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Intro to genomics

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Sean May

on 6 June 2016

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Transcript of Intro to genomics

"What's in a name? That which we call a rose
By any other word would smell as sweet.”
-- Romeo and Juliet (II, ii, 1-2)
Post -
Plant structure ontologies
For a new sequencing project
How would you start ?
Intellectual exercise.

What incentives
and what problems
can you foresee
in a genome project
for your choice of
organism?

-The order of genes within each“block” of DNA is conserved
despite vastly different numbers & length of chromosomes
Human/Mouse Synteny

In a conserved 'block' the orientation of genes are generally conserved.
Syntenic gene pairs are most likely orthologous
(direct evolutionary counterparts by vertical descent).
human


mouse
PVR
ZFP93
VASP
ERCC2
Pvs-rs1
Zfp93
Vasp
Erccs
orientation of transcription
Arabidopsis recombinant inbred maps

‘micro-linkage groups’

Made from the ‘performance’ or markers across 2-300 lines
Phenotype description in free text: Green dwarf. Broader leaves, glabra. Yellow seed.
EAV example
Molecular function (how)
Biological Process (what)
Crop circles
Gale & Devos
Cat vs human synteny
Why cats ?
ACTUAL ONLINE DATA
What is
genomics ?

Why sequence a genome ?
- Gene structures such as regulatory regions, splice sites, exon number,
exon length and sequence similarity (DNA and protein level) tend to be
more conserved

- Intronic sequences and length tend to be less conserved
Human/mouse synteny (gene level)
Monolith databases holding DNA sequences
Genbank at NCBI
(NATIONAL CENTRE FOR BIOTECHNOLOGY INFORMATION)
EMBL (EUROPEAN MOLECULAR BIOLOGY LABORATORY)
DDBJ (DNA DATABANK OF JAPAN)

EACH DB EXCHANGES DATA DAILY
Germplasm curation - standards
Plant phenotype ontologies are
concatenated controlled vocabularies


-
E
ntity, (structure)

Taken from Plant Ontology ( PO ) - e.g leaf, microspore.

With properties of that entity (size, shape, colour, etc):

-
A
ttribute and
V
alue (
EAV
) -or-
-
Q
uality (
EQ
)

Taken from the Phenotype, Attribute and Trait Ontology ( PATO ).
Many organisms
have now been
sequenced

Practical step 1.

Do you have a model framework to ‘fix’ your genome on ?

Synteny

Step 2.

Map your genome
Genetic maps
Physical maps
Step 3.

Break your genome up into manageable lengths:
YAC
BAC
Cosmids
Tagged HTS fragments
Hairy, Hirsute, Pubescent

'Stick on' ESTs or perform RNAseq to determine transcripts.

Analyse by example (training sets) to develop in-silico predictions of unknown genes.

Submit it to a database.
GO – GENE ONTOLOGY
HOW do you sequence a genome ?
Slow lifecycle
Can be cloned
Commercial interest
Transgenics ?
Genome size ?
Linkage groups ?
Funding ?
Knowledge
of the whole genome
of an organism

Knowledge of the function of a genome
http://www.genomesonline.org/
EACH SUBMISSION TO EACH DB HAS:
A unique identifier
Sequence data for entry
References and Medline/Pubmed link
Biologically relevant annotation
Bald
Smooth
Glabrous
Rapid lifecycle
Apomyctic
Commercial interest
Transgenics ?
Genome size ?
Linkage groups ?
Funding ?
B Misof et al. Science 2014;346:763-767

12 DEC 2014 • SCIENCE VOL 346 ISSUE 6215
Jaillon, O., et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
Nature 431, 946–957 (2004) doi:10.1038/nature03025

Sequence the ‘bits’
ONTOLOGIES
Ontologies are for Disambiguity
Simple and functional
Complex & heterogeneous
But must be practical
Gene set enrichment (GO enrichment)
Enrichment map (in Cytoscape)
E.g. reduction of dimensionality to aid visualisation: Network graphs, PCAs, GUIs.

Because humans are good at patterns but bad at raw numbers (especially big ones).
Cellular component (where)
A lot of Bioinformatics is about analysing data, storing it sensibly - and making it easy(ier) to assess.
Affordable personal Genomics

Controversial when they made associations
available
without a medic present...
Bio-ontologies are
defined
groupings
Not natural or philosophical absolutes
We are not there yet with most (any?) eukaryote genomes
So affordable (in 2012) I got myself done.
Bioinformatics changed ~2005
Trends Genet. 2013 Jan; 29(1): 51–58.
"Using a CRISPR -Cas9 approach, Church’s team replaced 14 loci in the elephant genome with the mammoth version of those sequences."
2006
1984
2008
2006
2016
2015
Full transcript