Manual The Human Genome

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The Human Genome Project (HGP) was an international scientific research project with the goal of determining the sequence of nucleotide base pairs that make.
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These sequencing methods have made a prospect realistic that, until now, would have be considered sheer fantasy: decoding the language that makes up the entire diversity of life on earth.

This does not mean that literally all unique genomes will be sequenced, however: The number of species on Earth is unknown, but current estimates point to several million species of eukaryotes organisms with complex cells containing a nucleus, like ourselves or fungi , and perhaps several billion of species of prokaryotes organisms with simple cells like bacteria.

However, a collection of representative genomes for all existing species seems a realistic goal—and for some particularly important species, including humans, there will be not one but thousands, if not millions, of representative genome sequences.

And then, what? What could—and should—we do with all that genomic data that stores the information of all organisms on earth? To begin with, we will know the entire range of biodiversity on Earth. This will allow reconstruction of the biochemical networks that define the functioning of every ecosystem and will eventually allow us to manipulate ecology. Unprecedented, deep understanding of the evolution of life will become possible as well. Complete knowledge of the history of life is unachievable because we will never have access to extinct evolutionary intermediates, but reconstruction by comparison of extant genomes will yield detailed information on these long-gone life forms.

Analysis of the complete genomic database will also enable understanding of the emergence of pathogenic bacteria and viruses. The relevance of such advances in this case is obvious—what if we could predict and control potential viral outbreaks? But the most immediate value will be a complete catalog of all the proteins genes encode. Scientists are already well aware of the most abundant genes and proteins think, for instance, of hemoglobin, which fills our blood and allows us to breathe. However, there is a huge mass of rare ones that could prove fascinating and, in quite a few cases, very useful for various technologies.

The recent identification of this relatively rare gene is a perfect example of this type of protein discovery. Discovered only a year or two ago, these enzymes are already changing the practice of genome engineering. The same applies to genes responsible for the synthesis of novel antibiotics, which will be essential to cope with antibiotic-resistant bacteria, which are currently on the rise. Even though we live in an information-dominated era, the principal bottleneck lies in the area of algorithms and computing power.

The computational power of human civilization keeps growing exponentially, but the amount of data we are generating grows even faster. And algorithms are struggling to keep up. To accomplish this, they electrophoresed the DNA through a gel matrix that permitted single-base differences in size to be easily distinguished.

Human Genome Project

Small fragments run more quickly through the gel, and larger fragments run more slowly Figure 6c. By putting the entire mixture into a single well of the gel, a laser can be used to scan the DNA bands as they move through the gel and determine their color; this data can be used to generate a sequence trace also called an electropherogram , showing the color and signal intensity of each DNA band that passes through the gel Figure 6d.

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Unfortunately, the initial hope of accelerating the discovery of new treatments for disease was not necessarily accomplished by the Human Genome Project. With the sequence of the human genome in hand, we have learned that it requires more than just knowledge of the order of the base pairs in our genome to cure human disease. Current efforts are therefore focused on understanding the protein products that are encoded by our genes.

When a gene is mutated, the corresponding protein is most often defective. The emerging field of proteomics aims to understand how protein function and expression are altered in human disease states. Furthermore, investigators are also turning their attention to the expansive regions of our genome devoid of traditional protein-encoding genes. We have already started to reap the benefits of our knowledge of the human genome, and future data-mining efforts will most certainly uncover many more exciting and unexpected links to human disease.

International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome.

What have we learned from the Human Genome Project?

Nature , — link to article. Finishing the euchromatic sequence of the human genome. Venter, J. Science , — link to article. Pufferfish and Ancestral Genomes. Simple Viral and Bacterial Genomes. Complex Genomes: Shotgun Sequencing. DNA Sequencing Technologies. Genomic Data Resources: Challenges and Promises. Transcriptome: Connecting the Genome to Gene Function. Behavioral Genomics.

Comparative Methylation Hybridization.

The Human Genome Project | Children's Hospital of Wisconsin

Pharmacogenomics and Personalized Medicine. Sustainable Bioenergy: Genomics and Biofuels Development. Thanks to the Human Genome Project, researchers have sequenced all 3. How did researchers complete this chromosome map years ahead of schedule? Aa Aa Aa. Phases of the Human Genome Project. The total is the sum of finished sequence red and unfinished draft plus predraft sequence yellow. Nature , Figure Detail. The BAC library is represented by short, disordered, squiggly black line segments. Next, the clones are organized and mapped into overlapping large clone contigs. One of the BAC clones is randomly chosen for sequencing.

It is fragmented into small pieces, which are subcloned into vectors to generate shotgun clones. These clones are then sequenced.

HGNC updates

Overlapping portions of the shotgun sequences are assembled to determine the genomic sequence. Minimally overlapping clones are picked from a fingerprint clone contig for sequencing. The clones are sequenced to at least draft coverage to form a sequenced-clone contig. The sequences are then merged and ordered to create a sequence-contig scaffold.

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Celera: Shooting at Random and Organizing Later. In whole-genome assembly, the BAC fragments red line segments and the reads from five individuals black line segments are combined to produce a contig and a consensus sequence green line. The contigs are connected into scaffolds, shown in red, by pairing end sequences, which are also called mates. If there is a gap between consecutive contigs, it has a known size. Next, the scaffolds are mapped to the genome gray line using sequence tagged site STS information, represented by blue stars.

This step produces a mixture of newly synthesized DNA strands that differ in length by a single nucleotide. C The DNA mixture is separated by electrophoresis. D The electropherogram results show peaks representing the color and signal intensity of each DNA band. From these data, the sequence of the newly synthesized DNA strand is determined, as shown above the peaks.

Dennis, C. Used with permission. Panel B shows nine newly synthesized DNA strands. Each of the strands differs in length by a single nucleotide and is labeled at the 3' end with a fluorescently-labeled ddNTP base. Panel C shows the electrophoresis results.


The DNA strands have been separated by size and appear as columns of colored bands. Panel D shows the electropherogram results, which are a series of colored peaks, with red representing T, black representing G, blue representing C, and green representing A. Shown above the peaks is the DNA sequence. From Rough Draft to Final Form. During this phase, the researchers filled in gaps and resolved DNA sequences in ambiguous areas that were not solved during the shotgun phase.

The final form of the human genome contained 2. Furthermore, the IHGSC reduced the number of gaps by fold; only gaps out of , gaps remained. The remaining gaps were associated with technically challenging chromosomal regions. Although the earlier draft publications had predicted as many as 40, protein-encoding genes, the finishing phase reduced this estimate to between 20, and 25, protein-encoding genes.

Future challenges identified by the IHGSC during this phase included the identification of polymorphisms as a platform for understanding genetic links to human disease , the identification of functional elements within the genome genes, proteins, elements involved in gene regulation , and structural elements , and the identification of gene and protein "modules" that act in concert with one another. From Digital Information to Molecular Medicine. One particularly striking finding of the Human Genome Project research is that the human nucleotide sequence is nearly identical However, a single nucleotide change in a single gene can be responsible for causing human disease.

Because of this, our knowledge of the human genome sequence has also contributed immensely to our understanding of the molecular mechanisms underlying a multitude of human diseases.