Principles And Analysis Of Genomics

Question 1

How have DNA sequencing technologies developed?

Answer 1

Sanger sequencing: chain termination method
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Autoradiograms
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Fluorescently labelled chain terminators (one automated reaction)
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Next Generation Sequencing: can look at the whole genome, exomes, gene panels and RNA. Platforms include 2nd (next) gen machines (the AB SOLiD, Illumina HiSeq), democratisation (LifeTech Ion Torrent, Illumina MiSeq) and single molecule sequencing.

Question 2

What is the definition of a gene?

Answer 2

A locatable region of genomic sequence corresponding to a unit of inheritance which is associated which regulatory regions, transcribed regions, or other functional sequence regions.

Question 3

What are the features of the Central Dogma?

Answer 3

Replication

Transcription

Translation

Question 4

What is the definition of the genome?

Answer 4

The entire DNA contents of the cell including all the genes and all the intergenic regions -
TA Brown.

Question 5

How were genetic markers developed?

Answer 5

Initial stages of the HGP:

• recognisable components of the membrane
• restriction fragment length polymorphisms (RFLPs)
• simple sequence length polymorphisms (SSLPs)
  - minisatallites (variable number tandem repeats)
  - up to 10 base pairs in length, found near chromosome ends
  - TTAGGG
  - microsatalites (simple tandem repeats)
  - GAGAGA
  - GAGAGAGAGA
  - SNPs

Question 6

What is the 1000 genomes project?

Answer 6

Seeks to create an integrated map of genetic variation from 1092 human genomes.

This has been extended to:

• the UK 10k genome project:
  - rare genetic variants in health and disease
  - 4000 whole genome sequences from TwinsUK and ALSPAC
  - 6000 exome samples of phenotypes for specific conditions
• the 100k genome project: Genomics England:
  - cancer
  - rare diseases
  - infectious diseases

Question 6

What is the ENCODE project?

Answer 6

The encyclopaedia of DNA elements is a public research project launched by the US National Human Genome Research Institute in September 2003.

Because having the sequence is only the first stage;

• gene regulation
• gene variation
• gene:gene and gene:protein interactions

Question 6

What are the stages of genomic analysis?

Answer 6

Primary:
- obtaining the raw data

Secondary:
- turning the raw data into the genome sequence

Tertiary
- biological interpretation

Question 7

How does human variation affect analysis?

Answer 7

There is a lot of it!

It can be difficult to distinguish normal variation from pathogenic variation

There are lots of different types:

• structural (large scale)
• small scale
• gene expression
• epigenetic

Question 8

What is the potential of genomics?

Answer 8

To link phenotypic and clinical data for

• personalised medicine
• screening
• risk management
• molecular understanding of disease
• therapeutic targets

IT IS ESSENTIAL TO LINK GENOTYPE WITH PHENOTYPE

Question 9

What are the clinical challenges?

Answer 9

• evaluating the cost:benefit (sample origin and quality)
• resolution and reproducibility of sequencing
• data analysis and reporting standards
• Storage
• ethics
• biological interpretation

Plus further technical challenges:

• volume
• processing time
• Storage
• network traffic
• algorithm development