Albany Medical College

Schaffer Library of Health

Sciences

LMI-2: Genetic
Variations
Traci Tosh, MSIS
2016

Objectives
Identify the basic genetic resources that are available for searching diseases
and disorders; such as Gene, ClinVar, dbSNP, and OMIM
Navigate NCBIs variation databases and tools to find specific types of
information related to variation data, such as clinical significance
Explain how genetic variations and mutations impact health

The next few slides are to teach you the

fundamental definitions, genetic terms
and concepts for genetic variations.
These are by no means
comprehensive.

Definitions click on each link for the definition

Allele
Base Pair
Codon
Deletion
DNA Sequencing
Exon
Frameshift mutation
Genetic Variations
Genotype
Insertion
Missense Mutation
Mutation
Nonsense Mutation
Phenotype
Single Nucleotide Polymorphisms (SNPs)

Small Variations
Small variations tend to be variations in a single base pair.

Small

AAGGATG
|||||||
TTCCTAC

G to T
C to A

AAGTATG
|||||||
TTCATAC

Source:
Matten, Wayne. A Librarians Guide to NCBI. National Center for Biotechnology Information. April 2013.

Types of Variations
Insertions & Deletions
Reference sequence

AAGGATGC

Insertion

AAGGCATGC

Deletion

AAG--TGC

Source:
Matten, Wayne. A Librarians Guide to NCBI. National Center for Biotechnology Information. April 2013.

Functional Variation Classification

Synonymous: no change to amino acid
silent

GGC
Gly

GGT
Gly

Non-synonymous: changes the amino acid

nonsense
frameshift
missense

Change to
a stop
codon

TCG
Ser

GGAAAGGTTAA
GlyLysVal

TCG
Ser

TAG
Ter
GGAAGGTTAA
GlyArgLeu

TGG
Trp

Source:
Matten, Wayne. A Librarians Guide to NCBI. National Center for Biotechnology Information. April 2013.

Genetic databases and tools are freely offered through the National Center for
Biotechnology Information (NCBI) website ( http://www.ncbi.nlm.nih.gov/). There are
three ways to search for genetic databases and tools, one, through the drop down box
next to the search box, two, from one of the subjects on the left side of the page, or
three, type your search into the search box, leave the drop down at All Databases and
click Search.

After an All Databases search, this is the screen that will display. It is called the
Entrez screen and is a quick way to access all NCBI databases: http
://www.ncbi.nlm.nih.gov/gquery/

NCBI Variation Resources

VariationDatabases
dbSNP
dbVar
Medical Genetics
ClinVar
MedGen
Genetic Testing Registry
OMIM (omim.org)
dbGaP

Viewers and Tools

SNP GeneView
Variation Viewer
Graphical Sequence Viewer
GaP Plus Browser
Phenotype Genotype
Integrator (PheGenI)
1000 Genomes Browser
Variation Reporter
Clinical Remap

Above is a list of the variation resources that are available through NCBI. We
are going to focus on the Variation resources in blue, as well as the Gene
database.

Quick Guide to NCBI Variation Resources

Gene database containing genetic sequencing, nomenclature, phenotype
characteristics, and variations
Genetic Testing Registry - central location for voluntary submission of genetic
test information by providers
Graphical Sequence Viewer - configurable graphical display of a nucleotide or
protein sequence and features that have been annotated on that sequence
OMIM (Online Mendelian Inheritance in Man) - database comprised of human
genes and genetic phenotypes
ClinVar - database containing records based on genetic variations and their
affiliation with medical disorders
MedGen - portal to information on medical genetics
dbSNP - database containing a catalog of short variations in nucleotide
sequences from a wide range of organisms
SNP GeneView - A list of short genetic variations of the gene and the functional
amino acid changes they cause. This will soon be replaced with the Variation
Viewer.
Variation Viewer genomic browser to search and view genomic variations listed
in dbSNP and ClinVar databases

Before we get started, here are a few Entrez Searching

rules!
Boolean operators (AND/OR/NOT) MUST be capitalized
If not, the operators are recognized as text words
Complicated Boolean strings with multiple components of ANDs and/or ORs
often do not run well
The order of search terms CAN make a difference in retrieving relevant results
Literal interpretation when searching no controlled vocabulary
You get back what you put in, including misspellings and typographical
errors
Enter plurals, include synonyms, and use truncation (*)
You can use quotes, but the phrase isnt always recognized
Source:
Rein, Diane. A Librarians Guide to NCBI. National Center for Biotechnology Information. April 2013.

Today we are going to search for Li Fraumeni. What is Li Fraumeni?

What is Li-Fraumeni syndrome?
Li-Fraumeni syndrome is a rare disorder that greatly increases the risk of developing several types of
cancer, particularly in children and young adults.
The cancers most often associated with Li-Fraumeni syndrome include breast cancer, a form of bone
cancer called osteosarcoma, and cancers of soft tissues (such as muscle) called soft tissue
sarcomas. Other cancers commonly seen in this syndrome include brain tumors, cancers of bloodforming tissues (leukemias), and a cancer called adrenocortical carcinoma that affects the outer layer
of the adrenal glands (small hormone-producing glands on top of each kidney). Several other types
of cancer also occur more frequently in people with Li-Fraumeni syndrome.
What genes are related to Li-Fraumeni syndrome?
The CHEK2 and TP53 genes are associated with Li-Fraumeni syndrome.
More than half of all families with Li-Fraumeni syndrome have inherited mutations in the TP53 gene.
TP53 is a tumor suppressor gene, which means that it normally helps control the growth and division
of cells. Mutations in this gene can allow cells to divide in an uncontrolled way and form tumors.
Other genetic and environmental factors are also likely to affect the risk of cancer in people with
TP53 mutations.
Source:
National Library of Medicine (US). Genetics Home Reference [Internet]. Bethesda (MD): The Library; 2014 Jun 16. LiFraumeni Syndrome; [reviewed 2007 Jan; Published 2016 Aug 2]; [about 1 screens]. Available from:
http://ghr.nlm.nih.gov/condition/li-fraumeni-syndrome

More on the TP53 gene and Li Fraumeni

What is the normal function of the TP53 gene?
The TP53 gene provides instructions for making a protein called tumor protein p53 (or p53). This protein acts as a tumor
suppressor, which means that it regulates cell division by keeping cells from growing and dividing too fast or in an
uncontrolled way.
The p53 protein is located in the nucleus of cells throughout the body, where it attaches (binds) directly to DNA. When
the DNA in a cell becomes damaged by agents such as toxic chemicals, radiation, or ultraviolet (UV) rays from sunlight,
this protein plays a critical role in determining whether the DNA will be repaired or the damaged cell will self-destruct
(undergo apoptosis). If the DNA can be repaired, p53 activates other genes to fix the damage. If the DNA cannot be
repaired, this protein prevents the cell from dividing and signals it to undergo apoptosis. By stopping cells with mutated
or damaged DNA from dividing, p53 helps prevent the development of tumors.
Because p53 is essential for regulating cell division and preventing tumor formation, it has been nicknamed the
"guardian of the genome."
Li-Fraumeni syndrome - associated with the TP53 gene. Although somatic mutations in the TP53 gene are found in
many types of cancer, Li-Fraumeni syndrome appears to be the only cancer syndrome associated with inherited
mutations in this gene. This condition greatly increases the risk of developing several types of cancer, particularly in
children and young adults. At least 140 different mutations in the TP53 gene have been identified in individuals with LiFraumeni syndrome.
Many of the mutations associated with Li-Fraumeni syndrome change single amino acids in the part of the p53 protein
that binds to DNA. Other mutations delete small amounts of DNA from the gene. Mutations in the TP53 gene lead to a
version of p53 that cannot regulate cell growth and division effectively. Specifically, the altered protein is unable to trigger
apoptosis in cells with mutated or damaged DNA. As a result, DNA damage can accumulate in cells. Such cells may
continue to divide in an uncontrolled way, leading to the growth of tumors
Source :
National Library of Medicine (US). Genetics Home Reference [Internet]. Bethesda (MD): The Library; 2014 Jun 16. TP53;
[reviewed 2015 May; cited 2015 Aug 24]; [about 1 screens]. Available from: http://ghr.nlm.nih.gov/gene/TP53

So lets do a search for Li Fraumeni from the Entrez page. Results

displayed in 36 databases across all the NCBI resources. For our search,
lets start with the Gene database.

The Gene database is where genetic sequencing, nomenclature, phenotype

characteristics, and variations can be found. For genomic research, the
Gene database is one of the best databases in which to start. We will start
here to view the TP53 gene, one of the genes that cause Li Fraumeni.

The results are organized by name and gene ID, description, chromosome location,
other known gene symbols, and the Online Mendelian Inheritance in Man (OMIM)
database number listed as MIM. OMIM will be mentioned later in this tutorial. If too
many results display, use the filters located on the left side to narrow down the search.
This should be familiar as PubMed has the same screen design.

Clicking on the link to the Gene database from the previous search on Li Fraumeni brings
up a list of gene results. Select the first listing for TP53 and human. Make sure to look
through the list of results to verify the record you are choosing is not an animal record.
The ability to filter by Organism is located on the right side of the screen.
Discontinued records display above the listed results.

In the selected TP53 gene record the top portion, or Summary, of the record textually
describes the gene; the official symbol and name, the gene type, the lineage, other
symbols this gene is known as, and a brief summary regarding TP53. Below the
Summary section is a section on Genomic Context with a diagram visually showing
which chromosome this gene is found on and the location.

On the right side of the screen is the Table of contents with quick links to sections
within this gene record for easier searching of the record. Located below the table of
contents are the Related Information links to related gene content in other databases,
primarily NCBI (these links will be displayed on the next slide). Remember, there is
also the ability to go directly to another resource from the Entrez search screen as well.

Scrolling down the page is the Sequence Viewer. This viewer is a visual
representation of where the gene is located on Chromosome 17 and where
the variations are located.

Related
Information
linkstoother
databasesthat
referencethe
TP53gene

Each of the
colored boxes
found under
ClinVar Short
Variations or
Cited Variants,
dbSNP has a
meaning (see
next slide) and
if hovered
over, will open
a pop-up
window with
information on
the variation
and links to
other NCBI
resources
such as
PubMed.

Variation box meanings

Source:
4.3. SNP Bins For Clinical Associations. Image. Graphical View Legend. National Center for Biotechnology Information,
Gene database. August 2016.

Continuing to scroll down the Gene page is where the section on Associated conditions for TP53 can
be found. Clicking on the condition link, for example Li-Fraumeni syndrome 1, will display the
Genetic Testing Registry page. Clicking on the Compare labs will display an alphabetical list of labs
with the different tests and services each lab runs. There are also links to other databases such as
MedGen and OMIM which will be discussed later in this module.

The Genetic Testing Registry (GTR) record of the disease provides a summary of the disease, available tests, associated
genes, and related conditions. It is a registry for voluntary submission of genetic test information by providers.
Notice the links on the right side of the screen for Reviews, Clinical resources, Practice guidelines, Molecular resources,
and Consumer resources.

Scrolling down the Genetic Testing Registry (GTR) record is where a breakdown of the
conditions related to Li Fraumeni along with linked icons to other resources. To look at the
full GeneReviews record for Li Fraumeni, click on the green G next to Li-Fraumeni 1.

GeneReviews are part of the NCBI Bookshelf. On the right side of the screen is a section
titled, In this GeneReview. These are quick links to sections of the currently displayed
GeneReview. Use the back arrow to return to the Gene database.

From the Gene record it is easy to move to another database simply by

choosing another resource from the Related Information links on the right
side of the page. Lets choose OMIM.

OMIM

OMIM stands for Online Mendelian Inheritance in Man. It is a database comprised of human
genes and genetic phenotypes. One of the pluses to OMIM are the external links it has in
each record to other NCBI and non-NCBI databases. To learn more about the information
located within each OMIM record, click on the FAQ link.

Linking to OMIM from the Gene database brings up a list of results on Li-Fraumeni
and TP53. Notice that the OMIM results list is similar in looks to a PubMed results
list. Scroll down the page until you find the listing for Tumor Protein p53 and click
the title.

The Tumor Protein p53 record in OMIM will display. OMIM is more textual in design
than the Gene database. To the left of the record is the table of contents; notice that
the OMIM record encompasses a wide variety of information on the Tumor Protein p53
gene record. To view a particular section of the record, click on the link in the table of
contents.

Selecting the Molecular Genetics section from the table of contents displays a listing of
diseases associated with the Tumor Protein 53. Within each disease section are
highlighted links to other resources as well as linked references to articles.

Currently the record displayed is the gene record. To link to the phenotype record use
the MIM Number link to the in the Gene-Phenotype Relationship table next to the
appropriate phenotype. The table in the phenotype record will then display as the
Phenotype-Gene Relationship table.

Located to the right of the record are the external links to other sites containing
information on the disease/gene. For more on information on the External
Links, select the External Links tab at the top of the screen. Click on the link for
Variation to access links to specific variation resources. Select ClinVar.

ClinVar

ClinVar is a database containing records based on genetic variations and their affiliation with medical
disorders. ClinVar is intended to meet the needs of the medical genetics community.

Disclaimer from ClinVar: ClinVar is based on direct submission, and not all variants known to cause or be
associated with medical disorders have been submitted to ClinVar or mapped to genomic coordinates.
You should not interpret the absence of medical information for a variant in a ClinVar file as a lack of
medical or functional effect for that variation

Selecting the ClinVar database link in OMIM brings up a list of all the TP53 variations in
ClinVar. There are quite a few listed so we will need to use filters to narrow down our
search. Similar to PubMed and the Gene database, additional filters are available on the
left side of the screen.

Filtering to Pathogenic narrows down our search to only display the genes with
pathogenic variations along with their corresponding conditions and locations.
Click on one of the results to view an individual record.

Choose the detailed pathogenic record for the TP53 gene with a coding DNA of c.637C>T and protein
changes of amino acid Arg213 to amino acid Ter. The ClinVar record lists the information on the
genetic variation, protein changes, clinical significance, and links to condition information.

Continue scrolling down the page to the tabs for Clinical Assertions (who the submitter is, clinical
significance, links to citations), Summary Evidence (laboratories, families, allele origin), and
Supporting Observations (phenotypes, description of genetic variation).

In ClinVar, clicking on the MedGen condition link

will display the MedGen record. MedGen is a
portal to information on medical genetics. The
information can include disease characteristics
and descriptions (found in GeneReviews
mentioned earlier in this module), guidelines,
clinical studies, systematic reviews, and links to
Genetic Testing Registry.

Click on the dbSNP link in the ClinVar record to bring up the result in the
dbSNP database.

dbSNP
dbSNP is a database containing a catalog of short variations in nucleotide
sequences from a wide range of organisms.

Selecting the dbSNP record in ClinVar retrieves one result. Click on the
result to retrieve the full dbSNP record.

At the top of the dbSNP record is where you will find the type of organism
(human) that the variation is associated with, the alleles that are affected (C/T),
and the clinical significance (with pathogenic allele).

A) The Integrated Maps section provides a summary of genome mapping information for the variation
by clicking on any value in the Chromosome Position (Chr Pos) column or the Contig Position
(Contig Pos) column.
B) The SNP GenView section is being replaced with the Variation Viewer which will be discussed
later in this tutorial.
C) The RefSeqGene Mapping table summarizes variation mapping information and protein changes.

A
B
C

As you scroll down the page

A) As in the The RefSeqGene Mapping table from the previous slide, the Gene Model table
summarizes variation mapping information and protein changes in chart form
B) The Sequence Viewer displays the variations similar to the sequence viewer in the Gene
database

The SNP GeneView page mentioned earlier displays a list of short genetic variations of the gene and
the functional amino acid changes they cause. However, it only reports human variation on GRCh38,
the new assembly for the human genome. A new Variation Viewer is available to view the gene TP53
variations in GRCh37p13 (previous human genome assembly) or GRCh38, and will replace SNP
GeneView later this year. The Variation Viewer is the genomic browser used to search and view
genomic variations listed in dbSNP and ClinVar databases
To search the new Variation Viewer, click the VarView button at the top of the dbSNP page and choose
which assembly in which you wish to view the variations.

The Variation Viewer is similar to PubMed in how the screen is structured - main search
topic is on the right and the limits/filters are on the left. The Sequence Viewer is the main
display and is a visual representation of where the gene is located on the Chromosome as
well as where the variations are located. Located under the Sequence Viewer is a table
with links to the variations, their locations, type of variant, the gene its associated with, the
clinical significance, and any publications associated with the variation.

To learn more about the Variation Viewer, click on the You Tube link located
at the top right of the screen.

Variation Portal

Up to this point I have shown you how to access the variation databases and portals
linking from one resource to another. A shortcut is through the Variation Portal which
contains many, but not all, of NCBIs variation resources all in one easy to reference
location.
http://www.ncbi.nlm.nih.gov/variation/

Youve reached the end of the Tutorial!

Final Test:

Click the Test link on sidebar of the LMI 2444 16-17

Sakai site to take the test.
The Test is due 11:59pm, Thursday, September 26.

Formative Assessment:

Follows after this slide

The formative assessment is for your benefit so that
you are aware you are studying at the level expected
of you.
There is no grade for the formative assessment and
it is open for the rest of the year so that you can
always refer back to it if need be.

Formative Assessment: Genetic

Variations

Answer

2
3
4

Question
Click on the corresponding button to see the answer!!
1.

Where is the best place find genetic databases and tools?

A. UpToDate
C. NCBI
B. Google
D. Visual Dx

2.

Can you filter your results in the Gene database? True or False?

3.

You must run a new search each time you wish to view other genetic databases and tools on
your topic. True or False?

4.

ClinVar is a database containing records on?

A. Drug Interactions
B. Dermatologic conditions
C. Genetic Variations and their affiliations with medical disorders