The DNA sequence, annotation and analysis of human chromosome

楼主 海贼王于 2004-04-05 16:34:22

The DNA sequence, annotation and analysis of human chromosome

The DNA sequence, annotation and analysis of human chromosome 3

DNA Sequence: Journal of DNA Mapping, Sequencing, and Analysis

DNA Sequence will accept original high quality reports based on mapping, sequencing and analysis of DNA and RNA, irrespective of supporting biological or functional data. Acceptable reports may describe coding or non-coding features of a single locus or whole genomes. Features of interest include e.g. genes (incl. RNA genes), variation, promoters, epigenetic modifications and any features affecting DNA/RNA function, structure and evolution. Experimental and computational method reports on the above topics are equally acceptable.

DNA sequencing is the determination of the precise sequence of nucleotides in a sample of DNA.

The most popular method for doing this is called the dideoxy method or Sanger method (named after its inventor, Frederick Sanger, who was awarded the 1980 Nobel prize in chemistry [his second] for this achievment).

DNA is synthesized from four The top formula shows one of them: deoxythymidine triphosphate (dTTP). Each new nucleotide is added to the 3′ -OH group of the last nucleotide added. The dideoxy method gets its name from the critical role played by synthetic nucleotides that lack the -OH at the 3′ carbon atom (red arrow). A dideoxynucleotide (dideoxythymidine triphosphate — ddTTP — is the one shown here) can be added to the growing DNA strand but when it is, chain elongation stops because there is no 3′ -OH for the next nucleotide to be attached to. For this reason, the dideoxy method is also called the chain termination method.

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The Asbestos & Mesothelioma Center is committed to providing the latest, up-to-date information to our visitors in hopes to create awareness about asbestos and its link with mesothelioma. The material on this site serves as a solid resource for those who are suffering from any of the lung related diseases caused by asbestos. Here you will also find complete lists of hospitals, doctors, and legal teams who specialize in mesothelioma cases. Since mesothelioma is a rare cancer, most people know little about asbestos, the disease, and its devastating effects on human health.

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Mesothelioma is considered a rare form of cancer. It affects the "mesothelial," the protective lining around our internal organs. Mesothelioma can attack cells in different linings of the body such as the lungs, heart, and abdomen. Many of the symptoms related to this disease (shortness of breath, severe cough, chest pain) do not appear for 30+ years, making it difficult to diagnose early. For this reason, the cancer is often found in the later stages, making it difficult for proper treatment and survival.

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Asbestosis usually shows no symptoms for years other than the presence of scars in the lung tissue. Those scars may be so microscopic that they don.t show up on X-rays for ten to fifty years. The earliest symptoms of asbestosis are a dry cough and shortness of breath, which are often mistaken for something else. As asbestosis gets worse, there may be chest pain and chest tightness, difficulty sleeping and loss of appetite, and the shortness of breath gets worse until it is difficult to breathe well, even when at rest.

Complications of Asbestosis

While there is no evidence that asbestosis causes mesothelioma, a virulent cancer associated with asbestos, there is a definite link between the two. People with asbestosis have a greatly increased risk of developing mesothelioma than those who have been exposed to asbestos, but haven.t developed asbestosis. Other complications include pulmonary hypertension, heart problems arising from the stress on the heart, a greatly increased risk of lung cancer and COPD, chronic obstructive pulmonary disease.

Abstract

After the completion of a draft human genome sequence1, the International Human Genome Sequencing Consortium has proceeded to finish2 and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B3. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

The sequence was generated using a clone-by-clone random shotgun sequencing and finishing strategy2 (see Methods). Each tiling path BAC clone was finished to community standards (http://genomeold.wustl.edu/Overview/g16stand.php). We finished 194,944,050 bp of euchromatic sequence to an independently measured accuracy of at least 99.99%7 and have covered more than 99.99% of the euchromatic chromosome. Each of the landscape features and annotations outlined here may be viewed as user-specified tracks on the Genboree Browser (http://www.genboree.org/Hs.chr3).

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1楼 无名于 2004-04-05 17:11:12

What is DNA

All living things, including humans, are made up of cells. Humans are made up of many different kind of cells, including skin cells, blood cells, buccal cells (inside the mouth), muscle cells, fat cells, and many more.Most of the cells in our bodies (with the exception of red blood cells) have a nucleus. The nucleus of all of our cells, doesn't matter which cell type, contains chromosomes, and chromosomes are responsible for storing our hereditary information. Chromosomes are made up of DNA (stands for deoxyribonucleic acid). DNA is like a blueprint because it holds the informational code for all of the genetic information for that person. The DNA for each individual is unique to that person.
With the exception of the egg and sperm cell, all of the cells in our body contain 23 pairs of chromosomes, 46 in total. One chromosome from the pair is inherited from our mother and the other one is passed down from our father. This is a picture of all of the chromosomes in a cell (this type of picture is called a karyotype).

Both males and females have 23 pairs of chromosomes. However, in male, the 23rd pair consists of an X-Chromosome and a Y-Chromosome, whereas females have two X-Chromosomes. The Y-Chromosome is special because it carries ancestral information regarding a male's paternal line.

DNA looks like a twisted ladder and is often referred to as a "double helix". The double helix consists of two complementary chains of DNA twisted together.

If we were to hypothetically untwist the DNA strand and lay it flat, it would look like a ladder. The two sides of the ladder are called the DNA's "backbone". The steps inside the ladder are representing "bases". There are 4 types of bases in DNA: A (for adenine), C (for cytosine), T (for thymine), and G (for guanosine). In the DNA strand, A always pairs with a T, and C always pairs with a G. The unique sequence of the A, C, T, and G in DNA forms codes which carry genetic information.

When DNA is deciphered by genetic testing, the DNA code can be written in the following manner:
A G C T G G G A C A A T G G G C G C T A G G C C C C C C...

No two individuals (except for identical twins) have exactly the same genetic code and that is what makes everyone unique. However, all males with the same surname who are originated from a common lineage will share the same or very similar genetic code in their Y-Chromosome. Unrelated males from a different family line will have a different Y-Chromosome code.

A male inherits his Y-Chromosome directly from his father. The Y-Chromosome that a male receives from his father is very special because it holds a lot of valuable information about his ancestry. This is because the Y-Chromosome is passed down along the male line, relatively unchanged from generation to generation. A forefather will pass his Y-Chromosome down to all of his sons, and they will then pass it down to all of their sons, and so on throughout the generations along the male line. Thus, males who are descendents of the same line will have the same or nearly identical Y-Chromosomes.

When a Y-Chromosome genealogy test is performed, the laboratory examines specific regions (markers) along the Y-Chromosome called "hypervariable" regions. Hypervariable regions are areas within the Y-Chromosome that may differ greatly between different family lines. The type of hypervariable region which is studied in Y-Chromosome testing is called STR markers (stands for "Short Tandem Repeat" markers). STR markers are regions of the Y-Chromosome where small chunks of the DNA are repeated over and over again. The number of times that these small chunks of DNA repeat themselves in the Y-Chromosome is variable amongst different family lines.

To follow is an example of a Y-Chromosome marker called DYS19. The section of DNA which repeats itself is TAGA. Thus, someone with a DYS19 marker of 6 will have TAGA repeated 6 times. The DNA test will indicate that the DYS19 marker is 6 for this individual. DYS19 = 6

Someone with a DYS19 marker of 4 will have TAGA is repeated 4 times. In this case, the DNA test will indicate that the DYS19 marker is 4 for this individual. DYS19 = 4

By testing your Y-Chromosome, a DNA laboratory can provide you with your Y DNA markers which is specific for your ancestry. Because all males with the same ancestors will have the same or similar Y DNA markers, you can enter your Y DNA markers into GeneBase to solve questions about your ancestry, to conclusively link family lines and to discover your distant relatives who share a common ancestor with yourself. DNA testing has become the most exciting and fastest growing branch of genealogy.

When a Y-Chromosome test is performed, up to 44 Y-Chromosome markers are analyzed to generate the unique "profile" for that individual. Two males with the same male lineage with the same forefathers will have the same or similar profiles. The closer the match in profiles, the more recently two individuals shared the same forefather. Obviously, the more markers that are tested, the more powerful your test becomes and the more information you will obtain when searching in GeneBase.

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