognize and cleave specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within organisms.This editing process has a wide variety of applications including basic biological research, development of biotechnology products, and treatment of diseases.
The CRISPR-Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity. RNA harboring the spacer sequence helps Cas (CRISPR-associated) proteins recognize and cut foreign pathogenic DNA. Other RNA-guided Cas proteins cut foreign RNA. CRISPR are found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
This presentation on Epigenetics is most advanced and evidence based one. Its Very helpful for Genetics students and research fellows, Reproductive Medicine specialist, Reproductive Biologist, Infertility practitioners
What is in situ hybridization
Radioactive ISH
Fluorescent ISH
Colorimetric ISH
ISH: three variables
The sample
The probe
Optimizing ISH Detection
ISH controls
Data Analysis
Genomic instability refers to changes in chromosome structure and number that can lead to cancer. It is caused by failures in DNA replication, damage sensing and repair, and cell cycle checkpoints. There are several types of genetic instability, including chromosomal instability (CIN), microsatellite instability (MIN), and DNA replication errors. CIN results in chromosome gains and losses, while MIN causes repetitive DNA expansions and contractions. Genomic instability can arise from defects in DNA damage response genes like p53 and ATM, problems with DNA replication, fragile sites in the genome, and DNA secondary structures. While genetic instability promotes evolution, it also contributes to pathological conditions like cancer by enabling the accumulation of mutations needed for malignant transformation.
The document discusses how epigenetics, through mechanisms like DNA methylation and histone modification, can influence gene expression and traits without changing the underlying DNA sequence. It provides examples of how environmental factors and early life experiences can alter the epigenome in ways that affect health conditions later in life, including cancer, mental illnesses like schizophrenia, and neurodevelopmental disorders. Epigenetic therapies targeting these epigenetic changes offer promising new medical approaches.
Next generation sequencing (NGS) provides a high-throughput and cheaper alternative to DNA sequencing through massively parallel sequencing of millions of DNA fragments simultaneously. NGS can be used for target sequencing to identify disease-causing mutations, RNA sequencing to study entire transcriptomes, and has various applications in cancer research and treatment including identifying mutations that predict responses to immunotherapy. However, NGS also faces challenges like accurately sequencing regions with repeats and detecting fusion genes.
Synopsis
Introduction
Some Facts
Types of SNPs
SNPs act as gene markers
Methods of Detection
Techniques to detect SNPs
Allelic Specific Cleavage
Differential Hybridization
Single Base Extension or minisequencing
Alternate Methods for Detecting SNPs
Mass Spectrometry
Microchips
SIGNIFICANCE OF SNPs
HAPLOTYPE
ADVANTAGES
Are SNP data available to the public?
Some important SNP database Resources
CONCLUSION
References
Epigenetics is the study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype — which in turn affects how cells read the genes. - [https://www.whatisepigenetics.com/fundamentals/]
Author of this presentation: The University of Western Australia
It contains information about- DNA Sequencing; History and Era sequencing; Next Generation Sequencing- Introduction, Workflow, Illumina/Solexa sequencing, Roche/454 sequencing, Ion Torrent sequencing, ABI-SOLiD sequencing; Comparison between NGS & Sangers and NGS Platforms; Advantages and Applications of NGS; Future Applications of NGS.
Exome seuencing (steps, method, and applications)Hamza Khan
This document summarizes exome sequencing methodology. It describes that exome sequencing sequences all expressed genes in a genome, which contains around 180,000 exons totaling 30 million base pairs in humans. There are two main steps: 1) selecting the exonic regions of DNA using either array-based or in-solution capture techniques, and 2) sequencing the captured exonic DNA using various platforms such as Sanger, 454, Illumina, or SOLiD sequencing. Exome sequencing has applications in rare variant mapping, discovering causes of Mendelian disorders, and clinical diagnostics.
This document describes the process of DNA microarray technology. It discusses:
- How DNA microarrays work by hybridizing DNA or RNA targets to probes arranged on a solid surface.
- The key steps of microarray experiments including array printing, sample preparation, hybridization, and data acquisition and analysis.
- Different types of microarrays like cDNA microarrays and high-density oligonucleotide arrays.
- Details of probe selection, target labeling, hybridization conditions, scanning, and data analysis.
CNVs have been found in many cancers including colon cancer and are thought to contribute to cancer development by altering gene dosage of oncogenes and tumor suppressors. Studies have shown that CNVs present in cancer cells are often absent in normal cells from the same patient. While the role of CNVs in cancer risk is still being explored, certain CNVs are associated with hereditary cancer syndromes that increase risk of colon cancer. Further research on cancer CNVs may lead to new biomarkers for cancer susceptibility, progression, and metastasis.
- Carcinogenesis is the process by which normal cells are transformed into cancer cells through genetic and epigenetic changes. It involves multiple steps including initiation, promotion and progression.
- Key events include transformation of cells, uncontrolled proliferation, invasion of surrounding tissues, and metastasis.
- DNA damage and defects in DNA repair can lead to mutations and epigenetic alterations that accumulate and drive carcinogenesis.
- Oncogenes and mutations in proto-oncogenes disrupt normal cell growth control and promote uncontrolled cell division.
ChIP-seq is a technique to identify where proteins bind to DNA in the genome. It involves cross-linking proteins to DNA in cells, fragmenting the DNA, immunoprecipitating the protein-DNA complexes using an antibody for the protein of interest, and then sequencing the retrieved DNA. This allows mapping of the genomic binding sites for the protein. The document discusses experimental design considerations for ChIP-seq, such as antibody choice and controls. It also reviews data analysis steps including read mapping, peak calling to identify enriched regions, and downstream analyses like motif finding. Higher resolution techniques like ChIP-exo are also introduced that can identify protein binding sites at base pair level.
This document discusses cancer genomics and tumor sequencing. It explains that tumor genotyping helps clinicians individualize cancer treatments by matching patients to the best treatment based on their tumor's DNA alterations. Next generation sequencing methods have made it possible to sequence entire cancer genomes and identify additional targets for new cancer therapies. Large-scale projects like The Cancer Genome Atlas and the International Cancer Genome Consortium are analyzing hundreds of cancer genomes to better understand the molecular changes driving different cancer types.
This document discusses epigenetics and cancer epigenetics. It defines epigenetics as heritable changes in gene expression that do not involve changes to DNA sequence. There are two forms of information in cells - genetic information encoded in the DNA sequence, and epigenetic information involving modifications like DNA methylation and histone acetylation. These epigenetic changes can contribute to oncogenesis along with genetic variations. The document discusses mechanisms of epigenetic changes like DNA methylation and histone acetylation/deacetylation and how they regulate gene expression. It provides examples of epigenetic changes in tumors and diseases and potential epigenetic therapies using demethylating and HDAC inhibitor drugs.
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
This document summarizes hereditary cancer syndromes and BRCA mutations. It discusses that most cancers are sporadic, but 5-10% are hereditary due to germline mutations passed down from relatives. Hereditary cancers often occur earlier and increase risk for multiple cancer types. Specific cancer susceptibility genes are discussed, including BRCA1 and BRCA2 mutations which increase lifetime risks of breast and ovarian cancers. Diagnostic testing and management strategies for individuals with BRCA mutations are outlined, including increased cancer screening, risk-reducing surgeries, and lifestyle modifications. Genetic counseling plays an important role in assessing cancer risks and managing hereditary cancer syndromes in families.
Gene expression and transcript profiling involves determining the pattern of genes expressed at the transcriptional level under specific circumstances by measuring the expression of thousands of genes simultaneously. This allows one to understand cellular function. Common techniques for profiling include DNA microarrays, RNA sequencing, and EST tags. DNA microarrays involve hybridizing cDNA or cRNA samples to probes on a chip to determine relative abundance of sequences. RNA sequencing uses next-generation sequencing to reveal presence and quantity of RNA in a sample.
Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows detection of copy number variations between a test and reference DNA sample without cell culturing. CGH involves labeling and hybridizing test and reference DNA to normal metaphase chromosomes before visualizing differences in fluorescence to identify regions of gains or losses. While CGH was originally used for cancer research, it can also detect chromosomal abnormalities associated with genetic disorders and has improved resolution over traditional cytogenetic methods. The main limitations of CGH are its inability to detect structural aberrations without copy number changes and resolutions above 5-10 megabases.
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
This document discusses genetic instability. It defines genetic instability as an increased rate of genomic alterations ranging from point mutations to chromosome rearrangements. It describes three main types: nucleotide instability, microsatellite instability, and chromosomal instability. Causes of genetic instability include replication errors, defects in DNA repair pathways, and issues during cell division. Methods for detecting instability include karyotyping, FISH, and array technologies. Genetic instability is a hallmark of cancer and helps accelerate tumor genesis by increasing mutations. Cells use mechanisms like DNA proofreading and cell cycle checkpoints to maintain stability.
CRISPR (clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found within the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacteriophages that have previously infected the prokaryote and are used to detect and destroy DNA from similar phages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes.
Cas9 (CRISPR-associated protein 9) is an enzyme that uses CRISPR sequences as a guide to recognize and cleave specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within organisms.This editing process has a wide variety of applications including basic biological research, development of biotechnology products, and treatment of diseases.
The CRISPR-Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity. RNA harboring the spacer sequence helps Cas (CRISPR-associated) proteins recognize and cut foreign pathogenic DNA. Other RNA-guided Cas proteins cut foreign RNA. CRISPR are found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
This presentation on Epigenetics is most advanced and evidence based one. Its Very helpful for Genetics students and research fellows, Reproductive Medicine specialist, Reproductive Biologist, Infertility practitioners
What is in situ hybridization
Radioactive ISH
Fluorescent ISH
Colorimetric ISH
ISH: three variables
The sample
The probe
Optimizing ISH Detection
ISH controls
Data Analysis
Genomic instability refers to changes in chromosome structure and number that can lead to cancer. It is caused by failures in DNA replication, damage sensing and repair, and cell cycle checkpoints. There are several types of genetic instability, including chromosomal instability (CIN), microsatellite instability (MIN), and DNA replication errors. CIN results in chromosome gains and losses, while MIN causes repetitive DNA expansions and contractions. Genomic instability can arise from defects in DNA damage response genes like p53 and ATM, problems with DNA replication, fragile sites in the genome, and DNA secondary structures. While genetic instability promotes evolution, it also contributes to pathological conditions like cancer by enabling the accumulation of mutations needed for malignant transformation.
The document discusses how epigenetics, through mechanisms like DNA methylation and histone modification, can influence gene expression and traits without changing the underlying DNA sequence. It provides examples of how environmental factors and early life experiences can alter the epigenome in ways that affect health conditions later in life, including cancer, mental illnesses like schizophrenia, and neurodevelopmental disorders. Epigenetic therapies targeting these epigenetic changes offer promising new medical approaches.
Next generation sequencing (NGS) provides a high-throughput and cheaper alternative to DNA sequencing through massively parallel sequencing of millions of DNA fragments simultaneously. NGS can be used for target sequencing to identify disease-causing mutations, RNA sequencing to study entire transcriptomes, and has various applications in cancer research and treatment including identifying mutations that predict responses to immunotherapy. However, NGS also faces challenges like accurately sequencing regions with repeats and detecting fusion genes.
Synopsis
Introduction
Some Facts
Types of SNPs
SNPs act as gene markers
Methods of Detection
Techniques to detect SNPs
Allelic Specific Cleavage
Differential Hybridization
Single Base Extension or minisequencing
Alternate Methods for Detecting SNPs
Mass Spectrometry
Microchips
SIGNIFICANCE OF SNPs
HAPLOTYPE
ADVANTAGES
Are SNP data available to the public?
Some important SNP database Resources
CONCLUSION
References
Epigenetics is the study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype — which in turn affects how cells read the genes. - [https://www.whatisepigenetics.com/fundamentals/]
Author of this presentation: The University of Western Australia
It contains information about- DNA Sequencing; History and Era sequencing; Next Generation Sequencing- Introduction, Workflow, Illumina/Solexa sequencing, Roche/454 sequencing, Ion Torrent sequencing, ABI-SOLiD sequencing; Comparison between NGS & Sangers and NGS Platforms; Advantages and Applications of NGS; Future Applications of NGS.
Exome seuencing (steps, method, and applications)Hamza Khan
This document summarizes exome sequencing methodology. It describes that exome sequencing sequences all expressed genes in a genome, which contains around 180,000 exons totaling 30 million base pairs in humans. There are two main steps: 1) selecting the exonic regions of DNA using either array-based or in-solution capture techniques, and 2) sequencing the captured exonic DNA using various platforms such as Sanger, 454, Illumina, or SOLiD sequencing. Exome sequencing has applications in rare variant mapping, discovering causes of Mendelian disorders, and clinical diagnostics.
This document describes the process of DNA microarray technology. It discusses:
- How DNA microarrays work by hybridizing DNA or RNA targets to probes arranged on a solid surface.
- The key steps of microarray experiments including array printing, sample preparation, hybridization, and data acquisition and analysis.
- Different types of microarrays like cDNA microarrays and high-density oligonucleotide arrays.
- Details of probe selection, target labeling, hybridization conditions, scanning, and data analysis.
CNVs have been found in many cancers including colon cancer and are thought to contribute to cancer development by altering gene dosage of oncogenes and tumor suppressors. Studies have shown that CNVs present in cancer cells are often absent in normal cells from the same patient. While the role of CNVs in cancer risk is still being explored, certain CNVs are associated with hereditary cancer syndromes that increase risk of colon cancer. Further research on cancer CNVs may lead to new biomarkers for cancer susceptibility, progression, and metastasis.
- Carcinogenesis is the process by which normal cells are transformed into cancer cells through genetic and epigenetic changes. It involves multiple steps including initiation, promotion and progression.
- Key events include transformation of cells, uncontrolled proliferation, invasion of surrounding tissues, and metastasis.
- DNA damage and defects in DNA repair can lead to mutations and epigenetic alterations that accumulate and drive carcinogenesis.
- Oncogenes and mutations in proto-oncogenes disrupt normal cell growth control and promote uncontrolled cell division.
An oncogene is a gene that has the potential to cause cancer. In tumor cells, these genes are often mutated or expressed at high levels. Most normal cells will undergo a programmed form of rapid cell death (apoptosis) when critical functions are altered and malfunctioning
Neoplasia refers to abnormal growths or tumors. Cancer is a genetic disease caused by DNA mutations that cause uncontrolled cell growth. Tumors can be benign or malignant, with malignant tumors able to spread to other parts of the body and be life-threatening. The development of cancer is influenced by oncogenes, tumor suppressor genes, DNA changes, infiltration of surrounding tissue, metastasis, and failure of immune surveillance mechanisms. A variety of environmental and viral agents can also cause cancer by inducing DNA mutations.
This document discusses neoplasia and tumor biology. It begins with definitions of neoplasia and benign versus malignant tumors. It describes the molecular basis of carcinogenesis including genetic changes that lead to autonomous growth. The progression of malignancy is explained in terms of differentiation, dysplasia, anaplasia and metastatic ability. Risk factors for cancer development including heredity, environment, viral exposure and DNA repair defects are outlined. The key genetic changes involved in malignant transformation are deregulated growth signals, evasion of growth inhibition, apoptosis resistance, replication immortality, angiogenesis and invasion.
This document discusses the role of genetic regulatory elements in human evolution and longevity. It makes three key points:
1. There is evidence that longevity and aging are heritable and selection traits that vary between species and populations due to evolutionary history.
2. Recent genetic studies have provided a huge amount of data on human and other genomes but have found few genetic variants associated with common diseases and traits, suggesting regulatory elements play an important role.
3. Elements like copy number variations, transposons, microRNAs, epigenetic modifications and DNA repair genes likely co-evolve over time and influence traits like longevity. Understanding their interactions and co-evolution could help trace human adaptations like skin color or nutrition.
Cancer arises due to genetic aberrations that accumulate in somatic cells and alter gene expression. There are several types of genomic changes including mutations, chromosome defects, and changes to oncogenes and tumor suppressor genes. Genetic testing can identify inherited cancer risk genes and guide diagnosis and treatment, while gene therapy holds promise for directly treating cancer at the genetic level.
This document discusses molecular biology concepts related to cancer, including:
1) Cells divide through proliferation and differentiation to replenish tissues, but mutations can render cells capable of uncontrolled growth (cancer).
2) A successful cancer cell must accumulate multiple mutations in genes controlling proliferation and apoptosis to evade homeostasis mechanisms.
3) Oncogenes are genes that drive cell growth when mutated or overexpressed. Common oncogenes include RAS, MYC, and others involved in signaling pathways.
4) Tumor suppressor genes normally inhibit cell growth but are inactivated in cancer, allowing uncontrolled proliferation. Understanding genetic damage causes is key to cancer prevention.
This document provides an overview of neoplasia (new abnormal growth) and cancer. It discusses the history and nomenclature of cancer, the difference between benign and malignant tumors, epidemiology, and the molecular basis and hallmarks of cancer development. Specifically, it describes how cancer arises from genetic mutations that cause cells to grow uncontrollably, evade growth controls, develop new blood vessels, and spread to other areas of the body. The document also examines in more detail the roles of tumor suppressor genes like RB and p53, which normally inhibit cell growth but are inactivated in cancer.
This document provides information about cancer genetics and cell biology. It defines cancer as uncontrolled cell growth and classifies tumors as benign or malignant. The main cancer types - carcinomas, sarcomas, and leukemias/lymphomas - are described based on their cell of origin. Key concepts in cancer development are discussed, including the roles of oncogenes, tumor suppressor genes, DNA repair genes, and failures in cell cycle control. Cancer results from mutations that disable normal controls on cell growth and division.
Clinical Validation of Copy Number Variant Detection by Next-Generation Seque...Golden Helix
Despite the great advances achieved in clinical genetics thanks to the incorporation of NGS (Next Generation Sequencing), a significant percentage of patients with diseases of genetic origin still do not have a conclusive molecular diagnosis. The incorporation of state-of-the-art bioinformatic methods has allowed the implementation of CNVs (Copy Number Variants) detection in NGS analysis, improving its diagnostic efficiency. In this study, the clinical utility of the detection of CNVs by NGS has been proven.
During 2018, 275 patients were studied using the NGS technique without obtaining an accurate genetic diagnosis. Bioinformatic tools that compare the normalized sequencing depth between patients and controls were used to determine CNVs. The results obtained were compared with patients own laboratory database and controls to rule out polymorphisms and false positives. All causal CNVs were confirmed by MLPA.
Pathogenic CNVs causing the disease were detected in 11 of the 275 patients (4%). Specifically, CNVs were detected for pathologies with autosomal dominant inheritance patterns (TSC2, MSH2, and FBN1), as well as for genes with autosomal recessive inheritance patterns, including two homozygous deletions (KCNV2 and RDX) and one heterozygous deletion with an SNV (Single Nucleotide Variant) in the PKHD1 gene. One of the most notable cases corresponds to a patient suspected of hypomagnesemia in which two deletions were identified in compound heterozygous mutation in the TRPM6 gene.
Carcinogenesis is the process by which normal cells are transformed into cancer cells. This involves changes at the cellular, genetic, and epigenetic levels. Cancers develop through a series of mutations that alter cell behavior and gene expression. There are two main categories of genes involved - oncogenes, which promote cell growth, and tumor suppressor genes, which suppress growth. For cancer to develop, mutations are generally required in both types of genes. Additionally, non-mutagenic carcinogens like alcohol and estrogen can increase cancer risk by stimulating faster cell division, leaving less time for DNA repair.
This document discusses liquid biopsies, which are non-invasive blood tests that detect circulating tumor cells and fragments of tumor DNA shed into the blood. Liquid biopsies provide information about cancers without invasive biopsy by analyzing biomarkers like circulating tumor cells, circulating tumor DNA, exosomes, and tumor-educated platelets. The document outlines the potential uses of liquid biopsy in cancer detection, diagnosis, monitoring treatment efficacy, and detecting recurrence. While tissue biopsy remains the gold standard, liquid biopsy is becoming more useful as technology advances and may provide information when a tissue biopsy is not possible or reveals limited information.
GTC group 8 - Next Generation SequencingYanqi Chan
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. Discuss the application of next generation sequencing in cancer treatment.
Next-generation DNA sequencing (NGS) provides high-throughput sequencing of DNA fragments in parallel to determine sequences exponentially faster and cheaper than Sanger sequencing. NGS can be used for whole genome, whole exome, or targeted gene panel sequencing. It has various clinical applications including cancer screening and management, diagnosis of complex genetic diseases, and identification of pathogenic variants. Tumor mutation burden (TMB) quantifies total mutations per tumor genome and higher TMB may predict better response to immunotherapy by expressing more neoantigens.
Como afrontar células madre de cáncer con alimentos Nutriline SRL
III Congreso mundial de medicina y nutrición moluecular e integrativa.
Alejandro Sacha Barrio Healey
"Como Afrontar Células Madre de Cáncer con Alimentos y Plantas"
This document discusses various cancer susceptibility syndromes. It begins by defining cancer susceptibility and the genetic and epigenetic factors that influence it. It then discusses several key syndromes in more detail, focusing on the genes involved, inheritance patterns, clinical features, and cancer risks. These include retinoblastoma (RB1 gene), Lynch syndrome (DNA mismatch repair genes), hereditary breast-ovarian cancer (BRCA1/2), neurofibromatosis type 1 (NF1 gene), and familial adenomatous polyposis (APC gene). It also outlines other syndromes categorized by the genes' functions in genomic integrity, proliferation, translation regulation, and angiogenesis.
This study investigated the relationship between MMP-9, TIMP-1, and sialic acid (NANA) in a human glial cell line and the effects of NANA on the expression of these genes. The study found that NANA upregulated the expression of both MMP-9 and TIMP-1 at lower concentrations in a way that maintained the MMP-9/TIMP-1 balance. However, at higher concentrations of 1000μM NANA, MMP-9 expression was upregulated to a significantly greater degree than TIMP-1 expression, causing an imbalance similar to reports in neurodegenerative diseases. This suggests NANA may be involved in signaling pathways regulating the expression of these genes linked to neuroinfl
This study investigated the relationship between matrix metalloproteinase 9 (MMP-9), tissue inhibitor of metalloproteinase 1 (TIMP-1), and sialic acid (NANA) in human glial cells. Treatment with NANA upregulated MMP-9 and TIMP-1 mRNA expression, indicating NANA involvement in signaling pathways regulating these genes. At lower NANA concentrations, MMP-9 and TIMP-1 expression increased similarly, but at the highest concentration MMP-9 increased more than TIMP-1, resembling an imbalance seen in multiple sclerosis. This suggests NANA affects MMP-9 and TIMP-1 expression and their balance, which may influence inflammatory demyelination.
This study investigated the relationship between MMP-9 gene expression and sialic acid (NANA) in human glial cell lines. Researchers treated glial cell lines with varying concentrations of NANA and found that MMP-9 mRNA expression increased with treatment, indicating NANA may be involved in signaling pathways regulating MMP-9 expression. The results suggest determining how NANA influences MMP-9 and other inflammatory molecules could provide insight into neurodegenerative diseases involving inflammation.
RNA interference (RNAi) is a biological process where RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. It was first discovered in plants and nematodes but is found in most eukaryotic organisms. The process involves specialized enzymes that cut long RNA molecules into short interfering RNAs which then guide other proteins to destroy any RNAs of the same sequence. RNAi plays important roles in regulating genes and defending against foreign DNA and RNA. It has many applications for studying gene function and as a potential therapeutic approach for diseases like cancer and infections.
Schizophrenia has a strong genetic component based on family and twin studies. While no single gene causes schizophrenia, genome-wide studies have implicated several genomic regions and candidate genes may play a role. Environmental factors like stress, abuse, and viruses during development can also influence risk. The dopamine and neurodevelopmental hypotheses propose that imbalances in brain chemistry like dopamine, or abnormalities in brain development, may underlie the disorder. Continued research on genetics, the brain, and environment aims to further elucidate the causes of schizophrenia.
Pharmacogenomics is the study of how an individual's genetic inheritance affects their body's response to drugs. It involves studying the genetic basis for variability in drug efficacy and toxicity. The goal is to develop personalized medicine by understanding how genetic factors influence an individual's ability to metabolize and respond to drugs. Key factors that can vary between individuals include drug metabolizing enzymes, drug transporters, and drug targets. Genetic variations in these factors are associated with differences in drug efficacy or risk of adverse effects. Pharmacogenomic testing helps identify genetic polymorphisms that can predict drug response and dosing requirements.
Here is the updated list of Top Best Ayurvedic medicine for Gas and Indigestion and those are Gas-O-Go Syp for Dyspepsia | Lavizyme Syrup for Acidity | Yumzyme Hepatoprotective Capsules etc
Does Over-Masturbation Contribute to Chronic Prostatitis.pptxwalterHu5
In some case, your chronic prostatitis may be related to over-masturbation. Generally, natural medicine Diuretic and Anti-inflammatory Pill can help mee get a cure.
ABDOMINAL TRAUMA in pediatrics part one.drhasanrajab
Abdominal trauma in pediatrics refers to injuries or damage to the abdominal organs in children. It can occur due to various causes such as falls, motor vehicle accidents, sports-related injuries, and physical abuse. Children are more vulnerable to abdominal trauma due to their unique anatomical and physiological characteristics. Signs and symptoms include abdominal pain, tenderness, distension, vomiting, and signs of shock. Diagnosis involves physical examination, imaging studies, and laboratory tests. Management depends on the severity and may involve conservative treatment or surgical intervention. Prevention is crucial in reducing the incidence of abdominal trauma in children.
Local Advanced Lung Cancer: Artificial Intelligence, Synergetics, Complex Sys...Oleg Kshivets
Overall life span (LS) was 1671.7±1721.6 days and cumulative 5YS reached 62.4%, 10 years – 50.4%, 20 years – 44.6%. 94 LCP lived more than 5 years without cancer (LS=2958.6±1723.6 days), 22 – more than 10 years (LS=5571±1841.8 days). 67 LCP died because of LC (LS=471.9±344 days). AT significantly improved 5YS (68% vs. 53.7%) (P=0.028 by log-rank test). Cox modeling displayed that 5YS of LCP significantly depended on: N0-N12, T3-4, blood cell circuit, cell ratio factors (ratio between cancer cells-CC and blood cells subpopulations), LC cell dynamics, recalcification time, heparin tolerance, prothrombin index, protein, AT, procedure type (P=0.000-0.031). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and N0-12 (rank=1), thrombocytes/CC (rank=2), segmented neutrophils/CC (3), eosinophils/CC (4), erythrocytes/CC (5), healthy cells/CC (6), lymphocytes/CC (7), stick neutrophils/CC (8), leucocytes/CC (9), monocytes/CC (10). Correct prediction of 5YS was 100% by neural networks computing (error=0.000; area under ROC curve=1.0).
Recomendações da OMS sobre cuidados maternos e neonatais para uma experiência pós-natal positiva.
Em consonância com os ODS – Objetivos do Desenvolvimento Sustentável e a Estratégia Global para a Saúde das Mulheres, Crianças e Adolescentes, e aplicando uma abordagem baseada nos direitos humanos, os esforços de cuidados pós-natais devem expandir-se para além da cobertura e da simples sobrevivência, de modo a incluir cuidados de qualidade.
Estas diretrizes visam melhorar a qualidade dos cuidados pós-natais essenciais e de rotina prestados às mulheres e aos recém-nascidos, com o objetivo final de melhorar a saúde e o bem-estar materno e neonatal.
Uma “experiência pós-natal positiva” é um resultado importante para todas as mulheres que dão à luz e para os seus recém-nascidos, estabelecendo as bases para a melhoria da saúde e do bem-estar a curto e longo prazo. Uma experiência pós-natal positiva é definida como aquela em que as mulheres, pessoas que gestam, os recém-nascidos, os casais, os pais, os cuidadores e as famílias recebem informação consistente, garantia e apoio de profissionais de saúde motivados; e onde um sistema de saúde flexível e com recursos reconheça as necessidades das mulheres e dos bebês e respeite o seu contexto cultural.
Estas diretrizes consolidadas apresentam algumas recomendações novas e já bem fundamentadas sobre cuidados pós-natais de rotina para mulheres e neonatos que recebem cuidados no pós-parto em unidades de saúde ou na comunidade, independentemente dos recursos disponíveis.
É fornecido um conjunto abrangente de recomendações para cuidados durante o período puerperal, com ênfase nos cuidados essenciais que todas as mulheres e recém-nascidos devem receber, e com a devida atenção à qualidade dos cuidados; isto é, a entrega e a experiência do cuidado recebido. Estas diretrizes atualizam e ampliam as recomendações da OMS de 2014 sobre cuidados pós-natais da mãe e do recém-nascido e complementam as atuais diretrizes da OMS sobre a gestão de complicações pós-natais.
O estabelecimento da amamentação e o manejo das principais intercorrências é contemplada.
Recomendamos muito.
Vamos discutir essas recomendações no nosso curso de pós-graduação em Aleitamento no Instituto Ciclos.
Esta publicação só está disponível em inglês até o momento.
Prof. Marcus Renato de Carvalho
www.agostodourado.com
Basavarajeeyam is an important text for ayurvedic physician belonging to andhra pradehs. It is a popular compendium in various parts of our country as well as in andhra pradesh. The content of the text was presented in sanskrit and telugu language (Bilingual). One of the most famous book in ayurvedic pharmaceutics and therapeutics. This book contains 25 chapters called as prakaranas. Many rasaoushadis were explained, pioneer of dhatu druti, nadi pareeksha, mutra pareeksha etc. Belongs to the period of 15-16 century. New diseases like upadamsha, phiranga rogas are explained.
Cell Therapy Expansion and Challenges in Autoimmune DiseaseHealth Advances
There is increasing confidence that cell therapies will soon play a role in the treatment of autoimmune disorders, but the extent of this impact remains to be seen. Early readouts on autologous CAR-Ts in lupus are encouraging, but manufacturing and cost limitations are likely to restrict access to highly refractory patients. Allogeneic CAR-Ts have the potential to broaden access to earlier lines of treatment due to their inherent cost benefits, however they will need to demonstrate comparable or improved efficacy to established modalities.
In addition to infrastructure and capacity constraints, CAR-Ts face a very different risk-benefit dynamic in autoimmune compared to oncology, highlighting the need for tolerable therapies with low adverse event risk. CAR-NK and Treg-based therapies are also being developed in certain autoimmune disorders and may demonstrate favorable safety profiles. Several novel non-cell therapies such as bispecific antibodies, nanobodies, and RNAi drugs, may also offer future alternative competitive solutions with variable value propositions.
Widespread adoption of cell therapies will not only require strong efficacy and safety data, but also adapted pricing and access strategies. At oncology-based price points, CAR-Ts are unlikely to achieve broad market access in autoimmune disorders, with eligible patient populations that are potentially orders of magnitude greater than the number of currently addressable cancer patients. Developers have made strides towards reducing cell therapy COGS while improving manufacturing efficiency, but payors will inevitably restrict access until more sustainable pricing is achieved.
Despite these headwinds, industry leaders and investors remain confident that cell therapies are poised to address significant unmet need in patients suffering from autoimmune disorders. However, the extent of this impact on the treatment landscape remains to be seen, as the industry rapidly approaches an inflection point.
Integrating Ayurveda into Parkinson’s Management: A Holistic ApproachAyurveda ForAll
Explore the benefits of combining Ayurveda with conventional Parkinson's treatments. Learn how a holistic approach can manage symptoms, enhance well-being, and balance body energies. Discover the steps to safely integrate Ayurvedic practices into your Parkinson’s care plan, including expert guidance on diet, herbal remedies, and lifestyle modifications.
share - Lions, tigers, AI and health misinformation, oh my!.pptxTina Purnat
• Pitfalls and pivots needed to use AI effectively in public health
• Evidence-based strategies to address health misinformation effectively
• Building trust with communities online and offline
• Equipping health professionals to address questions, concerns and health misinformation
• Assessing risk and mitigating harm from adverse health narratives in communities, health workforce and health system
Osteoporosis - Definition , Evaluation and Management .pdfJim Jacob Roy
Osteoporosis is an increasing cause of morbidity among the elderly.
In this document , a brief outline of osteoporosis is given , including the risk factors of osteoporosis fractures , the indications for testing bone mineral density and the management of osteoporosis
Osteoporosis - Definition , Evaluation and Management .pdf
Cancer and CNV
1. Presented by: Narjes Khatoon Shabani Sadr
Provided for : Cancer Genetics - Dr. Galedari
2.
3. Agenda for this Lecture
• Introduction of Copy number variations (CNV)
• types of CNV :bi-allelic and multi-allelic CNVs.
• Mechanism for the creation CNV
• Role in disease
• Define Cancer
• CNV role in cancer development
• Copy-number changes and cancer
• CNVs and cancer predisposition:
first hits to the tumor genome
• Common cancer CNVs
• Rare cancer CNVs
• Examples of cancer associated with CNVs
• CVN and Pharmacogenetics in oncology
• Conclusions
4. • The gene copy number (also "copy number variants" or CNVs) is the number
of copies of a particular gene in the genotype of an individual.
• Recent evidence shows that the can be elevated in
.
Introduction Copy number variations (CNV)
5. Introduction Copy number variations (CNV) :
A brief history of CNVs
• The first CNV in humans – discovered in the early – was found
to be widespread throughout all populations, with a range of striking
but largely benign phenotypic consequences.
• However, the first large, systematic structural comparisons of the
genomes of healthy humans were only carried out in and used
to identify large numbers of CNVs that are present at
significant frequency.
• Further studies have revealed well over a thousand CNVs, which at
one time were believed to account for of the human
genome, a figure inflated somewhat by the limited spatial resolution
of the methods used and consequent overestimation of the sizes of
the genomic regions involved.
6. • Copy-number variations (CNVs)—a form of structural
variation—are alterations of the DNA of a genome
that results in the cell having an abnormal or, for
certain genes, a normal variation in the number of
copies of one or more sections of the DNA.
• CNVs correspond to relatively large regions of the
genome that have been deleted (fewer than the
normal number) or duplicated (more than the normal
number) on certain chromosomes.
7. • For example, the chromosome that normally has
sections in order as A-B-C-D might instead have
sections A-B-C-C-D (a duplication of "C") or A-B-D (a
deletion of "C").
• This variation accounts for roughly 13% of human
genomic DNA and each variation may range from
about one kilo base (1,000 nucleotide bases) to
several megabases in size.
Introduction Copy number variations
(CNV)
8. Introduction Copy number variations
(CNV)
• DNA copy number variations (CNVs) are an important component of genetic
variation, affecting a greater fraction of the genome than single nucleotide
polymorphisms (SNPs).
9. • CNVs correspond to relatively large regions of
the genome that have been deleted or
duplicated on certain chromosomes.
• This variation accounts for roughly 13% of
human genomic DNA and each variation may
range from about 1 kb to several megabases
in size.
• CNVs contrast with SNPs, which affect only
one single nucleotide base.
10. What is a copy number variant?
• Human DNA has one copy of autosomal regions on each
chromosome.
• However, as discovered by the Human Genome Project,
many genetic regions display a variation in the number of
copies (more or less than two copies).
• Alleles containing 0 –13 gene copies have been reported
across the human population.
11. What is a copy number variant?
• These genetic variants are termed and are defined as
DNA segments ranging in size from to
among individuals owing to , ,
, , or .
• Although the contribution of CNVs to the of
common diseases is questionable, CNVs in some
genes play a clear role in drug efficacy
and toxicity.(especially in cancer)
12. Copy Number Variations in the Human
Genome
Chromosome Position
Person 1
Person 2
SignalSignal
Extra DNA
Missing DNA
14. Mechanism for the creation CNV
• Most CNVs are stable and , so CNV between
individuals is largely a product of genetic heritage,
however, arise through diverse mechanisms
at various stages of development.
• Multiple homologous recombination reactions on each
chromosome are required for the meiotic cell divisions
that give rise to gametes, and although these events are of
very high fidelity, occasional mistakes are inevitable.
• Therefore, most CNV in the human genome likely arises
through non-allelic homologous recombination events in
which unmatched regions of chromosomes are mistakenly
recombined during meiosis.
15. • However, two lines of evidence suggest that this is not
the whole story.
• Firstly, various studies have revealed extensive CNV
between different cells in the same individuals; these
CNVs must have arisen post-fertilization.
• Secondly, some complex genetic rearrangements cannot
be readily reconciled with a non-allelic homologous
recombination mechanism; these have been proposed to
arise through rare replication defects resulting from
broken DNA at one replication fork invading another fork,
resulting in a template switch.
• This was subsequently superseded by a more general
micro homology-mediated break-induced replication
(MMBIR) model.
Mechanism for the creation CNV
17. Non-homologous end joining (NHEJ) can result in a
genomic rearrangement that immediately or eventually
results in the or of genetic material after multiple
double-strand DNA breaks occur and are repaired.
18. Non-homologous end joining (NHEJ) can result in a
genomic rearrangement that immediately or eventually
results in the gain or loss of genetic material after multiple
double-strand DNA breaks occur and are repaired.
19. Role in disease
• Like other types of genetic variation, some CNVs have been
associated with or to disease.
• Gene copy number can be in cancer cells. For instance,
the copy number can be than normal in
.
• In addition, a higher copy number of CCL3L1 has been associated
with lower susceptibility to HIV infection, and a low copy number
of FCGR3B (the CD16 cell surface immunoglobulin receptor) can
increase susceptibility to systemic lupus erythematosus and similar
inflammatory autoimmune disorders. Copy number variation has also
been associated with autism, schizophrenia, and idiopathic learning
disability.
20. Define Cancer
is a term used to describe a large group
of diseases that are characterized by a cellular
malfunction.
• Healthy cells are programmed to “
”.
• Cancerous cells do not have this programming
and therefore and out of
control.
• They also serve no physiological function.
These cells are now termed a neoplasm.
• This neoplasmic mass often forms a clumping
of cells known as a tumor.
21. • Although the exact pathogenic mechanisms leading to
many cancers are unclear, the consensus view is that
cancer results from dysregulation of the activity or
expression of genes that control cell growth and
differentiation, leading to abnormal cell proliferation.
have been reported in ,
and presumably contribute to this dysregulation.
Define Cancer
22. Copy-number changes and cancer
• CNVs have clearly been shown to have the potential to indirectly
influence a healthy individual’s susceptibility to , for example
by the or .
• A more direct and immediate role of copy-number change is seen in
cancerous cells themselves, which frequently display CNVs that are
absent in the patient’s normal cells in characteristic (although cancer-
type specific) parts of the genome.
• Arguably, such copy-number changes in cancer cells should not be
called ‘variants’ because they do not fall within the spectrum of
normal human variation.
23. • Aneuploidy, double-minutes and nonreciprocal
translocations have long been recognized in many cancers
and are one form of CNV.
• But cancers have also been shown to gain additional copies
of certain smaller genomic regions.
• Such gains are of particular interest when they are found in
many patients with a given cancer type or in the early
stages of cancer because they can then be inferred to
harbor so-called ‘driver genes’ that favor the growth of
abnormal cells.
Copy-number changes and cancer
24. • By contrast, in the later stages of many cancers, ‘genomic
chaos’ often ensues, which makes it difficult to determine
which copy-number changes are significant or causative
and which are purely incidental or of minor importance.
Copy-number changes and cancer
25. CNVs and cancer predisposition:
first hits to the tumor genome
• The goal of cancer genetics is to discover all
that predispose to neoplasms.
• To this end, have been the most widely studied form
of genetic variation and, by using massive GWA studies,
many common SNPs have been shown to be associated
with cancer and other complex traits.
• However, the results of these efforts have not explained
much of the .
• This is perhaps because GWA studies have mostly ignored
the inter-individual genetic variation provided by CNVs,
which affect more than 10% of the human genome.
26. • CNVs, especially smaller variants, have been essentially
hidden from view until recently; thus, only a handful of
studies have found an association of CNVs with cancer.
• Once these CNVs have been identified, one can only
assume that CNVs will explain a larger portion of the
genetic basis of cancer.
• Once identified, common and rare CNVs should be
considered separately, as they may have very different roles
in cancer.
CNVs and cancer predisposition:
first hits to the tumor genome
27. Common cancer CNVs :Distribution of common
cancer CNVs in the human genome
As with SNPs, CNVs that are found frequently in the healthy population (common
CNVs) are very likely to have a role in cancer etiology.
28. Common cancer CNVs
:this is essential for DNA repair by homologous
recombination and has been shown by a GWA study to
contain a SNP that is strongly associated with
.
that seems to be associated with
a small deletion in Mtus1 is associated with a
decreased risk of familial and high-risk
29. Rare cancer CNVs
• There are over 200 cancer syndromes and although most
arise infrequently, they account for 5-10% of all cancer
cases.
• These are caused by base-pair-sized germline mutations
in many central
- such as: TP53, APC, BRCA1,
BRCA2, PTEN, and RB1
• and (fewer) , including HRAS and RET.
32. CNVs and tumor genomes: Copy
number alterations(CNA)
• Genome-scale analyses have found many formerly invisible
CNAs.
• In an analysis of 371 lung adenocarcinoma samples, Weir et al.
identified and
.
• The most significant amplification, at and containing
the novel oncogene .
• Mullighan et al found copy number changes in PAX5, a gene
within the B-cell development pathway, in 57 of 192 cases.
33. • In glioblastoma, CNA information, mRNA expression
levels and methylation changes have been measured and
nucleotide mutational analyses have been carried out.
• Integrative analysis has shown that over 70% of tumors
carry alterations in the retinoblastoma, p53 and receptor
tyrosine kinase pathways.
• Although cancer is driven primarily by alterations of the
genome, CNA profiles can be combined with other high-
throughput data to create insights that are 'greater than
the sum of their parts'.
CNVs and tumor genomes: Using
CNAs to define the key pathways of a
tumor
34. • CGH analysis has also shown that CNVs are associated
with , breast cancer, and
.
• Tse et al identified eight regions with CNVs including six
(on chromosomes 3, 6, 7, 8 and 19), and two
(on chromosomes 7 and 12) that were
significantly overrepresented in
patients compared with healthy
controls.
Examples of cancer associated
with CNVs
35. • Among these CNVs and gene deletions
on chromosome 6p21.3 showed the highest
association signal.
• Examining 51 BRCA1-associated ovarian cancer
patients, and 47 healthy women via Affymetrix
Genome-Wide Human SNP Array 6.0, Yoshihara et al
identified in BRCA1 associated ovarian
cancer patients.
Examples of cancer associated
with CNVs
39. Single-nucleotide
polymorphisms(SNPs) effect on
Pharmacogenomics
Single Nucleotide Polymorphism (SNP):
GAATTTAAG
GAATTCAAG
SNPs are defined as Single base-pair positions
in genomic DNA that vary among individuals
in one or several populations.
SNPs are believed to underlie susceptibility
to such common diseases as cancer, diabetes,
and heart disease and to contribute to the
traits that make individuals unique.
SNPs are used as genomic biomarkers.
Hence SNP analysis can be used to enhance
drug discovery and development.
DNA molecule 1 differs from DNA
molecule 2 at a single base-pair
location (a C/T polymorphism)
40. Examples of drugs where pharmacogenomics
testing is useful are listed in this Table
41. CVN and Pharmacogenetics in oncology
Pharmacogenetics focused on the effects of genetics in cancer
treatment.
Pharmacogenetics And selection of anticancer drugs:
• Thiopurine
• Irinotecan،
• Tamoxifen
42. Thiopurine such as :
6-mercaptopurine (6-MP)
thioguanine
and azathioprine (TPMT)
Metabolized by: thiopurine-S-methyl transferase (TPMT)
CVN and Pharmacogenetics in oncology
48. Tamoxifen (estrogen receptor-positive breast
cancer)
Tamoxifen is a prodrug
endoxifen (4-hydroxy-N-desmethyl-tomoxifer)
Tamoxifen
By CYP2D6
49. Conclusions
• The study of cancer and CNVs is in its infancy but is
maturing quickly.
• In considering the effect of this form of genetic variation
on cancer predisposition, cancer gene expression and
tumor genome profiling, there is much to learn from past
studies on genomic disorders.
• Denser micro-arrays, next-generation sequencing and
integrative informatics analyses are around the corner and
promise to uncover new CNVs and CNAs.
50. Conclusions
• There are, therefore, many exciting questions to be addressed:
• what role do CNVs have in cancer predisposition and how can we
use this newly discovered form of genetic variation to identify
those most at risk?
• Which cancer-related genes are affected by CNVs and, of these
changes, which are both necessary and sufficient to cause
neoplastic growth?
• Can incipient cancer cells use these constitutional deletions and
duplications to induce or accelerate tumorigenesis and tumor
proliferation?
51. • As these questions are resolved, the potential value of
cancer CNVs as novel biomarkers of cancer
susceptibility and initiation, and of cancer progression
and metastases, will become apparent. Whether
cancer CNVs offer insight into genes that might be
targets for novel drug development remains to be
determined.
Conclusions
52.
53. References
• Adam Shlien and David Malkin. (16 June 2009). Copy number vvariations and cancer.
Genome Medicine, 11:: 62.
• Ana CV Krepischi,Maria Isab el W Achatz,Erika MM San tos,, Silvia S Costa,Bianca CG
Lisboa,Helena Brentani,. (2012). Germline DNA copy number variation in familial and
early-onset breast cancer. Krepischi et al . Breast Cancer Research, 14-24.
• Andrew N. Shelling,Lynnette R. Ferguson. (2007). Genetic variation in human disease
and a new role for copy number variants. Mutation Research 622, 33–41.
• Antonis C Antoniou and Georgi a Chenev ix-Trench. (2010). Common genetic variants
and cancer risk in Mendelian cancer syndromes. Current Opinion in Gen etics &
Development, 299 –307.
• Bin Liu,ei Yang,Binf ang Huang,Mei C heng,Hui Wang,Yinyan Li,Do ngshen g Huang.
(August 10, 2012). A Functional Copy-Number Variation in MAPKAPK2. The American
Journal of Human Genetics 91, 384–390.
• Charles Lee , Courtney Hyland , Arthur S. Lee , Shona Hislop and Chunhwa Ihm. (2010).
Copy Number Variation and Human Health. In C. H. Charles Lee, Essentials of Genomic
and Personalized Medicine by Ginsburg & Willard (p. CHAPTER 5).
• Colin C . Pritchard, Stephen J. Salipante ,. (January 2014). Validation and Implem
entation of Targeted Capture and Sequencing for the Detection of Actionable
54. • Mutation, Copy Number Variation, and Gene Rearrangemen t in
Clinical Cancer Specimens. The Journal of Molecular Diagnostics.
• Dear, P. H. (July 2009). Copy-number variation: the end of the human
genome? Trends in Biotechnology, 448-456.
• Elsa Vanh ecke,Alexan der Valen t,Ximing Tang,Philippe Vielh,Luc Frib
oulet,Tao Tang,Aïcha Goubar,Yua nyuan Li,. (2013). 19q13- ERCC1
Gene Copy Number Incre ase in Non e Small-Cell Lung Cancer. Clinical
Lung Cancer, 549-57.
• Iuliana Ionita-Laza,Angela J . Rogers,, Christoph Lange,, Benjamin A .
Raby,Charles Lee. (2009). Genetic association analysis of copy-
number variation (CNV) in human disease pathogenesis. Genomics
93 , 22-26.
• Roland P Kuiper,Marjolijn JL Ligten berg,Nicoline Hoogerb rugge,and
Ad Geurt s van Kessel. (2010). Germline copy number variation and
cancer risk. Current Opinion in Gen etics & Development, 282 – 289.
References
55. • Tie-Lin Yang, Yan Guo,Christopher J. Papasian and
Hong-Wen Deng. (2013). Copy Number Variation. In
Y. G.-W. Tie-Lin Yang, Genetics of Bone Biology and
Skeletal Disease (p. chapter 9).
• Xiaosu Zhao,Qi Wu,Xinrong Fu,Bo Yu,Yong Shao,Hong
Yang,Ming Guan,Xiaojun Huang,. (2010).
Examination of copy number variations of CHST9 in
multiple types of hematologic malignancies. Cancer
Genetics and Cytogenetics 203 , 176 e179.
• Yijing He, Janelle M. Hoskins and Howard L. McLeod.
(May 2011). Copy number variants in pharmaco
genetic genes. Trends in Molecular Medicine.
References
56. “Human beings are ultimately
nothing but carriers-passageways-
for genes.
They ride us into the ground like
racehorses from generation to
generation. Genes don't think about
what constitutes good or evil.
They don't care whether we are happy or
unhappy. We're just means to an end for them.
The only thing they think about is what is
most efficient for them.”
Haruki Murakami, 1Q84
Editor's Notes
a) An example of a bi-allelic CNV that has a 1-copy allele and a 2-copy allele. The reference individual has two 1-copy alleles but 50% of individuals in this population have a total of three copies of this gene per cell. All bi-allelic CNVs have three genotypes per diploid cell, and in this case, copy numbers of 2, 3, and 4 per diploid cell. b) An example of a multi-allelic CNV that has a 0, 1, 2 and 3 copy alleles, resulting in six genotypes in this population. Only the allelic combinations for the three most common genotypes are shown.
Non-allelic homologous recombination (NAHR) is a mechanism for generating CNVs where recombination between non-allelic repeats with 90% sequence homology (indicated by black- and gray-colored DNA segments). Intervening DNA sequences are deleted and duplicated on different chromatids.
(a) A balanced rearrangement has occurred and there is no immediate net gain or loss of genomic material within the cell, but it will result in gains or losses of DNA in subsequent generations depending on which chromosome is inherited.
(b) In an unbalanced rearrangement, genomic material can be lost immediately (e.g., in this case, the acentric fragment containing one copy of genes b and c will be lost in subsequent cell divisions).
The chromosomes containing common cancer CNVs in the human genome are shown, with centromeric regions in red and Giemsa banding patterns in white, grey or black. Loci are in green if they were found to contain a cancer-related gene that is overlapped or encompassed by a CNV.
در یک پژوهش از 70 تا از ژنهای سرطانهای ژرم لاین در سرشماری ژنهای سرطان، 28 تا از ژنها گزارش شده است که به وسیله ی حذف ژنومی یا دوپلیکاسیون جهش یافته است (ژنها در جدول 1 نشان داده شد).
یک مدل بالقوه برای توضیح سهم CNVهای معمول و نادر برای سرطان در شکل 3 نشان داده شده است.
A model of copy-number-variable DNA regions in patients with sporadic (top) or inherited (bottom) cancer. We propose that healthy people maintain a similar low number of CNVs in their genomes (left; black blocks indicate inherited CNVs), whereas those at risk of developing early onset cancer have an excess of CNVs and a greater overall genomic burden of copy-number-variable DNA (middle; red blocks indicate somatically acquired CNVs). As a tumor grows, it acquires more copy-number-variable regions, including tumor-specific regions (blue).
(a) Testosterone is normally processed into DHT and other androgens. When there are two copies of UGT2B17 , the gene product converts excess molecules of DHT into the water-soluble glucuronic acid and is subsequently eliminated from the cell. (b) When there is a homozygous deletion of UGT2B17 , the DHT-sequestration pathway no longer exists, increasing endogenous interaction with androgen receptors (AR) and leading to elevated cell proliferation, which in some cases can result in the development of prostate cancer ( Park et al., 2006 ).
عمدهی ژنهای شناخته شد که در CNV های ژرم لاین گنجانده شدهاند در جدول یک نمایش داده میشوند.
ناقلین جهش BRCA2 که 2 کپی از آلل C در این SNP دارند مشخص شد که در معرض افزایش 3 برابری خطر پیشرفت سرطان سینه در مقایسه با هموزیگوتهای GG میباشند (جدول 2).
نتایج حاصله تاکنون برای 6 تا از این SNPها در MAP3K7 , LSP1 , TNRC , TONS, FGFR2 نواحی 3q20 , 2q35 منتشر شده است. (جدول 2)