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.