Suggested web readings etc :(in blue is the syllabus title, print is available for brown)
UNIT-I
1. Introduction, Methods, strategies and applications DNA markers,
Forensic Biology by Richard Li: pp.185-195-250, 287-364
Advanced/Reference material:
dna-analysis:
http://aboutforensics.co.uk/dna-analysis
DNA profiling
https://en.wikipedia.org/wiki/DNA_profiling
2. Mitochondrial, DNA the hypervariable regions and control region V,
Forensic Biology by Richard Li: pp.351-3643. Cytochrome b, Chloroplast DNA,
http://www.dnabarcoding101.org/introduction.html
4. Chromosomal DNA Amelogenin, Autosomal STRs, Y Chromosomal STRs, X
chromosomal STRs,
Forensic Biology by Richard Li: pp.317-326
extra:
Forensics, DNA Fingerprinting, and CODIS:
http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736
5. Variable Number Tandem Repeat (VNTR’s) and Short Tandem Repeat (STR’s)
markers,
Forensic Biology by Richard Li: pp. 287-308
Advanced/Reference material:
Minisatellite
https://en.wikipedia.org/wiki/Minisatellite
Forensic Biology by Richard Li: pp.185-195-250, 287-364
Advanced/Reference material:
dna-analysis:
http://aboutforensics.co.uk/dna-analysis
DNA profiling
https://en.wikipedia.org/wiki/DNA_profiling
2. Mitochondrial, DNA the hypervariable regions and control region V,
Forensic Biology by Richard Li: pp.351-3643. Cytochrome b, Chloroplast DNA,
http://www.dnabarcoding101.org/introduction.html
4. Chromosomal DNA Amelogenin, Autosomal STRs, Y Chromosomal STRs, X
chromosomal STRs,
Forensic Biology by Richard Li: pp.317-326
extra:
Forensics, DNA Fingerprinting, and CODIS:
http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736
5. Variable Number Tandem Repeat (VNTR’s) and Short Tandem Repeat (STR’s)
markers,
Forensic Biology by Richard Li: pp. 287-308
Advanced/Reference material:
Minisatellite
https://en.wikipedia.org/wiki/Minisatellite
6. Single Nucleotide Polymorphism (SNP’s)
UNIT-II
1. DNA Extraction, Organic and Inorganic extraction, Comparison of Extraction
methods, Commercial kits
Forensic Biology by Richard Li: pp.199-207
2. DNA Quantitation, Importance of quantitation, Spectrophotometric analysis,
Agarose Gel Electrophoresis, Slot Blot Hybridization, Real Time PCR.
Forensic Biology by Richard Li: pp. 211-219
3.Polymerase Chain Reaction
Forensic Biology by Richard Li: pp.223-234
4. Basic PCR mechanism, Real time PCR, Primer designing
5.Primer dimmer and Hairpins, Mismatch primers,Forensic Biology by Richard Li: pp.223-234
idt guidelines for primer design
https://www.youtube.com/watch?v=bJab6IG2KeQ
http://projects.nfstc.org/pdi/
UNIT-III
1. NGS (next generation sequencing techniques of DNA): principles
Illumina Sequencing by Synthesis
https://www.youtube.com/watch?v=fCd6B5HRaZ8
SMRT technique
www.youtube.com/watch?v=WMZmG00uhwU#action=share
Oxford Nanopore
https://www.youtube.com/watch?v=GUb1TZvMWsw
https://www.youtube.com/watch?v=hs0FdiTHMbc
https://nanoporetech.com/how-it-works
Next Generation Sequencing (NGS) - An Introduction
https://www.youtube.com/watch?v=jFCD8Q6qSTM
2. Protocols in NGS
Next Generation Sequencing (NGS) - Sample Preparation
https://www.youtube.com/watch?v=-kTcFZxP6kM&t=308s
protocol for SMRTbell Library prepration
http://smrt.med.cornell.edu/Services.html
http://files.pacb.com/Training/IntroductiontoSMRTbellTemplatePreparation/story_content/external_files/Introduction%20to%20SMRTbell%E2%84%A2%20Template%20Preparation.pdf
https://www.youtube.com/watch?v=x-z3MFkpvzE&list=PLxpxXZj-IgXyR0it4QjoBETC5JeEanW-o&index=10
3. Application of NGS in forensics
Next generation sequencing and its applications in forensic genetics:
https://www.ncbi.nlm.nih.gov/pubmed/25704953
4. Automation in DNA profilling: robotics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf
5. Miniaturisation in DNA profilling: microfluidics
http://www.avensonline.org/wp-content/uploads/JFI-2330-0396-02-0012.pdf
6. Recent developments in DNA profilling and databases
The future of forensic DNA analysis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf
UNIT-IV
Forensically relevant SNP classes
http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112806_O_3727a.pdf
Advanced/Reference material:
Developing a SNP panel for forensic identification
of individuals
http://www.sciencedirect.com/science/article/pii/S0379073805006134http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112806_O_3727a.pdf
Advanced/Reference material:
Developing a SNP panel for forensic identification
of individuals
UNIT-II
1. DNA Extraction, Organic and Inorganic extraction, Comparison of Extraction
methods, Commercial kits
Forensic Biology by Richard Li: pp.199-207
2. DNA Quantitation, Importance of quantitation, Spectrophotometric analysis,
Agarose Gel Electrophoresis, Slot Blot Hybridization, Real Time PCR.
Forensic Biology by Richard Li: pp. 211-219
3.Polymerase Chain Reaction
Forensic Biology by Richard Li: pp.223-234
4. Basic PCR mechanism, Real time PCR, Primer designing
5.Primer dimmer and Hairpins, Mismatch primers,Forensic Biology by Richard Li: pp.223-234
idt guidelines for primer design
6. Software’s packages, Multiplex PCR, PCR failures,
http://projects.nfstc.org/pdi/
http://projects.nfstc.org/pdi/
Forensic Biology by Richard Li: pp. 287-308
7. DNA degradation, Inhibition, DNA overload and Cycling.
7. DNA degradation, Inhibition, DNA overload and Cycling.
Forensic Biology by Richard Li: pp. 287-308
GeneMarker® HID Software - Introduction Part 1
https://www.youtube.com/watch?v=_Heupu3n8v0
GeneMarker® HID Software - Introduction Part 2
http://projects.nfstc.org/pdi/
UNIT-III
1. NGS (next generation sequencing techniques of DNA): principles
Illumina Sequencing by Synthesis
https://www.youtube.com/watch?v=fCd6B5HRaZ8
SMRT technique
www.youtube.com/watch?v=WMZmG00uhwU#action=share
Oxford Nanopore
https://www.youtube.com/watch?v=GUb1TZvMWsw
https://www.youtube.com/watch?v=hs0FdiTHMbc
https://nanoporetech.com/how-it-works
Next Generation Sequencing (NGS) - An Introduction
https://www.youtube.com/watch?v=jFCD8Q6qSTM
2. Protocols in NGS
Next Generation Sequencing (NGS) - Sample Preparation
https://www.youtube.com/watch?v=-kTcFZxP6kM&t=308s
protocol for SMRTbell Library prepration
http://smrt.med.cornell.edu/Services.html
http://files.pacb.com/Training/IntroductiontoSMRTbellTemplatePreparation/story_content/external_files/Introduction%20to%20SMRTbell%E2%84%A2%20Template%20Preparation.pdf
(Page 7 is most important)
VolTRAX – a small device designed to perform library preparation automatically
https://www.youtube.com/watch?v=x-z3MFkpvzE&list=PLxpxXZj-IgXyR0it4QjoBETC5JeEanW-o&index=10
3. Application of NGS in forensics
Next generation sequencing and its applications in forensic genetics:
https://www.ncbi.nlm.nih.gov/pubmed/25704953
4. Automation in DNA profilling: robotics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf
5. Miniaturisation in DNA profilling: microfluidics
http://www.avensonline.org/wp-content/uploads/JFI-2330-0396-02-0012.pdf
6. Recent developments in DNA profilling and databases
The future of forensic DNA analysis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf
UNIT-IV
1. Eukaryotic genome structure and concepts of genomic analysis
Eukaryotic Genome Complexity
http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437
2. Public sequence databases: DNA, RNA, proteins, whole genomes
http://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721
UCSC Genome Browser An Introduction tutorial movie
http://www.openhelix.com/showMovie2.cgi?id=27
3. Data mining for homologous sequences
http://www.ncbi.nlm.nih.gov/books/NBK1734/
Eukaryotic Genome Complexity
http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437
2. Public sequence databases: DNA, RNA, proteins, whole genomes
http://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721
UCSC Genome Browser An Introduction tutorial movie
http://www.openhelix.com/showMovie2.cgi?id=27
3. Data mining for homologous sequences
http://www.ncbi.nlm.nih.gov/books/NBK1734/
http://www.ncbi.nlm.nih.gov/books/NBK2590/
How to: Find a homolog for a gene in another organism:
http://www.ncbi.nlm.nih.gov/guide/howto/find-homolog-gene/
BLAST Results- Expect Values, part 1
https://www.youtube.com/watch?v=Z7ek7UoP7Bg
4. Multiple sequence alignment algorithms
https://en.wikipedia.org/wiki/Multiple_sequence_alignment
6. Phylogenetic trees and molecular evolution
Molecular phylogenetic analysis using ribosomal RNA (rRNA)
https://www.researchgate.net/file.PostFileLoader.html?id=55c2206660614b37738b4585&assetKey=AS%3A273825759989760%401442296556699
Molecular Phylogenetics:
http://www.ncbi.nlm.nih.gov/books/NBK21122/
7. Microarrays and transcriptome analysis
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_01_b.htm
How Does a DNA Microarray Work.mp4
https://www.youtube.com/watch?v=pWk_zBpKt_w
8. The proteome, metabolome, glycome, lipidome, and interactome
http://www.nature.com/scitable/topicpage/transcriptome-connecting-the-genome-to-gene-function-605
http://www.nature.com/scitable/topicpage/the-proteome-discovering-the-structure-and-function-613
9. Human genes and genetic disorders
Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders:
http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.220.1899
10. Ethics in human bioinformatics and genomics
Bioethics in Genetics:
http://www.nature.com/scitable/topicpage/bioethics-in-genetics-42093
11. Y Chromosome testing
Forensic Biology by Richard Li: pp.317-326
12 Non-Human, medical, and research applications
Genetic Inequality: Human Genetic Engineering:
http://www.nature.com/scitable/topicpage/genetic-inequality-human-genetic-engineering-768
Genetically Modified Organisms (GMOs): Transgenic Crops and
Recombinant DNA Technology:
http://www.nature.com/scitable/topicpage/genetically-modified-organisms-gmos-transgenic-crops-and-732
Practicals:
How to: Find a homolog for a gene in another organism:
http://www.ncbi.nlm.nih.gov/guide/howto/find-homolog-gene/
BLAST Results- Expect Values, part 1
https://www.youtube.com/watch?v=nO0wJgZRZJs
BLAST Results: Expect Values, part 2
4. Multiple sequence alignment algorithms
https://en.wikipedia.org/wiki/Multiple_sequence_alignment
6. Phylogenetic trees and molecular evolution
Molecular phylogenetic analysis using ribosomal RNA (rRNA)
https://www.researchgate.net/file.PostFileLoader.html?id=55c2206660614b37738b4585&assetKey=AS%3A273825759989760%401442296556699
Molecular Phylogenetics:
http://www.ncbi.nlm.nih.gov/books/NBK21122/
7. Microarrays and transcriptome analysis
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_01_b.htm
How Does a DNA Microarray Work.mp4
https://www.youtube.com/watch?v=pWk_zBpKt_w
8. The proteome, metabolome, glycome, lipidome, and interactome
http://www.nature.com/scitable/topicpage/transcriptome-connecting-the-genome-to-gene-function-605
http://www.nature.com/scitable/topicpage/the-proteome-discovering-the-structure-and-function-613
9. Human genes and genetic disorders
Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders:
http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.220.1899
10. Ethics in human bioinformatics and genomics
Bioethics in Genetics:
http://www.nature.com/scitable/topicpage/bioethics-in-genetics-42093
11. Y Chromosome testing
Forensic Biology by Richard Li: pp.317-326
12 Non-Human, medical, and research applications
Genetic Inequality: Human Genetic Engineering:
http://www.nature.com/scitable/topicpage/genetic-inequality-human-genetic-engineering-768
Genetically Modified Organisms (GMOs): Transgenic Crops and
Recombinant DNA Technology:
http://www.nature.com/scitable/topicpage/genetically-modified-organisms-gmos-transgenic-crops-and-732
Practicals:
ESPM 150: A brief tutorial on BLAST
nature.berkeley.edu/garbelotto/downloads/BLASTtutorial2010.doc
http://tools.thermofisher.com/content/sfs/manuals/chargeswitch_forensicdna_man.pdf
idt guidelines for primer design and ncbi primer design
primer design tutorial
Manual for general use, release by DBT, Govt of India
http://www.dbtindia.nic.in/wp-content/uploads/E-MANUAL.pdf
Practicals.
Detection, Isolation and Staining methods for different microorganisms of forensic application
yeast,
Restriction enzyme digestion - ligation of plasmid DNA
Isolation of RNA
http://vlab.amrita.edu/?sub=3&brch=186&sim=718&cnt=1
3. Study (observation) of some pathogenic Fungi and bacteria, (permanent slides)
4. Microbiological examination of water (Coli form test Microbiological examination of milk
milk
idt guidelines for primer design and ncbi primer design
primer design tutorial
Manual for general use, release by DBT, Govt of India
http://www.dbtindia.nic.in/wp-content/uploads/E-MANUAL.pdf
Practicals.
Detection, Isolation and Staining methods for different microorganisms of forensic application
yeast,
Gram Stain Technique
http://vlab.amrita.edu/?sub=3&brch=73&sim=208&cnt=2
2. Isolation of DNA RNA from biological material. Isolation of Plasmid DNA,Restriction enzyme digestion - ligation of plasmid DNA
Isolation of RNA
http://vlab.amrita.edu/?sub=3&brch=186&sim=718&cnt=1
Plasmid Isolation (Mini prep)
http://vlab.amrita.edu/?sub=3&brch=77&sim=314&cnt=1
Restriction Digestion
http://vlab.amrita.edu/?sub=3&brch=77&sim=694&cnt=1
Ligation ( Using T4 DNA Ligase)
http://vlab.amrita.edu/?sub=3&brch=186&sim=781&cnt=1
4. Microbiological examination of water (Coli form test Microbiological examination of milk
milk
Methylene Blue Reductase Test
http://vlab.amrita.edu/?sub=3&brch=73&sim=1630&cnt=1
