Draft 1 Essay2: Somatic and germ line mutations

Somatic and germ line mutations

Draft 1

In genetics, a gene mutation is known as a change in the DNA sequence.  A mutation can be of small or large proportions, and cause a gene to lose its function and therefore prevent the organism from working correctly. It can change only a single DNA base, or a big piece of DNA sequence in a chromosome.  Some mutations can be silent, having no effect on the organism’s phenotype but other s can cause great changes in the organism’s physical traits. There are two ways in which gene mutations occur: they can be inherited or can develop throughout lifetime.  While somatic mutations are not inherited, are caused by mutations in the individual cells and have no effect on the overall organism’s phenotype, germ line mutations are inherited, and have effects on the phenotype; it is evident that these two types of mutations play a key role in evolution.

Somatic mutations affect somatic cells: regular cells that make up tissues of the body. Somatic mutations occur while a cell is undergoing regular cell division, or mitosis.  They can be found by comparing DNA from different cells from the same individual. These mutations occur after fertilization and throughout life, therefore they cannot be inherited. There are two general categories of mutations: point and chromosomal mutations. Point mutations are ones that change one nucleotide either by a deletion or substitution of a nucleotide in the DNA sequence. Chromosomal mutations change the DNA sequence with insertions, inversions or translocations of more than nucleotide. The most common mutations that occur in somatic cells are point mutations. Somatic mutations can have no effect on the phenotype, but more often affects the genotype.  Some of these changes can go unnoticed or silent.  If the mutation is cancerous then the body will keep producing these cells until the person dies.  Somatic mutations can cause damages in the bladder, liver and kidney function.  Among somatic mutations the most dangerous are the ones that occur in the regulation of growth and cellular division.  Cells start reproducing without control and start forming cancerous cells.

Germ cells or sexual reproductive cells are developed either into a sperm or an egg.  The process of creating reproductive cells is known as meiosis and it is in this process that germ line mutations occur. If a germ line mutation occurs all the germ cells in the body will contain this mutation. If a parent has a mutation in their germ cells its offspring will inherit these cells and carry the mutation.  Germ line mutations have a higher incidence of occurring in male gametes since males carry more sperm that are constantly produced through meiosis, compared to the fixed amount of eggs women carry.  To be able to find a germ line mutation, germ cells from two different individuals must be compared.  Germ line mutations are associated with genetic diseases.  Different types of mutations that occur in the chromosomes can have effects on the phenotype or can cause cancer.  Some examples are: Down syndrome, Cri du chat syndrome (cry of the cat), Turner Syndrome and breast cancer. Most dangerous germ line mutations are the ones that interfere with the function of the organism.  Such mutations may change the way we interact with diseases’, or the environment. For example, red-greed blindness (Daltonism) affects your ability to distinguish colors, and type 1 diabetes is a mutation that prevents you from producing insulin and digesting sugar. However, there are germ line mutations that increase your chances of getting cancer.  If an individual carries such mutation in all its cells, fewer somatic mutations are needed to change it to the cancerous state.  For example, BRCA1 mutation is known to increase the chances of breast cancer hundreds of times.  This explains why cancers tend to run in certain families but not in others.

Not all the mutations are the same: they are different by type, effect, mechanism, and location.  Fortunately, there is repair mechanism: or cells can fix mutations, otherwise there would be too many of them.  However, not all mutations are harmful.  Some of germ line mutations are neutral, or can actually improve your body.  These mutations are rare, but they happen often enough to contribute to the variation between individuals, or serve as material for evolution of the species.  

What do I need to find out about germ line and somatic mutations? What did my research tell me?

1.What are the type of mutations between germline and somatic mutations?

a. The mutations that occur in the germ line and somatic cells can be of the same type.

Some mutations that change a single nucleotide are called point mutations. These type of mutations cause deletion or substitution of nucleotide. Chromosomal mutations are mutations that cause insertions, inversions or translocations of more than one nucleotide.

 2. What are the different effects between germ line and somatic mutations?

a.The most important difference between germ line and somatic mutations is that germ line mutations are inherited through the germ cells or gametes, while somatic mutations occur during life in somatic or regular cells, and therefore cannot not be inherited by the following generation.

b.Germ line mutations are shared by all the cells of the same organism. To be able to find them it must be compared to a different individual. While somatic cells can be found by comparing DNA from different cells from the same individual.

3. Effects

a. Germ line mutations are associated with genetic diseases.  Different types of mutations that occur in the chromosomes can have effects on the phenotype or can cause cancer. Some examples are: Down Syndrome, Cri du chat syndrome (cry of the cat), Turner Syndrome and breast cancer.

b. Somatic mutations can have no effect on the phenotype, usually causes changes in the genotype. Some of these changes can go unnoticed or silent. If the the mutation is cancerous then the body will keep producing these cells until the person dies. Somatic mutations can affect damages in the bladder, liver and kidney function.

c. The effects of these mutations are different. Most dangerous germ line mutations are the ones that  interfere with the function of the organism.  Such mutations may change the we interact with diseases, or the environment. For example, sickle cell anemia,is a mutation that causes a change in shape of the red blood cell from concave to sickle form. Another example is  red-green blindness (Daltonism) affects your ability to distinguish colors, and Type 1 diabetes is a mutation that prevents you from producing insulin and digesting sugar.

Among somatic mutations the most dangerous are the ones that occur in the regulation of growth and cellular division. Cells start reproducing without control and start forming cancerous cells.

http://www.ncbi.nlm.nih.gov/books/NBK21578/ 

http://www.ncbi.nlm.nih.gov/books/NBK21578/figure/A1886/?report=objectonly 

http://www.medterms.com/script/main/art.asp?articlekey=15923 

http://www.thetech.org/genetics/art04_bad.php 

http://www.your-cancer-prevention-guide.com/kinds-of-cancer.html 

What do I know about somatic and germ line mutations?

1. The most important difference between germ line and somatic mutations is that germ line mutations are inherited while somatic mutations occur during life and are not inherited.

2.  Germ line mutations occur during the process of cell division known as meiosis. The cells produced in this process are the ones that will become either an egg or a sperm.

3. Somatic mutations occur while a cell is undergoing mitosis. The cells produced in this process will form part of organ tissue. Somatic mutations also occur after conception and during life.
 

Mitosis                Meiosis

  

4.  Germline mutations are associated with genetic diseases.  Different types of mutations that occur in the chromosomes can have effects on the phenotype or can cause cancer. Some examples are: Down Syndrome, Cri du chat syondrome (cry of cat), Turner Syndrome and breast cancer.

5.  Somatic mutations can have no effect on the phenotype, usually causes changes in the genotype. Some of these changes can go unnoticed or silent. If the the mutation is cancerous then the body will keep producing these cells until the person dies. Somatic mutations can affect damages in the bladder, liver and kidney function.

http://www.nature.com/scitable/topicpage/genetic-mutation-441

What is Genomics

Final Draft

What is Genomics?

      Genomics is the study of genomes. A genome is the entire DNA code found in the chromosomal set of an organism.  A comprehensive study of a genome would include three parts: (1) structural genomics, (2) functional genomics, and (3) comparative genomics (Brown, 2006).  This essay presents a short review of the three steps for a complete genome analysis.

The study of a genome begins with an examination of the sequence, or structural analysis.  A structural analysis refers to determining the sequence and location of each genetic element on a given DNA sequence. This is done by molecular and computing techniques including sequencing and assembly respectively.  Today, there are several sequencing techniques used for the study of genomes, but the first technique applied was the Sanger method (Sanger and Coulson, 1975).  Sanger sequencing method is based on a chain termination reaction that involves synthesis of DNA strands complementary to a single- stranded DNA template. The end product of this process is a library of short DNA fragments. To reconstruct the whole genome, these fragments have to be arranged together to form a long continuous sequence, in a process called sequence assembly (Myers et al., 2000).   
The ultimate goal of structural genomics is to identify every gene in the genome assembly.  Sequence inspection can be used to locate genes because they are not random series of nucleotides (structural units of DNA), but can be recognized for their distinctive features.  Since genes code for proteins, these features are well known.  For example, genes always start with a specific sequence, the initiation codon (ATG).  This codon (a three-nucleotide sequence that codes for one amino acid) codes for the amino acid methionine (Met) found at the beginning of each protein (Brown, 2006).
The issue of finding genes is actually more complicated, because they are not continuous, and are often interrupted by the non-coding sequences called introns. Fortunately, these elements can also be identified, because they share common features between genes.  Finally, gene sequences always end with a termination codon (for example: UGA). Termination codon interrupts the process of transcription (copying of DNA into RNA), and thus always ends a gene.  The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF).  Once all the genes have been located, a complete structural analysis of the genome has been completed.  

As part of a genome study, it is required to narrow down the study and focus in a chromosome and the genes that it contains.  By doing this, it is easier to find the functions of the genes; this part is known as functional genomics.  As the genes regularly have many different functions, this task is often difficult.  
There are several approaches to determine the function of a gene.  For example, a common procedure is gene silencing, a method that uses mutations that change the original function of the gene and observe what happens to the organism (McManus and Sharp, 2002). The result of gene silencing is termination of gene expression which provides insights into the function.  Another way to determine gene function is to study the differences caused by the distinct alleles (an alternate form of a gene) of the same gene.  Usually, there is a common allele, or wild type, encoded by a certain sequence of a gene.  Individuals with genetic mutations in a gene sequence are compared to the wild type to see if they cause changes in function.  In addition, the location of gene expression can also be relevant to the gene function.  By observing where the gene is expressed within the organism, its purpose can be determined.  Usually, this is done either by attaching fluorescent tags to the sequences and tracking them with a microscope (Chalfie et al., 1994), or by identifying the increase in the amounts of the relevant RNA or protein in tissues (VanGuilder et al., 2008).  For example, if the protein that the gene encodes is found in the brain, then its function has to do with the brain activity.  Finally, the data gathered from the approaches described above can be used to study genetic pathways, in other words, tracking interactions between different genes. The goal of functional genomics is to determine gene function, to know how all the genes in an organism work, and to establish all the characteristics it has.

The final approach of the comprehensive genome study is comparative genomics. This area focuses on comparisons of genomes between related species and determines how they differ in structure and function.  This part of genomics is concerned with evolutionary processes, which describe how genomes acquired their structure.  It has been observed that different organisms often carry the same genes known as homologous.  Even distantly related organisms share common genes because of their common ancestry. Genes that are important change slowly because random changes can disturb their function, while genes that are not so critical change faster, and are found to be more different when compared between species (Oleksyk et al., 2010). This is an important point, because comparative analysis of genome sequences can point out the important genes maintained by selection. On the other hand, finding genes that are divergent between species can explain differences between them.  For example, comparisons between the human genome and that of the chimpanzee, shows genes that are involved in developing superior brain structure and allows humans to use speech (Enard et al., 2002; Fisher and Scharff, 2009).  In other words, comparative genomics can give a scientific answer to one of the most important questions: “what makes us human”?

In short, this essay has reviewed the three stages of the study of a genome.  Together they are combined in Genomics, a science that studies genomes, the entire DNA codes found in each of the chromosomes that a given organism carries.  A comprehensive genome study involves all three major parts: structural genomics, functional genomics and comparative genomics.  Structural genomics focuses in sequencing and assembly of the genome for gene location.  Functional genomics is the area that determines that function of the genes.  Finally, comparative genomics focuses on comparing genomes of related species to determine the differences and similarities found between them.

Works Cited

Brown T.A. (2006). Genomes 3. 3rd ed. Garland Science Publishers. Oxford.713p.

Chalfie M, Tu Y, Euskirchen G, Ward W, Prasher D (1994). "Green fluorescent protein as a marker for gene expression". Science 263 (5148): 802–5

Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monaco AP, Pääbo S (2002). "Molecular evolution of FOXP2, a gene involved in speech and language". Nature 418 (6900): 869–72.

Fisher SE, Scharff C (2009). "FOXP2 as a molecular window into speech and language". Trends Genet. 25 (4): 166–77

McManus, M.T. & Sharp, P.A. (2002) “Gene silencing in mammals by small interfering RNAs”. Nature reviews. Genetics 3, 737-47

Myers EW, Sutton GG, Delcher AL, et al. (2000). "A whole-genome assembly of Drosophila". Science 287 (5461): 2196–204

Oleksyk TK, Smith MW, O'Brien SJ (2010) “Genome-wide scans for footprints of natural selection”.  Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 365(1537):185-205.

Sanger F, Coulson AR (1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase". J. Mol. Biol. 94 (3): 4418

VanGuilder H D, Vrana KE, Freeman WM (2008). "Twenty-five years of quantitative PCR for gene expression analysis". Biotechniques 44 (5): 619–626

What is Genomics?

 Draft 2

 What is Genomics?

                Genomics is the study of genomes. A genome is the entire DNA code found in the chromosomal set of an organism. A comprehensive genome study would include three parts: (1) structural genomics, (2) functional genomics, and (3) comparative genomics (Brown, 2006).  This essay presents a short review of steps for complete genome analysis.

The study of a genome begins with the first examination of the sequence, or structural analysis.  A structural analysis refers to determining the location of each gene on a given DNA sequence. This is done by molecular and computing techniques which include sequencing and assembly respectively.  Today, there are several sequencing techniques used for the study of genomes, but the first technique used was the Sanger method (Sanger and Coulson, 1975).  Sanger sequencing method is a chain termination reaction that involves synthesis of DNA strands that are complementary to a single- stranded DNA template. The end product of this process is a library of short segmented fragments of DNA. To reconstruct the whole genome, these fragments are then arranged together to form a long continuous sequence, in a process called sequence assembly (Myers et al., 2000).

The ultimate goal of structural genomics is to identify every gene in the assembly.  Sequence inspection can be used to locate genes because they are not random series of nucleotides (structural units of DNA and RNA), but can be recognized for their distinctive features.  Since genes code for proteins, these features are well known.  For example, genes always start with a specific sequence, the initiation codon (ATG).  This codon (a three-nucleotide sequence that codes for one amino acid) codes for the amino acid methionine (Met) found at the beginning of each protein (Brown, 2006).

The issue of finding genes is actually more complicated, because they are not continuous, and are often interrupted by the non-coding sequences called introns. Fortunately, these elements can also be identified, because they share common features between the genes. Finally, gene sequences always end with a termination codon (for example: UGA). Termination codon interrupts the process of transcription (copying of DNA into RNA), and thus always ends a gene. The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF).  Once all the genes have been located, a complete structural analysis of the genome has been completed.

As part of a genome study, it is required to narrow down the study and focus in a chromosome and the genes that it contains.  By doing this, it is easier to find the functions of the genes; this part of the study  is known as functional genomics.  As the genes regularly have many different functions, this task is often difficult.  Functional genomics is also concerned with interactions between genes and functional differences between different variants of the same gene. There are several approaches to determine the function of a gene. For example, a common procedure is gene silencing which is a method that uses mutations that change the original function and observe whats happens to the organism (McManus and Sharp, 2002). The result of gene silencing is termination of gene expression. The result of gene silencing provides insights into the function Another way to determine gene function is to study the differences caused by distinct alleles (an alternate form of a gene) of the same gene.  Usually there is a common allele, or wild type, encoded by a certain sequence of a gene.  Individuals with genetic mutations in a gene sequence are compared to the wild type to see if they cause change in function. Sometimes the location of gene expression can be relevant to gene function.  Therefore, by observing where the genes is expressed in the organism its purpose can be determined.  This is usually done either by attaching fluorescent tags to the sequence and tracking it with the microscope (Chalfie et al., 1994), or identifying the increase of the RNA or protein in tissues (VanGuilder et al., 2008). For example, if the protein that gene encodes is found in the brain then its function has to do with brain activity. Finally, the data gathered from the approaches described above can be used to study  genetic pathways, in other words, tracking interactions between different genes. The goal of functional genomics is to determine gene function, to know how all the genes in an organism work, and to establish the characteristics it has.

The final approach of the comprehensive genome study is comparative genomics. This area focuses on comparisons of  genomes between related species and determines how they differ in structure and function.  This part of genomics is concerned with evolutionary processes, which describes how  genomes acquired their structure.  Often, it has been observed that different organisms carry the same genes, they are known as homologous.  Even distantly related organisms share common genes because of their common ancestry. Genes that are important for organisms function change slowly because random changes can disturb their function, while genes that are not so critical change faster, and are found to be more different when compared between species (Oleksyk et al., 2010). The importance of this is that comparative analysis of genome sequences can point out the important genes, those that have been maintained by selection. On the other hand, finding genes that are different between species can help find differences between them. For example, comparisons between the human genome and  the chimpanzee genomes show genes that are involved in developing superior brain structure, and allows humans to have speech (Enard et al., 2002; Fisher and Scharff, 2009).  In other words, comparative genomics can give a scientific answer to one of the most important questions: “what makes us human”?

Genomics is a science that studies genomes, and a genome is the entire DNA code found in each of the chromosomes that a given organism carries. A comprehensive genome study involves three major parts which are structural genomics, functional genomics and comparative genomics. Structural genomics focuses in sequencing and assembly of the genome for gene location. Functional genomics is the area that determines that function of the genes.  Finally,  comparative genomics focuses on comparing genomes of related species to determine the differences and similarities found between them.

REFERENCES

Brown T.A. (2006). Genomes 3. 3rd ed. Garland Science Publishers. 713 p.
Sanger F, Coulson AR (1975). "A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase". J. Mol. Biol. 94 (3): 441–8
VanGuilder H D, Vrana KE, Freeman WM (2008). "Twenty-five years of quantitative PCR for gene expression analysis". Biotechniques 44 (5): 619–626
Chalfie M, Tu Y, Euskirchen G, Ward W, Prasher D (1994). "Green fluorescent protein as a marker for gene expression". Science 263 (5148): 802–5
Oleksyk TK, Smith MW, O'Brien SJ (2010) Genome-wide scans for footprints of natural selection.  Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 365(1537):185-205.
Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, Kitano T, Monaco AP, Pääbo S (2002). "Molecular evolution of FOXP2, a gene involved in speech and language". Nature 418 (6900): 869–72.
Fisher SE, Scharff C (2009). "FOXP2 as a molecular window into speech and language". Trends Genet. 25 (4): 166–77
McManus, M.T. & Sharp, P.A. (2002) Gene silencing in mammals by small interfering RNAs. Nature reviews. Genetics 3, 737-47
Myers EW, Sutton GG, Delcher AL, et al. (2000). "A whole-genome assembly of Drosophila". Science 287 (5461): 2196–204

What is Genomics?

Draft 1

What is Genomics?

Thesis statement:  Genomics is the study of genomes. A genome is the entire DNA code found in the chromosomal set of an organism. A comprehensive genome study would include three parts: (1) structural genomics, (2) functional genomics, and (3) comparative genomics.

Topic Sentence 1: To begin the study of a genome, the first examination is structural analysis of the genome.  A structural analysis refers to the location of each gene on a given DNA sequence. Structural analysis is done by molecular and computing techniques which include sequencing and assembly respectively.  Today, there is several sequencing techniques used for the study of a genome. The first technique that was used is the Sanger method.  Sanger sequencing method is a chain termination reaction that involves the synthesis of DNA strands that are complementary to a single- stranded DNA template (1). The end product of sequencing by the Sanger method is short segmented fragments of DNA. To form the whole genome sequence, the DNA fragments are arranged back together, forming a long continuous sequence of DNA, in short terms, sequence assembly.   The ultimate goal of structural genomics is to identify every gene in the genome sequence.  Sequence inspection can be used to locate genes because genes are not random series of nucleotides (structural unit of DNA and RNA) but instead have distinctive features. For example, genes always start with a specific sequence, the initiation codon (ATG).  This codon (a three-nucleotide sequence that codes for one amino acid) codes for the amino acid methionine (Met).

The issue is complicated, because genes are not continuous, and are interrupted by the non-coding sequences called introns. However, these elements can also be identified, because they have common features. Finally, gene sequences always end with a termination codon (for example: UGA). Termination codon interrupts the process of transcription (copying of DNA into RNA), and thus always ends a gene. The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF).  Once all the genes have been located, a complete structure of the genome has been completed.   

Topic Sentence 2: As part of a genome study, it is required to narrow down the study and focus in a chromosome and the genes that it contains.  By doing this it is easier to find the functions of the genes. Functional genomics is the part of genome study where the functions of genes are determined.  As the genes regularly have many different functions, this task is often difficult.  Functional genomics is also concerned with interactions between genes and functional differences between different variants of the same gene, as in cancer studies.
function
 Topic Sentence 3: Comparative genomics is the part of that compares genomes of related species and determines how they differ in structure and function.  This part of genomics is concerned with evolutionary processes, which is how did genomes acquire their present characteristics.  And one of the most important questions it studies is “what makes us human”?

Are my links good enough?

http://www.ncbi.nlm.nih.gov/books/NBK21117/
Yes, its a good reliable source of information
1. It is a book and has an author: Wiley-Liss
2. Its in the bookshelf of the National Cancer Institute
3. It has a publisher and publishing date: Bio Scientific, 2002

Things that I should know about Genomics

Q3.  If we compare genome and found 5% differences between them, does this mean that the two organisms are really different from each other?

The percentage difference is not necessarily the best indicator of divergence between species.  The genomes consist of different elements, some of them more important for the organism than the others.  For example, genes change very little, since they are restricted by their function.  On the other hand, the intergenic (between genes) sequence and introns often change a lot, because it has no protein coding purpose. Still the differences can be very deceiving.  For example, humans and chimpanzees are 5% different.  This seems like definitely a lot of difference.  However, these differences are not found in genes, and it is not clear which ones of them make us human.  On the other hand, two sea urchins born from the same individual, are often almost 4% apart, almost as much as humans and chimpanzees.  This may seem surprising, but there is an objective explanation: there is a lot of variation inside the same species.  A lot of this is explained by the adaptation to the changing environments, most of the differences are found in the immune genes.

http://www.nsf.gov/news/news_summ.jsp?cntn_id=108174

Things that I should know about Genomics

Q2. The DNA sequence is not enough to understand the functions of a genome, a functional unit of a genome is a gene, so how do you find one?

The are three different approaches to gene identification and localization.  First, genes can be found by sequence inspection, either by eye, or by computer methods (bioinformatics).  Second, genes can be found experimentally by identifying protein or RNA sequence found in tissues, and finding a corresponding DNA sequence on the chromosome.  Third, genes can be identified by comparing sequences between genomes of different species (comparative genomics).

1. Gene location by sequence inspection Sequence inspection can be used to locate genes because genes are not random series of nucleotides (structural unit of DNA and RNA) but instead have distinctive features. For example, genes always start with a specific sequence, the initiation condon (ATG) (Figure 1).  The issue is complicated, because genes are not continuous, and are interrupted by the non-coding sequences called introns.  However, these elements can also be identified, because they have common features.  Finally, gene sequences always end with a termination codon (for example: UGA).  The sequence identified in this manner between initiation and termination codon is called an open reading frame (ORF

Figure 1. Start and stop codons

2. Experimental techniques for gene location

Experimental methods for gene location use RNA molecules that are transcribed (copied) from genes. All genes are by definition transcribed into RNA.  In these methods, you collect RNA that was transcribed from the DNA, and convert it back to DNA code using molecular methods.  Since it is no longer the original DNA, but a copy, we call it a cDNA, and a library of fragments obtained by this methods, a cDNA library.  Once gene sequences have been identified in the DNA code, all we need to do is to find them in the genome.

3. Comparative methods for gene location

Once a gene is identified in one species, it is often easy to find it in a related species, because their sequences are likely to be similar.  This can be done by comparing sequences computationally (homology search), or by hybridizing (attaching sequences) genes between different species.  One way of doing this is zoo blotting (Figure 2). The objective is to determine if a fragment of human DNA hybridizes to DNAs from related species.

Figure 2. Zoo Blotting

http://www.ncbi.nlm.nih.gov/books/NBK21136/#A6613

Things that I should know about Genomics

Continuation to Question 1 (Q1)

Next Generation Sequencing Technologies

The next generation sequencing methods can be subdivided into three general categories:

1. Approach:  Emulsion PCR  

    Technology: Roche 454: http://454.com/products/technology.asp
 

2. Approach:  Substrate based 

    Technology:  Illumina: http://www.illumina.com/technology/sequencing_technology.ilmn
 

3. Approach:  Single molecule sequencing

    Technology:  Pacific Bio technology: http://www.pacificbiosciences.com/products/pacificbio-rs-workflow?quicktabs_2=0

 

 In general, next generation sequencing works by obtaining many small DNA fragments that need to be assembled like it was done in the shotgun method.  The short length (number of bp) of the  DNA fragments is compensated by the large number of the reads (how many copies of the DNA fragments are made), sometimes as many as 100 copies cover the same area on the chromosome. This is called coverage, and the number of overlapping sequences in the same place is denoted by X, in our example that would be 100X coverage.

However, since the human genome sequence is already known, it is not necessary to assemble DNA fragments anymore.  It is sufficient to find where the piece fits on the reference genome sequence (a standard sequence provided by the Human Genome Project).  

Another reason to use this advanced technology is that while Human genome project cost $3 billion dollars, today the sequencing cost is below $10,000.  

Thus the answer to the question is, no, I would not use the same method, or the same approach, because the progress in Genomics in the last 10 years has made it possible to sequence and assemble a genome for  much less and with a better coverage.
 

http://www.genome.gov/11006943

Things that I should know about Genomics

Q1. If I want to sequence a genome today, could I use the same approach with which human genome was sequenced?

 The human genome was sequenced more than ten years ago, and at the time the only available method for sequencing was the Sanger method.

Figure1. Sanger method

Figure 1. Sanger method. Chain termination sequencing involves the synthesis of DNA strands that are complementary to a single-stranded DNA template.

 http://www.wellcome.ac.uk/Education-resources/Teaching-and-education/Animations/DNA/WTDV026689.htm
http://www.dnalc.org/resources/animations/sangerseq.html

 The human genome sequence was done with two different approaches: clone-contig approach and the shotgun approach.

 1. The clone-contig approach uses a map of a chromosome which had previously identified genes or genetic markers. After the markers are located, the chromosome is cut into small fragments and many clones of the fragments are created. These clones are put together into contigs (from contiguous) to form what are called contig libraries (Figure 2). These contig libraries are then assembled back into the chromosome using the  reference map.

Figure 2. Clone-contig approach

2.  The shotgun method does not use a reference map to assemble the contigs. This approach is done by taking the whole master sequence and break (shotgun) it into short sequences. Then, the short reads are assembled into sequence by examining the the sequence overlaps. In the picture seen below, the first step demonstrates the sequenced braked  into many pieces, only the segments that are 2,000 base pair long (bp) are sequenced (Figure 3). The size restriction is because the Sanger sequencing method works best with sequences that are 1000-2000 bp long. The next step is to assemble the contigs into th chromosome directly, without a map.

Figure 3. Shotgun approach

For more information go to: http://www.ncbi.nlm.nih.gov/books/NBK21117/
 

Today, Sanger method is no longer used for large genome projects, but for short sequences only. Instead, the new generation sequencing methods are used for acquiring the whole genomic sequence.