BGM1004/L16 Genetic Analysis of Human Disease

Question 1

What percentage of human DNA is the same across the whole species?

Answer 1

> 99%

Question 2

Why do chromosomes become ‘mixed’?

Answer 2

Crossover during meiosis

Question 3

What are sequence variations?

Answer 3

Sequences that co-segregate with variants through generations
E.g., SNO, RFLPs, microsatellites

Question 4

What are variable number tandem repeats?

Answer 4

Repeated sequences organised at sequential (tandem) repeats

Question 5

Why do variable number tandem repeats vary between individuals?

Answer 5

Unequal corssover, replication errors etc.

Question 6

How long are simple sequence repeats and short tandem repeats?

Answer 6

3-7 nucleotides

Question 7

How many times are SSRs and STRs repeated?

Answer 7

<100x

Question 8

How are SSRs and STRs distributed in the genome?

Answer 8

Every few 1000 base pairs

Question 9

What are minisatellites?

Answer 9

GC-rich variant repeats of 10-100 bases

Question 10

Where do 90% of minisatellites occur in humans?

Answer 10

Sub-telomeric region of chromosomes

Question 11

What method can be used to detect numbers of repeats at various loci?

Answer 11

PCR

Question 12

What are single nucleotide polymorphisms?

Answer 12

Single base differences (SNPs)

Question 13

How often do SNPs occur?

Answer 13

Every -300 nucleotides

Question 14

What are changes to base sequence that change the size of the restriction fragments on a Southern Blot?

Answer 14

RFLPs

Question 15

What are CpG islands?

Answer 15

Regions of DNA highly enriched in CpG sites

Question 16

What region are CpG islands frequently associated with?

Answer 16

5’ region (promoters) of genes

Question 17

How can CpG islands be identified?

Answer 17

When sequence is not known since sites for some restriction enzymes cluster in CpG-rich regions

Question 18

Approximately what percentage of genes contain CpG islands?

Answer 18

70%

Question 19

How were the causative mutations of Cystic Fibrosis found?

Answer 19

Linkage and RFLP analyses
Positional cloning

Question 20

What kind of protein is encoded by the Cystic Fibrosis gene?

Answer 20

Chloride transporter

Question 21

What kind of mutation leads to Cystic Fibrosis?

Answer 21

3 nucleotide deletion of Phe 508

Question 22

What is the term describing a set of linked polymorphic markers?

Answer 22

Haplotype

Question 23

What are SNP maps useful for? (2)

Answer 23

Locating genes that might be associated with particular phenotypes
Diagnosing potential (future) problems/phenotypes

Question 24

Describe BeadChips (Illumina). (5 steps)

Answer 24

PCR amplification of whole genome
Fragment and hybridise to primers bound to beads on a chip
Each primer ends 1 base before the position of a known SNP
Extend the primer by 1 nucleotide
Read in scanner to identify labelled bases added

Question 25

What is the GWAS approach?

Answer 25

Genome-Wide Association Study

Question 26

How is a GWAS conducted? (4)

Answer 26

Collect large number of case & control samples
Put through assays for SNPs spread across genome
Analyse data for significant association of particular variants with cases
Use other SNPs in region of interest to confirm association

Question 27

How can information from GWAS be used? (2)

Answer 27

Informs patient care/screening
Identify genes/pathways influencing particular phenotypes
Informs about human history

Question 28

Where is the great majority of human DNA sequencing focused?

Answer 28

High income countries