11/18/05 "Omics" Experimental Approaches 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 1
Bioinformatics Seminars Nov 18 Fri 12: 10 BCB Seminar in E 164 Lago Using P-Values for the Planning and Analysis of Microarray Experiments Dan Nettleton, Stat 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 2
Protein Structure Prediction Genome Analysis Mon Protein 3' structure prediction Wed Genome analysis & genome projects Comparative genomics; ENCODE, SNPs, Hap. Maps, medical genomics Thur Lab Protein structure prediction, SNPs Fri Experimental approaches: microarrays, proteomics, metabolomics, medical genomics 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 3
Reading Assignment (Fri & after break) Mount Bioinformatics • Chp 13 Microarray Analysis http: //www. bioinformaticsonline. org/ch/ch 13/index. html • Ck Errata: http: //www. bioinformaticsonline. org/help/errata 2. html 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 4
BCB 544 Additional Readings Required: • Human Hap. Map (Nature 437, Oct 27, 2005) • Commentary (437: 1233) http: //www. nature. com/nature/journal/v 437/n 7063/full/4371233 a. html • News & Views (437: 1241) http: //www. nature. com/nature/journal/v 437/n 7063/full/4371241 a. html Optional: • Article (437: 1299) A haplotype map of the human genome The International Hap. Map Consortium 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 5
Review last lecture & New: Genomics 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 6
Genomics - for excellent overview lectures, see these posted by NHGRI & Pevsner: 1 - Genomic sequencing Mapping and Sequencing Eric Green, NHGRI CTGA 2005 Lecture 1. pdf 2 - Human genome project The Human Genome 2005 -10 -19_ch 17. pdf Jonathan Pevsner, Kennedy Krieger Institute 3 - SNPs Studying Genetic Variation II: Computational Techniques Jim Mullikin, NHGRI CTGA 2005 Lecture 13. pdf 4 - Comparative Genomics Comparative Sequence Analysis Elliott Margulies, NHGRI CTGA 2005 Lecture 8. pdf 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 7
1 - Genomic sequencing Many thanks to: Eric Green, NHGRI for the following slides extracted from his lecture on: Mapping and Sequencing CTGA 2005 Lecture 1. pdf 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 8
Genomic Sequencing - Brief Review E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 9
Comparison of Sequenced Genome Sizes E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 10
Comparison of Genetic & Physical Maps E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 11
STSs: Provide common markers for "linking" genetic & physical maps E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 12
With complete genomes (now), why bother to generate physical maps? E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 13
Genomic sequencing requires assembly of sequences obtained from DNA cloned in vectors E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 14
Advances in DNA Sequencing Technology E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 15
Sequencing Method #1: Gilbert-Maxim "Chemical Degradation" E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 16
Sequencing Method #2: Sanger "Di-deoxy Chain Termination" E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 17
Automated Sequencing for Genome Projects: Sanger method - with improvements Another recent improvement: rapid & high resolution separation of fragments in capillaries instead of gels (E Yeung, Ames Lab, ISU) E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 18
Human Genome Sequencing Two approaches: • Public (government) - International Consortium (6 countries, NIH-funded in US) • "Hierarchical" cloning & BAC-by-BAC sequencing • Map-based assembly • Private (industry) - Celera (Craig Ventner) • Whole genome random "shotgun" sequencing • Computational assembly (took advantage of public maps & sequences, too) Guess which human genome they sequenced? Craig's 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 19
"Hierarchical" BAC-by-BAC Shotgun Sequencing E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 20
Whole-Genome "Shotgun" Sequencing E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 21
"Hierarchical" Subcloning Strategy E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 22
"Shotgun" Sequencing Stategy E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 23
Computational Assembly of Shotgun Sequences E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 24
Either Strategy: Sequence "Finishing" = Hard !! E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 25
1 st Eukaryotic Genome Sequence: S. cerevisiae E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 26
1 st Animal Genome Sequence: C. elegans E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 27
Timetable for Human Genome Sequencing: Faster than expected! E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 28
1 st Draft Human Genome - "Finished" in 2001 E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 29
Public Sequencing - International Consortium E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 30
"Finishing" the Human Genome - continues… E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 31
"Complete" Human Genome Sequence - What next? E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 32
Interpreting the Human Genome Sequence E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 33
Comparative Genomics: now with entire genomic sequences E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 34
Comparing Genomes: Functional Elements E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 35
ENCODE Project E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 36
ENCODE - Web Sites E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 37
Eric Green's Genomic Sequencing Challenges (2005 List) E Green 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 38
2 - Human Genome Project Many thanks to: Jonathan Pevsner Kennedy Krieger Institute for the following slides extracted from his lecture on: The Human Genome 2005 -10 -19_ch 17. pdf 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 39
J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 40
Human Genome Sequence - Where is it? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 41
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 42
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 43
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 44
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 45
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 46
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 47
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 48
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 49
Human Genome Project: What have we learned? J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 50
The Human Genome - 3 Major Access Sites: J Pevsner 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 51
3 - SNPs Many thanks to: Jim Mullikin, NHGRI for the following slides extracted from his lecture on: Studying Genetic Variation II: Computational Techniques CTGA 2005 Lecture 13. pdf 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 52
J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 53
SNPs: Single Nucleotide Polymorphisms J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 54
SNPs: Single Nucleotide Polymorphisms J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 55
SNP Discovery Methods J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 56
SNPs - from EST Mining J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 57
SNPs: from Clone Overlap J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 58
The SNP Consortium (TSC) J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 59
Haplotype Map (Hap. Map) Project J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 60
SNPs: from Targeted Resequencing J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 61
Using Poly. Phred to Visualize SNPs J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 62
SNPs: from Sequencing Chips J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 63
"SNP Chips": an example J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 64
SNPs: How are they distributed? J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 65
SNPs: How are they distributed? J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 66
SNPs: Where are they stored? J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 67
SNPs: Access via 3 Major Genome Browsers J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 68
Haplotype - What is it? J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 69
Haplotypes: an example J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 70
Hapmap Project J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 71
Hap. Map Project Goals J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 72
Significance of SNP Analyses J Mullikin 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 73
4 - Comparative Genomics Many thanks to: Elliott Margulies, NHGRI for the following slides extracted from his lecture on: Comparative Sequence Analysis CTGA 2005 Lecture 8. pdf 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 74
E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 75
Comparative Genomics E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 76
Comparative genomics provides important clues re: biological function E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 77
Many different terms are used to describe different types of conserved sequences E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 78
Sequence Comparisons via Alignments E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 79
Visualization Tools for Comparative Genomics E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 80
Two major tools: E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 81
Best of both tools: E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 82
Comparing multiple species with z. Picture E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 83
What have we learned from comparative genomics? An example E Margulies 2005 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 84
New topic today: Microarrays, proteomics, metabolomics & medical genomics: Experimental approaches 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 85
"Omics" - for excellent overview lectures, see these posted by NHGRI & Pevsner: 1 - Gene expression analysis Gene Expression 2005 -10 -19_Chp 6. pdf Jonathan Pevsner, Kennedy Krieger Institute 2 - Microarrays Microarray Analysis (& more) Paul Meltzer, NHGRI CTGA 2005 Lecture 14. pdf 3 - Proteomics Proteins and Proteomics 2005 -10 -19_Chp 8. pdf Jonathan Pevsner, Kennedy Krieger Institute 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 86
Resources for Genomics & Gene Expression Analysis Servers: • NCBI (National Center for Biolotechnology Information) • Genomics: Genomic Biology, COG, Homolo. Gene, Genetic Analysis Software • Microarrays: GEO (Gene Expression Omnibus) • Ex. PASy (Expert Protein Analysis System) • Microarrays: GOCluster • Proteomics: Proteomics Server URLs for Resources: http: //pevsnerlab. kennedykrieger. org/wiley/chapt 6. htm http: //pevsnerlab. kennedykrieger. org/wiley/chapt 7. htm 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 87
ISU Resources & Experts Facilities: Biotech - Instrumentation Facilities CIAG - Center for Integrated Animal Genomics PSI - Plant Sciences Institute PSI Centers Faculty: BCB - Bioinformatics & Computational Biology Baker Center - for Bioinformatics & Biological Statistics CIAG - Center for Integrated Animal Genomics CILD - Computational Intelligence, Learning & Discovery 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 88
ISU Resources & Experts Genomic sequencing & comparative genomics Facilities: Biotech DNA Facility - Polking Carver Co-lab - Schnable Experiments: Microbial: Minion, others Plant: Schnable, Bogdonave, others Animal: Rothschild, Tuggle, Reecy, others Analysis: Huang, Chou, Brendel, Proulx, Gu 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 89
ISU Resources & Experts Microarrays Facilities: Carver Co-lab - Schnable Experiments: Microbial: Beattie, Beetham, others Plant: Schnable, Bogdonave, Wise, many others Animal: Rothschild, Tuggle, many others Analysis: Nettleton, Honavar, Gu, Proulx 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 90
ISU Resources & Experts Proteomics Facilities: Biotech Protein Facility - Tabbatabai Carver Co-lab Proteomics Facility - Lewis Experiments: Microbial: ? (not sure!) Plant: Rodermel, Voytas, others? Animal: Greenlee, others? Analysis: Honavar, Dobbs 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 91
ISU Resources & Experts Metabolomics Facilities: Keck Metabolomics Facility - Nikolau Ames Lab - Yeung, others Experiments: Wurtele, Nikolau, Yeung Analysis: Dickerson, Shanks 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 92
ISU Resources & Experts Medical genomics Hmmm - not a lot at ISU (yet) But, see: Ellinwood in Animal Science 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 93
ISU Resources & Experts Other "Omics: " "Glycomics" - Carbohydrate modifications: Facilities, Experiments, Analysis: 3/19/2018 Pohl D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 94
Overview of Experimental Methods 1 - Gene expression analysis Gene Expression 2005 -10 -19_Chp 6. pdf Jonathan Pevsner, Kennedy Krieger Institute 2 - Microarrays Microarray Analysis (& more) Paul Meltzer, NHGRI CTGA 2005 Lecture 14. pdf 3 - Proteomics Proteins and Proteomics 2005 -10 -19_Chp 8. pdf Jonathan Pevsner, Kennedy Krieger Institute 3/19/2018 D Dobbs ISU - BCB 444/544 X: "Omics" - Experimental Approaches 95
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