1. Sucheta Tripathy, IICB, 15th Dec 2012

2. Mutation and disease
 Many of the diseases occur because of mutation
 4000 diseases have altered gene.
 Heart disease
 Cancer
 Auto immune disorders
 Diabetes

8. http://www.cancer.gov/cancertopics/understandingcancer/genetesting/
GENETEST.PDF

9. Cancer Genetics
 RB1 mutation leads to Retinoblastoma.
 BRCA1 mutation is linked with breast cancer.

10. The Cancer Genome Atlas
 Project to catalogue all mutations in cancer (2005).
 Glioblastoma
 Ovarian cancer
 Lung cancer
Gene Expression Profiling
Copy number variation
SNP Genotyping
Genome wide DNA methylation
MicroRNA
Exome sequencing

11. Immunogenetics
 Genetic link leading to Immune related dis-orders.
 Father of Immuno Genetics is Edward Jenner. In year
1796 predicted human smallpox can be treated with
cowpox.
Multiple Sclerosis
Type-1 Diabetes
Rheumatoid arthritis.
Ref: http://www.idi.harvard.edu/uploads/investigators/Immunogenetics-
coi.pdf

12. IMGT

13. IMGT

14. Human Genome Project
NHGRI
Solicited RFAs were
First
pilot sought for
Publicati
proposal for full
on in
ENCODE ENCODE
2000
In October GWAS -
Finished 90% lies First Report
1990 Human ENCODE
paper in outside on Encode
Genome coding published
2003 Published in
project started 2005 2012
2007

15. Genome Mapping
 What does it mean?
 Mapping multiple variation of the same gene.
HapMap Project:
Mapping Haplotype of human genome Genetic
variants
affecting
health
Disease and
Environme response to
ntal Effects drugs

16. HapMap Project
• To study the effect of environment and their
effects on diseases.
• 99.5% DNA are similar.
• 269 individuals genotype.
• One million SNPs genotyped
– Rose to 10 million including polymorphic sites.
http://en.wikipedia.org/wiki/International_HapMap_Project

17. What we knew
• 95% of the genome is “junk”.
– 2.94% of the genome is coding
• cis regulatory elements occur within a limited
genome distance.
• Most of the genome is transposable elements that
are of obscure origin are dying.
• Transcribed elements are most often translated
than not.

18. 1000 genomes project
Copy Number
Variation
SNPs
Indels
http://en.wikipedia.org/wiki/1000_Genomes_Project
Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with
ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in
Kinyawa, Kenya; Toscani in Italy; Peruvians in Perú; Gujarati Indians in Houston;
Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles

19. HapMap Project
 SNPs occurring at least 1% of the population.
 If a SNP in one site is known, then the SNP in the
nearest site can be identified.

20. Reference
 http://www.nature.com/ejhg/journal/v21/n1/full/ejhg2
01169a.html
 http://nar.oxfordjournals.org/content/34/suppl_1/D78
1.full