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Course Detail

Course Name Genomic Technologies
Course Code 25CLG512
Program M. Sc. Clinical Genomics
Semester 2
Credits 3
Campus Kochi

Syllabus

Unit 1

(Lectures 12)
DNA sequencing technologies and its applications: Sanger sequencing, Next-generation sequencing (NGS) chemistry of different platforms, NGS applications: Whole-genome sequencing (WGS) and whole-exome sequencing (WES), High-throughput genotyping methods (e.g., SNP arrays), Epigenomic and transcriptomic profiling techniques (e.g., ChIP-seq, RNA-seq) Single-cell genomics in clinical research.

Unit 2

(Lectures 10)
Clinical Applications of Genomics: Prenatal and newborn screening, Carrier screening, Tumor profiling for precision oncology, Genomic markers in risk prediction and prognosis

Unit 3

(Lectures 8)
Genomics in Clinical Practice: Genetic privacy and data security (e.g., HIPAA, GDPR), Ethical challenges in genomic medicine, Ethical, Legal, and Social Implications (ELSI)

Unit 4

(Lectures 5)
Genetic counseling: Best practices and communication.

Unit 5

(Lectures 10)

Artificial intelligence in genomic medicine.

Introduction

Pre-requisites: Understanding the technologies in genomics and their clinical applications

Total number of classes: 45

Objectives and Outcomes

Course Outcome

CO1 Students will develop a comprehensive understanding of DNA sequencing by different technologies.

CO2 Using these techniques, student will be able to understand how these technologies are applied for clinical use.

CO3 Students will develop a comprehensive understanding of how genomics are applied in clinical practice.

CO4: Students will gain an in-depth understanding of based on the genomic abnormality how counselling is done and its significance in clinical practice.

CO5: Students will develop an understanding of how artificial intelligence is made use in genomics and its applications in clinical practices.

Programme Outcomes (PO) (As given by NBA and ABET)

PO1: Bioscience Knowledge

PO2: Problem Analysis

PO3: Design/Development of Solutions

PO4: Conduct Investigations of complex problems

PO5: Modern tools usage

PO6: Bioscientist and Society

PO7: Environment and Sustainability

PO8: Ethics

PO9: Individual & Team work

PO10: Communication

PO11: Project management & Finance

PO12: Lifelong learning

CO–PO Mapping Table:

COs

PO1

PO2

PO3

PO4

PO5

PO6

PO7

PO8

PO9

PO10

PO11

PO12

CO1

3

2

–

2

3

–

–

–

–

–

–

2

CO2

3

3

–

3

3

2

–

–

–

–

–

2

CO3

3

3

–

3

3

2

–

–

–

–

–

2

CO4

3

2

–

2

2

3

–

3

–

3

–

2

CO5

3

3

2

3

3

2

–

–

–

–

–

2

Program Specific Outcomes. (PSO)

PSO 1 – NGS Data Formats and Quality Control

PSO 2 – Read Mapping Algorithms

PSO 3 – Variant Detection and CNV Analysis

PSO 4 – RNA Sequencing (RNA-seq)

PSO 5 – Differential Expression Analysis

PSO 6 – Gene Ontology (GO) and Pathway Enrichment Analysis

PSO 7 – Genome Assembly Algorithms

PSO 8 – Application of NGS in Epigenomic Studies

PSO 9 – Processing and analysis of epigenomic data

PSO 10 – understanding gene regulation and disease

CO–PSO Mapping Table:

COs

PSO1

PSO2

PSO3

PSO4

PSO5

PSO6

PSO7

PSO8

PSO9

PSO10

CO1

3

3

–

3

–

–

–

–

–

–

CO2

3

3

3

3

3

–

–

–

–

–

CO3

3

–

3

3

3

–

2

2

3

3

CO4

3

–

3

2

3

–

3

–

2

3

CO5

2

–

3

2

3

–

3

3

2

3

Evaluation Pattern

Evaluation Pattern: 50+50 = 100

Internal Assessment – 50%
Periodical 1 Exam 20%
Periodical 2 Exam 20%
Continuous Assessment Assignment/Test/Quiz 10%
50%
End Semester Examination- 50%
Theory Exam 50%
50%
Total 100%

 

Textbooks/ References

Textbooks:

  • Clinical Genomics: A Guide to Clinical Next Generation Sequencing; 2nd Edition – May 1, 2024; Editors: Shashikant Kulkarni, Somak Roy
  • Next Generation Sequencing, Methods and Protocols, 2018, Volume 1712, Steven R. Head, Phillip Ordoukhanian, Daniel R. Salomon (Eds), Humana Press. ISBN : 978-1-4939-7512-9

References

  • New Clinical Genetics by Andrew Read and Dian Donnai, Scion Publishing Limited, Oxfordshire, UK, 2007, ISBN: 9781904842316

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