Trends in Biomedical Science 02 Mapping of disease genes GWAS 1

Genome-wide association studies (GWAS)  recently developed research technique  used to identify the single nucleotide polymorphisms (SNPs, pronounced "snips") – common to the human genome – find how SNPs are spread across different populations.  help scientists associations between individual SNPs and disorders that are passed from one generation to the next  can be used to determine an individual's risk of developing a particular disorder 2

The most common type of genetic variation is a single nucleotide polymorphism (pronounced 'snip'), a difference in a single DNA base. There are approximately 10 million SNPs estimated to occur commonly in the human genome. 3

4

5

Depends upon researchers' understanding of the interacting factors behind common genetic disorders. 6

SNP(Single Nucleotide Polymorphism) 단일염기변이, 스니프스 (SNPs). 인종이나 개인별 염기의 차이를 말한다. 즉 세포핵 속에 염색체가 갖고 있는 30 억개의 염기 서열 가운데 개인 편차를 나타내는 한개 또는 수십개의 변이염기를 일컫는다. 500~1000 염기당 1 개꼴로 나타나며, 인간지놈에는 약 300 만개의 SNP 가 존재하고 있다. 인간은 인종이나 민족과 상관없이 유전자가 99.9% 일치하지만 0.1% 의 SNP 때문에 키와 피부색이 달라지게 된다. 한국인이 서양인에 비해 위암과 간암이 잘 걸리는 것도 이런 차이에서 생기는 것으로 추정된다. 7

Other methods quantitative trait locus (QTL) analysis – identify a QTL, or a chromosomal region associated with a given phenotype – study the candidate genes within that region microsatellite DNA sequences – short stretches of chromosomal DNA – contain a two- to five-base-pair sequence (such as CA) repeated multiple times (e.g., CACACACACACACA). – polymorphic, and the number of base-pair repeats often varies between individuals. 8

SNPs: Variations in the Human Genome After Human Genome Project  find areas of the genome that varied between individuals  discovered that the most common type of DNA sequence variation found in the genome is the single nucleotide polymorphism; – an estimated 10 million SNPs that commonly occur in the human genome. – HapMap Project 9

HapMap Project identify and localize these and other genetic variants, learn how the variants are distributed within and among populations from different parts of the world. identified over 3.1 million SNPs that are common to individuals of African, Asian, and European ancestry. 10

The HapMap information → the genome-wide association study (GWAS). find distribution of SNPs in hundreds or even thousands of people with and without a particular disease. find which SNPs co-occur with disease symptoms, → statistical estimate regarding the level of increased risk associated with each SNP. 11

For instance, 2007 study in the United Kingdom: Found people affected by seven common disorders, – genotyped 2,000 people in each disease category (for a total of 14,000 people) – compared to 3,000 genotyped controls who did not have the disorders – identified new genetic markers that point to an increased risk for multifactorial disorders such as heart disease and diabetes 12

July 2008 – study will be expanded to add 36,000 individuals – will examine the genetic contributions to a total of 14 common disorders – individuals' responses to certain drugs. 13

The Role of DNA Microarrays in GWAS DNA microarray (sometimes called a DNA chip) a small glass slide with short DNA probes attached to it in a specific pattern – a sample of fragmented DNA is washed over the microarray, – pieces of this DNA hybridize to the chip – detected by scanning software. 14

Affymetrix is one manufacturer of DNA microarrays sells a chip containing approximately 1.8 million different genetic markers a fragment of DNA from a test sample hybridizes to a probe on this microarray the scanning software can document exactly which genetic marker is present in that DNA sample allows a single sample to be searched for changes at almost 2 million known genetic variants. 15

16

Microarray experiments Two color experiment (panel a) DNA from individuals or different tissue from a single individual (e.g., normal and diseased cells) is extracted and differentially labeled with compatible fluorophores (e.g., Cy3, Cy5). Equal amounts of labeled DNA is hybridized to the microarray. At most probes, equal amounts of the two samples will hybridize (yellow features on the array), so most loci in the two genomes are present in equal amounts (for example region 3). One-color experiments (panel b in the figure). DNA is labeled with a single color and hybridized to a microarray without a reference sample. The difference between two-color and one- color experiments is that in the former case two samples are compared within an experiment, whereas in the latter case two separate experiments are required to compare the samples. 17

Using GWAS to Estimate Disease Risk 18

Finding a correlation between a genetic change and the incidence of a complex disease limited to statistical estimation of increased risk for developing the disorder rather than a hard-and-fast prediction significant number of genetic and environmental variables interact to cause the onset of a complex disease any genetic variant, such as a SNP, makes only a small contribution to an individual's overall risk. 19

Findings from a GWAS: usually cannot be directly applied to the prevention or treatment of disease. before doctors are able to recommend medicinal, behavioral, and environmental interventions the full pathway of disease development must be understood the involvement of all variables must be understood. 20

Eg., a SNP may not be located within an exon of a gene – Maybe the SNP lies in a promoter or enhancer region – somehow affects regulation of the causal gene. 21

Sometimes results of a GWAS can be directly applied; often when a gene contains a variant that gives susceptibility to a multifactorial disorder the effect of that variant or other alleles of the gene is one of many factors influencing disease risk the predictive power of the various alleles is not absolute 22

eg. certain alleles of the apolipoprotein E (ApoE) gene found on chromosome 19 linked to the development of Alzheimer's disease. ApoE codes for a protein that helps carry cholesterol in the bloodstream, – three common alleles: e2, e3, and e4. – having one or two copies of the ApoE e4 allele significantly increases a person's risk for developing Alzheimer's disease, – does not guarantee development of this disorder. Not clear how certain forms of ApoE influence cerebral plaque formation, - Alzheimer's disease 23

Personal SNP Profiles 24

Very large amounts of information derived from the use of genome-wide association studies. most SNPs are only partial contributors to an individual's risk for developing a disease, researchers must be cautious about giving too much weight to SNP profiles. entrepreneurs capitalizing on existing GWAS research – eg., consumer genomics companies such as 23andMe, deCODE genetics, Navigenics, and Knome – used to offer a range of personal genotyping and sequencing services to clients – regulated so much → cannot offer services 25

Summary 26

genome-wide association studies have played an important role in research to identify possible connections between SNPs and various disorders. knowledge of the genetic risk factors for disease has increased → apply GWAS research to risk assessments for various disorders. GWASs are not absolute predictors of disease due to the role of environmental factors in complex disease development 27

Genome-Wide Association Studies and Human Disease Networks Adapted from Pray,L.(2008)Genome-wide association studies and human disease networks.NatureEducation1(1):220 28

Organizing Gene Association Data Research institutions in the United States and Korea developed what they call the "human disease network," a visual map of all human diseases with known underlying genetic associations; details the genetic connections between these diseases 29

Map made of nodes and branches node a disease, size - number of genes known to be associated with that disorder. thickness of the branches the number of genes shared by the connected diseases. 30

31

Most diseases with known genetic associations share most of their genes with other diseases. such as type 2 diabetes and prostate cancer – appear to be influenced by variation in the JAZF1 gene 32

Genetic connections among diseases  Show the molecular pathways that cause disease  aid in the design and development of new ways of treating or curing disease.  eg. a treatment that works well for one of the diseases may work for the other 33

34

Benefits of Gene Association Mapping 35

Gene-disease networking  first step toward making GWAS data useful for health care,  changes how physicians think about disease 36

eg. how doctors categorize various illnesses. – Stop thinking of human sickness in terms of the tissue involved (e.g., cancer of the breast), – Start thinking in terms of the molecular pathways involved. 37

Eg. invasive breast cancer, – categorized as being either Her2/neu- positive or Her2/neu-negative. Her2/neu is a receptor on the surface of breast cancer cells that is coded for by the Her2/neu gene. – Her2/neu-positive have many more of these receptors – Benefit more from certain forms of treatment than are Her2/neu-negative patients 38

Example Database

40