Swayam Central

Introduction to Proteogenomics

By Prof. Sanjeeva Srivastava   |   IIT Bombay
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 : Upcoming
Course Type : Elective
Duration : 12 weeks
Start Date : 29 Jul 2019
End Date : 18 Oct 2019
Exam Date : 17 Nov 2019
Category :
  • Biological Sciences & Bioengineering
  • Level : Undergraduate
    This is an AICTE approved FDP course


    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


    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


    Prof. Sanjeeva Srivastava
    Proteomics describes the study and characterization of complete set of proteins present in a cell, organ or organism at a given time. My laboratory is using high throughput proteomic techniques such as mass spectrometry and protein microarray etc. for biomarker discovery in cancer & tropical diseases of India, to study protein-protein interactions and drug target discovery. Information obtained from research program is also used for in silico studies and computing models to enhance our understanding in systems approach. Academic Background . Ph.D. University of Alberta, Canada (2006) .Post-doc, Harvard Institute of Proteomics, Harvard Medical School, USA (2007-2009).Assistant Professor, Department of Biosciences and Bioengineering, IIT Bombay (2009-2014) .Associate Professor, Department of Biosciences and Bioengineering, IIT Bombay (2014-onwards)


    • 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