Centre for Human Genetics Bangalore Course-Syllabus final version with... · 2020-01-09 ·...
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Syllabus: MSc in Human Disease Genetics 15th July 2016
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Centre for Human Genetics
Bangalore
Master’s Program in Human Disease Genetics
Credit Matrix
Semester Theory
Course
Credits
(L)
Tutorial
Credits
(T)
Practicals (P)
(Includes Research Credits:
Term Paper and Dissertation)
Total
Credits
1 11 2 6 19
2 8 3 7 18
3 5 - 6 4 - 5 8 18 - 19
4 8 - 9 4 8 20 - 21
Total Credits 76
Theory courses consist of lectures to be attended, tutorials are discussion sessions and the ‘practicals’ consist
of experiments performed in a laboratory also called ‘lab’ modules. Most theory courses are compulsory and
are called hard core (HC) courses. The soft core (SC) courses offer you a choice from a range available each
semester. In addition we offer Open Elective (OE) courses consisting of a choice of courses in subjects
unrelated to the subject area of the Master’s programme.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Semester 1: August to December
Paper Code Title of Course
(Course coordinator)
HC/SC
/OE
Credits
L T P Total
HDG01 Fundamentals of Genetics
(Gurudatta Baraka)
HC 2 0 0 2
HDG02 Biochemistry
(Sudha Srinivasan)
HC 2 0 0 2
HDG03 Cell Biology and cytogenetics
(Prathibha Ranganathan and
Jayarama S K)
HC 2 0 0 2
HDG04 Human Embryology and Anatomy
(Carmen Coelho)
HC 2 0 0 2
HDG05 Statistical Methods*
(Carmen Coelho)
SC 2 1 0 3
HDG06 History of Genetics* SC 2 1 0 3
HDG07 Scientific writing and presentation (Carmen Coelho)
HC 1 1 0 2
HDGP1 Lab Module I – Genetics
(Gurudatta Baraka)
HC 0 0 3 3
HDGP2 Lab Module II – Cytogenetics
(Jayarama S K)
HC 0 0 3 3
Total Credits 11 2 6 19
Hours /
week
11 4 12 27
Assignments this semester 5
* One soft-core course (for 3 credits) to be taken this semester.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Semester 2: January to May
Paper Code Title of Course
(Course coordinator)
HC/SC/
OE
Credits
L T P Total
HDG08 Molecular Biology
(Nishtha Pandey)
HC 2 1 0 3
HDG09 Biotechniques
(Prathibha Ranganathan)
HC 2 0 0 2
HDG10 Principles of Development*
(Carmen Coelho)
SC 2 1 0 3
HDG11 Bioinformatics*
(Kshitish Acharya)
SC 2 1 0 3
HDG12 Therapeutics: Pharmacogenomics
and vaccines*
SC 2 1 0 3
HDGP3 Lab Module III - Biochemistry &
Molecular Biology (Prameela
Kantheti)
HC 0 0 4 4
HDGP4 Lab Module IV – Cell Biology
(Prathibha Ranganathan)
HC 0 0 3 3
Total Credits 8 3 7 18
Hours / week 8 6 14 28
Assignments this semester 4
* Two soft-core courses (amounting to 6 credits) to be taken this semester.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Semester 3: August to December
Paper Code Title of Course
(Course coordinator)
HC/S
C/OE
Credits
L T P Total
HDG13 Human Molecular Genetics
(Nishtha Pandey)
HC 2 1 0 3
HDG14 Biochemical Genetics
(Sudha Srinivasan)
HC 1 1 0 2
HDG15 Advanced Bioinformatics* SC 1 1 0 2
HDG16 Population Genetics and Evolution*
(Vidyanand Nanjundiah)
SC 1 1 0 2
HDG17 Cancer Biology*
(Prathibha Ranganathan)
SC 1 0 0 1
HDGS1 Model Organisms (Seminar series)*
(Carmen Coelho)
SC 0 1 0 1
HDGS2 Developmental disorders (Seminar
series)
HC 1 0 0 1
HDGT1 Term Paper (Carmen Coelho) HC 0 0 1 1
HDGP5 Lab Module V - Molecular Diagnostics
(Swathi Shetty)
HC 0 0 4 4
HDGP6 Dissertation HC 0 1 3 4
Total Credits 5-
6
4 - 5 8 18 - 19
Hours / week 5-
6
8 - 10 10 24 - 25 +
dissertatio
n
Assignments this semester 5 or 6
* Soft-core courses amounting to 3 to 4 credits to be taken this semester.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Semester 4: January to May
Paper Code Title of Course
(Course coordinator)
HC/S
C/OE
Credits
L T P Total
HDG18 Human Genome Organization*
(Gurudatta Baraka)
SC 1 0 0 1
HDG19 Genetic Counselling and
Epidemiology
(Meenakshi Bhat)
HC 2 1 0 3
HDG20 Ethics in Clinical and Biomedical
Research*
(Meenakshi Bhat)
SC 2 1 0 3
HDG21 Intellectual Property and Patents* SC 2 1 0 3
HDG22 Humanities courses OE 4 4
HDGP7 Dissertation HC 0 2 8 10
Total Credits 8 – 9 4 8 20 – 21
Hours / week 8 - 9 8 0 16 – 17 +
dissertation
Assignments this semester 2 or 3 + OE
* Soft-core courses (3 or 4 credits) to be taken this semester to complete the programme credit
requirement of 76 credits.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Syllabus SEMESTER 1
HDG01. FUNDAMENTALS OF GENETICS (Lecture CREDITS-2)
Unit I 2 Hrs
Heredity and Variation: Definition, history, terminology and significance of study of
genetics for mankind.
Unit II 3 Hrs
Mendelian Inheritance in Humans: Dominance and recessivity, the example of ABO
blood groups in humans, qualitative and quantitative traits, patterns of inheritance;
the contributions of Gregor Johann Mendel: his experimental approach, hypotheses,
the publication and reception of his work.
Unit III 3 Hrs
Chromosomal Basis of Inheritance: Historical experiments, the relationship
between Mendel’s laws and chromosome transmission in mitosis and meiosis,
transmission of genes located on human sex chromosomes.
Unit IV 4 Hrs
Gene Interaction, Inheritance of Complex Traits, Extra-chromosomal
Inheritance: Modified dihybrid ratios; concept of penetrance (illustrated by
Huntington’s disease), expressivity and pleiotropy; maternal inheritance in humans
(mitochondrial inheritance, Leigh syndrome); mosaicism and chimerism.
Unit V 4 Hrs
Mapping of Genetic Loci in Humans: Linkage, crossover and map distance, 2 test of linkage,
mapping function, genetic polymorphisms, chromosomal mapping.
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Unit VI 4 Hrs
Human Pedigree analysis: Test-cross, back-cross in other systems; pedigree analysis
in humans.
Unit VII 4 Hrs
Identification of Genetic Material and the Concept of a Gene: Classical
experiments: those by Griffith; Avery, MacLeod and McCarty; Hershey and Chase;
Beadle and Tatum; Benzer’s deletion mapping and complementation; McClintock’s
jumping genes.
Unit VIII 4 Hrs
Identifying Human Disease Genes: Positional cloning illustrated using as examples,
Duchenne muscular dystrophy, cystic fibrosis and Huntington’s disease.
Unit IX 4 Hrs
Introduction to Microbial Genetics: Bacterial transformation and conjugation,
bacteriophage genetics and transduction, bacterial and viral gene maps.
HDG02. BIOCHEMISTRY (Lecture CREDITS-2)
Unit I 1 Hr
Water, pH and buffers: Chemical properties of water, acids, bases, the pH scale,
buffers.
Unit I I 8 Hrs
Molecules of life: Structure and functions of amino acids, peptides, proteins,
carbohydrates, nucleic acids, lipids, vitamins and minerals.
Unit III 2 Hrs
Enzymes: Properties, classification and kinetics.
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Unit IV 1 Hr
Bioenergetics: Generation and utilization of ATP etc. in cells.
Unit V 6 Hrs
Metabolism of biomolecules: Synthesis and degradation of carbohydrates, lipids,
nucleic acids and amino acids; urea cycle.
Unit VI 3 Hrs
Liver in metabolism: Functions of liver; intermediary metabolism; metabolism of
xenobiotics, including drugs.
Unit VII 1 Hr
Cancer metabolism: Warburg effect.
Unit VIII 5 Hrs
Blood: Haematopoiesis; physical and chemical properties of blood; coagulation
cascade; chemistry of haemoglobin and related molecules; structure of
immunoglobulins; biochemical basis of inherited haematological disorders such as
haemoglobinopathies and coagulation disorders.
Unit IX 5 Hrs
Hormones: The overview of the endocrine system (chemical nature of hormones,
biosynthesis and degradation of hormones, mechanism of action of hormones,
regulation of biosynthesis and secretion hormones); classical endocrine glands and
the hormones secreted by them; functions of various hormones.
HDG03 CELL BIOLOGY AND CYTOGENETICS (Lecture CREDITs-2)
PART 1 – CELL BIOLOGY
Unit I 4 Hrs
Cell Theory and Introduction to Cell Biology: History and breakthroughs in cell
biology; properties and behaviour of cells; structure of biological membranes, lipids
and lipid modification, membrane proteins; cell organelles and functions.
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Unit II 3 Hrs
Cell Division: Mitosis and meiosis, cell cycle, cell cycle controls, phases of cell cycle.
Unit III 2 Hrs
Nuclear Architecture and Organization: Nuclear membrane, nuclear transport,
nuclear organizer region, kinetochore and centrosome.
Unit IV 2 Hrs
Protein and Small Molecule Trafficking: Receptor-mediated endocytosis; intra-
cellular transport, lysosomes, organelle biogenesis; extra-cellular transport:
biogenesis of membrane proteins, protein modification, glycosylation; pumps,
channels and transporters.
Unit V 3 Hrs
Cell Adhesion and Tissue Formation: Organization of cells into tissues and
specialized cell types; extra cellular matrix, cell motility and cytoskeleton; stem cells
and cancer.
Unit VI 1 Hr
Principles of Cell Signalling: Receptors as a basis of signal transduction.
Unit VII 1 Hr
Cell Proliferation, Senescence and Programmed Cell Death
PART 2 – CYTOGENETICS
Unit I 1 Hr
Introduction to Cytogenetics and Clinical Cytogenetics
Unit II 2 Hrs
Introduction to Cytogenetic Techniques: Conventional banding patterns of
chromosomes; specialized banding techniques – C banding, silver staining; nucleolus
organizer region (NOR), sister chromatid exchange (SCE), etc.
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Unit III 2 Hrs
Application of Cytogenetics in Medical Genetics: Chromosome abnormalities and
human genetic diseases: structural and numerical abnormalities; Chromosome
Breakage Studies and their Applications
Unit IV 1 Hr
International System for Human Cytogenetic Nomenclature (ISCN) and Quality
Assurance
Unit V 2 Hrs
Introduction to Cancer Cytogenetics: Application of cytogenetics in cancer
diagnosis, analysis and interpretation of results, quality assurance.
Unit VII 1 Hr
Introduction to Molecular Cytogenetics
Unit VIII 1 Hr
Clinical Applications of Fluorescence in situ Hybridization (FISH)
Unit IX 1 Hr
Application of FISH in Prenatal Diagnosis
Unit X 2 Hrs
Application of FISH in Cancer Diagnosis
Unit XI 2 Hrs
Advanced Molecular Cytogenetic Techniques: Primer in situ labeling (PRINS),
comparative genome hybridization (CGH), spectral karyotyping (SKY), multicolor FISH
(mFISH), multicolor banding (mBAND), Fluorescent in situ hybridization on stretched
DNA known as Fiber FISH, etc.: principles, procedures and applications.
Unit XII 1 Hr
Quality Assurance: International System for Human Cytogenetic Nomenclature
(ISCN), FISH nomenclature, Analysis and Interpretation of Results
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HDG04 HUMAN EMBRYOLOGY and ANATOMY (Lecture CREDITS-2)
PART 1 - HUMAN ANATOMY and PHYSIOLOGY
Unit I 1Hr
Tissue Organization: Overview of tissue organization and organ systems in humans
Unit II 3Hrs
Epithelial Tissue: Structure of epithelia and tissue specific variations.
Muscular Tissue: Structure and classification of muscles, structure of the neuro-
muscular junction.
Connective Tissue: Cartilage, bone, joints; classification and growth of bones.
Integumentary system: Skin and Hair.
Secretory organs: Various kinds of exocrine and endocrine secretory organs.
Unit III 2Hrs
Digestive System: Anatomy and physiology.
Unit IV 2Hrs
Nervous System: Anatomy of the central nervous system and the peripheral nervous
system; an overview of the autonomic nervous system.
Unit V 2Hrs
Vascular and Respiratory System: arterial and venous systems; gross anatomy of
the heart and major blood vessels; blood cells and the physiology of blood; anatomy
and physiology of the respiratory tract.
Unit VI 2Hrs
Excretory System: Anatomy and physiology.
Unit VII 2Hrs
Reproductive System: Anatomy and physiology.
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Unit VIII 2Hrs
Endocrine System: Anatomy and physiology.
PART 2 - HUMAN EMBRYOLOGY
Unit I 2Hrs
Gametogenesis, Fertilization and Assisted Reproductive technologies.
Unit II 3Hrs
Early Embryogenesis: cleavage, the germinal stage, gastrulation, formation of the
germ layers, the embryonic period, body axis specification and pattern formation.
Cell fate and Cell Lineage: Commitment, specification, determination and
differentiation
Development of the Placenta.
Unit III 1 Hr
Development of the Bronchial Apparatus, Face, Nose and Palate.
Unit IV 10Hrs
Development of organ systems:
Gastrointestinal tract.
Respiratory system and Cardio-vascular system.
Urinary system.
Reproductive system.
Nervous system.
Special sense organs.
HDG05. STATISTICAL METHODS
(Lecture CREDITS-2)(TUTORIAL-1)
Unit I 4 Hrs
General Introduction and Probability: Descriptive statistics versus inferential
statistics; measures of central tendency: mean, median, mode; measures of spread:
Syllabus: MSc in Human Disease Genetics 15th July 2016
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variance, standard deviation, coefficient of variation; studying grouped data, graphic
methods; introduction to and definition of probability; conditional probability; Bayes’
rule and screening tests, Bayesian inference; ROC curves; prevalence and incidence.
Unit II 3 Hrs
Distributions: Introduction; random variables and their properties; permutations
and combinations; The Binomial distribution: expectation (mean) and variance; The
Poisson distribution: expectation and variance, computation of Poisson probabilities.
Unit I II 3 Hrs
Estimation: Introduction; the relationship between population and sample; random-
number tables, randomized studies; estimation of the mean of a distribution;
estimation of the variance of a distribution; estimation for the Binomial distribution;
estimation for the Poisson distribution.
Unit IV 4 Hrs
Hypothesis Testing: One-sample inference, one-sample test for the mean of a normal
distribution: one-sided alternatives; one-sample test for the mean of a normal
distribution: two-sided alternatives; the relationship between hypothesis testing and
confidence intervals; Bayesian inference; one-sample χ2 test for the variance of a
normal distribution, one-sample inference for the binomial distribution, one-sample
inference for the Poisson distribution; two-sample inference; the paired t-test; interval
estimation for the comparison of means from two paired samples; two-sample t-test
for independent samples with equal and unequal variances, interval estimation for the
comparison of means from two independent samples (equal variance case); testing for
the equality of two variances.
Unit V 4 Hrs
Categorical Data: Two-sample test for binomial proportions, Fisher’s exact test; two-
sample test for binomial proportions for matched-pair data (McNemar’s test);
estimation of sample size and power for comparing two binomial proportions, R×C
contingency tables; chi-square goodness-of-fit test, the kappa statistic.
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Unit VI 2 Hrs
Nonparametric Methods: the sign test, the Wilcoxon signed-rank test, the Wilcoxon
rank-sum test.
Unit VII 4 Hrs
Regression and Correlation Methods: General concepts; fitting regression lines,
assessing the goodness of fit including the method of least squares; inferences to be
made from the parameters of regression lines; interval estimation for linear
regression; the correlation coefficient, inferences from correlation coefficients;
multiple regression, partial and multiple correlation, rank correlation, interval
estimation for rank correlation coefficients.
Unit VIII 4 Hrs
Multisample Inference: Introduction to the one-way analysis of variance (ANOVA):
fixed effects model, hypothesis testing; comparisons of specific groups, using one-way
and two-way ANOVA; The Kruskal-Wallis test; the random effects models in one-way
ANOVA, the intra-class correlation coefficient; mixed models.
Unit IX (part of tutorial) 4 Hrs
An introduction to Data Analysis using ‘R’: an introduction to handling data using
computers; general programming skills used in visualizing raw data, interpreting data
and inferring relationships between data and models; use of the R language to load
data, create basic summaries and graphics for homework or reports.
HDG07. SCIENTIFIC WRITING AND PRESENTATION
(Lecture CREDITS-1)(TUTORIAL-1)
This course will consist of lectures, written exercises and seminar presentation
workshops aimed at setting an appropriate standard in writing and presentation
skills. The lectures will include lessons in English grammar, composition and
argument mapping. The exercises will include critiquing written scientific material,
composing abstracts, titles and introductions to scientific papers along with exercises
on simple seminar presentations using everyday themes as subject material.
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HDGP1. LAB MODULE I - GENETICS (CREDITS-3)
1. Introductory Genetics; Drosophila genetics
Life cycle of Drosophila, husbandry and handling
Observation and identification of genetic markers of Drosophila
Basics of genetic crosses
2. Examination of phenotypes from monohybrid and dihybrid crosses in
Drosophila.
3. Homozygosity test, back-cross, test-cross; complementation groups; X-linked
inheritance (segregation analysis).
4. Creating a genetic map using Drosophila markers.
5. P-elements and transgenesis.
6. Mapping of P-elements to chromosomes.
7. Genetic tool kit in Drosophila to understand gene function.
8. Reverse genetics
9. RNAi using Drosophila
HDGP2. LAB MODULE II - CYTOGENETICS (CREDITS -3)
PART 1 - BASIC CYTOGENETICS
1. Use of patient tissue samples: blood/percutaneous umbilical blood sampling
(PUBS)/amniotic fluid/chorionic villus specimen (CVS)/products of conception
(POC)/Skin/bone marrow (BM)/solid tumor, etc.
2. Microscopy – Principles
3. Karyotyping – conventional and software based (Karyotype workstation)
4. Conventional cytogenetic techniques: G-banding, C-Banding, nucleolus
organizer region (NOR) staining: principles, procedures and applications.
5. Specialized techniques – Chromosome breakage and Sister-chromatid
Exchange (SCE).
6. Conventional Cytogenetics, for example, peripheral blood (PB) cytogenetics,
prenatal cytogenetics, cancer cytogenetics: case study analysis and inference.
7. Analysis and interpretation of results.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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PART 2 - MOLECULAR CYTOGENETICS
1. Specimen culture; preparation of slides and probes for fluorescence in situ
hybridization (FISH).
2. Fluorescence Microscopy – Principles
3. FISH, signal detection and analysis.
4. Methods in spectral (Color) image capture and analysis.
5. Advanced FISH techniques – spectral karyotyping (SKY) or multiplex
fluorescent in situ hybridization (mFISH).
6. Analysis and interpretation of results.
7. Quality assurance.
SEMESTER 2
HDG08. MOLECULAR BIOLOGY
(Lecture CREDITS-2) (TUTORIAL-1)
Unit I 2 Hrs
Biomolecules and Central Dogma of Molecular Biology: Molecular organization of
genes and chromosomes; the genetic-code and the central dogma connecting DNA to
RNA to Protein; structures of these macromolecules.
Unit II 4 Hrs
DNA Replication: Prokaryotic and Eukaryotic replication: mechanisms and molecular
machinery.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit III 5 Hrs
DNA Recombination: Models suggesting how recombination might occur: the
Holliday model, the Messelson-Radding heteroduplex model and the double-strand-
break repair model; gene conversion.
Unit IV 5 Hrs
Transcription: Prokaryotic and Eukaryotic transcription: mechanisms and molecular
machinery.
Unit V 4 Hrs
Post-transcriptional Processing and Nuclear Transport: processing of mRNA: 5'-
capping, 3'-polyadenylation, splicing; processing of tRNA and rRNA; RNA editing.
Unit VI 4 Hrs
Translation: Prokaryotic and eukaryotic translation: mechanisms and molecular
machinery.
Unit VII 4 Hrs
Post-translational Processing of Proteins: Polypeptide cleavage, chemical
modifications and ribozymes.
Unit VIII 1 Hr
Gene Regulation: Elements of gene regulation: promoters, enhancers, silencers,
repressors; hox gene regulation during development.
Unit IX 2 Hrs
Mutations and Human Diseases: Mutagens, intrinsic mechanisms of DNA damage
and repair mechanisms; coding and non-coding mutations, types of amino-acid
substitution, substitution rates, mutation-rate differences between the sexes;
sequence repeats and their pathogenic effects; transposons and retro-transposons.
Unit X 1 Hr
Mitochondrial DNA: Genome organization and codon usage; mitochondrial mutations
and associated diseases.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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HDG09. BIOTECHNIQUES (Lecture CREDITS-2)
Unit I
Genotyping and Sequencing: DNA polymorphisms and genotyping: restriction site
polymorphisms (RSP), minisatellites, microsatellites, single nucleotide polymorphisms
(SNP), restriction fragment length polymorphisms (RFLP), DNA-fingerprinting;
sequencing: Sanger, Maxim-Gilbert, pyro, de novo; polymerase chain reaction (PCR):
principle, modifications and applications; next-generation sequencing.
Unit II
Nucleotide Hybridization, Principles and its Application: Introduction to probe
preparation, hybridization, autoradiography, fluorescent detection; types of
hybridization assays: dot, Southern, northern, colony blots, plaque lift, array
hybridization, fluorescence in situ hybridization.
Unit III
Identification of Genes and their Structure: Open reading frame (ORF) analysis: zoo
blot, exon-trapping, rapid amplification of complementary DNA ends (RACE),
transcription start site mapping, exon-intron boundary identification, database
homology search.
Unit IV
Analysis of gene expression: Detection of gene expression: reverse transcriptase-
quantitative (real time) PCR (RT-qPCR), in situ hybridization; detection of protein
expression: immunocyto/histo-chemistry, western blotting, protein tagging and
reporter gene expression analysis including Luciferase, Green fluorescent protein
(GFP), beta-D Galactosidase (LacZ), Chloramphenicol acetyltransferase (CAT)
expression.
Unit V
Gene Manipulation: Mutagenesis methods: chemical, radiation, site-directed,
insertion mutagenesis; transgenic model systems.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit VI
Study of Proteins and Protein Complexes: Introduction and expression of cloned
genes in bacterial and mammalian systems: transformation, transfection, inducible
systems; protein purification, antibody production and immunoprecipitation; mapping
of protein-binding sites on DNA: gel-retardation assay, DNase-I footprinting; protein-
protein interaction study: far-western, co-immunoprecipitation and fluorescence
resonance energy transfer (FRET).
Unit VII
Cloning: Principles of cell-based cloning and cloning systems: plasmid, lambda,
cosmid, bacterial artificial chromosomes (BACs), P1 derived artificial chromosomes
(PACs) and yeast artificial chromosomes (YACs); expression systems: bacterial, phage
and eukaryotic cells.
Unit VIII
Introduction to Functional Genomics and Proteomics: Comparative genomics;
transcriptome analysis: serial analysis of gene expression (SAGE), DNA microarrays;
2-dimensional gel electrophoresis (2DGE), mass spectrometry; protein structural
studies: macro-molecular structure, nuclear magnetic resonance (NMR), protein
structure predictions; protein-protein interaction screening: phage display, yeast two-
hybrid system.
HDG10 PRINCIPLES OF DEVELOPMENT (Lecture CREDITS-2)
Unit I 1 Hr
Developmental Biology: Basic Principles and Concepts
Unit II 5 Hrs
Origins of polarity in the embryo: Differences in the origins of polarity between
different kinds of embryos, inheritance in most cases of polarity from the egg;
specification of Dorso-ventral and Anterio-posterior polarity.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit III 5 Hrs
Formation of the germ layers: Early specification of germ layers and the derivatives
of each germ layer in insects and vertebrates; Spemann’s organizer; gastrulation in
invertebrates and vertebrates; morphogenetic movements and cell shape changes
accompanying the formation of each germ layer; induction between germ layers.
Unit V 2 Hrs
Basics of pattern Formation: Formation of protein gradients during development,
pattern formation within simple epithelia and within mesenchymal cells; long range
and short range pattern formation.
Unit IV 6 Hrs
Emergence of the Body Plan: Segmentation in insects and vertebrates; segment
identity specification by Hox genes; left-right asymmetry; the emergence of limbs in
insects and vertebrates.
Unit VI 2Hrs
Specification of Cell Fate: Signaling events accompanying cell fate specification in
certain well characterized contexts, for example, Notch-Delta signalling in neuroblast
specification; the role of lineage, asymmetric and symmetric cell divisions.
Unit VII 4 Hrs
Cell Migration: role of migration during development, epithelial to mesenchymal
transition, directed migration of individual cells; branching of tubular structures.
Unit VIII 5 Hrs
Determination of size: Organ intrinsic and extrinsic (systemic) regulation of organ
size; cell size versus cell number; pathways that regulate growth; the determination of
organ size and shape by morphogens; bone growth in vertebrates
Unit IX 2 Hrs
Germ cell development: Specification and migration of germ cells to form gonads in
invertebrates and vertebrates
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HDG11. BIOINFORMATICS (Lecture CREDITS-2)(TUTORIAL-1)
Unit I 1 Hr
Introduction to Bioinformatics and its Scope: An overview of activities in
bioinformatics with emphasis on the types of information in modern biology and the
need for databases and software.
Unit II 3 Hrs
Operating Systems and Basics of Computer Languages and Commands: Use of
Linux operating system, commonly used open software; introduction to shell, Perl
Unit III 4 Hrs
Databases and Data-mining: General concepts of databases; an overview of database types; common databases, related software and their utilities (Medline, Entrez Gene, dbEST, Unigene, HPRD, PubMed, NEBcutter, Primer3plus, Primer Blast); concepts in primer designing and restriction site analysis and relevant tools.
Unit IV 4 Hrs
Human genome analysis: Relationship between mutations, SNPs, indels, CNVs and
alleles; significance of SNPs; GWAS; SNP databases and analysis using the databases;
NGS analysis for SNP detection; genomic vs. exomic analysis; case studies.
Unit V 4 Hrs
Metagenomics: concepts and case studies; demonstration of data analysis.
Unit VI 6 Hrs
Sequence analysis: Significance of sequence analysis; common methods used in sequence analysis and alignment; basic concepts of sequence similarity, identity and homology, definitions of homologs, orthologs, paralogs; common databases used to retrieve gene, mRNA and protein sequences; phylogenetic analysis with reference to nucleic acids and proteins, and their significance; comparison of operation and applications of BLAST and MSA, and interpretation of results; concepts in DNA and RNA motif analysis, relevant databases and software.
Unit VII 6 Hrs
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Transcriptome Analysis: Commonly used databases for transcriptomic data; micro-
array technology and analysis; RNA-seq analysis; miRNA analysis; ChIP-seq
technology and data analysis.
Unit VIII 4 Hrs
Bioinformatics for Proteins: Review of protein structures and domains; Obtaining
basic data/information on proteins of interest using databases; Use of databases for
protein-structures, gene ontologies, protein-interactions and pathways; concepts in
homology modeling, drug discovery and designing; biosimilars vs. traditional APIs and
concept of clinical trials.
HDGP3 LAB MODULE III: BIOCHEMISTRY & MOLECULAR BIOLOGY (CREDITS -4)
1. Basic Principles and Techniques I: Preparation of solutions: stock and
working solutions, concept of serial dilution; storing of solutions: making
aliquots, freezing, thawing; ways to express concentration of solutions: concept
of molarity; measuring and adjusting pH; appropriate handling of various
chemical compounds.
2. Analysis of proteins in cell lysates: Preparation of cell lysates;
chromatography (column and paper), dialysis, salting out, etc., estimation of
total protein (Lowry/Bradford); analysis of protein of interest by western
blotting.
3. Use of Antibodies in antigen analysis: ELISA.
4. Isolation of nucleic acids: DNA and RNA from E. coli, eukaryotic cells and
tissues; estimation and agarose gel electrophoresis; preparation of plasmid DNA
from bacterial cells, restriction digestion, analysis of products through agarose
gel electrophoresis.
5. Nucleic acid hybridization techniques and analysis: Southern, Northern and
reverse dot blots; probe preparation including labelling and purification.
6. Extraction of chromatin; Micrococcal nuclease and DNase-I digestion of
chromatin and analysis of DNA and proteins of nuclease sensitive and resistant
fractions.
7. Culturing bacteria and analysing phases of growth through a growth curve.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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HDGP4. LAB MODULE IV - CELL BIOLOGY
(CREDITS-3)
1. Basics of cell culture: Media preparation and filtration; sub-culturing and
reviving frozen stocks.
2. Cell counting, cell viability assay: Trypan blue exclusion.
3. Transfection and gap junction localization: Transfection and estimation of
transfection efficiency using wild-type and mutant Connexin-GFP expressing
constructs.
4. Cell viability assays: MTT assay, IC50 determination
5. Wound healing assay: Scratch test performed using a confluent culture of
Human cells.
6. Basics of light microscopy: Lecture plus demonstration
7. Early development of Drosophila melanogaster: collecting sychronised egg
lays, watching cellularisation and gastrulation in live embryos, staining with
nuclear dyes; using GFP expressing strains that label organelles, cytoskeleton,
mitotic spindles and cell-cell junctions during early development of Drosophila
embryos.
*********************************************************************************************
SEMESTER 3
HDG13. HUMAN MOLECULAR GENETICS (Lecture CREDITS-2) (TUTORIAL–1)
Introduction to Human Genetics 1 Hr
Unit I 3 Hrs
Genetic Disorders and Single Gene Inheritance: Overview of genetic disorders:
consequences and mechanisms; Nomenclature of mutations, importance of the
Syllabus: MSc in Human Disease Genetics 15th July 2016
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position of a Base, databases of known mutations; from genotype to phenotype: loss of
function mutations, gain of function mutations, expanding repeats.
Unit I I 6 Hrs
Genetic Mapping of Monogenic Traits: Linkage analysis: genetic markers,
recombinants and non-recombinants, development of genetic markers; two-point
mapping, multipoint mapping: calculation of logarithm of odds (LOD) scores, Bayesian
calculation of linkage threshold, haplotype analysis and defining critical linked interval
in large pedigrees; autozygosity mapping; principles and strategies of identifying
disease genes, positional cloning and position independent approaches.
Unit I II 6 Hrs
Multifactorial Traits or Complex Disorders: Polygenic theory of quantitative traits;
partitioning of variance; polygenic theory of discontinuous characters; genetic
component assessment: twin and adoption studies; mapping of complex traits by non-
parametric linkage analysis and association studies.
Unit IV 4 Hrs
Identification of Candidate Disease Genes in a Post-Genomic Scenario: Genomic,
transcriptomic and proteomic approaches, genome-wide association studies (GWAS)
illustrated by whole genome/exome sequencing in the study of obesity.
Unit V 4 Hrs
Sex Linked Disorders, Sex Limited, Sex Influenced Traits, Genomic Imprinting
Unit VI 8 Hrs
Gene Action-Tracking Defects in Gene Function: Epigenetics and gene expression
defects with respect to (a) haemoglobinopathies, haemophilia, beta-thalassemia, sickle
cell anaemia (b) cystic fibrosis (c) laminopathies, Hutchinson-Gilford progeria
syndrome (d) glaucoma (e) genetics of epilepsy (f) infertility (g) macromolecular
storage disorders (glycogen and other carbohydrates) (h) Rett syndrome: an example
of genetic disorders in neurodevelopment (i) fragile X syndrome (j) dermatological
disorders (k) hearing impairment (l) genetics of intellectual disability and autism (m)
molecular basis for ataxia telangiectasia - one kinase, multiple function, (above list of
disorders will be reviewed according to availability of teachers).
Syllabus: MSc in Human Disease Genetics 15th July 2016
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HDG14. BIOCHEMICAL GENETICS (Lecture CREDITS-1)(TUTORIAL-1)
Unit I 5 Hrs
Inborn Errors of Metabolism (IEM)
Basic concepts, including history; types of IEM; diagnosis, symptoms; inborn errors in
the metabolism of amino acids, carbohydrates, nucleic acids, lipids, vitamins and
minerals; treatment of IEM.
Unit II 5 Hrs
Lysosomal Storage Disorders (LSD)
Types of LSD, diagnosis, symptoms, disease mechanisms, biomarkers, and treatment.
Unit III 4 Hrs
Endocrine and Metabolic Diseases
Overview of diseases associated with the biosynthesis, degradation and action of
hormones; pathophysiology and treatment of diabetes mellitus; monogenic endocrine
diseases such as multiple endocrine neoplasia and congenital adrenal hypoplasia;
endocrine disruptors.
Unit IV 2 Hrs
Development of Drugs
Principles of pharmacology, including pharmacogenomics; Development of small
molecules and biopharmaceutical agents; cell based assays and preclinical models.
HDG16. POPULATION GENETICS AND EVOLUTION (Lecture CREDITS-1) (TUTORIAL-1)
Unit I
Overview and Evolution of the Physical Universe: Origins of the universe, big bang
theory, formation of the solar system, early earth; rock formation, plate tectonics,
geological time scale.
Syllabus: MSc in Human Disease Genetics 15th July 2016
26
Unit II
The origins of life on Earth: emergence of macromolecules, cells, role of RNA;
Precambrian life, brief introduction to Cambrian explosion and terrestrial life.
Unit III
Tree of Life: “Living forms are related”, fossil record, classification and phylogeny,
evolutionary transitions among genera, major transitions during evolution.
Unit IV
Adaptation and Natural Selection: phenotypic variation vs. genetic variation; theory
of Natural Selection; the ‘selfish gene’ concept; individual selection vs. group selection;
parasite-host adaptation; biogeographic evidence for evolution, major patterns of
distribution of species.
Unit V
Genes and evolution: origins of genetic variation, mutation rate, erosion and release
of variation by recombination, effect on fitness; alterations in karyotype; external
sources of genetic variation, hybridization, horizontal gene transfer
Unit VI
Fundamental principles of genetic variation in Populations: Frequencies of alleles
and genotypes, Hardy-Weinberg principle and significance in evolution; genetic
variation in natural populations, geographic variation, genetic distance.
Unit VII
Population structure and Genetic drift: Theory of genetic drift, genetic drift in
natural populations; Inbreeding and its effects on genetic drift; models of gene flow
and genetic drift, genetic hitchhiking; migration, extinction and recolonization; the
‘Neutral theory of molecular evolution’; population structure and gene trees,
haplotype diversity, gene trees and species trees.
Unit VIII
Speciation and macroevolution: Sympatric, allopatric and parapatric speciation;
ontogeny and phylogeny; rates of evolution; developmental principles of evolutionary
Syllabus: MSc in Human Disease Genetics 15th July 2016
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change, developmental constraints, non-adaptive characters and discontinuity of
evolutionary change, evolution of novelty.
Unit IX
Evolution of Sex and sexual selection: evolution in asexual and sexual populations;
mate choice and signal detection; male vs. female reproductive fitness, cost of
reproduction.
Unit X
Evolution of Social behavior: evolution of different forms of social behavior,
evolution of cooperation and apparent altruism.
Unit XI
Evolution of Life Histories: major life history traits and fitness; evolution of
demographic traits, life span and senescence, age schedules of reproduction, number
and size of offspring.
Unit XII
The Evolution of Homo sapiens: Phylogenetic relationships, fossil record, origin of
modern human populations, migration and genetic variation in human populations;
the evolutionary future of humans; evolution of human behavior and cultural
evolution.
Unit XIII
The Implications of our Evolutionary Heritage on our Health: frequency of alleles
that cause disease among different populations, rare deleterious alleles; assortative
mating behavior and allele frequency; consanguinity, genetic drift and genetic diseases
in populations with a reduced number of founders; the occurrence of mutation
hotspots.
Unit XIV
Alternatives to natural selection.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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HDG17. CANCER BIOLOGY (Lecture CREDITS-1)
Unit I 6 Hrs
Basics about the Origins of Cancer: Basic mechanisms regulating normal tissue
homeostasis: regulation of cell-proliferation, growth, differentiation and apoptosis; the
regulation of growth in terms of volume/mass increase; the determination of cell size,
cytoplasmic to nuclear size ratio, the balance between signals that drive cell division
versus increase in cell volume; the role of stem cells in tissue homeostasis; DNA
replication and repair mechanisms; the loss of regulatory mechanisms that result in
cancer.
Unit II 3 Hrs
Genetic Alterations in Cancer: The nature of commonly occurring mutations: gain of
function, loss of function, copy number variation (CNV), chromosomal-translocations
etc.; methods of detecting genetic alterations and their use as diagnostic/prognostic
tools; disease management; mouse models for understanding the role of these gene
products in the development of cancer.
Unit III 5 Hrs
Epigenetic Mechanisms of Carcinogenesis: Epigenetic changes during normal
development and homeostasis, role of the Polycomb group (PcG) and Trithorax (Trx)
proteins in maintaining the balance between stem cell renewal and differentiation;
known alterations that occur in cancer; the basis of epigenetic therapy; insights from
mouse models.
Unit IV 1 Hr
Roles of Viruses in the development of Cancer
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit V 1 Hr
Current strategies in Therapeutics and Drug Design
HDGS1. MODEL ORGANISMS (LECTURES AND SEMINARS) (TUTORIAL CREDITS-1)
The course will consist of seminars and discussions led by invited speakers who use
model organisms in their research. This course is aimed at an interactive learning
experience for the students. The course could also consist of workshops conducted,
coordinated or sponsored by the Centre for Human Genetics.
Insights into the mechanisms of human disease obtained from studying the
biology of human diseases using model systems.
The following model systems could be studied, depending on the expertise available:
Unit I 3 Hrs
Planaria: Using a simple micro-organism to study the cell biology of regeneration.
Unit II 2 Hrs
C.elegans: Using orthologous genetic, mutant models to study the biology of metabolic
disorders such as diabetes, ageing and neuronal disorders such as Alzheimer’s disease,
muscular dystrophy, ion-channelopathies.
Unit III 3 Hrs
D. melanogaster: Using orthologous genetic, mutant models to study the biology of
diseases such as Alzheimer’s disease, neurodegenerative disorders, Parkinson’s
disease, triplet repeat expansion diseases, Fragile X syndrome, metabolic disorders
and diabetes.
Unit IV 2 Hrs
Zebrafish: Using vertebrate orthologous genetic, mutant models to study
haematological diseases such as sideroblastic anemia, polycythemia, and porphyria; T-
cell leukaemia models, Melanomas, heart defects resembling human dilated
Syllabus: MSc in Human Disease Genetics 15th July 2016
30
cardiomyopathies (DCMs), modeling Duchenne muscular dystrophy, Polycystic kidney
disease (PKD), etc.
Unit V 4 Hrs
Mouse: Studying humanised mouse models containing transplanted human cells or
the human orthologues of specific genes; genetic disorders such as hearing-loss
disorders; treatment of early onset cancers such as acute promyelocytic leukaemia
(APL); role of the protein Leptin in controlling obesity.
Unit VI 2 Hrs
Human Induced Pluripotent Stem Cells: as tools in drug development and modeling
diseases; the ability to create patient and disease specific stem cells.
HDGS2. DEVELOPMENTAL DISORDERS (Lecture CREDITS-1)
This course will consist of guest lectures by established medical practitioners and
scientists and will deal with diseases pertaining to specific organ systems. The topics
covered will include:
Unit I 2 Hrs
The genetics of breast cancer and kidney disorders.
Unit II 2 Hrs
Ophthalmic molecular genetics, focusing on the identification of genes responsible
for eye diseases such as retinoblastoma, corneal dystrophies, congenital cataracts
and retinitis pigmentosa.
Unit III 2 Hrs
Dermatology: skin diseases, such as eczema, epidermolysis bullosa.
Unit IV 1 Hr
Syllabus: MSc in Human Disease Genetics 15th July 2016
31
Immunology with specific emphasis on host-pathogen interactions and cohort based
studies to address susceptibility to co-infections.
Unit V 1 Hr
Immuno-endocrinology with emphasis on immuno-modulation during pregnancy.
Unit VI 1 Hr
The development of vaccines such as vaccines against Abrin toxin and Hepatitus C
viruses.
Unit VII 1 Hr
Host-pathogen interactions in the development of tuberculosis as a disease
condition.
Unit VIII 1 Hr
Nephrology with a particular emphasis on critical care nephrology and preventive
nephrology.
Unit IX 1 Hr
Differentiation of embryonic stem cells.
Unit X 2 Hrs
Pathology and therapy of neurodegenerative diseases and the screening of natural
products for any potential therapeutic role.
Unit XI 2 Hrs
Epilepsy and neurodegenerative disorders; brain-banking as an aid in brain research.
HDGT1. TERM PAPER (PRACTICAL-1)
The student will write and present an up to date review of literature on a selected
topic or alternately, a project proposal. This would serve as a platform to enhance the
Syllabus: MSc in Human Disease Genetics 15th July 2016
32
student’s skills in reading scientific literature, critical analysis of the literature and
communication skills. Special attention will be given to discouraging plagiarism.
HDGP5. LAB MODULE V- MOLECULAR DIAGNOSTICS (CREDITS -4)
1. Polymerase chain reaction (PCR) and its multiple applications
2. Primer design for PCR and sequencing.
3. DNA gel electrophoresis of PCR amplified products
4. Sanger sequencing of gene exons for mutation detection.
5. Analysis of Sequence-electropherograms and analysis of identified sequence
variations.
6. Quantitative PCR (qPCR) for estimation of gene copy or transcript expression
level.
7. Genotyping with PCR for deletion screening.
8. STR-based Human Identification
9. Detection of Fragile X mutation though capillary electrophoresis.
10. Multiplex Ligation Dependent Probe Amplification (MLPA)
HDGP6. DISSERTATION (PRACTICAL CREDITS-3) (TUTORIAL-1)
Each student will have one supervisor and a research committee of at least three
people including the supervisor.
This course consists of an individual research project to be carried out in one of the
research laboratories in CHG. This will be for the duration of the third and fourth
semesters. During the third semester the students will be expected to master the
literature behind the project and present a proposal of work, including preliminary
results.
Syllabus: MSc in Human Disease Genetics 15th July 2016
33
**************************************************************************************
SEMESTER 4
HDG18. HUMAN GENOME ORGANIZATION (Lecture CREDITS-1)
Unit I 2 Hrs
Regulation of Gene Expression (An overview): Transcriptional regulation: RNA
polymerase II promoters, enhancers and insulators; post transcriptional regulation:
alternative splicing, alternative poly-Adenylation, and alternative translation start
sites; nonsense-mediated decay and other mRNA surveillance mechanisms; microRNA,
RNA-interference.
Unit II 2 Hrs
Chromatin Organization and its effects on Gene Expression: Organization of
Euchromatin and Heterochromatin; Long-range gene regulation: DNA-methylation,
Histone modifications, imprinting, allelic exclusion, X-inactivation, multi-tiered
regulation of Homeobox genes; organization of the Y-chromosome; organization of
certain specific loci: immunoglobulin gene loci, T-cell receptor gene loci, Haemoglobin
gene locus; special stage specific chromosomal organization: for example, chromatin
during gametogenesis
Unit III 4 Hrs
Genome: Human genome mapping, structure of genome, genome organization and
variation.
Unit IV 8 Hrs
Analysis of the Human Genome: The genome landscape, gene number in comparison
to other organisms, sequence analysis, human genome mapping.
Syllabus: MSc in Human Disease Genetics 15th July 2016
34
HDG19. GENETIC COUNSELLING and EPIDEMIOLOGY (Lecture CREDITS-2)(TUTORIAL-1)
PART 1-GENETIC COUNSELLING
Unit I 1Hr
Introduction to genetic counseling
Unit II 3Hrs
Impact of illness on patients and families: Morbidity and support services, access to
education and economic support, social practices and health cost issues. Incidental detection
of other genetic disorders on pedigree evaluation and NGS testing, manifesting carriers,
later onset genetic disorders including neuro-genetic disorders, e.g., Huntington’s disease,
Myotonic dystrophy and Inherited cancers
Unit III 3Hrs
Congenital anomalies and rare medical disorders, its impact on community health and
health priorities: Incidence of common congenital anomalies and risk factors, pre-
pregnancy evaluation and intervention strategies, newborn screening for rare metabolic
disorders, Consanguinity and its impact on genetic disorders, registries and support groups
for rare medical disorders
Unit IV 3Hrs
Social and cultural issues in rare medical disorders: Evaluation of social attitudes and
customs, caste, consanguinity, economic status and cultural perceptions in the evaluation of
genetic disorders. Impact of disorders of sexual development (DSDs) and genetic
counselling in these disorders, eg., sex reversal, androgen insensitivity disorder and
Syllabus: MSc in Human Disease Genetics 15th July 2016
35
Klinefelter and Turner syndrome. Impact of rare disorders on decisions about marriage,
reproduction, prenatal diagnosis and integration in mainstream education and society
Unit V 3Hrs
Predictive counselling for late onset disorders, e.g., Huntington’s disease, breast and
ovarian cancer: Principles about predictive counselling and testing in late onset disorders,
imparting results of predictive testing, counselling and management in follow up sessions,
ethical issues in testing of minors, prenatal diagnosis in late onset disorders, ethical and
social issues
Unit VI 3Hrs
Genetic counseling in Clinics: Time spent in clinics (Clinical rotations) during the
semester.
These rotations will provide an opportunity for students to learn directly about medical
genetic conditions and their impact on individuals and families and interpretation of
medical diagnosis in real life clinical sessions based in a hospital outpatient setting. They
will gain practical insight in pedigree evaluation, recent advances in medical genetics,
therapy options, prenatal diagnosis and practical genetic counseling.
PART 2-GENETIC EPIDEMIOLOGY
Unit I 2 Hrs
Epidemiology: the study of the interplay between genetic and environmental factors
that result in human disease
Unit II 4 Hrs
Infectious Diseases: spread and management
Unit III 4 Hrs
Immunogenetics: Auto-immune diseases, HLA typing
Syllabus: MSc in Human Disease Genetics 15th July 2016
36
Unit IV 2 Hrs
Human Vaccines
Unit V 2 Hrs
Pharmacogenomics: genetic variations in patients that cause varied responses to a
drug.
Unit VI 2 Hrs
Genomes and Society: Topics related to modern medicine and treatment. Special
emphasis will be placed on the principles of human genomics (including human
genome organization, complex disease and large scale genomic analysis) and how they
relate to the field of translational genomics (connecting human genetics with drug
design); brief discussion on ethical and societal issues concerning personalized
medicine as well as its implications on modern health care.
HDG20. ETHICAL IN CLINICAL AND BIOMEDICAL RESEARCH
(Lecture CREDITS-2) (TUTORIAL-1)
Unit I: Clinical Ethics Unit II: Ethical issues in prenatal diagnosis and newer reproductive technologies
Unit III: Genetic testing in adult onset disorders
Unit IV: Testing of vulnerable populations
Example: children of intellectually incapacitated individuals, consent and confidentiality.
Unit V: Research Ethics
The use of placebos, conflicts of interest and clinical trials, research on animals and
vulnerable populations, research in developing countries
Unit VI: Role and Scope of Institutional review board in scientific research.
Unit VII: Global & Population Ethics: global disparities in health and public health, global
pandemics, population growth, human rights to health and health care, Role of foreign aid
Syllabus: MSc in Human Disease Genetics 15th July 2016
37
Unit VIII: Ethics of New Technologies:
Embryonic stem cells, cloning, genetic engineering, synthetic biology
Unit IX: Environmental & Animal Ethics: species preservation, biodiversity loss,
ecosystem services, the use and misuse of animals, ethics
Unit X: Medico-legal Issues: Surrogacy, Organ donation, Paternity testing
Students will also work on a short-term project on Ethics in Biomedical sciences at various
organizations in around Bangalore.
HDGP7. DISSERTATION (PRACTICAL CREDITS-8) (TUTORIAL-2)
Each student will have one supervisor and a research committee of at least three
people including supervisor.
This course is a continuation of the individual research project started in the third
semester in one of the research laboratories in CHG. During the fourth semester, the
students will be expected to complete the project and present their results through a
seminar and written dissertation.
*******************************************************************************************************
References
SEMESTER1
HDG01. Fundamentals of Genetics
1. AH Sturtevant (2001) History of Genetics, Cold Spring Harbor Laboratory Press
2. AJF Griffiths, JH Miller, DT Suzuki, RC Lewontin, and WM Gelbart (2000) An
Introduction to Genetic Analysis, W.H Freeman Publication, 7th Edition
3. DP Snustad and MJ Simmons (2012) Principles of Genetics, John Willey & Sons
Publication, 6th Edition
4. DL Hartl and EW Jones (2008) Genetics: Analysis of Genes and Genomes, Jones and
Bartlett Publication
Syllabus: MSc in Human Disease Genetics 15th July 2016
38
5. R Nussbaum, RR McInnes, HF Willard (2007) Thompson and Thompson Genetics in
Medicine, Elseiver Health Sciences, 7th Edition
6. SR Maloy, JE Cronan, D Freifelder(1994) Microbial Genetics, Jones and Bartlett
Publication, 2nd edition
7. Educational resource built around Mendel’s work: http://www.mendelweb.org/
HDG02. Biochemistry
1. DL Nelson and MM Cox (2013) Lehninger, Principles of Biochemistry, WH Freeman
Publication, 6th Edition
2. D Voet and JG Voet (2010) Biochemistry, John Willey & Sons Publication, 4th Edition
3. JM Berg, JL Tymoczko and L Stryer (2010) Biochemistry, WH Freeman Publication, 7th
Edition
4. V Rodwell, D Bender, KM Botham, PJ Kennelly and PA Weil (2015) Harper’s Illustrated
Biochemistry, Mc Graw Hill Publication, 30th Edition
5. Varki A, Cummings RD, Esko JD, et al., editors. Essentials of Glycobiology. 2nd edition.
Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. Available from:
http://www.ncbi.nlm.nih.gov/books/NBK1908/
6. Nussey S, Whitehead S. Endocrinology: An Integrated Approach. Oxford: BIOS Scientific
Publishers; 2001. Chapter 1, Principles of endocrinology. Available from:
http://www.ncbi.nlm.nih.gov/books/NBK20/
7. Robert A. Weinberg, The Biology of Cancer, Garland Science; 2nd edition, 2013
HDG03. Cell and Biology and Cytogenetics
1. JD Watson (2013) Molecular Biology of the Gene, Pearson Publication, 7th Edition
2. B Alberts, A Johnson, J Lewis, M Raff, K Roberts and P Walter (2014) Molecular Biology
of the Cell, Taylor and Francis Publication, 6th Edition
3. H Lodish, A Berk, SL Zipursky, P Matusdaira, D Baltimore and J Darnell (2012) Molecular
Cell Biology, W. H. Freeman and Company, 7th Edition
4. JE Krebs, ES Goldstein and ST Kilpatrick (2012) Lewin’s Gene XI, Jones and Bartlett
Learning Publication, 11th Edition
HDG04. Human Embryology and Anatomy
1. TW Sadler (2011) Langman’s Medical Embryology, Lippincott Williams and Willkins
Publication
2. S Standring (2008) Gray’s Anatomy, Churchill Livingstone Publication, 40th Edition
Syllabus: MSc in Human Disease Genetics 15th July 2016
39
3. E Hall (2010) Guyton and Hall, Text book of Medical Physiology, Saunders
Publication, 12th Edition
4. SF Gilbert (2013) Developmental Biology, Sinauer Publication, 10th Edition
5. L Wolpert, C Tickle and AM Arias (2015) Principles of Development, Oxford University
Press, 5th Edition
6. EF Keller (2002) Making Sense of Life: Explaining Biological Development with
Models, Metaphors and Machines, Harvard University Press, 1st Edition
7. Scott F. Gilbert and Anne M. Raunio (1997) Editors, Embryology, Constructing the
Organism, Elsevier Science.
HDG05. Statistical Methods
1. JH Zar (2010) Biostatistical Analysis, Prentice Hall Publication, 5th Edition
HDGP1. Lab Module I-Genetics
1. RJ Greenspan (2004) Fly Pushing: The Theory and Practice of Drosophila Genetics,
Cold Spring Harbor Laboratory Press
2. S Chyb and N. Gompel (2013) Atlas of Drosophila Morphology: Wild Type and
Classical Mutants, Academic Press, Elseiver
3. DS Henderson (2004) Drosophila Cytogenetics Protocols, Humana Press Inc.
4. PA Lawrence (1992) The Making of a Fly: the Genetics of Animal Design, Wiley
Publications
5. C Dahmann (2010) Drosophila: Methods and Protocols (Methods in Molecular
Biology), Humana Press Inc.
6. M Ashburner(2011) Drosophila A Laboratory Handbook, Cold Spring Harbor
Laboratory Press
7. W Sullivian, M Ashburner, RS Hawley (2000) Drosophila Protocols, Cold Spring Harbor
Laboratory Press
HDGP2. Lab Module II-Clinical and molecular cytogenetics
1. JL Hamerton (2013) Human Cytogenetics: Clinical Cytogenetics, Academic Press
2. S Gersen and MB Keagel (2013) The Principles of Clinical Cytogenetics, Springer
Science and Buisness Media Publication
*******************************************************************************************************
SEMESTER2
HDG08. Molecular Biology
Syllabus: MSc in Human Disease Genetics 15th July 2016
40
1. JD Watson (2013) Molecular Biology of the Gene, Pearson Publication, 7th Edition
2. B Alberts, A Johnson, J Lewis, M Raff, K Roberts and P Walter (2014) Molecular
Biology of the Cell, Taylor and Francis Publication, 6th Edition
3. H Lodish, A Berk, SL Zipursky, P Matusdaira, D Baltimore and J Darnell (2012)
Molecular Cell Biology, W. H. Freeman and Company, 7th Edition
4. JE Krebs, ES Goldstein and ST Kilpatrick (2012) Lewin’s Gene XI, Jones and Bartlett
Learning Publication, 11th Edition
HDG09. Biotechniques
1. H Lodish, A Berk, SL Zipursky, P Matusdaira, D Baltimore and J Darnell (2012)
Molecular Cell Biology, W. H. Freeman and Company, 7th Edition
2. B Alberts, A Johnson, J Lewis, M Raff, K Roberts and P Walter (2014) Molecular Biology
of the Cell, Taylor and Francis Publication, 6th Edition
3. T Strachan and AP Read (2011) Human Molecular Genetics, Garland Science, Taylor
and Francis Group Publication, 4th Edition
4. J Sambrook and DW Russell (2001) Molecular Cloning: a Laboratory Manual. Cold
Spring Laboratory Press, 6th Edition
5. SB Primrose, R Twyman and B Old (2004) Principles of Gene Manipulation.
University of California Press Publication, 6th Edition
HDG10. Principles of Development
1. SF Gilbert (2013) Developmental Biology, Sinauer Publication, 10th Edition
2. L Wolpert, C Tickle and AM Arias (2015) Principles of Development, Oxford University
Press, 5th Edition
3. Jonathan M W Slack (2012), Essential Developmental Biology, Wiley-Blacwell, 3rd
Edition.
HDG11. Bioinformatics
1. T Lengauer (2001) Bioinformatics-From Genomes to Drugs, Willey VCH Publication,
1st Edition
2. SM Brown (2000) Bioinformatics: A Biologist’s Guide to Computing and the
Internet, Eaton Pub Co Publication, 1st Edition
3. R Blum and C Bresnahan (2015) Linux Command Line and Shell Scripting Bible,
Wiley and Sons Publication, 3rd Edition
4. J Tisdall (2001) Beginning Perl for Bioinformatics, O’Reilly Media Publication, 1st
Edition
Syllabus: MSc in Human Disease Genetics 15th July 2016
41
5. S Mitra and T Acharya (2003) Data Mining Soft Multimedia, Soft Computing and
Bioinformatics, John Willey and Sons Publication, 1st Edition
Databases:
1. NCBI Genome Browser and databases: http://www.ncbi.nlm.nih.gov/
2. UCSC Genome Browser: http://genome.ucsc.edu/
3. Ensemble Genome Browser: http://www.ncbi.nlm.nih.gov/
4. Protein Catalog ExPAsy: http://www.expasy.org/
5. Protein Catalog Uniprot: http://www.uniprot.org/
HDGP3. Lab Module III-Biochemistry and Molecular Biology
1. K Willson and J Walker (2010) Principles and Techniques of Practical
Biochemistry, Cambridge University Press, 7th Edition
2. Protocols Online: http://www.protocol-online.org/
3. Sambrook and DM Russell (2001) Molecular Cloning: a Laboratory Manual. Cold
Spring Laboratory Press Publication, 6th Edition
4. FM Ausubel (1990) Current Protocols in Molecular Biology, John Willey and Sons
Publication
5. Protocols Online: http://www.protocol-online.org/
HDGP4. Lab Module IV-Cell Biology
1. JS Bonifacino (2003) Current Protocols in Cell Biology, John Willey & Sons
Publication
2. Protocols Online: http://www.protocol-online.org/
3. PA Lawrence (1992) The Making of a Fly: the Genetics of Animal Design, Wiley
Publications
4. C Dahmann (2010) Drosophila: Methods and Protocols (Methods in Molecular
Biology), Humana Press Inc.
5. M Ashburner(2011) Drosophila A Laboratory Handbook, Cold Spring Harbor
Laboratory Press
6. W Sullivian, M Ashburner, RS Hawley (2000) Drosophila Protocols, Cold Spring
Harbor Laboratory Press
*******************************************************************************************************
SEMESTER 3
Syllabus: MSc in Human Disease Genetics 15th July 2016
42
HDG13. Human Molecular Genetics
1. T Strachan and AP Read (2011), Human Molecular Genetics, Garland Science/Taylor
and Francis Group Publication, 4th Edition.
2. For information on Mendelian phenotypes: http://www.omim.org
3. Access to Biomedical Literature: http://www.ncbi.nlm.gov/entrez
HDG14. Biochemical Genetics
1. CR Scriver, A Beaudet, WS Sly, D Valle, B Childs, KW Kinzler and B Vogelstein (2000)
The Metabolic and Molecular Basis of Inherited Disease, McGraw-Hill Publication,
8th Edition
2. L Buckingham (2011) Molecular Diagnostics: Fundamentals, Methods and Clinical
Applications, FA Davis Company Publication, 2nd Edition
3. CA Burtis, D Bruns and ER Ashwood (2007) Fundamentals of Molecular
Diagnostics, Saunders, Elsevier Publication
4. P George, GP Patrinos and WJ Ansorge (2010) Molecular Diagnostics, Academic
Press, Elsevier Publication, 2nd Edition
HDG16. Population Genetics and Evolution
1. DL Hartl and AG Clark (2006) Principles of Population Genetics, Sinauer
Associates Publication, 4th Edition
2. LL Cavalli-Sforza and WF Bodmer (2013) The Genetics of Human Population,
Dovers Publication
3. M Jobling, E Hollox, M Hurles, T Kivisild and C Tyler-Smith (2013) Human
Evolutionary Genetics, Garland Science/Taylor and Francis Group Publication,
2nd Edition
HDG17. Cancer Biology
1. RA Weinberg (2012) Biology of Cancer, Garland, Taylor and Francis Group
Publication, 2nd Edition
2. B Alberts, A Johnson, J Lewis, M Raff, K Roberts and P Walter (2008) Molecular
Biology of Cell, Taylor and Francis group Publication, 5th Edition
3. VT DeVita, TS Lawrence and SA Rosenberg (2015) Devita, Hellman, and Rosenberg's
Cancer: Principles & Practice of Oncology, Wolters Kluwer Publication, 10th Edition
HDGS1. Model Organisms (Seminars)
Syllabus: MSc in Human Disease Genetics 15th July 2016
43
1. SF Gilbert, AM Raunio, NJ Haver (1997) Embryology: Constructing the
Organism, Sinauer Associates Inc. Publication
2. T Strachan and AP Read (2011) Human Molecular Genetics, Garland Science,
Taylor and Francis Group Publication, 4th Edition
3. A Spradling, B Ganetsky,P Hieter,M Johnston,M Olson,T Orr-Weaver,J Rossant,A
Sanchez, R Waterston (2006) New roles for model genetic organisms in
understanding and treating human disease: report from the 2006 Genetics
Society of America meeting. Genetics. 172: 2025-2032.
4. Online resource -Using Model organisms to study Health and Disease:
http://www.nigms.nih.gov/Education/Pages/modelorg_factsheet.aspx
5. Online resource-Model organisms for Biomedical research:
http://www.nih.gov/science/models/
HDGS2. Diseases of Organ Systems
1. DL Rimoin, RE Pyeritz, B Korf (2013), Emery and Rimoin’s Principles and
Practice of Medical Genetics, Elseivier Science Publication, 6th Edition.
2. Genes and Diseases (NCBI Bookshelf):
http://www.ncbi.nlm.nih.gov/books/NBK22185/
HDGP5. Lab Module V. Molecular Diagnostics
1. JL Hamerton (2013) Human Cytogenetics: Clinical Cytogenetics, Academic Press
2. S Gersen and MB Keagel (2013) The Principles of Clinical Cytogenetics, Springer
Science and Buisness Media Publication
3. RL Nussbaum, RR. McInnes and HF Willard (2007) Thomson and Thomson Genetics
in Medicine, Saunders, Elseivers Publication
4. LB Jorde, JC Carey and MJ Bamshad (2009) Medical Genetics, Elseivers Publication
5. S Heim, F Mitelman (2011) Cancer Cytogenetics: Chromosomal and Molecular
Genetic Aberrations of Tumor Cells, John Willey and Sons Publications
6. L Buckingham (2011) Molecular Diagnostics: Fundamentals, Methods and Clinical
Applications, FA Davis Company Publication, 2nd Edition
7. CA Burtis, D Bruns and ER Ashwood (2007) Fundamentals of Molecular
Diagnostics, Saunders, Elseivers Publication
8. P George, GP Patrinos and WJ Ansorge (2010) Molecular Diagnostics, Academic
Press, Elseiver Publication, 2nd Edition
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Syllabus: MSc in Human Disease Genetics 15th July 2016
44
SEMESTER4
HDG18. Human Genome Organization
1. TA Brown (2006) Genomes 3, Garland Science Publication, 3rd Edition
2. H Lodish, A Berk, SL Zipursky, P Matusdaira, D Baltimore and J Darnell (2012)
Molecular Cell Biology, W. H. Freeman and Company, 7th Edition
HDG19. Genetic Counseling and Genetic Epidemiology
1. K Park (2011) Park's Textbook of Preventive and Social Medicine, Banarsidas
Bhanot Publication, 21st Edition.
2. J Owen, J Punt and S Stranford (2013) Kuby Immunology, WH Freeman
Publication, 7th Edition.
3. T Strachan and A Read (2011), Human Molecular Genetics, Garland
4. Science/Taylor and Francis Group Publication, 4th Edition.
5. Peter Turnpenny and Sian Ellard (Eds) (2012) Emery’s Elements of Medical
Genetics, Elsevier, 14th Edition.
6. R.J. MKinlay Gardner, Grant R Sutherland, and Lisa G. Shaffer (2011), Chromosome
abnormalities and Genetic counselling, Oxford University Press, 4th Edition.
7. David L. Rimoin, Reed E. Pyeritz and Bruce Korf. (Eds.) (2013) Emery and
Rimoin's Principles and Practice of Medical Genetics, Elsevier, 6th Edition.
8. Peter S Harper (2010), Practical Genetic Counselling Elsevier, 7th Edition.
9. Jean-Marie Saudubray, Georges van den Berghe, John H. Walter, (Eds.)(2012),
Inborn Metabolic Diseases: Diagnosis and Treatment, Springer, 5th Edition.
HDG20. Ethics in Clinical and Biomedical Research
1. T Smith (1999) Ethics in Medical Research: A Handbook of Good Practice,
Cambridge University Press
2. IS Shergill, A Thompson and N Temple (2011) Ethics, Medical Research, and
Medicine: Commercialism versus Environmentalism and Social Justice,
Springer Science and Business Media Publication
**************************************************************************************************************
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Syllabus for Alternative Courses (Soft Core)
SEMESTER 1
HDG06. HISTORY OF GENETICS
(CREDITS-2)(TUTORIAL-1)
Unit I 2 Hrs
Theories on Inheritance before Mendel: Views of Hippocrates, Darwin and
Aristotle, experiments of Maupertuis, Kolreuter and others.
Unit II 4 Hrs
Mendel and the Birth of Mendelism (1822-1884): Mendel’s Life History, Mendel’s
experiments, results, hypothesis, their publication and reception.
Unit III 3 Hrs
The 1866-1900 Period: Weismann’s theory of the germplasm, cell theory and the
early cytological studies of chromosomes, mitosis and meiosis, (Flemming,
Strasburger, Van Beneden and Caldwell), Roux’s experiments and the views of Hugo
de Vries, Bateson and Korschinsky.
Unit IV 4 Hrs
Rediscovery of Mendel’s Work: Roles of Hugo de Vries, Carl Correns and Erich von
Tschermak; Bateson’s view on Mendel’s work and the origin of genetic terminology.
Unit V 2 Hrs
Relationship of Inheritance, Chromosomes and Mendel’s Law: Cytological studies
of Boveri, Correns, Cannon, Montgomery and Sutton.
Unit VI 3 Hrs
Concept of Linkage, Linkage Mapping and Drosophila Genetics: Genes on a
chromosome, problems of independent assortment, first report of Linkage (Correns),
incomplete linkage (coupling and repulsion by Bateson and Punnett), the observations
of Janssens (Chiasma); Henking and McClung’s findings of the X-Chromosome, Nettie
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Stevens’s XX and XY Genotypes and Gender, Bridges’ contribution on sex linkage and
non-disjunction, Morgan’s explanation of autosomal linkage and cross-over,
Sturtevant’s linkage map and mapping genes in the fruit fly, Drosophila melanogaster.
Unit VII 3 Hrs
Genetics of Continuous Variation: Contributions of Francis Galton.
Unit VIII 2 Hrs
The Discontinuous Variation: Mutation theory of Hugo de Vries and H J Muller’s
induced mutations in the fruit fly, Drosophila melanogaster.
Unit IX 2 Hrs
Cytological Map and Cytology of Crossing Over
Unit X 3 Hrs
Sex Determination, Concepts of Position and Maternal Effects: Contributions of
Morgan, Bridges, Metz, Stern, Heitz and Painter (sex-determination in Drosophila),
Warmke and Blakeslee’s studies on sex-determination in Melandrium; Baltzer’s
findings on the role of the environment on sex determination; the study of “Bar” eye
reversion and the 16A locus by May, Morgan, Sturtevant and others.
Unit XI 4Hrs
Genetics and Branches of Science: Genetics and Immunology, Biochemical Genetics,
Population Genetics and Evolution, Microbial Genetics and Human Genetics: origin,
initial studies and contributing scientists.
Syllabus: MSc in Human Disease Genetics 15th July 2016
47
SEMESTER 2
HDG12. THERAPEUTICS: PHARMACOGENOMICS AND VACCINES
(CREDITS-2)(TUTORIAL-1)
PART 1: DEVELOPMENT OF VACCINES
Unit I 1Hr Public Health and Vaccine Development Process Unit II 2Hrs Vaccine Immunology and Preclinical Research Unit III 2Hrs Vaccine Manufacture and Quality Control Processes Unit IV 2Hrs Infectious Diseases and Vaccine Prevention Unit V 2Hrs Clinical Development Methodology, Biostatistics and Clinical Data management Unit VI 2Hrs Pharmaco-vigilance Unit VII 2Hrs Epidemiology, Health Systems and Economics Unit VIII 1Hr Good Clinical Practices, Clinical Quality Assurance and Clinical Trial Operations Unit IX 1Hr Regulatory Affairs Unit X 1Hr Policies and Recommendations for Vaccines in the World
Syllabus: MSc in Human Disease Genetics 15th July 2016
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PART 2: PHARMACOGENOMICS Unit I 1Hr Introduction Unit II 1Hr Pharmacokinetics: Drug absorption, distribution, metabolism and excretion; types of drugs: pro-drugs and active drugs. Unit III 2Hrs Understanding Drug Response: Types of metabolizers: extensive, intermediate, poor and ultra-rapid metabolizers; drug-gene interactions, drug-drug interaction, toxicity of drugs, multidrug resistance. Unit IV 2Hrs From Pharmacogenetics to Pharmacogenomics: Genes, genome and epigenetics. Unit V 2Hrs Identifying Genes for Drug Response: GWAS, expression analysis and cheminformatics, pathway-based methods. Unit VI 2Hrs Role of Pharmacogenetics in Drug Discovery: A pharmacogenetic study design. Unit VII 2Hrs Applications of Pharmacogenetics in Clinic: Drug prescription, personalized medicine and pretreatment screening, drug toxicity, drug dose, drug efficacy, drug labeling. Unit VIII 1Hr Computation Advances and Pharmacogenetics Resources: PharmGKB, DrugBank. Unit IX 1Hr Challenges of Pharmacogenetic Studies: Drug safety, drug response in populations, ethics: privacy and confidentiality, informed consent in research and treatment; legal Implications.
Syllabus: MSc in Human Disease Genetics 15th July 2016
49
Unit X 2Hrs Therapeutic Areas: Pharmacogenetics in oncology, pain management, psychiatry, cardiology and forensics.
SEMESTER 3
HDG15. ADVANCED BIOINFORMATICS (lecture CREDITS-1) (TUTORIAL-1)
Unit I
Linux: Introduction to computers, software and operating systems; history and
features of UNIX and GNU/Linux; Unix file system, file and directory commands, file
permissions; basic commands, I/O redirection and piping, simple and advanced filters;
sed command, vi as text editor; archives and file compressions; processes: background
processes and scheduled processes; alias and environmental variables.
Unit II
Shell Programming: Multiple commands as a shell script simple shell script creation
and execution; variables: system variables and user defined variables, read values to
variables, mathematic and string handling; decisions and loopings: if, for and while
loops, case statement; awk programming, terminal formatting using echo and tput;
functions: calling functions; passing arguments; receiving parameters; local variables;
returning values from functions; unsetting functions; Signals: handling signals;
ignoring signals.
Unit III
C Programming: Programming basics: algorithm and flowcharts, compiling, linking,
executing, testing and debugging; C: variables and data types in C; operators:
arithmetic, relational, boolean and bitwise operators; I/O and formatted I/O. Loops: if,
for and while loops, goto and switch statements; functions, subroutines, recursions;
application to simple problems; the pre-processor; simple macros; macros with
arguments; macros v/s functions; #include; conditional compilation; passing
command line arguments.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit IV
Arrays, Strings, Storage classes and Pointers: Arrays in C; defining and using 2D
arrays; multi-dimensional arrays; array operations; strings: string operations using
string.h, storage of strings in arrays; extern, static, auto and register; linking modules;
pointers: declaring and using pointers; operations on pointers; void pointers; NULL
pointers; function pointers; pointers and functions: passing by value, passing by
pointers; pointers and arrays: array storage and properties, array and pointer
conversions; pointers and strings: string operations using pointers; passing arrays to
functions.
Unit V
Structures and Unions, Memory allocation and File handling: Structures: defining,
instantiating and operating on structures, pointers to structures; structure memory
organisation; nested structures; arrays of structures; bit-fields; need for unions;
memory organisation of unions; memory allocation: static memory allocation; need
for dynamic memory allocation; malloc() and calloc(); free(); memory problems:
memory leaks, dangling pointers, invalid deallocation; file handling: opening files in
various modes; closing files; reading and writing characters; reading and writing
strings; formatted I/O on files; raw I/O on files; seeking in files; application to
bioinformatics problems.
SEMESTER 4
HDG21. INTELLECTUAL PROPERTY AND PATENTS
(CREDITS-2)(TUTORIAL-1)
PART I - INTRODUCTION TO IPR & PATENTS
Unit I 1Hr
Understanding Intellectual Property Rights: Introduction, history of patent
protection, rationale behind the patent system
Unit II 2Hrs
Syllabus: MSc in Human Disease Genetics 15th July 2016
51
An Overview of the IPR Regime: The industrial property system, patents,
trademarks, copyrights, industrial design, layout design of integrated circuits,
undisclosed information - trade secrets
Unit III 2Hrs
Definition and Content of Patents System: Definition of patents, TRIPS, definition,
various kinds of patent systems, inventions and invention excluded from patentability,
process and product patent, acquiring a patent, method of acquiring a patent, patent
specification, patent claims
Unit IV 2Hrs
Enforcement of Patents: The term of a patent, the working of a patent, compulsory
licensing, licenses of rights, obligations of a patentee
Unit V 1Hr
Exploitation of Patents: Rights of the patentee, infringement & remedies, literal
infringement, infringement by equivalents – doctrine of equivalents; defenses of
infringement.
Unit VI 1Hr
Abuse of Patents: Statement on working of patents, voluntary licensing & compulsory
licensing, licenses of rights, the concepts of meeting “reasonable requirement of the
public at reasonable cost”, revocation of patents
PART II - PATENTING IN INDIA
Unit I 2Hrs
Legislations and Salient Features: Indian Patents Act 1970, Patent Amendment Act
2005, WTO TRIPS - Indian legislation.
Unit II 2Hrs
Syllabus: MSc in Human Disease Genetics 15th July 2016
52
Patent Search: Patent offices in India, patent information and databases, search
methods/tools, patent information centers, advantages of patent search, international
patent classification, patent search.
Unit III 2Hrs
Procedures for Patent Applications: Patentability, exclusions from patentability,
acquisition of patents, preparation of patent specification, patent office procedure,
construction of patent claims
Unit IV 1Hr
Drafting of Patents: Patent infringement
PART III - AMERICAN & EUROPEAN PATENT REGIMES
Unit I 2Hrs
US Patent Regime: Title 37 CFR, patentability, utility, novelty, non obviousness,
patent specification – best mode
Unit II 2Hrs
European Patent Regime: European patent convention, patentable inventions in
European patent systems, history of the broad definition of patentability, final form of
European patent system, development of EPO practice in relation to software
industries
Unit III 1Hr
Business Model Patents - Biotech Patents
Unit IV 1Hr
Software Patents
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit V 1Hr
Patentability of Life Forms
PART IV- INTERNATIONAL TREATIES/CONVENTIONS ON IPR
Unit I 1Hr
Paris Convention: Background, salient features of Paris convention, governing rules
of Paris convention
Unit II 1Hr
World Intellectual Property Organization (WIPO): Background, salient features of
WIPO, organization of WIPO
Unit III 1Hr
World Trade Organization: Evolution of WTO, organization of WTO
Unit IV 1Hr
TRIPS Agreement: Background, salient features of TRIPS, TRIPS and Indian IPR,
TRIPS and PARIS convention – a comparison
Unit V 1Hr
Patent Co-operation Treaty: Background, objectives of PCT, salient features of PCT
Unit VI 1Hr
Budapest Treaty
Unit VII 1Hr
Convention of Bio-Diversity
Syllabus: MSc in Human Disease Genetics 15th July 2016
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Unit VIII 1Hr
Madrid Agreement
Unit IX 1Hr
Discussions: Opinions of patentability, preparation of patent specifications,
patentability of software & biotechnology related inventions, licenses of Rights,
infringement issues in patents
References
SEMESTER1
HDG06. History of Genetics
1. AH Sturtevant (2001) History of Genetics, Cold Spring Harbor Laboratory Press
SEMESTER2
HDG12. Therapeutics: Pharmacogenomics and vaccines
1. RG Hill (2012) Drug Discovery and Development: Technology in Transition, Churchill Livingston Publication
2. RB Altman, D Flockhart, DB Goldstein (2012) Principles of pharmacogenetics and pharmacogenomics. Cambridge: Cambridge University Press. 400 p.
3. RB Altman, HK Kroemer, CA McCarty, MJ Ratain and D Roden (2010) Pharmacogenomics: will the promise be fulfilled? Nat Rev Genet 12: 69–73.
4. RB Altman (2011) Pharmacogenomics: ‘noninferiority’ is sufficient for initial implementation. Clin Pharmacol Ther 89: 348–350.
5. TE Klein, JT Chang, MK Cho, KL Easton, R Fergerson (2001) Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J 1: 167–170.
6. AD Roses (2000) Pharmacogenetics and the practice of medicine. Nature 405: 857–865.
7. AD Roses (2004) Pharmacogenetics and drug development: the path to safer and more effective drugs. Nat Rev Genet 5: 645–656.
Syllabus: MSc in Human Disease Genetics 15th July 2016
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SEMESTER3
HDG15. Advanced Bioinformatics
1. C. Negus (2004) Red Hat linux 7.2 Bible (2004); Wiley India Pvt Ltd Publication
2. B. McCarty (1999) Learning Red Hat linux, O'Reilly & Associates Inc. Publication
3. V. Rajaraman (1994) Computer programming in C Prentice-Hall of India Publication
4. D Ritchie (2007) The C programming language, Pearson Education Publication
5. Y Kanetkar (1999) Let us C, BPB Publications
SEMESTER4
HDG21. Intellectual Property and Patents
1. RP Merges, PS Menell, MA Lemley (2012) Intellectual Property in the New Technological Age, Sixth Edition (Aspen Casebook Series) Hardcover, Robert P. Aspen Publishers; 6th edition