Raj Lab Meeting presentation (05/01/19)
by Katia Lopes and Ricardo Vialle
Discussing the paper "The impact of rare variation on gene expression across tissues" - Li et al. Nature (2017)
FunGen JC Presentation - Mostafavi et al. (2019)BrianSchilder
The document summarizes a study that used RNA sequencing data from over 500 brain samples to construct gene coexpression networks and identify modules of genes associated with Alzheimer's disease traits like cognitive decline and amyloid pathology. They prioritized one module (m109) associated with cognitive decline and validated two genes (INPPL1 and PLXNB1) within that module that reduced amyloid levels in vitro. However, these genes did not fully account for the effects of the entire module, suggesting more work is needed to identify additional driver genes related to cognitive decline in Alzheimer's disease.
Functional Genomics Journal Club presentation on the following publication:
Kuzawa, C. W., Chugani, H. T., Grossman, L. I., Lipovich, L., Muzik, O., Hof, P. R., … Lange, N. (2014). Metabolic costs and evolutionary implications of human brain development. Proceedings of the National Academy of Sciences, 111(36), 13010–13015. https://doi.org/10.1073/pnas.1323099111
Genome-wide association study (GWAS) technology has been a primary method for identifying the genes responsible for diseases and other traits for the past ten years. GWAS continues to be highly relevant as a scientific method. Over 2,000 human GWAS reports now appear in scientific journals. Our free eBook aims to explain the basic steps and concepts to complete a GWAS experiment.
This document summarizes research applying genome-wide association studies (GWAS) and transcriptomics to study gene-trait associations in banana. A GWAS was performed on a panel of 106 banana accessions to identify genomic regions associated with seedlessness. Five regions were identified, with two genes directly linked to female sterility in Arabidopsis. Additional studies explored drought tolerance by measuring leaf temperatures under drought and conducting transcriptomics analyses of three genotypes under osmotic stress. The research aims to aid banana breeding through gene discovery using these complementary genomic and phenomic approaches.
This document is a seminar submission by Varsha Gayatonde on the topic of genome wide association studies. It includes an introduction to genetic mapping, key terminology used in GWAS such as linkage disequilibrium and minor allele frequency. It then discusses the history and concepts of GWAS, including a comparison to biparental mapping. Specific examples of GWAS in crops such as Arabidopsis, rice, and maize are also mentioned.
Genome-wide association studies (GWAS) allow researchers to scan the entire human genome to find genetic variations associated with particular diseases. The document describes a multi-stage GWAS that identified genetic variants associated with type 2 diabetes. It involved initial genome-wide scans followed by focused validation stages with increasing sample sizes. Several loci were confirmed, including regions near TCF7L2, SLC30A8, and HHEX genes. A variant near IRS1 was also identified. Association results were assessed in additional populations and metabolic trait analyses.
This document summarizes research on developing a human cancer coessentiality network using data from pooled shRNA screens across 107 cancer cell lines. Key points:
- A network of 866 genes and 1877 edges was constructed based on correlations in essentiality profiles across cell lines.
- Network clustering identified groups of genes essential for similar cell line subtypes (e.g. breast, ovarian, pancreatic cancers).
- One cluster involved in oxidative phosphorylation was particularly essential for luminal/HER2 breast cancers.
- The network provides a functional genomics resource, though opportunities exist to improve coverage and accuracy.
FunGen JC Presentation - Mostafavi et al. (2019)BrianSchilder
The document summarizes a study that used RNA sequencing data from over 500 brain samples to construct gene coexpression networks and identify modules of genes associated with Alzheimer's disease traits like cognitive decline and amyloid pathology. They prioritized one module (m109) associated with cognitive decline and validated two genes (INPPL1 and PLXNB1) within that module that reduced amyloid levels in vitro. However, these genes did not fully account for the effects of the entire module, suggesting more work is needed to identify additional driver genes related to cognitive decline in Alzheimer's disease.
Functional Genomics Journal Club presentation on the following publication:
Kuzawa, C. W., Chugani, H. T., Grossman, L. I., Lipovich, L., Muzik, O., Hof, P. R., … Lange, N. (2014). Metabolic costs and evolutionary implications of human brain development. Proceedings of the National Academy of Sciences, 111(36), 13010–13015. https://doi.org/10.1073/pnas.1323099111
Genome-wide association study (GWAS) technology has been a primary method for identifying the genes responsible for diseases and other traits for the past ten years. GWAS continues to be highly relevant as a scientific method. Over 2,000 human GWAS reports now appear in scientific journals. Our free eBook aims to explain the basic steps and concepts to complete a GWAS experiment.
This document summarizes research applying genome-wide association studies (GWAS) and transcriptomics to study gene-trait associations in banana. A GWAS was performed on a panel of 106 banana accessions to identify genomic regions associated with seedlessness. Five regions were identified, with two genes directly linked to female sterility in Arabidopsis. Additional studies explored drought tolerance by measuring leaf temperatures under drought and conducting transcriptomics analyses of three genotypes under osmotic stress. The research aims to aid banana breeding through gene discovery using these complementary genomic and phenomic approaches.
This document is a seminar submission by Varsha Gayatonde on the topic of genome wide association studies. It includes an introduction to genetic mapping, key terminology used in GWAS such as linkage disequilibrium and minor allele frequency. It then discusses the history and concepts of GWAS, including a comparison to biparental mapping. Specific examples of GWAS in crops such as Arabidopsis, rice, and maize are also mentioned.
Genome-wide association studies (GWAS) allow researchers to scan the entire human genome to find genetic variations associated with particular diseases. The document describes a multi-stage GWAS that identified genetic variants associated with type 2 diabetes. It involved initial genome-wide scans followed by focused validation stages with increasing sample sizes. Several loci were confirmed, including regions near TCF7L2, SLC30A8, and HHEX genes. A variant near IRS1 was also identified. Association results were assessed in additional populations and metabolic trait analyses.
This document summarizes research on developing a human cancer coessentiality network using data from pooled shRNA screens across 107 cancer cell lines. Key points:
- A network of 866 genes and 1877 edges was constructed based on correlations in essentiality profiles across cell lines.
- Network clustering identified groups of genes essential for similar cell line subtypes (e.g. breast, ovarian, pancreatic cancers).
- One cluster involved in oxidative phosphorylation was particularly essential for luminal/HER2 breast cancers.
- The network provides a functional genomics resource, though opportunities exist to improve coverage and accuracy.
MAGIC :Multiparent advanced generation intercross and QTL discovery Senthil Natesan
MAGIC or multiparent advanced generation inter-crosses is an experimental method that increases the precision with which genetic markers are linked to quantitative trait loci (QTL). This method was first introduced by (Mott et al., 2000) in animals as an extension of the advanced intercrossing (AIC) approach suggested by (Darvasi and Soller , 1995)for fine mapping multiple QTLs for multiple traits. Advanced Intercrossed Lines (AILs) are generated by randomly and sequentially intercrossing a population initially originating from a cross between two inbred lines.
MAGIC involves multiple parents, called founder lines, rather than bi-parental control. AILs increase the recombination events in small chromosomal regions for the purpose of fine mapping. These lines are then cycled through multiple generations of outcrossing. Each generation of random mating reduces the extent of linkage disequilibrium (LD), allowing the QTL to be mapped more accurately.
Emerging Clinical Applications of CRISPR-Cas9 as Promising Strategies in Gene...Chi-Ping Day
CRISPR/Cas9 gene editing shows promise for correcting diseases through gene therapy and targeted changes. Current applications include editing T-cells to produce CAR T-cells for cancer therapy and editing retinal cells in rats to treat retinitis pigmentosa. Additional areas of focus include eliminating HIV from cells, correcting the Fah mutation in mice, and overcoming issues like delivery efficiency and off-target effects. Looking ahead, cell therapies and local treatments for eye/ear diseases appear promising applications for CRISPR's precise gene editing capabilities.
The IMPACT of INDEL realignment: Detecting insertions and deletions longer th...Ronak Shah
Cancer is a disease of the genome –most of its forms result from a buildup of genetic alterations that, directly or indirectly, allow the patient’s cells to proliferate without restraint. For decades, identifying and targeting cancer mutations for treatment was impractical due to the limitations of sequencing technology. However, the rise of high-throughput next-generation sequencing (NGS) tools has allowed researchers to rapidly and cheaply sequence large, targeted regions of DNA. MSK-IMPACT(Memorial Sloan Kettering-IntegratedMutation Profiling of Actionable Cancer Targets), a sequencing platform with an associated computational pipeline, takes advantage of improvements in sequencing technology to analyzetumor specimensfor clinically actionable variants in341 cancer-associatedgenes.Criticalto IMPACT’s efficacy is the detection of somatic DNAalterationslike INDELs, which are insertions or deletions of nucleotides. Current sequence aligners have difficulty accuratelymapping reads (short, overlapping DNA sequences) containing morethan a single base change, let alone reads containing INDELs. This flaw necessitates the use of INDEL realigners, whichrearrange reads inregions where INDELs might exist in order to identify them more easily. Currently, the INDEL realignment software associated withMSK-IMPACT’scomputational pipeline, the Genome Analysis Toolkit’s IndelRealigner (GATK), canonly efficiently resolveINDELsshorter than 30 base pairs, which limits theplatform’sreliability forINDELdetection. Thus, wetested and compared the performance of a new INDEL realigner called ABRA (Assembly BasedRe-Aligner) to that of GATK’s IndelRealigner.
Detecting clinically actionable somatic structural aberrations from targeted ...Ronak Shah
Structural aberrations including deletions, insertions, inversions, tandem duplications, translocations, and more complex rearrangements constitute a frequent type of alteration in human tumors. Here, we sought to explore the potential to discover such events from targeted DNA sequence data in our CLIA-compliant molecular diagnostics laboratory. To detect somatic structural aberrations in individual tumors, we have developed an analytic framework in Perl & Python to detect these events in data generated by a hybridization capture-based, targeted sequencing clinical assay (MSK-IMPACT), which can reveal structural rearrangements as small as 500bp.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
Comparative analysis of gene regulation in mouse rat and humanconstantina mylona
Which is the most suitable model mouse or rat even in the use of the latest gene editing tool-CRISPR/Cas 9 ?
Final Project presentaion on BSc Human Biology
Creative Biogene, a global provider and manufacture, offers professional products and services to help our clients in gene research. CRISPR/Cas9 PlatformCB, which provides comprehensive gene editing services and products, is one of Creative Biogene’s platforms.
https://www.creative-biogene.com/crispr-cas9/about-us.html
The document describes an analysis of gene expression data from a glioblastoma cell line before and after treatment with the chemotherapeutic drug temozolomide (TMZ). RNA sequencing data was analyzed using the Deseq2 model to identify differentially expressed genes between untreated and treated conditions. Weighted gene co-expression network analysis (WGCNA) was also used to cluster genes into modules and identify co-expression patterns. Additionally, a software application was developed to analyze single-cell RT-PCR data on 96 genes of interest identified from the RNA-seq analysis, in order to investigate tumor heterogeneity. The results highlighted genes and gene modules related to drug resistance in glioblastoma.
Gene drives are a new genetic engineering technique that uses CRISPR to bias inheritance and spread genetic modifications throughout populations at rates much higher than normal Mendelian inheritance. Researchers have successfully created a gene drive in mosquitoes that causes fluorescent eyes as a proof of concept. This technique could potentially be used to eradicate malaria by modifying mosquitoes unable to transmit the disease. However, gene drives face technical challenges and raise significant ethical concerns about human control over natural evolution that require extensive public discussion and new regulations before deployment.
CRISPR Gene Editing Congress, 25-27 February 2015 in Boston, MADiane McKenna
Key industry leaders will gather at the inaugural CRISPR Precision Gene Editing Congress with an ultimate purpose of addressing the importance of overcoming specificity, efficiency and delivery challenges associated with the CRISPR/Cas9 system. Pioneers will showcase the expanding biomedical and therapeutic potential of gene editing tools for drug discovery and development.
Developing a framework for for detection of low frequency somatic genetic alt...Ronak Shah
Cancer is a complex, heterogeneous disease of the genome. Most cancers result
from an accumulation of multiple genetic alterations that lead to dysfunction of cancer-associated
genes and pathways. Recent advances in sequencing technology have enabled comprehensive
profiling of genetic alterations in cancer. We have established a targeted sequencing platform
(IMPACT: Integrated Mutation Profiling of Actionable Cancer Targets) using hybridization capture and
next-generation sequencing (NGS) technology, which can reveal mutations, indels and copy number
alterations involving 340 cancer related genes.
This document discusses genomic technologies that can be used to observe the human genome and their applications. It covers microarrays, next-generation sequencing, DNA methylation, copy number variation, and more. Challenges include the cost of these technologies and integrating the large amounts of data they produce to improve healthcare.
APPLICATION OF NEXT GENERATION SEQUENCING (NGS) IN CANCER TREATMENTDinie Fariz
Next generation sequencing (NGS) has revolutionized cancer treatment by enabling high throughput DNA sequencing. This document discusses several applications of NGS in cancer treatment including whole exome sequencing of tumors from 25 patients to identify genetic mutations, using avatar mouse models to test proposed treatment strategies, detecting mutations in liquid biopsies, and identifying somatic mutations in leukemia patients. Challenges of NGS include analyzing large amounts of data, accurately interpreting variants, and addressing ethical issues.
Bioinformatics and NGS for advancing in hearing loss researchJoaquin Dopazo
This document discusses the importance of bioinformatics and next-generation sequencing (NGS) for advancing hearing loss research. It summarizes the Spanish 1000 genomes project, which sequenced over 1000 samples across various rare and familial diseases to search for novel disease genes, responsible genes with unknown modifier genes, susceptibility genes, and therapeutic targets. The organization and analysis pipeline of the project is described, including initial quality control, mapping, variant calling, annotation, filtering, and gene prioritization. Results identified 36 new disease variants in known genes and 27 disease variants in 13 new genes.
The document discusses the growth of genomic sequence data due to falling costs of DNA sequencing. This creates both a "big data" problem of how to store and analyze large amounts of data, as well as a "diminishing discovery" problem as it becomes harder to find new discoveries within the data. The document proposes several solutions to these problems including pre-competitive collaboration between organizations to share data and analytics platforms. It provides examples of existing data sharing platforms like tranSMART and describes how next generation sequencing is revealing different types of human genetic variation including single nucleotide polymorphisms and their role in pharmacogenomics.
Speaker: Benedict C. S. Cross, PhD, Team leader (Discovery Screening), Horizon Discovery
CRISPR–Cas9 mediated genome editing provides a highly efficient way to probe gene function. Using this technology, thousands of genes can be knocked out and their function assessed in a single experiment. We have conducted over 150 of these complex and powerful screens and will use our experience to guide you through the process of screen design, performance and analysis.
We'll be discussing:
• How to use CRISPR screening for target ID and validation, understanding drug MOA and patient stratification
• The screen design, quality control and how to evaluate success of your screening program
• Horizon’s latest developments to the platform
• Horizon’s novel approaches to target validation screening
This document summarizes research on estimating the population fitness and genetic load of single nucleotide polymorphisms (SNPs) that affect mRNA splicing. The authors develop an objective function to relate differences in the information content of alleles to the fitness of genotypes in a population. They analyze over 1 million SNPs from the HapMap project and identify thousands that alter natural splice site information. By calculating genetic load based on changes in information content and allele frequency, they partition SNPs according to their predicted effect on splicing and population fitness. Many predicted effects are supported by gene expression studies. Their analysis provides insights into how natural selection acts on splicing-related SNPs.
This document summarizes a study that analyzed genetic variants called single nucleotide polymorphisms (SNPs) that affect mRNA splicing. The researchers developed a method to estimate the population fitness and genetic load of SNPs based on how they alter the information content of mRNA splicing sites. They analyzed SNPs in human populations that were known to affect splicing sites. Many of the predicted effects of SNPs on splicing and gene expression were supported by gene expression data. The researchers integrated various genetic and genomic datasets into a database to relate SNPs to changes in splicing and gene expression. They computed the genetic fitness and load for all SNPs in databases to analyze their potential effects on populations based on changes to splicing site information content and allele frequencies.
MAGIC :Multiparent advanced generation intercross and QTL discovery Senthil Natesan
MAGIC or multiparent advanced generation inter-crosses is an experimental method that increases the precision with which genetic markers are linked to quantitative trait loci (QTL). This method was first introduced by (Mott et al., 2000) in animals as an extension of the advanced intercrossing (AIC) approach suggested by (Darvasi and Soller , 1995)for fine mapping multiple QTLs for multiple traits. Advanced Intercrossed Lines (AILs) are generated by randomly and sequentially intercrossing a population initially originating from a cross between two inbred lines.
MAGIC involves multiple parents, called founder lines, rather than bi-parental control. AILs increase the recombination events in small chromosomal regions for the purpose of fine mapping. These lines are then cycled through multiple generations of outcrossing. Each generation of random mating reduces the extent of linkage disequilibrium (LD), allowing the QTL to be mapped more accurately.
Emerging Clinical Applications of CRISPR-Cas9 as Promising Strategies in Gene...Chi-Ping Day
CRISPR/Cas9 gene editing shows promise for correcting diseases through gene therapy and targeted changes. Current applications include editing T-cells to produce CAR T-cells for cancer therapy and editing retinal cells in rats to treat retinitis pigmentosa. Additional areas of focus include eliminating HIV from cells, correcting the Fah mutation in mice, and overcoming issues like delivery efficiency and off-target effects. Looking ahead, cell therapies and local treatments for eye/ear diseases appear promising applications for CRISPR's precise gene editing capabilities.
The IMPACT of INDEL realignment: Detecting insertions and deletions longer th...Ronak Shah
Cancer is a disease of the genome –most of its forms result from a buildup of genetic alterations that, directly or indirectly, allow the patient’s cells to proliferate without restraint. For decades, identifying and targeting cancer mutations for treatment was impractical due to the limitations of sequencing technology. However, the rise of high-throughput next-generation sequencing (NGS) tools has allowed researchers to rapidly and cheaply sequence large, targeted regions of DNA. MSK-IMPACT(Memorial Sloan Kettering-IntegratedMutation Profiling of Actionable Cancer Targets), a sequencing platform with an associated computational pipeline, takes advantage of improvements in sequencing technology to analyzetumor specimensfor clinically actionable variants in341 cancer-associatedgenes.Criticalto IMPACT’s efficacy is the detection of somatic DNAalterationslike INDELs, which are insertions or deletions of nucleotides. Current sequence aligners have difficulty accuratelymapping reads (short, overlapping DNA sequences) containing morethan a single base change, let alone reads containing INDELs. This flaw necessitates the use of INDEL realigners, whichrearrange reads inregions where INDELs might exist in order to identify them more easily. Currently, the INDEL realignment software associated withMSK-IMPACT’scomputational pipeline, the Genome Analysis Toolkit’s IndelRealigner (GATK), canonly efficiently resolveINDELsshorter than 30 base pairs, which limits theplatform’sreliability forINDELdetection. Thus, wetested and compared the performance of a new INDEL realigner called ABRA (Assembly BasedRe-Aligner) to that of GATK’s IndelRealigner.
Detecting clinically actionable somatic structural aberrations from targeted ...Ronak Shah
Structural aberrations including deletions, insertions, inversions, tandem duplications, translocations, and more complex rearrangements constitute a frequent type of alteration in human tumors. Here, we sought to explore the potential to discover such events from targeted DNA sequence data in our CLIA-compliant molecular diagnostics laboratory. To detect somatic structural aberrations in individual tumors, we have developed an analytic framework in Perl & Python to detect these events in data generated by a hybridization capture-based, targeted sequencing clinical assay (MSK-IMPACT), which can reveal structural rearrangements as small as 500bp.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
Comparative analysis of gene regulation in mouse rat and humanconstantina mylona
Which is the most suitable model mouse or rat even in the use of the latest gene editing tool-CRISPR/Cas 9 ?
Final Project presentaion on BSc Human Biology
Creative Biogene, a global provider and manufacture, offers professional products and services to help our clients in gene research. CRISPR/Cas9 PlatformCB, which provides comprehensive gene editing services and products, is one of Creative Biogene’s platforms.
https://www.creative-biogene.com/crispr-cas9/about-us.html
The document describes an analysis of gene expression data from a glioblastoma cell line before and after treatment with the chemotherapeutic drug temozolomide (TMZ). RNA sequencing data was analyzed using the Deseq2 model to identify differentially expressed genes between untreated and treated conditions. Weighted gene co-expression network analysis (WGCNA) was also used to cluster genes into modules and identify co-expression patterns. Additionally, a software application was developed to analyze single-cell RT-PCR data on 96 genes of interest identified from the RNA-seq analysis, in order to investigate tumor heterogeneity. The results highlighted genes and gene modules related to drug resistance in glioblastoma.
Gene drives are a new genetic engineering technique that uses CRISPR to bias inheritance and spread genetic modifications throughout populations at rates much higher than normal Mendelian inheritance. Researchers have successfully created a gene drive in mosquitoes that causes fluorescent eyes as a proof of concept. This technique could potentially be used to eradicate malaria by modifying mosquitoes unable to transmit the disease. However, gene drives face technical challenges and raise significant ethical concerns about human control over natural evolution that require extensive public discussion and new regulations before deployment.
CRISPR Gene Editing Congress, 25-27 February 2015 in Boston, MADiane McKenna
Key industry leaders will gather at the inaugural CRISPR Precision Gene Editing Congress with an ultimate purpose of addressing the importance of overcoming specificity, efficiency and delivery challenges associated with the CRISPR/Cas9 system. Pioneers will showcase the expanding biomedical and therapeutic potential of gene editing tools for drug discovery and development.
Developing a framework for for detection of low frequency somatic genetic alt...Ronak Shah
Cancer is a complex, heterogeneous disease of the genome. Most cancers result
from an accumulation of multiple genetic alterations that lead to dysfunction of cancer-associated
genes and pathways. Recent advances in sequencing technology have enabled comprehensive
profiling of genetic alterations in cancer. We have established a targeted sequencing platform
(IMPACT: Integrated Mutation Profiling of Actionable Cancer Targets) using hybridization capture and
next-generation sequencing (NGS) technology, which can reveal mutations, indels and copy number
alterations involving 340 cancer related genes.
This document discusses genomic technologies that can be used to observe the human genome and their applications. It covers microarrays, next-generation sequencing, DNA methylation, copy number variation, and more. Challenges include the cost of these technologies and integrating the large amounts of data they produce to improve healthcare.
APPLICATION OF NEXT GENERATION SEQUENCING (NGS) IN CANCER TREATMENTDinie Fariz
Next generation sequencing (NGS) has revolutionized cancer treatment by enabling high throughput DNA sequencing. This document discusses several applications of NGS in cancer treatment including whole exome sequencing of tumors from 25 patients to identify genetic mutations, using avatar mouse models to test proposed treatment strategies, detecting mutations in liquid biopsies, and identifying somatic mutations in leukemia patients. Challenges of NGS include analyzing large amounts of data, accurately interpreting variants, and addressing ethical issues.
Bioinformatics and NGS for advancing in hearing loss researchJoaquin Dopazo
This document discusses the importance of bioinformatics and next-generation sequencing (NGS) for advancing hearing loss research. It summarizes the Spanish 1000 genomes project, which sequenced over 1000 samples across various rare and familial diseases to search for novel disease genes, responsible genes with unknown modifier genes, susceptibility genes, and therapeutic targets. The organization and analysis pipeline of the project is described, including initial quality control, mapping, variant calling, annotation, filtering, and gene prioritization. Results identified 36 new disease variants in known genes and 27 disease variants in 13 new genes.
The document discusses the growth of genomic sequence data due to falling costs of DNA sequencing. This creates both a "big data" problem of how to store and analyze large amounts of data, as well as a "diminishing discovery" problem as it becomes harder to find new discoveries within the data. The document proposes several solutions to these problems including pre-competitive collaboration between organizations to share data and analytics platforms. It provides examples of existing data sharing platforms like tranSMART and describes how next generation sequencing is revealing different types of human genetic variation including single nucleotide polymorphisms and their role in pharmacogenomics.
Speaker: Benedict C. S. Cross, PhD, Team leader (Discovery Screening), Horizon Discovery
CRISPR–Cas9 mediated genome editing provides a highly efficient way to probe gene function. Using this technology, thousands of genes can be knocked out and their function assessed in a single experiment. We have conducted over 150 of these complex and powerful screens and will use our experience to guide you through the process of screen design, performance and analysis.
We'll be discussing:
• How to use CRISPR screening for target ID and validation, understanding drug MOA and patient stratification
• The screen design, quality control and how to evaluate success of your screening program
• Horizon’s latest developments to the platform
• Horizon’s novel approaches to target validation screening
This document summarizes research on estimating the population fitness and genetic load of single nucleotide polymorphisms (SNPs) that affect mRNA splicing. The authors develop an objective function to relate differences in the information content of alleles to the fitness of genotypes in a population. They analyze over 1 million SNPs from the HapMap project and identify thousands that alter natural splice site information. By calculating genetic load based on changes in information content and allele frequency, they partition SNPs according to their predicted effect on splicing and population fitness. Many predicted effects are supported by gene expression studies. Their analysis provides insights into how natural selection acts on splicing-related SNPs.
This document summarizes a study that analyzed genetic variants called single nucleotide polymorphisms (SNPs) that affect mRNA splicing. The researchers developed a method to estimate the population fitness and genetic load of SNPs based on how they alter the information content of mRNA splicing sites. They analyzed SNPs in human populations that were known to affect splicing sites. Many of the predicted effects of SNPs on splicing and gene expression were supported by gene expression data. The researchers integrated various genetic and genomic datasets into a database to relate SNPs to changes in splicing and gene expression. They computed the genetic fitness and load for all SNPs in databases to analyze their potential effects on populations based on changes to splicing site information content and allele frequencies.
This document summarizes a presentation given by Minoru Kubo on single cell analyses for plant reprogramming studies. The presentation covered how next generation sequencing and single cell analyses have changed biological research. It discussed single cell transcriptomics for analyzing plant reprogramming at the single cell level. The goal is to identify reprogramming genes, understand cell-cell interactions during reprogramming, and validate theories of reprogramming using the moss Physcomitrella patens as a model organism. Positioning information from single cell analyses could provide new insights into cell lineages, interactions, and multicellular development.
This document discusses high-resolution views of the cancer genome using various technologies including DNA microarrays, comparative genomic hybridization, tiling arrays, next-generation sequencing, and DNAse-Seq. It describes how these technologies can be used to analyze gene expression, copy number variation, chromatin structure, and more to better understand cancer at the genomic level. Integrating data from all these sources presents challenges but may help improve individual health outcomes.
A New Generation Of Mechanism-Based Biomarkers For The ClinicJoaquin Dopazo
The document discusses moving from single gene biomarkers to more functional, modular biomarkers for disease. It argues that most diseases are caused by combinations of variants affecting functional modules rather than single genes. The document proposes analyzing genomic data like SNPs and gene expression in the context of protein interaction networks and gene ontologies to better capture disease mechanisms and identify more informative biomarkers. Examples show how this approach can prioritize genes interacting with known disease genes and find enriched functional groups associated with diseases.
This document summarizes a presentation on using synthetic DNA controls called "sequins" to represent the human genome for quality control in next-generation sequencing experiments. Key points:
1. Sequins are synthetic DNA or RNA molecules created to represent features of the human genome like genes and genetic variants.
2. Sequins are added to real DNA or RNA samples prior to sequencing to act as internal controls for alignment, variant detection, and gene expression quantification.
3. Analysis of sequin controls can provide metrics like accuracy, precision, sensitivity and limits of detection for sequencing experiments and bioinformatics pipelines.
Global Gene Expression Profiles from Breast Tumor Samples using the Ion Ampli...Thermo Fisher Scientific
Thousands of genes are expressed in a controlled fashion in each eukaryotic cell
determining what a cell can do and dictate normal tissue function. The measurement of
the entire gene expression pattern of a given sample is critical in understanding the
natural homeostatic state of a healthy tissue, as well as providing useful information
when a system is altered due to environmental queues or potentially disease state.
Many technologies have been utilized to measure the entire gene expression profile of a
RNA test sample. DNA microarrays have become a key method to acquire a
comparative snapshot of the gene expression profile from test samples in a high
throughput manner. Quantitative PCR and newer sequencing techniques are popular
alternatives offering highly accurate gene expression measurements, but with limitations
due to cost and complex analysis needs.
To address the challenges of current sequencing based methods of global gene
expression profiling and take advantage of the simplicity of analysis that comes with
defined expression profiling content from technologies such as microarrays, we have
tested the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit using RNA
isolated from invasive ductal tumor samples. This novel approach allows profiling the
global mRNA expression of human RNA in a highly multiplexed fashion using the Ion
Torrent sequencing platform. The results show detection of more genes than popular
microarray platforms with comparable differential gene expression measurements to
quantitative PCR (r = 0.96) and RNA-Seq methods (r = 0.94).
Data presented here demonstrates high on target mapping (>91% of reads) for all
human breast carcinoma libraries. Gene expression values correlated with R>0.99 for
all technical replicates. We saw >64% of the over 22,800 genes in the single pool panel
detected for all libraries. The most highly expressed genes include genes expected to
be over-expressed in breast tumor samples. The Ion AmpliSeq™ Transcriptome Human
Gene Expression Kit is a novel method to measure global gene expression profiles from
human RNA samples in a timely, cost effective, and high throughput manner resulting in
sensitive and accurate gene expression measurements.
ASHG 2015 - Redundant Annotations in Tertiary AnalysisJames Warren
After obtaining genetic variants from next generation sequencing data, a precursory step in tertiary analysis is to annotate each variant with available relevant information. There is no standardized compendium for this purpose; researchers instead are required to compile data from a motley of annotation tools and public datasets. These sources for annotation are independently maintained, and accordingly there is limited concordance between their reported contents. The choice of annotation datasets thus has a direct and significant impact on the results of the analysis.
The document discusses the evolving concept of what constitutes a gene. It provides a brief history of how the gene concept has changed over time as scientific understanding has progressed, from early ideas of genes as discrete units representing traits, to the modern understanding of genes as complex genomic regions encoding functional products. The document examines problems with defining genes, and summarizes several proposed definitions, including the Gerstein-Snyder definition of a gene as a union of genomic sequences encoding overlapping functional products, and the Stadler-Prohaska definition of a gene representing the duality between a functional biomolecule and its genomic footprint.
1) The study analyzed genetic diversity in 66 finger millet accessions from Ethiopia and Eritrea using RAPD markers.
2) A total of 123 RAPD fragments were amplified using 15 primers, of which 89 (72%) were found to be polymorphic.
3) Genetic similarity between accessions ranged from 0.585 to 0.984. Cluster analysis grouped the 66 accessions into nine clusters at a similarity index of 0.83, showing high genetic variability among the accessions.
Genetic variation and its role in health pharmacologyDeepak Kumar
Genetic variation exists at different scales, from single nucleotide polymorphisms within individuals of a species to larger structural differences between species. Genetic variation arises through mutations, recombination, gene flow, genetic drift, and the interaction of these processes over time. The effective population size of a species influences how genetic variation is shaped by these evolutionary forces.
1. The study performed whole-exome sequencing on 72 cases of familial Meniere's disease to identify rare variants in genes associated with sensorineural hearing loss (SNHL).
2. Analysis identified that 40% of cases carried at least one novel or ultra-rare variant in SNHL genes, suggesting these genes play a role in Meniere's disease.
3. The OTOF gene showed a significant accumulation of rare variants compared to controls. A common intronic variant in OTOF, rs34796712, which regulates its expression, occurred less frequently in cases also carrying a rare variant, suggesting it may play a protective role.
Comparative sequence studies of the repeat elements in diverse insect species can provide useful information on how to make use of them for developing abundant markers that can be used in those species;
$ At the moment, a total of 8 species are in genome assembly stages and another 35 are in progress for genome sequencing;
$ Different molecular marker systems in the field of entomology are expected to provide new directions to study insect genomes in an unprecedented way in the years to come
Human genetic variation and its contribution to complex traitsgroovescience
This document summarizes a meeting discussing the human genome and human genetic variation.
The key points are:
1) In June 2000, the first draft of the human genome was announced, with fully sequenced publications in 2001. This marked a major milestone in understanding the human genome.
2) Since then, over 11 million SNPs and thousands of structural variants have been discovered through projects like HapMap and large sequencing studies. However, the majority of rare variants are still unknown.
3) Genome-wide association studies since 2006 have identified over 300 genetic loci associated with over 80 human traits and diseases. However, determining the functional consequences and molecular mechanisms remains a major challenge.
1. Association mapping uses linkage disequilibrium in natural populations to identify markers closely linked to genes influencing traits, allowing for higher resolution than traditional linkage mapping.
2. Key factors for successful association mapping include choosing diverse germplasm with extensive recombination history, collecting high-quality phenotypic data across environments, genotyping candidate genes and markers, and using statistical methods to account for population structure.
3. Combining association mapping with traditional QTL mapping and the various available software tools allows for rapid dissection and evaluation of complex traits.
RT-PCR and DNA microarray measurement of mRNA cell proliferationIJAEMSJORNAL
For mRNA quantification, RT-PCR and DNA microarrays have been compared in few studies
(RT-PCR). Healing callus of adult and juvenile rats after femur injury was found to be rich in mRNA at
various stages of the healing process. We used both methods to examine ten samples and a total of 26 genes.
Internal DNA probes tagged with 32P were employed in reverse transcription-polymerase chain reaction
(RT-PCR) to identify genes (RT-PCR). Ten Affymetrix® Rat U34A cRNA microarrays were hybridized with
biotin-labeled cRNA generated from mRNA. There was a wide range of correlation coefficients (r) between
RT-PCR and microarray data for each gene. Meaning became genetically unique because of this diversity.
Relatively lowly expressed genes had the highest r values. The distance between PCR primers and
microarray probes was found to be higher than previously assumed, leading to a drop in agreement between
microarray calls and PCR outcomes. Microarray research showed that RT-PCR expression levels for two
genes had a "floor effect." As a result, PCR primers and microarray probes that overlap in mRNA expression
levels can provide good agreement between these two techniques.
The group analyzed the relationship between gene expression, genetics, and phenotypes using pedigree data. Three subgroups looked at: gene expression alone, the genetics of expression, and the genetics of expression and their relationship to phenotypes like systolic blood pressure. Methods included linear mixed models, causal modeling, and assessing if incorporating both genetics and expression data improved association tests compared to single omics. Results did not reach statistical significance after accounting for multiple testing, likely due to low power, but papers presented their top findings. Analyzing expression, genetics and their relationship to phenotypes provides insights but large sample sizes are still needed.
This document discusses a study that found significant differences in gene expression variability between knockout and wild-type mice using microarray data from 25 publicly available datasets. The study found that knockouts exhibited either significantly increased or decreased variability compared to wild-types in virtually every dataset analyzed. Examination of the data distributions indicated that these differences were due to broad changes in variability across most genes, rather than being driven by outliers. The findings suggest that changes in gene expression variability due to gene knockouts may have important phenotypic consequences.
Suzanne Lagerweij - Influence Without Power - Why Empathy is Your Best Friend...Suzanne Lagerweij
This is a workshop about communication and collaboration. We will experience how we can analyze the reasons for resistance to change (exercise 1) and practice how to improve our conversation style and be more in control and effective in the way we communicate (exercise 2).
This session will use Dave Gray’s Empathy Mapping, Argyris’ Ladder of Inference and The Four Rs from Agile Conversations (Squirrel and Fredrick).
Abstract:
Let’s talk about powerful conversations! We all know how to lead a constructive conversation, right? Then why is it so difficult to have those conversations with people at work, especially those in powerful positions that show resistance to change?
Learning to control and direct conversations takes understanding and practice.
We can combine our innate empathy with our analytical skills to gain a deeper understanding of complex situations at work. Join this session to learn how to prepare for difficult conversations and how to improve our agile conversations in order to be more influential without power. We will use Dave Gray’s Empathy Mapping, Argyris’ Ladder of Inference and The Four Rs from Agile Conversations (Squirrel and Fredrick).
In the session you will experience how preparing and reflecting on your conversation can help you be more influential at work. You will learn how to communicate more effectively with the people needed to achieve positive change. You will leave with a self-revised version of a difficult conversation and a practical model to use when you get back to work.
Come learn more on how to become a real influencer!
This presentation by Professor Giuseppe Colangelo, Jean Monnet Professor of European Innovation Policy, was made during the discussion “The Intersection between Competition and Data Privacy” held at the 143rd meeting of the OECD Competition Committee on 13 June 2024. More papers and presentations on the topic can be found at oe.cd/ibcdp.
This presentation was uploaded with the author’s consent.
XP 2024 presentation: A New Look to Leadershipsamililja
Presentation slides from XP2024 conference, Bolzano IT. The slides describe a new view to leadership and combines it with anthro-complexity (aka cynefin).
This presentation by Yong Lim, Professor of Economic Law at Seoul National University School of Law, was made during the discussion “Artificial Intelligence, Data and Competition” held at the 143rd meeting of the OECD Competition Committee on 12 June 2024. More papers and presentations on the topic can be found at oe.cd/aicomp.
This presentation was uploaded with the author’s consent.
This presentation by Katharine Kemp, Associate Professor at the Faculty of Law & Justice at UNSW Sydney, was made during the discussion “The Intersection between Competition and Data Privacy” held at the 143rd meeting of the OECD Competition Committee on 13 June 2024. More papers and presentations on the topic can be found at oe.cd/ibcdp.
This presentation was uploaded with the author’s consent.
Carrer goals.pptx and their importance in real lifeartemacademy2
Career goals serve as a roadmap for individuals, guiding them toward achieving long-term professional aspirations and personal fulfillment. Establishing clear career goals enables professionals to focus their efforts on developing specific skills, gaining relevant experience, and making strategic decisions that align with their desired career trajectory. By setting both short-term and long-term objectives, individuals can systematically track their progress, make necessary adjustments, and stay motivated. Short-term goals often include acquiring new qualifications, mastering particular competencies, or securing a specific role, while long-term goals might encompass reaching executive positions, becoming industry experts, or launching entrepreneurial ventures.
Moreover, having well-defined career goals fosters a sense of purpose and direction, enhancing job satisfaction and overall productivity. It encourages continuous learning and adaptation, as professionals remain attuned to industry trends and evolving job market demands. Career goals also facilitate better time management and resource allocation, as individuals prioritize tasks and opportunities that advance their professional growth. In addition, articulating career goals can aid in networking and mentorship, as it allows individuals to communicate their aspirations clearly to potential mentors, colleagues, and employers, thereby opening doors to valuable guidance and support. Ultimately, career goals are integral to personal and professional development, driving individuals toward sustained success and fulfillment in their chosen fields.
This presentation by OECD, OECD Secretariat, was made during the discussion “Competition and Regulation in Professions and Occupations” held at the 77th meeting of the OECD Working Party No. 2 on Competition and Regulation on 10 June 2024. More papers and presentations on the topic can be found at oe.cd/crps.
This presentation was uploaded with the author’s consent.
This presentation by Thibault Schrepel, Associate Professor of Law at Vrije Universiteit Amsterdam University, was made during the discussion “Artificial Intelligence, Data and Competition” held at the 143rd meeting of the OECD Competition Committee on 12 June 2024. More papers and presentations on the topic can be found at oe.cd/aicomp.
This presentation was uploaded with the author’s consent.
This presentation by Juraj Čorba, Chair of OECD Working Party on Artificial Intelligence Governance (AIGO), was made during the discussion “Artificial Intelligence, Data and Competition” held at the 143rd meeting of the OECD Competition Committee on 12 June 2024. More papers and presentations on the topic can be found at oe.cd/aicomp.
This presentation was uploaded with the author’s consent.
This presentation by Nathaniel Lane, Associate Professor in Economics at Oxford University, was made during the discussion “Pro-competitive Industrial Policy” held at the 143rd meeting of the OECD Competition Committee on 12 June 2024. More papers and presentations on the topic can be found at oe.cd/pcip.
This presentation was uploaded with the author’s consent.
This presentation by OECD, OECD Secretariat, was made during the discussion “Pro-competitive Industrial Policy” held at the 143rd meeting of the OECD Competition Committee on 12 June 2024. More papers and presentations on the topic can be found at oe.cd/pcip.
This presentation was uploaded with the author’s consent.
This presentation by Tim Capel, Director of the UK Information Commissioner’s Office Legal Service, was made during the discussion “The Intersection between Competition and Data Privacy” held at the 143rd meeting of the OECD Competition Committee on 13 June 2024. More papers and presentations on the topic can be found at oe.cd/ibcdp.
This presentation was uploaded with the author’s consent.
This presentation by Professor Alex Robson, Deputy Chair of Australia’s Productivity Commission, was made during the discussion “Competition and Regulation in Professions and Occupations” held at the 77th meeting of the OECD Working Party No. 2 on Competition and Regulation on 10 June 2024. More papers and presentations on the topic can be found at oe.cd/crps.
This presentation was uploaded with the author’s consent.
This presentation by OECD, OECD Secretariat, was made during the discussion “Artificial Intelligence, Data and Competition” held at the 143rd meeting of the OECD Competition Committee on 12 June 2024. More papers and presentations on the topic can be found at oe.cd/aicomp.
This presentation was uploaded with the author’s consent.
Artificial Intelligence, Data and Competition – OECD – June 2024 OECD discussion
Raj Lab Meeting May/01/2019
1. The impact of rare
variation on gene
expression across tissues
Katia Lopes, PhD
Ricardo Vialle, PhD
Raj Lab
Department of Neurosciences
May 1st 2019
2.
3. Background
Currently is hard to distinguish pathogenic from benign rare non-
coding variants
Association studies (like GWAS) usually works fine for common
variants, however they are not practical for rare variants (large
sample sizes are required)
Analyzing the effect of rare non-coding variants in the expression
across different tissues may help to elucidate their roles in
diseases!
4. GTEx project v6p release
RNA-seq + Whole-genome sequencing (WGS)
449 individuals
44 tissues
log2(RPKM + 2)
Allele-specific expression (ASE)
Gencode v.19 annotation
Protein coding genes + long intergenic noncoding RNAs (lincRNA)
Estimated hidden factors using PEER
Standardized the expression for each gene with Z-scores
Data
5. PEER correction
Total expression removed by PEER
A noticeable difference between the brain and other tissues ???
Linear Regression between the covariate values
and the PEER factors
White = missing values
6. Outlier definition
Focus: Individuals with extremely high or extremely low expression of
a particular gene compared with the population
OUTLIERS
|Z-score| >= 2
AKR1C4
Single-tissue outlier
Single-tissue outlier
Single-tissue outlier
Multi-tissue outlier
At least 5 tissues
For each gene… e.g.
Pair Gene + Individual
7. Multi-tissue outlier distribution
Ext Fig 2 - Distribution of the number of genes with a multi-tissue outlier.
a, Each individual was an outlier for a median of 10 genes. Individuals with 50 or more outliers
are colored in grey and were excluded from downstream analyses. b – c, Distribution of the
number of genes for which individuals, stratified by common covariates, were multi-tissue
outliers.
Number of genes
Multi-tissue outliers
8. GTEx
449 individuals
44 tissues
10 brain tissues
18,830 genes tested
b, Outlier expression sharing between
tissues measured by the proportion of
single-tissue outliers that have a |Z-
score| >= 2
Single tissue outlier
9. Replication of expression outliers
2 groups of expression data:
Discovery set of 34 tissues
Replication set of 10 tissues
For t = 10, 15, 20, 25 and 30
Multi-tissue outlier replication
Replication = 60% | Z-score >=1
Replication = ~30% | Z-score >=2
10. In order to investigate the influence of rare genetic variation on extreme
expression levels they focused on individuals of European ancestry with
WGS data (1,144 multi-tissue outliers)
Autosomal variants that passed all filters in the VCF (PASS in the filter
column)
Rare variants were defined as having MAF ≤ 0.01 in GTEx
SNVs and indels with MAF ≤ 0.01 in the European population of the 1000
Genomes Project Phase 3 data
They checked if the allele frequency was similar in the 1000 Genome Project
Rare genetic variation
11. Multi-tissue outliers were strongly enriched for nearby rare variants. The enrichment was most
pronounced for structural variants (SV) and greater for short insertions and deletions (indels)
than for single-nucleotide variants (SNVs)
Enrichment of rare variants in outliers
Figure 2 | Enrichment of rare variants and allele-specific expression (ASE) in outliers.
a, Enrichment within 10 kb of the transcription start site (TSS) among outliers.
Rare Common
1144 multi-tissue outlier
(WGS)
Y = Enrichment as the
relative risk of having a
nearby rare variant
12. Figure 2 | Enrichment of rare variants and allele-specific expression (ASE) in outliers.
b, Rare SNV enrichments at increasing Z-score thresholds.
Rare genetic variation
14. Under vs Over expressed outliersAllele-specificexpression(ASE)
15. Figure 3 | Stratification of multi-tissue outliers by rare variant classes.
16. RIVER (RNA-informed variant effect on regulation)
A Bayesian statistical model that jointly analyses genome and transcriptome
data from the same individual to estimate the probability that a variant has
regulatory impact!
Software - RIVER
Roadmap Epigenomics
CADD
VEP
F = binary variable
representing the
functional regulatory
status of the rare variant
E = binary node
representing expression
outlier status
17. Software: RIVER
Figure 5 | Performance of RIVER for prioritizing functional regulatory variants.
b, Predictive power of RIVER compared to an L2-regularized logistic regression model using
only genomic annotations.
3.766 pairs shared by 2 individuals
Computes test posterior
probabilities of FR for 1st
individual, and compares them
with outlier status of 2nd
individual from the list
18. Software: RIVER
Figure 5 | Performance of RIVER for prioritizing functional regulatory variants.
c, Distribution of RIVER scores as a function of expression and genomic annotation scores.
20. GAMT is associated with cerebral
creatine deficiency syndrome 2, and
causes neurological deficiencies and
also lead to low body fat
SBDS is associated with the
recessive Shwachman–Diamond
syndrome
Software: RIVER
21. Applications for Raj Lab
1. Correlate factors with covariates (PEER, PCA … )
2. Z-scores for gene-individual outlier detection
3. Enrichment of rare variants near outliers
4. Use RIVER to prioritize rare variants in each individual genome by their
predicted impact on gene expression
5. Single vs Multi-tissue data (or multi cell types?)