Blog

Lecture 14: Next-Generation Sequencing Technologies (2016) - Elaine Mardis

Highlights

  • Massively parallel sequencing (MPS) basics
  • Transformed medical inquiry
  • Massively parallel sequencing instruments
  • Library construction for MPS
  • PCR related problems in MPS
  • Massively parallel sequencing synthesis
  • Synthesis platforms
  • Integrated Genomics Viewer (IGV)
  • Data and Coverage Statistics
  • False Negativity / Positivity
  • Real time sequencing of single DNA molecules
  • Gold genomes, 10X genomics
  • Oxford Nanopore sequencing

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 13: Genomics of Microbes and Microbiomes - Julie Segre (2016)

Highlights

  • Why the human microbiome?
  • The human microbiome and elucidating the diversity
  • Direct sequencing vs. Culture-based methods
  • Bacterial diversity - 16s rRNA gene
  • DNA Sequencing to assess bacterial diversity
  • Analysis tools - QIIME, Mothur, CloVR
  • Databases - Ribosomal Database Project, SILVA,
  • Human microbiome project
  • Signature taxa and Operational Taxonomic units (OTUs)
  • Comparing bacterial diversity between communities
  • Richness, Evenness and Diversity
  • Assemblers and evaluating assemblies
  • Metagenomics and Shotgun sequencing

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 12: Genomic Medicine - Bruce Korf (2016)

Highlights

  • Hype cycle of genomic medicine
  • Genomic Newborn screening
  • Diagnostic testing and the Diagnostic odyssey
  • Incidental findings
  • Preconceptional Screening
  • Genomic Carrier Screening
  • Prenatal diagnosis
  • Pre-symptomatic testing
  • Pre-dispositional testing
  • Direct-to-Consumer testing
  • Pharmacogenetics
  • Genomics as a library of life

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 11: Pharmacogenomics - Howard McLeod (2016)

Highlights

  • The Clinical Problem
  • Probabilistic data for clinical interventions
  • Why focus of drugs?
  • The precision medicine initiative
  • Drivers of Precision Medicine
  • Cancer pharmacogenomics
  • CPIC - Clinical Pharmacogenomics Implementation Consortium
  • Reasons for Precision Medicine
  • Competing and Cumulative risk analysis
  • Candidate gene approach - Chemotherapy Neurotoxicity
  • Practical Choices

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 10: Expression Analysis, Functional Enrichment, and Network Inference - John Quackenbush (2016)

Highlights

  • A brief history of expression analysis
  • Early techniques of understanding gene expression
  • Quantification requires normalization
  • Northern blots, Quantitative RT-PCR (Small and Large Scale)
  • DNA Microarrays and RNASeq
  • Disease progression and precision care
  • Expression analysis pipelines (Microarrays and RNASeq)
  • Experimental design, normalization, clustering
  • Limma - Microarray analysis pipeline
  • Biological interpretation, GO and Functional analysis
  • DAVID bioinformatics resources
  • MSigDB and Gene Set Enrichment Analysis (GSEA)
  • Biological Networks and Network analysis

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 9: Genomic Approaches to the Study of Complex Genetic Diseases - Karen Mohlke (2016)

Highlights

  • Fundamentals of complex traits and diseases
  • Gene mapping in populations
  • Scale of genetic architecture - Effect size and Allele frequency
  • Genome Wide Association Studies (GWAS) and Identification of loci
  • GWAS Design, Samples / Study participants, Genotyping, tests of association, Imputation and Meta-analysis
  • Confounding and population stratification
  • Genome-wide genotyping panels
  • Haplotype Tags
  • Illumina Infinium Assay and Affymetrix Axiom Assay
  • Effect size and significance of locus characteristics
  • Sequencing and rare variants studies
  • Variant discovery at GWAS locus
  • Future of complex trait analysis


Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 8: Identifying the Genomic Basis of Rare Diseases - David Valle (2016)

Highlights

  • Foundational features of Mendelian diseases
  • Case studies - a metabolic and a neurological disorder
  • Finding the responsible variants and genes
  • Evolution and rise of field of clinical DNA Sequencing
  • Sequencing by target and its types
  • Clinical vs. Research Whole exome sequencing
  • Characteristics of current sequencing approaches
  • Value of Precision Diagnosis
  • Disease gene discovery
  • Tools from Baylor-Hopkins Center for Mendelian Genomics
  • PhenoDB, GeneMatcher, and the human disease network
  • Short and long term consequences of identifying disease genes

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 7: Introduction to Population Genetics - Lynn Jorde (2016)

Highlights

  • Patterns of human genetic variation
  • Four major factors of evolution
  • Mutation and Genetic Variation
  • Assessment of these variations at population and at individual level
  • Evolutionary factors influencing these variations
  • Biomedical implications of genetic variations
  • Linkage disequilibrium, evolution and disease-gene associations
  • Population genetics in understanding role of rare variants in disease

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 6: Applications of Genomics to Improve Public Health - Colleen McBride (2016)

Highlights

  • Importance of conducting translational research
  • Translational research for optimal applications
  • Overview of Social and Behavioral research
  • Health promotion - Theories by Intervention Level
  • Principles of public health
  • Clinical health vs. Public health
  • Translational research in priority areas
  • Public understanding of genomics
  • Genetic risk communication
  • Challenges for research on clinical integration of genomics
  • Public health campaign and genetic susceptibility education
  • A transdisciplinary model

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.




Lecture 5: Regulatory and Epigenetic Landscapes of Mammalian Genomes - Laura Elnitski (2016)

Highlights

  • Blueprint (genome) to Implementation (phenome)
  • Genome Composition
  • Functional Elements
  • Histone Modifications
  • DNA methylation
  • Phenomics
  • Future of Regulatory and Epigenetic Landscapes

Lecture Series Description:

  • Current Topics in Genome Analysis 2016
  • National Human Genome Research Institute

A lecture series covering contemporary areas in genomics and bioinformatics

Given the rapid advances in genomics and bioinformatics that have taken place in the past few years, an intensive review of the major areas of ongoing genome research would be of great value. To that end, the National Human Genome Research Institute (NHGRI) has once again sponsored the Current Topics in Genome Analysis lecture series.

The series consists of 14 lectures, covering the major areas of genomics. Instead of splitting the lectures into "laboratory-based" and "computationally-based" blocks, this lecture series has been organized by general subject area, in hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future.