(Week 2) [T4-1] Precision Medicine Data

Question 1

What is Precision Medicine? And what is Bioinformatics?

Answer 1

• Precision medicine. Bringing genomics to healthcare. Requires management/analysis of clinical/molecular data.
• Bioinformatics. Application of computer science to solve molecular biology problems. For example, genome assembly, sequence alignment, and other applications.

Question 2

State the 3 sources of genetic variability.

Answer 2

• DNA replication (produce 2 identical replicas of DNA from one original DNA molecule). Potential source of large and small-scale mutations.
• Meiosis (1 set of chromosomes for each parent in a gamete). Random segregation of parental chromosomes. Crossover recombination.
• Retroviruses. Virus that uses RNA as its genomic material. Upon infection, a cell converts his RNA into DNA, which in turn is inserted into the DNA of the host cell.

Question 3

State the 3 types of genetic variability.

Answer 3

• Single nucleotide polymorphisms (SNPs). Genomic variant at a single base position in the DNA.
• Insertions/deletions.
• CNVs.

Question 4

Explain what is the adaptive immune system.

Answer 4

Relies on the capacity of immune cells to distinguish between the body’s own cells and unwanted invaders.

Lymphocytes are a type of white blood cells.
T-cells protect us from infection.
B-cells create antibodies (protein).

Question 5

What is the Gene Ontology (GO)?

Answer 5

The GO (Gene Ontology) is a controlled vocabulary divided into 3 orthogonal ontologies describing protein function at different levels (molecular function, biological process, cellular component).

Question 6

Explain the relation (sequence, structure, function) of proteins. Is structure tied with function?

Answer 6

Protein sequence can be used to predict structure and function. Can only be done experimentally through destructive methods (for example, with mass spectrometry).

Protein structure is closely tied with function (there are exceptions, but similar structures tend to perform similar functions). It is challenging and expensive to do experimentally.

Question 7

DNA sequence directly determines protein sequence. What are the 3 generations of sequencing?

Answer 7

• 1st generation sequencing
  4 separate reactions each containing DNA polymerase, primers and all four dNTPs, but only one ddNTP (to stop the systenshis).
  Use gel electrophoresis to separate oligonucleotides by size and determine sequence.
• 2nd generation sequencing
  Illumina sequencing. High-throughput, low cost, can detect DNA epigenetics. Although, has short reads.
• 3rd generation sequencing
  Single-molecule real-time (SMRT). Long reads, and can detect DNA epigenetics. Although, worst accuracy and higher cost than Illumina, now it’s better in both factors.

Question 8

What is PCR?

Answer 8

Polymerase chain reaction (PCR) is a technique to make many copies of a specific DNA region in vitro (in a test tube). The applications are the following.
- Amplify RNA to determine if a gene is being expressed.
- DNA profiling, identification of a pathogenic species (COVID-19 tests), or identification of genetic disorders or cancer.

Question 9

Why is it useful to use DNA microarrays?

Answer 9

DNA microarrays are used to determine whether the DNA from a particular individual contains a mutation in genes. Also useful for gene expression analysis.

Question 10

State 2 advantages of precision medicine.

Answer 10

• Better accuracy in defining a diagnosis.
• Treatment tailored for the individual and not for a population.