Introduction to Proteogenomics

By Prof. Sanjeeva Srivastava   |   IIT Bombay
Learners enrolled: 924
Cancer research has been significantly aided by advancements in proteogenomics technologies, where proteomics information derived from mass spectrometry is used to complement genomics using next generation sequencing. With the recent advent of Cancer Moonshot Project, the critical role that proteogenomics can play in improving cancer patient treatment is increasingly being recognized. This course will utilize advanced genomic and proteomic technologies and their data from high-quality human biospecimens to identify potentially actionable therapeutic molecular targets. This course is a part of a workshop by experts in the fields of proteomics and proteogenomics in cancer research from the Broad Institute of MIT and Harvard and Indian Institute of Technology Bombay. The course will comprise interactive lectures with case studies, hands-on sessions and demonstrations on proteogenomics aimed at accelerated understanding of cancer and will cover the principles of proteogenomics followed by experimental sessions, where proteomics data using LC-MS/MS will be processed and analyzed. The next step will be to integrate the proteomics data with genomics data, from The Cancer Genome Atlas for the proteogenomics analysis. Lectures and demonstrations on different computational methods will be performed for statistical data analysis of proteogenomics data.

INTENDED AUDIENCE : Biotechnology or Engineering background students having interest in latest technologies,(BE/B.Tech)
                                         Biotechnology. Students with science or engineering background but course is open to all
PREREQUISITES :          Nill
INDUSTRY SUPPORT :  Thermofisher Scientific, Illumina
Course Status : Completed
Course Type : Elective
Duration : 12 weeks
Start Date : 29 Jul 2019
End Date : 18 Oct 2019
Exam Date : 17 Nov 2019 IST
Category :
  • Biological Sciences & Bioengineering
Credit Points : 3
Level : Undergraduate

Page Visits

Course layout

Week 1: Proteogenomics overview- Part I, Proteogenomics overview- Part II, Introduction to Genomics- Part I : Gene 
                sequencing and mutations Introduction to Genomics-Part II : Sequence alignment, Introduction to Genomics-
                Part III :Transcriptome, SL1: Advancement in Cancer Genomics, SL2: Advancement in Cancer Genomics
Week 2: Introduction to Genomics IV : Epigenome, Introduction to Genomics : cBioPortal, Genotype, Gene expression & 
                Phenotype - Part I, Genotype, Gene expression & Phenotype- Part II, An overview of NGS technology, SH1: 
                NGS-Sequencing by synthesis, SH2: NGS- Sequencing by synthesis
Week 3: Introduction to Proteomics, Proteomics: Sample Prep & Protein Quantification, Proteomics: Sample Prep & 
                Protein Quantification (Hands-on), Introduction to MS-based Proteomics- Part I, Introduction to MS-based 
                Proteomics- Part II, SL 3: Applications of NGS – Ion Torrent, SL4: Applications of NGS – Ion Torrent
Week 4: Introduction to MS-based Proteomics- Part I (Hands-on), Introduction to MS-based Proteomics- Part II 
                (Hands-on), Data analysis: Normalization, Data analysis: Batch Correction and Missing values, Data analysis: 
                Statistical Tests, SH3: NGS- Ion Torrent, SH4: NGS- Ion Torrent
Week 5: Machine learning and Clustering, Hypothesis testing, ProTIGY- Part I, ProTIGY- Part II, Proteogenomics 
                approach to unravel proteoforms, SL5: Genomic Analysis using Droplet PCR, SL6: Genomic Analysis using 
                Droplet PCR
Week 6: Workflow to Automated Data Processing, Introduction to Fire Cloud, Fire Cloud and Data Model, Bioinformatics 
                solutions for ‘Big Data’ Analysis- Part I, Bioinformatics solutions for ‘Big Data’ Analysis-Part II, SH5: Genomic 
                Analysis using Droplet PCR, SH6: Genomic Analysis using Droplet PCR
Week 7: Data Science infrastructure management- Part I, Data Science infrastructure management- Part II, Data 
                Science infrastructure management- Part III, DIA-SWATH Atlas-Part I, DIA-SWATH Atlas-Part II, SL7: 
                Introduction to Targeted Proteomics, SH7: Data Analysis using Skyline
Week 8: Human Protein Atlas-Part I Clinical, Human Protein Atlas-Part II, Affinity based proteomics & HPA, Clinical 
                Considerations for OMICS-Part I, Considerations for OMICS- Part II, SL8: Proteomics: PTMs, SL9: Clinical 
Week 9: ntroduction to Proteogenomics-Part I, Introduction to Proteogenomics-Part II, Sequence centric 
                proteogenomics, Gene Variant Analysis, Proteomics in Clinical studies,SH8: ProTIGY
Week 10:Supervised Machine learning- Predictive Analysis Part I, Supervised Machine learning- Predictive Analysis 
                Part II, Supervised Machine learning- Marker Selection, Gene Set Analysis using WebGestalt- Part I, Gene Set 
                Analysis using WebGestalt- Part II, SH9: Supervised Machine Learning
Week 11:Biological Network Analysis- Part I, Biological Network Analysis- Part II, Mutation and Signaling - Part I, 
                Mutation and Signaling- Part II, Pathway Enrichment,SH10: Pathway Enrichment and Network Analysis
Week 12:Gene Set Enrichment Analysis (GSEA), Pathway enrichment: GSEA, Linked Omics, Linked Omics
               (Hands-on), Proteogenomics Conclusions, SL10: Topics in Proteogenomics- Malaria and Cancer case study

Books and references

Proteomics: A Cold Spring Harbor Laboratory Course Manual, A.J. Link and J. LaBaer, Cold Spring Harbor Laboratory Press, 2009. Selected papers from scientific journals

Instructor bio

Prof. Sanjeeva Srivastava
Dr. Sanjeeva Srivastava is a Professor and group head of proteomics laboratory at the Indian Institute of Technology, Bombay. He obtained his Ph.D. from the University of Alberta and post-doc from the Harvard Medical School in the area of proteomics, stress physiology and has specialized expertise in applications of data enabled sciences in global health, developing country and resource limited settings. He joined IIT Bombay in 2009 as an Assistant Professor and currently working as Professor. Current research in his group centers on biomarker and drug target discovery and deciphering the protein interaction networks in complex human diseases (gliomas) and infectious diseases (malaria) using high throughput proteomics, protein microarrays and mass spectrometry.
Dr. Srivastava is an active contributor to global proteomics science and innovation. He serves on the Executive Council of Human Proteome Organization (HUPO) and Proteomics Society, India (PSI). He has organized three successful international conferences & workshops at IIT Bombay – PSI-2014, Targeted Proteomics International Symposium in 2015 and 2018. He has published four special issues as editor, “Proteomics in India” for Journal of Proteomics; “Proteomics Research in India” for Nature India, “Protein Arrays” for Proteomics and “Neglected Tropical Infectious Diseases” for Proteomics Clinical Applications. Having an extensive teaching experience at IITB and experience of conducting proteomics courses at CSHL, New York provided him with the background to increase proteomics education for the global community. One of his special contributions has been the development of e-learning resources (MOOC – mass spectrometry and interactomics courses; Virtual Proteomics Laboratory). He has made first ever proteomics documentaries – “Proteomics: Translating the Code of Life” and “Human Proteome Project (HPP)”. He has directed HUPO “Perspective in Proteomics” video interview series, which is hosted on HUPO website.

Recently we have signed a MOU on clinical proteogenomics cancer research with National Cancer Institute, along with Tata Memorial Centre and India has now become 12th country to join the International Cancer Proteogenome Consortium (ICPC). Dr. Srivastava continues to develop proteomics & omics science and innovation together with and for the next generation of keen students, researchers and the research and education commons in Asia and global OMICS community.

Click here to view Faculty Profile: http://www.bio.iitb.ac.in/~sanjeeva/ 

About the Instructor: https://youtu.be/sb4faypvWwk 

Course certificate

  • The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
  • The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
  • Date and Time of Exams: 17 November 2019, Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
  • Registration url: Announcements will be made when the registration form is open for registrations.
  • The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
  • Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

  • Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments given in the course. 
  • Exam score = 75% of the proctored certification exam score out of 100
  • Final score = Average assignment score + Exam score

  • If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.
  • Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Bombay. It will be e-verifiable at nptel.ac.in/noc.
  • Only the e-certificate will be made available. Hard copies are being discontinued from July 2019 semester and will not be dispatched

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