This document discusses various topics related to genomics and systems biology, including DNA sequencing methods, finding and identifying genes, genetic mapping, genome sequencing, the human genome, single nucleotide polymorphisms (SNPs), bioinformatics, systems biology, and applications of genomics such as functional genomics, comparative genomics, metagenomics, toxicogenomics, and epigenetics. DNA sequencing methods determine the order of nucleotides, genes can be located using sequence tagged sites and expressed sequence tagged sites, and genetic mapping aims to locate genes on chromosomes.

1. Genomics and Systems Biology
Dr. Nawfal Hussein
Email: nawfal_hm@yahoo.com
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2. DNA Sequencing
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 DNA sequencing, process by which the precise order of
nucleotides in a piece of DNA can be determined
Sequencing Methods
 The chain termination method (Sanger dideoxy (enzymatic)
sequencing) in which the sequence of a single-stranded DNA
molecule is determined by enzymatic synthesis of
complementary polynucleotide chains, these chains terminating
at specific nucleotide positions
 The chemical degradation method (Maxam-Gilbert method),
in which the sequence of a double-stranded DNA molecule is
determined by treatment with chemicals that cut the molecule at
specific nucleotide positions. Cleaves DNA template at different
nucleotide positions, G, A+G, T+C and C and labels these
cleaved fragments.Read A and T by interpreting double bands
also including G (with A) and C (with T) .Not used very much
historically

3. Finding and Identifying Genes
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 Sequence tagged sites (STSs) and expressed sequence tagged
sites (ESTs) are unique regions of DNA sequence that are used
in mapping the human genome, and other large genomes.
 STSs and ESTs are mapped relative to each other using linkage
analysis on yeast artificial chromosomes (YAC) clones or in
radiation hybrid cells.
 STSs are 100–500 bp unique sequences located in non-
repetitive regions of the genome. These sequences can be
amplified by PCR. An EST is a type of STS, but is located within
genome regions that are expressed into RNA. ESTs are shorter
and many may be located in the same expressed region. ESTs
can be assayed by generating cDNA using an oligo(dT) primer
that binds to the 3´ poly(A) tail, and elongation by reverse
transcriptase.

4. Genetic mapping
♠ Genetic mapping aims to locate genes to a specific locus or
position on a chromosome. Mapping genomes requires more
than RFLPs and VNTRs as these are not specific enough.
Instead, for mapping something large like the human genome,
sequence tagged sites (STSs) and expressed sequence tagged
sites (ESTs) are used due to their relative uniqueness.
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5. Genome sequencing
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 The shotgun approach, in which the genome is randomly
broken into short fragments. The resulting sequences are
examined for overlaps and these are used to build up the
contiguous genome sequence.
 The clone contig approach, which involves a pre-sequencing
phase during which a series of overlapping clones is identified.
This contiguous series is called a contig. Each piece of cloned
DNA is then sequenced, and this sequence placed at its
appropriate position on the contig map in order to gradually
build up the overlapping genome sequence.
 A complementary, approach to sequencing the genome is to
identify mRNAs. Expressed mRNAs are much less complex
than genomic DNA

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7. Human genome
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 Human genome contains 3.2 * 109 base pairs. A majority of the
base pairs are from euchromatin areas, which contain more
relaxed DNA, and thus are easier to access. The remaining
sequence is in heterochromatin regions that are condensed.
 1.5% of the total genome is estimated to code for protein
 The actual number of human genes is predicted to fall between
20,000 and 25,000, some of which produce non-coding RNA
such as rRNA, tRNA, snRNA, and snoRNA.
 snoRNAs: Small nucleolar RNAs modify ribosomal RNAs
 snRNAs: Small nuclear RNAs are part of the spliceosome, that
helps to produce mRNA by removing introns of genes and
piecing together the exons to be translated into proteins.
 About half of human genome is non-coding repetitive
sequences such as tandem repeats, SINEs, LINEs, and defunct
retroviruses and transposons.

8. Human genome
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 Between the genome of one individual to the next are variations
or polymorphisms such as different bases, insertions, and/or
deletions. A single nucleotide polymorphism (SNP) is a single
base change. A simple sequence length polymorphism (SSLP) is
any insertion and/or deletion different between two individuals.
Copy number variations (CNVs) are variations in the number of
tandem repeats.
 SNP analysis is used to screen for hereditary defects and test
individuals for phenotypic variations in response to
pharmaceuticals.
 The non-coding parts of the human genome were originally
called “junk,” but further analysis has indicated that these are a
major source of human genomic variation that perhaps can
cause some diseases.

9. SNP analysis
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 SNP analysis is useful to identify different alleles for a specific
gene, particularly the cytochrome P450 gene, which is used to
degrade different pharmaceutical drugs.
 Individuals do not always react the same to certain clinical
drugs, most likely due to natural variations in DNA sequences.
Pharmacogenomics is a new field that focuses on an
individual’s predisposition (based upon the genomic data) to
respond to certain pharmaceuticals. An analysis of SNP is
useful to find patterns associated with specific reactions to the
drugs.

10. Bioinformatics and Systems
Biology
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 Bioinformatics uses computers to analyze the large amounts of
genetic sequence data. Data mining filters or sifts the data,
whereas genome mining specifically applies to identifying the
genomic sequence data of interest, cleaning the data of
unnecessary information, reformatting the data into convenient
forms for analysis, and then interpreting the genomic data for
different patterns or relationships.

11. Systems biology
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 Systems biology studies how a particular organism adapts its
entire genetic expression patterns in response to a different
condition.
 Systems biology compiles information from many different
sources to provide an overview of how an organism functions,
as a whole. Looking at the big picture provides a valuable
assessment of exactly what is occurring because the sum of the
parts (meaning the research into individual genes) does not
necessarily equal the whole. Often, one condition or
environmental difference completely alters the expression
profile of genes.

12. Applications of Genomics
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 Functional genomic attempt to relate the genome to
functional changes in an organism. defining the genes present
in the genome. What genes they code for, what regulates their
expression, and how this expression varies among tissues,
environments/ disease, or individuals.
 Comparative genomics, the use of other genomes from
diverse species, to understanding genomes.
Evolutionary comparisons among genomes are used to better
annotate genes (providing information on function), define
genomic architecture and roles of genes, and develop insights
into the creation of novel structures.
fish genomic sequences were used to identify many human
genes, and these were used as one of the primary pieces of
evidence that the vertebrate genome had 30,000 – 40,000
genes and not 70,000 – 140,000

13. Applications of Genomics
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 Metagenomics is the study of genomes from multiple
organisms that inhabit a particular environment.
 Toxicogenomics is the study of the complex interaction
between an organism ’ s genome and chemicals in the
environment, and disease.
 Epigenetics refers to modifications in DNA that do not involve
changes in sequence. These types of changes include
methylation patterns, histone modification patterns, and
inactivation of certain genes or chromosomes by converting the
area into heterochromatin.

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