genome sequencing

Examples of genome sequencing in the following topics:

• Uses of Genome Sequences

  • Genome sequences and expression can be analyzed using DNA microarrays, which can contribute to detection of disease and genetic disorders.
  • Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome.
  • Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function.
  • Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities.
  • It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely.

• Use of Whole-Genome Sequences of Model Organisms

  • The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs).
  • Several other organelle and viral genomes were later sequenced.
  • It took this long because it was 60 times bigger than any other genome that had been sequenced at that point.
  • Having entire genomes sequenced aids these research efforts.
  • The process of attaching biological information to gene sequences is called genome annotation.

• DNA Sequencing Techniques

  • Next generation sequencing can sequence a comparably-sized genome in a matter of days, using a single machine, at a cost of under $10,000.
  • Many researchers have set a goal of improving sequencing methods even more until a single human genome can be sequenced for under $1000.
  • Most genomic sequencing projects today make use of an approach called whole genome shotgun sequencing.
  • Whole genome shotgun sequencing involves isolating many copies of the chromosomal DNA of interest.
  • Genome sequencing will greatly advance our understanding of genetic biology.

• Predicting Disease Risk at the Individual Level

  • Genome analysis is used to predict the level of disease risk in healthy individuals.
  • The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information.
  • Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics.
  • In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases.
  • Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level remain to be addressed.

• Strategies Used in Sequencing Projects

  • The strategies used for sequencing genomes include the Sanger method, shotgun sequencing, pairwise end, and next-generation sequencing.
  • All of the segments are then sequenced using the chain-sequencing method.
  • This was sufficient for sequencing small genomes.
  • However, the desire to sequence larger genomes, such as that of a human, led to the development of double-barrel shotgun sequencing, more formally known as pairwise-end sequencing.
  • Compare the different strategies used for whole-genome sequencing:  Sanger method, shotgun sequencing, pairwise-end sequencing, and next-generation sequencing

• Noncoding DNA

  • Noncoding DNA are sequences of DNA that do not encode protein sequences but can be transcribed to produce important regulatory molecules.
  • In genomics and related disciplines, noncoding DNA sequences are components of an organism's DNA that do not encode protein sequences.
  • For example, over 98% of the human genome is noncoding DNA, while only about 2% of a typical bacterial genome is noncoding DNA.
  • Other noncoding sequences have likely, but as-yet undetermined, functions.
  • More than 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA.

• Physical Maps and Integration with Genetic Maps

  • The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping.
  • A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location.
  • An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs.
  • Information obtained from each technique is used in combination to study the genome.
  • Genomic mapping is being used with different model research organisms.

• Biotechnology

  • Relying on the study of DNA, genomics analyzes entire genomes, while biotechnology uses biological agents for technological advancements.
  • Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species.
  • The advances in genomics have been made possible by DNA sequencing technology.
  • The ways in which genomic information can contribute to scientific understanding are varied and quickly growing.
  • In genomics, the DNA of different organisms is compared, enabling scientists to create maps with which to navigate the DNA of different organisms.

• Genome Evolution

  • The evolution of the genome is characterized by the accumulation of changes.
  • The analaysis of genomes and their changes in sequence or size over time involves various fields.
  • There are various mechanisms that have contributed to genome evolution and these include gene and genome duplications, polyploidy, mutation rates, transposable elements, pseudogenes, exon shuffling and genomic reduction and gene loss.
  • The most common transposable element in the human genome is the Alu sequence, which is present in the genome over one million times.
  • Good examples are the genomes of Mycobacterium tuberculosis and Mycobacterium leprae, the latter of which has a dramatically reduced genome.

• Variations in Size and Number of Genes

  • Genetic diversity at its most elementary level is represented by differences in the sequences of nucleotides (adenine, cytosine, guanine, and thymine) that form the DNA (deoxyribonucleic acid) within the cells of the organism.
  • The C-value is another measure of genome size.
  • For example, the predicted size of the human genome is not much larger than the genomes of some invertebrates and plants, and may even be smaller than the Indian rice genome.
  • In eukaryotic organisms, there is a paradox observed, namely that the number of genes that make up the genome does not correlate with genome size.
  • It is also possible that genomes can shrink due to deletions.