Term Paper

On

“Single-nucleotide Polymorphism”

Submitted to: Submitted by:Ms. Tulasi Adapa Ojasvi Ahuja

RE7602B36 3040060064

Contents

Single-nucleotide polymorphism

Types of SNPs

Needles in Haystack

Use and importance of SNPs

SNPs and Disease Diagnosis

SNPs and Drug Development

SNPs and NCBI

NCBI's "Discovery Space" Facilitating SNP Research

Examples of SNPs

Databases of SNPs

Nomenclature

Human Genome Project and SNP Mapping Goals

FAQs

Conclusion & Discussion

References

Single-nucleotide polymorphism

DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (a C/T polymorphism)

A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation

occurring when a single nucleotide — A, T, C, or G — in the genome (or other shared

sequence) differs between members of a species (or between paired chromosomes in an

individual). For example, two sequenced DNA fragments from different individuals,

AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say

that there are two alleles : C and T. Almost all common SNPs have only two alleles.

Within a population, SNPs can be assigned a minor allele frequency — the lowest allele

frequency at a locus that is observed in a particular population. This is simply the lesser of the

two allele frequencies for single-nucleotide polymorphisms. There are variations between

human populations, so a SNP allele that is common in one geographical or ethnic group may

be much rarer in another.

"SNP"

In the past, SNPs with a minor allele frequency of greater than or equal to 1% (or 0.5%, etc.)

were given the title "SNP". Some used "mutation" to refer to variations with low allele

frequency. With the advent of a better understanding of evolution, this definition is no longer

necessary, e.g., a database such as dbSNP includes "SNPs" that have lower allele frequency

than 1%.

Types of SNPs

Non-coding region

Coding region

o Synonymous

o Nonsynonymous

Missense

Nonsense

Single nucleotides may be changed (substitution), removed (deletions) or added (insertion) to

a polynucleotide sequence. Ins/del SNP may shift translational frame.

Single nucleotide polymorphisms may fall within coding sequences of genes, non-coding

regions of genes, or in the intergenic regions between genes. SNPs within a coding sequence

will not necessarily change the amino acid sequence of the protein that is produced, due to

degeneracy of the genetic code. A SNP in which both forms lead to the same polypeptide

sequence is termed synonymous (sometimes called a silent mutation) — if a different

polypeptide sequence is produced they are nonsynonymous. A nonsynonymous change may

either be missense or nonsense, where a missense change results in a different amino acid,

while a nonsense change results in a premature stop codon. SNPs that are not in protein-

coding regions may still have consequences for gene splicing, transcription factor binding, or

the sequence of non-coding RNA.

Needles in a Haystack

Finding single nucleotide changes in the human genome seems like

a daunting prospect, but over the last 20 years, biomedical

researchers have developed a number of techniques that make it

possible to do just that. Each technique uses a different method to

compare selected regions of a DNA sequence obtained from

multiple individuals who share a common trait. In each test, the

result shows a physical difference in the DNA samples only when a SNP is detected in one

individual and not in the other.

Many common diseases in humans are not caused by a genetic variation within a single gene

but are influenced by complex interactions among multiple genes as well as environmental

and lifestyle factors. Although both environmental and lifestyle factors add tremendously to

the uncertainty of developing a disease, it is currently difficult to measure and evaluate their

overall effect on a disease process. Therefore, we refer here mainly to a person's genetic

predisposition, or the potential of an individual to develop a disease based on genes and

hereditary factors.

Genetic factors may also confer susceptibility or resistance to a disease and determine the

severity or progression of disease. Because we do not yet know all of the factors involved in

these intricate pathways, researchers have found it difficult to develop screening tests for

most diseases and disorders. By studying stretches of DNA that have been found to harbor a

As a result of recent advances in SNPs research, diagnostics for many diseases may improve.

SNP associated with a disease trait, researchers may begin to reveal relevant genes associated

with a disease. Defining and understanding the role of genetic factors in disease will also

allow researchers to better evaluate the role non-genetic factors—such as behavior, diet,

lifestyle, and physical activity—have on disease.

Because genetic factors also affect a person's response to drug therapy, DNA

polymorphisms such as SNPs will be useful in helping researchers determine and understand

why individuals differ in their abilities to absorb or clear certain drugs, as well as to

determine why an individual may experience an adverse side effect to a particular drug.

Therefore, the recent discovery of SNPs promises to revolutionize not only the process of

disease detection but the practice of preventative and curative medicine.

Use and Importance of SNPs

Variations in the DNA sequences of humans can affect how humans develop diseases and

respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also thought to

be key enablers in realizing the concept of personalized medicine. However, their greatest

importance in biomedical research is for comparing regions of the genome between cohorts

(such as with matched cohorts with and without a disease).

The study of single-nucleotide polymorphisms is also important in crop and livestock

breeding programs (see genotyping). See SNP genotyping for details on the various methods

used to identify SNPs.

They are usually biallelic and thus easily assayed.

SNPs and Disease Diagnosis

Each person's genetic material contains a unique SNP pattern that is made up of many

different genetic variations. Researchers have found that most SNPs are not responsible for a

disease state. Instead, they serve as biological markers for pinpointing a disease on the human

genome map, because they are usually located near a gene found to be associated with a

certain disease. Occasionally, a SNP may actually cause a disease and, therefore, can be used

to search for and isolate the disease-causing gene.

To create a genetic test that will screen for a disease in which the disease-causing gene has

already been identified, scientists collect blood samples from a group of individuals affected

by the disease and analyze their DNA for SNP patterns. Next, researchers compare these

patterns to patterns obtained by analyzing the DNA from a group of individuals unaffected by

the disease. This type of comparison, called an "association study", can detect differences

between the SNP patterns of the two groups, thereby indicating which pattern is most likely

associated with the disease-causing gene. Eventually, SNP profiles that are characteristic of a

variety of diseases will be established. Then, it will only be a matter of time before physicians

can screen individuals for susceptibility to a disease just by analyzing their DNA samples for

specific SNP patterns.

SNPs and Drug Development

As mentioned earlier, SNPs may also be associated with the absorbance and clearance of

therapeutic agents. Currently, there is no simple way to determine how a patient will respond

to a particular medication. A treatment proven effective in one patient may be ineffective in

others. Worse yet, some patients may experience an adverse immunologic reaction to a

particular drug. Today, pharmaceutical companies are limited to developing agents to which

the "average" patient will respond. As a result, many drugs that might benefit a small number

of patients never make it to market.

In the future, the most appropriate drug for an individual could be determined in advance of

treatment by analyzing a patient's SNP profile. The ability to target a drug to those

individuals most likely to benefit, referred to as "personalized medicine", would allow

pharmaceutical companies to bring many more drugs to market and allow doctors to

prescribe individualized therapies specific to a patient's needs.

SNPs and NCBI

Because SNPs occur frequently throughout the genome and tend to be relatively stable

genetically, they serve as excellent biological markers. Biological markers are segments of

DNA with an identifiable physical location that can be easily tracked and used for

constructing a chromosome map that shows the positions of known genes, or other markers,

relative to each other. These maps allow researchers to study and pinpoint traits resulting

from the interaction of more than one gene. NCBI plays a major role in facilitating the

identification and cataloging of SNPs through its creation and maintenance of the public

SNP database (dbSNP). This powerful genetic tool may be accessed by the biomedical

community worldwide and is intended to stimulate many areas of biological research,

including the identification of the genetic components of disease.

NCBI's "Discovery Space" Facilitating SNP Research

NCBI Discovery Space

Records in dbSNP are cross-annotated within other internal information resources such as

PubMed, genome project sequences, GenBank records, the Entrez Gene database, and the

dbSTS database of sequence tagged sites. Users may query dbSNP directly or start a search in

any part of the NCBI discovery space to construct a set of dbSNP records that satisfy their

search conditions. Records are also integrated with external information resources through

hypertext URLs that dbSNP users can follow to explore the detailed information that is

beyond the scope of dbSNP curation.

 

Reproduced with permission from Sherry ST, Ward MH, Kholodov M, Baker J, Phan L,

Smigielski EM, Sirotkin K."dbSNP: the NCBI database of genetic variation." Nucleic Acids

Research. 2001; 29:308-311.

To facilitate research efforts, NCBI's dbSNP is included in the Entrez retrieval system which

provides integrated access to a number of software tools and databases that can aid in SNP

analysis. For example, each SNP record in the database links to additional resources within

NCBI's "Discovery Space". Resources include: GenBank, NIH's sequence database; Entrez

Gene, a focal point for genes and associated information; dbSTS, NCBI's resource

containing sequence and mapping data on short genomic landmarks; human genome

sequencing data; and PubMed, NCBI's literature search and retrieval system. SNP records

also link to various external allied resources.

Providing public access to a site for "one-stop SNP shopping" facilitates scientific research in

a variety of fields, ranging from population genetics and evolutionary biology to large-scale

disease and drug association studies. The long-term investment in such novel and exciting

research promises not only to advance human biology but to revolutionize the practice of

modern medicine.

Examples

rs6311 and rs6313 are SNPs in the HTR2A gene on human chromosome 13.

A SNP in the F5 gene causes a hypercoagulability disorder with the variant Factor V

Leiden.

rs3091244 is an example of a triallelic SNP in the CRP gene on human chromosome

1.

TAS2R38 codes for PTC tasting ability, and contains 6 annotated SNPs.

Databases

As there are for genes, there are also bioinformatics databases for SNPs. dbSNP is a SNP

database from National Center for Biotechnology Information (NCBI). SNPedia is a wiki-

style database from a hybrid organization. The OMIM database describes the association

between polymorphisms and, e.g., diseases in text form, while HGVbaseG2P allows users to

visually interrogate the actual summary-level association data.

Nomenclature

The nomenclature for SNPs can be confusing: several variations can exist for an individual

SNP and consensus has not yet been achieved. One approach is to write SNPs with a prefix,

period and greater than sign showing the wild-type and altered nucleotide or amino acid; for

example, c.76A>T.

Human Genome Project SNP Mapping Goals

In 1998, as part of their last 5-year plan, the DOE and NIH Human Genome programs

established goals to identify and map SNPs. These goals follow.

Develop technologies for rapid, large-scale identification and scoring of SNPs and

other DNA sequence variants.

Identify common variants in the coding regions of most identified genes.

Create a SNP map of at least 100,000 markers.

Develop the intellectual foundations for studies of sequence variation.

Create public resources of DNA samples and cell lines.

FAQs

What is The SNP consortium (TSC)?

In April 1999, ten large pharmaceutical companies and the U.K. Wellcome Trust

philanthropy announced the establishment of a consortium lead by Arthur L. Holden to find

and map 300,000 common SNPs. The goal was to generate a widely accepted, high-quality,

extensive, publicly available map using SNPs as markers evenly distributed throughout the

human genome. In the end, many more SNPs (1.8 million total) were discovered. Now that

the SNP discovery phase of the TSC project is essentially complete, emphasis has shifted to

studying SNPs in populations. Various TSC member laboratories are genotyping a subset of

SNPs as part of the Allele Frequency Project. The goal of the TSC allele frequency/genotype

project is to determine the frequency of certain SNPs in three major world populations. See

the TSC website for more information.

Who are members of the SNP consortium?

The international member companies, which together committed at least $30 million to the

consortium's efforts, are APBiotech, AstraZeneca Group PLC, Aventis, Bayer Group AG,

Bristol-Myers Squibb Co., F. Hoffmann-La Roche, Glaxo Wellcome PLC, IBM, Motorola,

Novartis AG, Pfizer Inc., Searle, and SmithKline Beecham PLC. The Wellcome Trust

contributed at least $14 million.

Laboratories funded by these companies to identify SNPs are located at the Whitehead

Institute, Sanger Centre, Washington University (St. Louis), and Stanford University. Data

management and analysis take place at Cold Spring Harbor Laboratory.

See Consortium Updates:

News related to The SNP Consortium SNP Consortium collaborates with HGP, publishes first progress reports , 2000.

Human Genome News.

International SNP meeting updates , 2000. Human Genome News.

Why should private companies fund a publicly accessible genome map?

The SNP consortium views its map as a way to make available an important, precompetitive,

high-quality research tool that will spark innovative work throughout the research and

industrial communities. The map will be a powerful research tool to enhance the

understanding of disease processes and facilitate the discovery and development of safer and

more effective medications.

Whose DNA was analyzed to create the consortium's SNP map?

The SNP consortium used DNA resources from a pool of samples obtained from 24 people

representing several racial groups. This is a subset of the DNA reference panel for SNP

identification collected by the NIH National Human Genome Research Institute. The

anonymous, voluntary DNA contributions were made with informed consent specifically for

this use.

Are SNP data available to the public?

SNP data were made available through a consortium website at quarterly intervals during the

project's first year and at monthly intervals during the second year. This cycle of releases

ceased in fall 2001 once the discovery phase was finished, but with recent additions of

genotype and allele frequency information, new data were released in fall 2002.

Besides the TSC website, SNP data are also available from the following resources:

dbSNP database - From the National Center for Biotechnology Information (NCBI).

HGVbase (Human Genome Variation Database) - A human gene-based

polymorphism database.

Conclusion & Discussion

Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most

common type of genetic variation among people. Each SNP represents a difference in a

single DNA building block, called a nucleotide. For example, a SNP may replace the

nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.

SNPs occur normally throughout a person’s DNA. They occur once in every 300 nucleotides

on average, which means there are roughly 10 million SNPs in the human genome. Most

commonly, these variations are found in the DNA between genes. They can act as biological

markers, helping scientists locate genes that are associated with disease. When SNPs occur

within a gene or in a regulatory region near a gene, they may play a more direct role in

disease by affecting the gene’s function.

Most SNPs have no effect on health or development. Some of these genetic differences,

however, have proven to be very important in the study of human health. Researchers have

found SNPs that may help predict an individual’s response to certain drugs, susceptibility to

environmental factors such as toxins, and risk of developing particular diseases. SNPs can

also be used to track the inheritance of disease genes within families. Future studies will work

to identify SNPs associated with complex diseases such as heart disease, diabetes, and cancer.

Various scientific endeavors had already started even before the completion of the first

human genome reference sequence to identify unique genetic differences between

individuals. 99.9% of one individual DNA sequences will be identical to that of another

person. Of the 0.1% difference, over 80% will be single nucleotide polymorphisms (SNPs). A

SNP is a single base substitution of one nucleotide with another, and both versions are

observed in the general population at a frequency greater than 1%. Human DNA is comprised

of only four chemical entities, e.g. A, G, C, T, whose specific chemical order is the alphabet

of the genome. An example of a SNP is individual "A" has a sequence GAACCT while

individual "B" has sequence GAGCCT, the polymorphism is a A/G. The most recognized

public effort was spearheaded by The SNP Consortium (TSC) whose mission was to

determine and map about 300,000 evenly spaced single nucleotide polymorphisms within the

human genome.

Current estimates are that SNPs occur as frequently as every 100-300 bases. This implies in

an entire human genome there are approximately 10 to 30 million potential SNPs. More than

4 million SNPs have been identified and the information has been made publicly available

through the efforts of TSC and others. Many of these SNPs have unknown associations.

Compilation of public SNPs by NCBI has produced a subset of SNPs defined as a non-

redundant set of markers that are used for annotation of reference genome sequence and are

thus referred to as reference SNPs (rsSNPs). Over 2.6 million SNPs have currently been

assigned as "rsSNPs".

References

en.wikipedia.org/wiki/Single-nucleotide_polymorphism

www.ncbi.nlm.nih.gov/About/primer/snps.html

las.perkinelmer.com/content/snps/genotyping.asp

www.medterms.com/script/main/art.asp?articlekey=30716

encyclopedia.farlex.com/single+nucleotide+polymorphisms

www.ncbi.nlm.nih.gov/About/primer/snps.html

www.ornl.gov/sci/techresources/Human.../faq/snps.shtml