Bioinformatics

Question 1

What is bioinformatics

Answer 1

Development and application of computer science to the analysis of large amounts of biological information

Question 2

What is systems biology

Answer 2

Study of biological systems accounting for the interactions of the key elements (DNA, RNA, proteins and cells) with respect to one another

Question 3

Meaning of metagenomics

Answer 3

Direct genetic analysis of genomes contained with an environmental sample. Study of all genes in a system/ environment

Question 4

When a variation is found, what questions need to be asked ( in regard to clinical significance)

Answer 4

Is it pathogenic
Is it in one or both chromosomes
What are the consequences
What action can be taken

Question 5

Research approach to find the clinical significance of a variation found in a gene

Answer 5

PCR part of the gene- design primers from reference genome
Sequence DNA- sanger sequencing
Computer clean up- remove poor quality sequence DNA
Similarity search against human reference genome eg BLAST
Use ClinVar to see if pathogenic
Clinical action eg counselling, treatment

Question 6

Types of BLAST

Answer 6

Blastn= DNA-DNA
Blastp= protein-protein
Blastx= DNA-protein
tblastn= protein-DNA
tblastx= DNA-DNA

Question 7

ClinVar pathogenicity scale

Answer 7

Benign, likely benign, likely pathogenic, pathogenic

Difficult variants= variant of uncertain significance (VUS) or conflicting evidence

Question 8

How does bioinformatics link into the clinical importance of variation example

Answer 8

PCR- designing primers from reference genome
Computer cleanup
Searching against human reference- BLAST