BIN300 - W1: what is statistical genomics?

Genome

Totality of genes on all chromosomes (1930s)

Genetic material of organism DNA

DNA discovered in the 1950s

chromosomes → double helix: two strands of DNA

DNA codes to make all cell types

DNA code

…ACGATAAGAAACT…

nucleotides

cytosine (C), guanine (G), adenine (A), thymine (T)

DNA contains the code for live

Genomics

investigations into the structure and function of large numbers of genes/nucleotides in a simultaneous fashion

large scale research of genomics

high throughput, new tehcnologies required, e.g. recording, analyisng etcsu

subdisciplines genomics

structural, comparative, functional, bioinfomatics

why so much interest in genomics - exepctations are high for

new approaches for drug discovery, new understanding on cancer formation, new approaches to genetic engineering

• disease resistance, improved nutrient contents of food, new selection methods involving new traits, gene-editing

genetic mapping

order of genes (distance between them)

physical mapping

where are the genes in the sequence of the genome

sequencing of entire genomes

human genome, 3 million baspeairs, cattle, horse, chicken, dog, pig, sheep, salmon

structural genomics

genetic mapping, physical mapping, sequencing of entire genomes

comparative genomics

many species: too many genomes to sequence? not a problem since genomes are similar, e.g. sequence species A gives info over B

Study of relationships of genomes

• across species, across breeds within species, between individuals, acorss genes (gene families)

functional genomics

from genotype to phenotype

mutagenesisf

genotype

mutant, changed DNA sequence

phenotype

all biologicla consequences, on physiological level, on animal/trait level

mutagenesis

study effects of mutations

invoking changes in DNA of model organism, studies the effect of DAN changes, expect similar effects in other species

proteomics

structure function and spatial localisation of protiens

proteome: all proteins in a cellp

physiomic

proteom => biochemistry and physilogy of organismp

phenomics

biochemistry → anatomy and function

bioinformatics

genomics studies not 1 gene but all 30.000

very large quentities of data, coming from high throughput machinery

bioinformatics

• computational, algortihimic and statistical analysis of large amounts of genomics data, database techniques, prediction of genes from DNA sequence, prediction of protein structure, i.e. how it folds

statistical genomics

biostatics part of bioinformatics

detection of genes for complex traits, quenatitiative trait loci (QTL)

genomic selection, use of genomics data for selection

gene

inherited phyiscal DNA that affects traits

locus

position on chromosome

alleles

position on chromosomea

allele frequency

number of allele A/ total number of alleles

segregation

sampling of alleles in meiosis, individual AB → gamete A or gamete B

genes are lying on chromosomes

true

polymorphic gene

more than 1 allele

genotype

allelic constituitation at 1, …., all loci

for 1 locus: A1A2H

homozygous

same 2 alleles at locus A

E.G. A1A

Heterozygouos2

2 different alleles at locus A

E.G. A1A2

quantitative traits

continuous variation, e.g. height or weightph

phenotype

recordable effect of genotype

qualitative traits

2 or few alternative forms, e.g. brown vs white coat, or blue vs borwn eyes

QTL

A quantitative trait locus (QTL) is a region of DNA associated with a specific phenotype or trait that varies within a population. Typically, QTLs are associated with traits with continuous variance, such as height or skin color, rather than traits with discrete variance, such as hair or eye color.