Variation and the VEP: Ensembl Online Webinar series

Denise Carvalho-‐Silva Ensembl Outreach team

European Molecular Biology Laboratory

European Bioinforma9cs Ins9tute

Ensembl online

training series 2016

Course Objec=ves

What is Ensembl?

What type of data can you get in Ensembl?

How to navigate the Ensembl browser website?

How to connect with Ensembl

This online course Date Webinar topic Instructor

24th March

Introduc9on to Ensembl Emily Perry

31st March

Ensembl genes Denise Carvalho-‐Silva

7th April Data export with BioMart Helen Sparrow

14th April

Varia=on data in Ensembl and the Ensembl VEP Denise Carvalho-‐Silva

21st April

Comparing genes and genomes with Ensembl Compara Helen Sparrow

28th April

Finding features that regulate genes – the Ensembl Regulatory Build

Emily Perry

5th May Uploading your data to Ensembl and advanced ways to access Ensembl data

Ben Moore

hSp://www.ebi.ac.uk/training/events/2016/ensembl-‐online-‐training-‐series-‐2016

Our Polls: finding more about you

• Previous webinars

Introduc9on, Genes and Transcripts, BioMart

• Poll 1: ASendance • Poll 2: Exercises

Structure for this hour webinar

Presenta=on: SNPs, CNVs, SV available in Ensembl VEP: tool for variant annota9on

Demo: View variants/

run the VEP

Exercises: On the train online course

Ques=ons?

• We’ve muted all the microphones •  Ask ques9ons in the Chat box in the webinar interface

• My Ensembl colleagues will respond during my talk

•  Please respond with @username

Helen Sparrow Ben Moore Emily Perry

EBI is an Outstation of the European Molecular Biology Laboratory.

Compara9ve Genomics Gene models

Regula9on Varia9on

Custom data display Programma9c access

Toolkit

Ensembl Features

EBI is an Outsta9on of the European Molecular Biology Laboratory.

Module 4: Gene=c Varia=on in Ensembl

Outline

•  Classes of varia9on, species and sources

•  Browsing varia9on data: some entry points Loca9on tab Gene tab Varia9on tab

•  Phenotype and popula9on gene9cs data

•  How to annotate your own variants

1) Large scale: structural (> 50 base pairs)

Gene=c varia=on

duplica9on dele9on inversion transloca9on loss

2) Short scale: SNPs (or SNVs), indels

G A C T G A C T A T C G G G G T T T C C C A A A

G A A T G A C T T T C G G -‐ G -‐ T T C C -‐ A A A

Species with varia=on data

Understand the types of gene9c varia9on data and how to view them in the context of our genomes

Sources of varia=on data

•  Import alleles and frequencies

•  Annotate variants

hSp://www.ensembl.org/info/docs/varia9on/sources_documenta9on.html

Loca=on tab: across a region

SVs SNPs

Ensembl genes

Gene tab: gene-‐centric SNPs

SVs

Varia=on tab: variant centric

summary data

SNP or SV

Variants on the karyotype

Phenotype data in Ensembl species and sources

Popula=on data for variants

hSp://hapmap.ncbi.nlm.nih.gov/

hSp://www.1000genomes.org

pie charts: 1KG super popula9ons

Human Popula=on Gene=cs

Coffee intake is a worldwide phenomenon

with Finland at the top, and UK in the 44th

place. Is caffeine consump9on in our genes?

A)  What are the chromosome loca9ons of variants associated with this phenotype?

B)  Which variant has got the most significant associa9on?

C)  What is the ancestral allele of this variant? Is it conserved in eutherian mammals?

D)  What is the most frequent allele in Great Britain?

E)  Can you download this variant and 200 nt upstream and downstream flanking sequence in RTF (Rich Text Format)?

Live demo

You can annotate your SNPs and SVs too!

•  Variant Effect Predictor

•  Different input formats

•  SIFT/PolyPhen for missense variants

PMID: 20562413

Perl script Web interface REST API

XML

CODING Synonymous

INTRONIC 5’ UTR

ATG AAAAAAA

Regulatory

Splice sites

CODING Missense

3’ UTR 5’ Upstream 3’ downstream

Mapping variants on transcripts

Iden9fy transcripts that overlap variants and predict the consequence of these on Ensembl (or RefSeq) transcripts using

Consequence terms for variants

www.ensembl.org/info/genome/varia9on/predicted_data.html#consequence_type_table

* defined by the Sequence Ontology (SO) project (hSp://www.sequenceontology.org/)

Consequence: missense GAG >GGG Glu > Gly

SIFT sift.jcvi.org/

PolyPhen-2 genetics.bwh.harvard.edu/pph2/ Condel

dbNSFP

Ensembl tools hSp://www.ensembl.org/tools.html

hSp://www.ensembl.org/vep

Inpu[ng data into the

Chromosome Start End Alleles Strand

Output op=ons in the

GAG > GGG Glu > Gly

GAG > GAA Glu > Glu

Queued Running Done Failed

Save to your account (log in) Edit and resubmit your job

Delete job

Ticket system in the

Ticket iden9fier Job name

Viewing the results

SO consequence terms*

*hSp://www.sequenceontology.org/index.html

ensembl.org/info/docs/tools/vep/online/results.html#summary

Table •  Before / aper filtering •  novel / exis9ng variants

Pie charts (consequence terms) •  total observed (more than one per variant) •  Separate chart: coding consequences

Viewing the results

Navigate results (one row per variant/ transcript overlap)

Show/hide columns in results table more columns: scroll right

•  Download results •  Send results to BioMart

Create and edit filters

ensembl.org/info/docs/tools/vep/online/results.html#table

results table

Filters consist of three components Field •  e.g. Consequence, biotype

Operator •  e.g. is, matches (par9al string matches)

Value •  the value to compare against •  some fields have autocomplete values

Mul9ple filters allowed with logical rela9onship (AND, OR) Ac9ve filters can be edited too!

ensembl.org/info/docs/tools/vep/online/results.html#filter

Filtering the e results

I’ve got a list of gene9c variants from my resequencing project of a cohort study of breast cancer in Cambridge. The posi9ons are all on chromosome 9, GRCh37 assembly:

131084628 C/A (posi9ve strand)

131085358 C/G (posi9ve strand)

131085196 G/A (posi9ve strand)

1)  Do any of these cause a change at the amino acid level?

2)  Are these predicted to be deleterious?

3)  Can I get the flanking sequence (200 nucleo9de both up and downstream)

for the known variants in this set?

Tutorial: VEP

Tutorial: VEP 1)  Have I got genomic coordinates? Ensembl default format

9 131084628 131084628 C/A + 9 131085358 131085358 C/G + 9 131085196 131085196 G/A +

VEP video

hSp://9nyurl.com/vep-‐video

Things to bear in mind

1)  No dis9nc9on between polymorphisms and muta9ons. Excep9on HGMD and COSMIC: all muta9ons;

2)  C/T à first allele is the one in the reference genome, not necessarily the major or the ancestral;

3)  Ensembl reports all alleles on the forward strand (different from dbSNP).

Next webinar – Comparing genes and genomes

Ensembl allows you to perform detailed analysis of gene models between species. During this webinar we will take a look at the gene trees and homologues of a set of genes, and at whole genome alignments between pairs and groups of species. See you next week, same 9me.

Helen Sparrow

Course exercises hSp://www.ebi.ac.uk/training/online/course/ensembl-‐

browser-‐webinar-‐series-‐2016

This text will be replaced by a YouTube (link to YouKu too) video of the webinar and a pdf of the slides.

The “next page” will be the exercises

A link to exercises and their solu9ons will appear in the page

hierarchy The “previous page”contains the solu9on of previous modules’ exercises

Get help with the exercises

•  Use the exercise solu9ons in the online course

•  Join our Facebook group and discuss the exercises with everybody (see the online course for the link)

•  Email us [email protected]

Connect with Ensembl

? ? ? ? ?

? ?

? ? ?

[email protected]

www.youtube.com/user/EnsemblHelpdesk www.ensembl.org/info/genome/genebuild/index.html

Acknowledgements The En=re Ensembl Team

Funding

Co-funded by the European Union

Variation and the VEP: Ensembl Online Webinar series

Science

Transcript of Variation and the VEP: Ensembl Online Webinar series