Editing Final Report/Thesis 2019 (section)

==Background==

===DNA===

DNA is the hereditary material which stores the genetic information in humans.
There are two types of DNA in human beings, one is known as nuclear DNA which is
located in cell nucleus and another type is mitochondrial DNA which is located in the
mitochondria. This project only focuses on the analysis of nuclear DNA. DNA stores
genetic information as a sequence built up with four types of nitrogen bases which
are adenine (A), guanine (G), cytosine (C), and thymine (T) [2]. Also, a sugar
molecule and a phosphate molecule are
attached to each nitrogen base to form a
molecule called nucleotide. The bases
would pair up (A with T and C with G)
and multiple nucleotides are placed in
two strands to form a double helix which
looks like a spiral [2]. In general, a DNA
is a genetic sequence formed by multiple
base pairs. The genetic instructions of
building and maintaining an organism
are obtained from the order of these
base pairs [2]. There are about 3 billion
bases in human DNA, in which more
than 99% of the bases are common in all human beings, and the physiological
differences among people depends on these 1% DNA.
[[File:DNA.png|thumb|300px|center|Figure 2: DNA structure]]

===Chromosome===
[[File:chromosome1.png|thumb|300px|Figure 3: Chromosome structure]]   [[File:chromosome2.png|thumb|300px|Figure 4: 23 pairs of chromosomes in human]]
Chromosome is an integrated package of DNA molecules. It has thread-like
structures, and DNA molecules are coiled up around hi stones proteins to form the
structure. There are 23 pairs of chromosomes in human body's cell, which is 46
chromosomes in total. 22 pairs are called autosomes which are common for both
males and females and the last 23rd pair is sex chromosomes which differ males and
females. In this project, the DNA data analysis would only focus on autosomes.

===SNP===

Single nucleotide polymorphism (SNP) is a genetic variation
among human beings. Each SNP represents a difference in a nucleotide which is
a single DNA molecule. For instance, one SNP may replace a nucleotide of base
guanine (G) with cytosine (C). These SNPs can be found nearly once in every 1,000
nucleotides on average in a person's DNA. Most SNPs do not effect health of owner.
However, some of these variations may associate with diseases.

===DNA reference file===
A DNA reference file stores a group of SNPs data of owner's DNA. The format of DNA reference files used in this project are of the same format which is 23andMe company's file, where 23andMe is a company that attended to provide personal genetic information for customers by using advanced genetic analysis techniques and web-based interactive tools. A screenshot of a sample file is shown below.
[[File:Dna_ref.png|thumb|center|300px|Figure 5: Sample DNA file from 23andMe]]
As shown in the figure, there are 4 columns in the DNA reference file: rsid, chromosome, position and genotype. The rsid is a unique id used to identify a specific SNP.
The format of rsid starts with “rs” and followed by a number (eg. rs123456). These rsids are commonly used by researchers and databases. There is another special format of rsid that starts with “i” and followed by a number (eg. i123456). This “i” format is used internally by 23andMe to identify the unknown SNP and cannot be used in public database. The second column chromosome identify which chromosome the SNP belongs to (1st to 22nd chromosome). The third column, position, indicates positions of SNPs in owner's DNA sequence. The last column, genotype, is the column for base pairs of variants (A, T, G, C). Note that there are some cases where the genotype result for some SNPs are not able be provided and “--” would be displayed in genotype column. It is important to note that only the SNPs with identified base pairs can be used for DNA analysis.