Molecular Genetics Diagnosis

Question 1

How is molecular diagnostics different than molecular biology?

Answer 1

Diagnostics - use of molecular technology to identify inherited and non-inherited genetic variations for the purpose of diagnosis, counseling/management, and treatment

Question 2

What is a compound heterozygote?

Answer 2

Two different mutant alleles at the same locus

Question 3

What defines a polymorphism at a locus? What is an example? What are they good for?

Answer 3

Two or more changes seen at the same locus in a population, that is present in >1% of the population. I.e. eye color, hair color. Useful for genes (i.e. single nucleotide polymorphisms - SNPs).

Question 4

How are nucleotides numbered in a gene?

Answer 4

1 = the A of the ATG start codon, last number = last nucleotide of stop codon

Intron nucleotides are numbered for the counting away from the end of an exon (i.e. 362+1, +2, +3) or from the beginning of the next exon (363-1, -2, -3)

Question 5

What does c.83G>A mean?

Answer 5

c = coding reference sequence

The G which is normally present at position 83 of the reference sequence is now mutated to an A

Question 6

What does p.V312A mean?

Answer 6

p = protein reference squence

The valine which is normally present at position 312 has been replaced with an alanine

Question 7

What are the five categories of sequence variants? What is this for?

Answer 7

For describing the impactfulness of genetic mutation

1. Pathogenic
2. Likely pathogenic
3. Unknown signifiance
4. Likely benign
5. Benign

Question 8

What is an example of a large and small dosage change?

Answer 8

Large: Trisomy 21
Small: F508del = deletion of phenylalanine 508, as in cystic fibrosis

Question 9

What is a silent mutation and how can it be pathogenic?

Answer 9

A mutation of the wobble nucleotide which causes no change in amino acid, but affects synthesis rate due to requirement of a different tRNA

Question 10

What is the significance of a single nucleotide polymorphism?

Answer 10

Every 100 to 300 bases there will be an insignificant 1 nucleotide change which makes up 90% of human genetic variation. These can be used in population genetic studies.

Question 11

What can SNP arrays identify? How do they work?

Answer 11

Copy number, consanguinity and incest, uniparental disomy, loss of heterozygosity in tumor specimens, deletion / duplication syndromes

They work by probing for known polymorphisms in alleles

Question 12

What is uniparental disomy?

Answer 12

You are diploid for a chromosome, but both of those chromosomes came from the same parent (may or may not be homologous)

Question 13

What is targeted mutation analysis?

Answer 13

Testing for a specific genetic condition - i.e. CF due to F508del

Question 14

What is comprehensive gene sequencing and what are its limitations?

Answer 14

Sequence an entire gene, i.e. CF gene, looking for variants (known or unknown). It is difficult to use when there is more than one gene that can cause disease

Question 15

What do you use multiplex ligation dependent probe amplification (MLDPA) for?

Answer 15

Small dosage changes, and deletions and duplications which can be very large (Sanger sequencing will not pick this up)

Question 16

What are the three types of next generation sequencing?

Answer 16

1. Targeted gene panels - probe for all genes which cause a specific disease
2. Whole Exome sequencing - 85% of mutations occur in exon region, finds most of these via exons which make up 1% of genome
3. Whole genome sequencing, can find all mutations

Question 17

What factors should be considered when determining if you should carrier screen?

Answer 17

Condition severity, race/ethnicity, carrier frequency, and detection rate.

Also, expensiveness of test, whether it was of public interest, and whether counseling is available for that specific condition

Question 18

What type of risk remains if you screen negative for a carrier?

Answer 18

Residual risk -> risk that the test failed to detect the carrier mutation (i.e. the CF carrier panel for Caucasians only has a 90% detection rate)

Question 19

What technology does expanded carrier testing use, and what does a negative result mean?

Answer 19

Next generation screening -> use a panel to test for >100 disorders, with less concern about demographic information. It is casting a wide net.

Negative result = carrier chance reduced, but not zero as the screening tests cannot detect all mutations

Question 20

What is presymptomatic testing and what is the model disease?

Answer 20

Screening of individuals at risk for a disease during the time when they are asymptomatic. The model disease is Huntington’s and there are positive and negatives to doing this

Question 21

What is the molecular mechanism of Huntington’s disease, and what does a higher copy number mean?

Answer 21

CAG repeats in Huntington gene. More CAG repeats = earlier age of onset of Striatal degradation. Fully penetrant at >40 repeats

Question 22

What is predisposition (susceptibility) genetic testing?

Answer 22

Developing a risk estimate based on genotype, i.e. for inherited thrombophilia disorders. Not all carriers will develop symptoms, but it can increase your risk for developing symptoms some there is some ambiguity on who to test.