next generation sequence with pathway studio

| 1

Country Long Distance

Australia +61 3 8488 8993

Austria +43 (0) 7 2088 2171

Belgium +32 (0) 42 68 0164

Canada +1 (647) 497-9386

Denmark +45 (0) 89 88 04 43

Finland +358 (0) 931 58 4587

France +33 (0) 182 880 933

Germany +49 (0) 692 5736 7304

Ireland +353 (0) 19 036 186

Country Long Distance

Italy +39 0 294 75 15 36

Netherlands +31 (0) 108 080 115

New Zealand +64 (0) 9 801 0293

Norway +47 21 03 72 89

Spain +34 911 23 4247

Sweden +46 (0) 852 500 292

Switzerland +41 (0) 435 0824 40

United Kingdom +44 (0) 330 221 9921

United States +1 (646) 307-1726

TO USE YOUR COMPUTER'S AUDIO: When the webinar begins, you will be connected to audio using

your computer's microphone and speakers (VoIP). A headset is recommended. --OR--

TO USE YOUR TELEPHONE: If you prefer to use your phone, you must select "Use Telephone" after

joining the webinar and call in using the numbers below.

Dial your country’s number and then use Access Code: 131-004-283

Next Generation Sequence Data Analysis in Pathway Studio

Our Webinar will begin in a few minutes

Next Generation Sequence Data Analysis in Pathway Studio For Current Pathway Studio Users

May 6, 2014

| 3

Pathway Studio Web Now Includes Analysis

Capabilities for NGS (Variant and RNA-Seq data)

Pathway Studio Web customers with a subscription to the

Mammal+ChemEffect+DiseaseFx database

can now analyze Next Generation Sequencing (NGS) data results

using new tools released in Pathway Studio Web v. 11.0

Variant analysis requires the data included in the

ChemEffect and DiseaseFx database.

| 4

Types of Output and Analysis Options for NGS Data

Two data output types can be analyzed in Pathway Studio

RNA-Seq Whole Genome Sequence

or Exome Sequence

RNA-Seq Analysis

in Pathway Studio

Web

| 6

Analysis of RNA-Seq Data in Pathway Studio Web

File Format Requirements

X

?

1. Gene Identifiers that can be used in

Pathway Studio

a) Identifiers in the database

b) Identifiers that are mapped (using

a mapping file) to identifiers in the

database

2. Normalized measured values for each

gene

a) Can be RPKM, FPKM or fold

change

b) Need to pedestal data to avoid “0”

values. Zero values will remove

genes from inclusion in enrichment

analysis.

Cannot have multiple values in one field

Identifiers not in the database require a mapping file

| 7


File Format Requirements

Gene ID Normalized Measured Values

| 8


The import steps are similar to the Gene Expression analysis options

for microarray data.

| 9


Variant Analysis

| 11

Variant Analysis in Pathway Studio

Data from the dbSNP database is includes in Pathway Studio

http://www.ncbi.nlm.nih.gov/snp



| 12


Data from the dbNSFP and 1000 Genomes databases are includes

in Pathway Studio

1000 Genomes [http://www.1000genomes.org/about] A Catalog of

Human Genetic Variation information provided by The 1000 Genomes

Project Consortium

dbNSFP [https://sites.google.com/site/jpopgen/dbNSFP and

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109890/#R19 ] A

database developed for functional prediction and annotation of all

potential non-synonymous single-nucleotide variants (nsSNVs) in the

human genome.

http://www.1000genomes.org/about

https://sites.google.com/site/jpopgen/dbNSFP

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109890/#R19

| 13


Search dbSNP database

Find variants in an individual genome

Analyze variants in a population

Upload genomic files

| 14


Search the dbSNP database – targeted filters

• Is the mutation within the coding region of a gene, the intron, the

regulatory region for expression of the gene, or is it in a region between

genes?

• Does the SNP affect the protein’s sequence, and if so, will the amino acid

change have a profound deleterious effect on the structure and function

of the protein, or will the change be well tolerated by the protein (not

impact its function and activity)?

• Is the mutation in a specific protein’s amino acid position or within a

region of the protein sequence that is known to be generally conserved

(very few changes) within the human population?

• Is the protein mutation within a region that is known to be conserved

(very few changes) across species other than just human?

• What chromosome and region of a chromosome is the SNP is located

on?

| 15



• What diseases or cell processes are associated with the gene containing

the SNP of interest? (This information is derived from Elsevier’s Pathway

Studio database.)

• Is there any known clinical impact reported for a specific SNP (such as:

pathogenic, drug response, etc.)?

• Does the SNP alter the splicing of the gene, or terminate the protein

sequence prematurely?

• How common or frequently is a particular SNP found within the standard

1000 Genome Project reference data?

[http://www.1000genomes.org/about]

http://www.1000genomes.org/about

| 16


Search dbSNP database

| 17



| 18


Search the dbSNP database – filter definitions

| 19



| 20



| 21



| 22



| 23



| 24


Search the dbSNP database – example

Example biological query:

Find SNP(s) that are potentially deleterious to the function of a protein(s) that

are known to be associated with Hodgkin Lymphoma.

| 25






| 26


Search the dbSNP database – example filter definitions




| 27






| 28






| 29






| 30






Importing Genomic

Data into Pathway

Studio Web

| 32


Importing individual genomic data into Pathway Studio


| 33


Importing individual genomic data into Pathway Studio – file formats

The format required for both genomic or exome

data is .vcf files

[http://www.1000genomes.org/node/101].

The time to upload a file is dependent on the size

of the file and the number of files.

.vcf files need to have been generated using the

same version of the reference genome as is loaded

into the database.

http://www.1000genomes.org/node/101

| 34



| 35



| 36



Find variants in an individual genome

| 37



Analysis of an

Individual Genome

| 39


Search single exome file for interesting variants


Question: Are there any novel (not yet reported) potentially damaging variants in this

dataset in genes known through Elsevier’s text-mining to be associated with the

cellular processes apoptosis.

| 40







| 41







| 42







| 43







| 44







Analysis of an

Multiple Genomes

| 46


Variant analysis of multiple genomes – import


| 47


Variant analysis of multiple genomes – import

| 48


Analyze variants in a population

| 49


Variant analysis of multiple genomes - comparisons

| 50



| 51



| 52


Variant analysis of multiple genomes


Question: Find homozygous variants that are present in at least three of the case

samples but not in any of the control samples that are also in the coding region and

are known to be associated with breast cancer.

| 53







| 54







| 55







| 56







| 57







Note: in the Case and Control column, the

number of times the specific variant is identified

are represented by four numbers in this order:

• homozygous

• heterozygous

• hemizygous

• ambiguous

| 58







| 59







| 60

NGS data analysis Pathway Studio

Where to find help

| 61


http://help.elsevier.com/app/answers/detail/a_id/5549/p/9047/

Where to find help

| 62


Where to find help

| 63


Where to find help

http://help.elsevier.com/app/pathway_select/p/9048

Questions?

next generation sequence with pathway studio

Health & Medicine

pathway studio data

pathway studio http

pathway studio rnaseq

analysis of rna

current pathway studio

analysis capabilities

enrichment analysis

microarray data