Practicals - Bioinformatics

Question 1

What does the online dbSNP database examine?

Answer 1

SNPs

Question 2

What is the most frequent forms of genetic variation within the human genome?

Answer 2

• Single nucleotide variation (SNVs) and single nucleotide polymorphisms (SNPs)

Question 3

Are SNVs generally rare or common variants?

Answer 3

• SNVs are generally rare variants

Question 4

Why are SNPs commonly used as genetic markers?

Answer 4

They occur every 300bp within the genome and many are associated with disease

Question 5

What methods identify SNPs?

Answer 5

• microarrays, RFLP or PCR

Question 6

What methods does the 1000 genomes project use to identify SNPs?

Answer 6

Whole genome sequencing combined with deep exome sequencing

Question 7

How many individuals did the 1000 genome project initially use? How many now?

Answer 7

1092 humans from various populations, now over 2500 genomes

Question 8

Other than 1000 genomes project and dbSNP what are some similar databases?

Answer 8

GnomAD, ExAC and the 100K genomes project

Question 9

What do GWAS do?

Answer 9

Identify genomic variants (e.g. SNPs) that are associated with disease. These studies provide unbiased in vivo association of a gene or genetic pathway with disease pathogenesis

Question 10

Why is it important to perform further analysis after GWAS?

Answer 10

The identification of an association does not necessarily indicate the discover of a causal disease variant (e.g. a variant may be in LD with the actual causal variant). Therefore, it’s important to perform further analysis of associated variants to determine their functional effect(s) and how this relates to disease

Question 11

What online databases are useful for analysis of genetic variants?

Answer 11

• dbSNP and the 1000 genomes browser

Question 12

What information do the databases dbSNP and 1000 genomes provide?

Answer 12

• the genomic context, allele frequency and population data for SNPs

Question 13

What can NCBI BLAST be used to identify?

Answer 13

Identifies nucleotides in a sequence that differ from the reference genome. Allowing identification of SNVs and SNPs

Question 14

What does the database ClinVar allow?

Answer 14

Understanding the complexity associated with genetic variation by reporting the relationships between human variations and phenotypes

Question 15

What is the 1000 genomes project useful for?

Answer 15

Identifying the genotypes of individuals from a large number of populations.

Also useful when you have performed a GWAS in one population and identified SNPs associated with a particular disease

Question 16

What is the goal of ENCODE?

Answer 16

The goal of the Encyclopedia of DNA Elements (ENCODE) is to identify functional elements that affect gene expression

Question 17

What is the UCSC Genome Browser?

Answer 17

Information from ENCODE available in this data base, as well as dbSNP

Question 18

What does PCR require?

Answer 18

Both a forward and a reverse primer which bind to different strands of the DNA and amplify a particular target region

Question 19

What tools can be used to assess primer specificity?

Answer 19

BLAST or in silico PCR

Question 20

What does RFLP allow the identification of?

Answer 20

Restriction Fragment Length polymorphism (RFLP) allows identification of differences between homologous DNA between individuals