Human Genome Project (HGP) Main objectives Human Genome Project (HGP) Goals for the HGP Medical Implications Applications of HGP Timeline of HGP Technical aspects in HGP Mapping strategies Sequencing strategies . Shotgun sequencing method Sanger sequencing method Outcomes of HGP

1. Human Genome
Project

2. Presented by:
Muhammad Sohail Riaz
Presented to:
Miss Iqra Munir

3. Table of Content
 Human Genome Project (HGP)
 Main objectives Human Genome Project (HGP)
 Goals for the HGP
 Medical Implications
 Applications of HGP

4. Human Genome Project (HGP)
 HGP was conceived in 1984 & officially begun in
earnest in October 1990
 The US side of the Human Genome Project was
initially led by James Watson (one half of Crick and
Watson, who discovered the structure of DNA), and
later by Francis Collins
 HGP is a large multicentric, international
collaboration

5. Cont…..
 The main aim of which is to determine the
nucleotide sequence of the entire human nuclear
genome
 In 1997, United States established the National
Human Genome Research Institute (NHGRI)
 The HGP was an international research groups from
six countries- USA, UK, France, Germany, Japan and
China, & several laboratories and a large no. of
scientists and technicians from various disciplines

8. Timeline of HGP
 1970 – Fredrick Sanger developed a technique for
DNA sequencing, known as the Sanger’s method of
DNA sequencing
 1985 - Robert Sinsheimer at UCSC proposed the
idea of sequencing the human genome
 1986 - the U.S. Dept of Energy and the National
Institute of Health came forward to fund the Human
Genome Project
 1989 - U.K’s medical research council (MRC) joined
the Human Genome Project

9. Cont…..
 1990 – HGP was officially launched with James
Watson as its Project Director
 The 1st gene to be mapped was BRCA1, which is the
gene for breast cancer
 1993 - 1st 5 year plan for HGP was published.
Sanger Institute(UK) joins HGP
 1994 – HGP’s Human genetic mapping goal was
achieved

11. Cont…….
 1995 - Genetic privacy act was passed. 1st bacterial
genome was sequenced (Hemophilus influenzae)
 1996 – 1st Human Gene map was published. Yeast
genome was sequenced. HGP’s mouse genetic
mapping goal was achieved
 1997 - NIH becomes NHGRI
• E.coli genome sequenced
• Genoscope, French National Genome Sequencing
Centre was established

14. Cont……
 1998 - 2nd 5 year plan for HGP was published.
Japan’s RIKEN Genomic Services Centre was
established. Genome of the roundworm
Caenorhabditis elegans was sequenced. SNP
sequencing was initiated. The Chinese National
Human Genome Centres were established in Beijing
and Shanghai
 1999 - sequencing of human chromosome 22 was
completed and was published in “The Nature.”

16. Cont…….
 2000 - working draft of human genome completed.
US president Clinton & UK’s PM Blair support free
access to genome information. Genomes of
D.melanogaster and A.thaliana were sequenced &
published in “The Nature”
 2001 – working draft of human genome sequence
was published in “The Nature” & “Science”

18. Cont……
 2002 – working draft of mouse genome sequence
was completed & published
 2003 - finished version of human genome sequence
was completed
 HGP ended with all the goals achieved

21. Technical aspects in HGP
 The process of determining the human genome first
involves genome mapping, or characterizing the
chromosomes. This is called a genetic map
 The next step is DNA sequencing ,or determining
the order of DNA bases on a chromosome. These
are physical maps

23. Mapping strategies
 Genetic markers are invaluable for genome
mapping
 Markers are any inherited physical or molecular
characteristics that are different among individuals
of a population (polymorphic)
 A genetic map shows the relative locations of these
specific markers on the chromosomes
 An example of a marker includes restriction
fragment length polymorphisms (RFLP)

24. Cont……
 Used in RFLP markers are restriction enzymes
 These enzymes recognize short sequences of DNA
and cut them at specific sites, therefore, DNA can be
cut into many different fragments
 These fragments are the DNA pieces used in
physical maps
 RFLPs reflect sequence differences in DNA sites
which are cleaved by restriction enzymes

26. Sequencing strategies
 To sequence DNA, it must be first be amplified, or
increased in quantity
 Two types of DNA amplifications are cloning and
Polymerase Chain Reactions (PCR)
 Now that the DNA has been amplified, sequencing
can begin

28. Primer
 A primer is a short nucleic acid sequence that provides
a starting point for DNA synthesis
 In living organisms, primers are short strands of RNA
Polymerases
 Polymerases are enzymes that catalyze the synthesis of
DNA

30. Cont…….
 Sequencing techniques used in HGP are:-
 1. Shotgun sequencing method
 2. Sanger sequencing method

31. Shotgun sequencing method
 Shotgun sequencing is a laboratory technique for
determining the DNA sequence of an organism's
genome
 The method involves breaking the genome into a
collection of small DNA fragments that
are sequenced individually

33. Sanger sequencing method
 Sanger sequencing, also known as the “chain
termination method”, is a method for determining
the nucleotide sequence of DNA
 The method was developed by two time Nobel
Laureate Frederick Sanger and his colleagues in
1977, hence the name the Sanger Sequence

35. Outcomes of HGP
 There are approximately 22,300 protein-coding
genes in human beings, the same range as in other
mammals
• Mouse – 23,000 genes (approx)
• Drosophila – 17,000 genes (approx)
• C.elegans - < 22,000 genes

38. Cont…..
 we share many homologous genes (called
"orthologs") with both these animals. But:-
• Many of our protein-encoding genes produce more
than one protein product (e.g., by alternative
splicing of the primary transcript of the gene)
• On average, each of our ORFs produces 2 to 3
different proteins
 So the human "proteome" (our total number of
proteins) may be 10 or more times larger than that
of the fruit fly and roundworm

39. CONT……
 A larger proportion of our genome :-
• Encodes transcription factors is dedicated to control
elements to which these transcription factors bind
• The combinatorial use of these elements provides
much greater flexibility of gene expression than is
found in Drosophila and C.elegans

40. Cont……
 Gene density :-
• 23 genes per million base pairs on chromosome
19(Chromosome 19 spans more than 58.6 million
base pairs, the building material of DNA)
• 5 genes per million base pairs on chromosome
13(Chromosome 13 spans about 114 million base
pairs, the building material of DNA)

41. Cont……
 Humans, and presumably most vertebrates, have
genes not found in invertebrate animals like
Drosophila and C. elegans. Few of those genes are
:-
• Antibodies and T cell receptors for antigen (TCRs)
the transplantation antigens of the Major
Histocompatibility Complex (MHC) & Human
Leucocyte Antigen (HLA)
• Cell-signaling molecules including the many types of
cytokines the molecules that participate in blood
clotting

42. Cont…..
 Human genome comprises of 2% of exons (coding
regions) and 98% of introns (non-coding regions)

43. Main objectives Human Genome
Project (HGP)
 This collaboration was named as International
Human Genome Sequencing Consortium (IHGSC)
 The main objectives set out early in history of the
project include:
 1. To obtain complete sequence of pooled DNA
extracted from cells donated by several anonymous
donors, so as to determine the sequence of DNA in
each chromosome

44. Cont……
 2. To construct genetic map for studies
 3. To discover all human genes to allow further
study of human genetic diseases
 4. To develop simplified and automated technology
for DNA sequencing process

45. Cont……
 The HGP results attracted worldwide attention
 This achievement was hailed with many description
in the media
• The mystery of life unraveled
• The library of life
• The periodic table of life
• The Holy grail of human genetics

46. Cont……
 The total no. of genes in the human genome is in
the range of 33,000 to 44,000
 Approximately 75% of these genes have the same
DNA sequence in all individuals, except for those
with rare mutations

47. Cont……..
 Any two human genomes are approximately 99.9%
identical in sequence
 The apparently insignificant difference of 0.1% has a
highly significant effect on personality, behaviour,
intelligence, disease susceptibility and other traits

48. Goals for the HGP
 1. Establish the complete human genome sequence
and to make it freely accessible
 2. Improve the sequencing technology by
developing new and more effective methods
 3. Analyze sequence variations in the human
genome, such as single nucleotide polymorphisms
(SNPs) and other DNA sequence variations

49. Single nucleotide polymorphisms
 A single-nucleotide polymorphism (SNP,
pronounced snip) is a DNA sequence variation
occurring when a single nucleotide adenine (A),
thymine (T), cytosine (C), or guanine (G]) in the
genome differs between members of a species

50. Cont…….
 4. Develop technology for functional genomics. It
includes
• Development of additional cDNA resources and
technology for detailed analysis of gene expression
• Comprehensive study of functions of non-protein
coding sequences
• Encourage development of technology for global
protein analysis

51. Cont…….
 5. Study comparative genomics by completing the
genome sequence of some model organism (e.g.
Mouse etc) which would enhance our
understanding of the human genome
 6. Develop bioinformatics and computational
biology, to impart advanced training to young
scientists and encourage establishment of academic
careers in genomic research

52. Cont…….
 7. Consider social implications of the vastly
expanding knowledge base
 It is anticipated that clash of this new and advanced
knowledge with the pre-existing philosophical
perspectives may result in undesirable
consequences, which have to be taken care of

53. Medical Implications
 The medical implications of the huge amount of
genetic information obtained from the HGP are
tremendous
 It would serve as resource for identification of the
human disease gene
 For example the oncogenic sequence changes in
cancer cells can be directly identified by comparing
cancer genome sequences against draft genome

54. Oncogenic gene
 Sequence of deoxyribonucleic acid (DNA) that has
been altered or mutated from its original form
 Oncogenes may cause the growth of cancer cells

55. Draft genomes
 Draft genomes can have segments of contiguous
base pairs interspersed with gaps for which the
sequence is unknown
 When two or more contigs are joined by
overlapping sequences but there is a gap between
them

56. Contig
 A contig--from the word "contiguous"--is a series of
overlapping DNA sequences used to make a
physical map that reconstructs the original DNA
sequence

57. Cont…….
 Advancement in biotechnology with regard to
development of useful genes would expand the
scope of gene therapy and open new ways of
combating disease
 It may even initiate new fields such as
pharmacogenomics which would individualized
therapies depending on genetic make up of the
patient

58. Applications of HGP
 1. Identification of human genes and their functions
 2. Understanding of polygenic disorders e.g. cancer,
hypertension, diabetes
 3. Improvements in gene therapy
 4. Improved diagnosis of diseases
 5. Development of pharmacogenesis: study of how
people respond differently to drug therapy based upon
their genetic makeup or genes

59. Cont……
 6. Genetic basis of psychiatric disorders
 7. Understanding of complex social trait
 8. Improved knowledge on mutations
 9. Better understanding of developmental biology
 10. Development of biotechnology