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General and in-depth analysis and knowledge about genomics and proteomics
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GBT 422 _ Genomics and Proteomics 2020_2021 SESSIONMr B.U. Umeh (GBT)
Genomics
Assignment
1. Genomes change over time, discuss the different types of events that can change their
sequence.
2. We can learn more about the genetic causes of inheritable diseases by comparing the
genomes of affected individuals to those of unaffected individuals. Discuss comparative
genomics
3. Discuss five applications of genomics
To be submitted before 31st October, 2022, 4pm
1
,Table of Contents
Genomes: A Brief Introduction ............................................................................................................... 3
Genomes as organismal blueprints..................................................................................................... 3
Determining a genome sequence ....................................................................................................... 3
Diversity of genomes .......................................................................................................................... 4
Dynamics of genome structure ............................................................................................................... 6
The study of genomes ............................................................................................................................. 6
Comparative genomics ....................................................................................................................... 6
Metagenomics: who is living somewhere and what are they doing? .................................................... 7
Genomics ................................................................................................................................................ 8
Mapping genomes .............................................................................................................................. 8
Whole genome sequencing .................................................................................................................. 10
Applying genomics ................................................................................................................................ 11
Predicting disease risk at the individual level ................................................................................... 11
Genome-wide association studies .................................................................................................... 11
Pharmacogenomics ........................................................................................................................... 13
Metagenomics .................................................................................................................................. 13
Creation of new biofuels ................................................................................................................... 14
Mitochondrial genomics ................................................................................................................... 14
Genomics in forensic analysis ........................................................................................................... 15
Genomics in agriculture .................................................................................................................... 15
Proteomics ........................................................................................................................................ 15
Summary ............................................................................................................................................... 17
2
, Genomes: A Brief Introduction
Genomes as organismal blueprints
A genome is an organism's entire collection of heritable information stored in DNA, not to be
confused with a gene. The diversity of life we observe all around us can be explained by
differences in information content. The primary forces behind the phenotypic diversity we
observe (and some we cannot) in the environment and which is then filtered by natural selection
are changes to the information encoded in the genome. These changes are therefore the forces
behind evolution. This raises inquiries. How can there be different cell types if every cell in a
multicellular organism carries the same DNA sequence (for instance, how can a liver cell be
so different from a brain cell if they both carry the same DNA)? And how do we read the
information?
Determining a genome sequence
Understanding life, its processes, diversity, and evolution requires knowledge that is encoded
in genomes. Therefore, it makes sense that reading the information content encoded in the
relevant genome(s) would be a good place to start biology studies. Understanding the
arrangement of the nucleotides (A, G, C, and T) into one or more independently replicating
units of DNA (such as chromosomes and/or plasmids) is a good place to start. This was a
challenging idea for more than 30 years after it was discovered that DNA is the hereditary
material. But the development of semi-automated tools for DNA sequencing in the late 1980s
set off a revolution that fundamentally altered how we approach the study of life. Twenty years
later, in the middle of the 2000s, we entered a period of accelerated technological advancement
in which advances in the fields of computer science, optics, electrical and computer
engineering, bioengineering, materials science (particularly, advances in our ability to make
things on a very small scale), and have all converged to bring us dramatic increases in our
capacity to sequence DNA and consequently dramatic decreases in the cost of numerous
advances in our capacity to sequence DNA. The cost of sequencing the human genome has
changed over time, which is a well-known example to demonstrate this point. The first draft of
the human genome took nearly 15 years and $3 billion dollars to complete. Today, 10's of
human genomes can be sequenced in a single day on a single instrument at a cost of less than
$1000 each (the cost and time continue to decrease). Today, companies like Illumina, Pacific
Biosciences, Oxford Nanopore, and others offer competing technologies that are driving down
the cost and increasing the volume, quality, speed, and portability of DNA sequencing.
3
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