Molecular Genetics Diagnosis Flashcards
How is molecular diagnostics different than molecular biology?
Diagnostics - use of molecular technology to identify inherited and non-inherited genetic variations for the purpose of diagnosis, counseling/management, and treatment
What is a compound heterozygote?
Two different mutant alleles at the same locus
What defines a polymorphism at a locus? What is an example? What are they good for?
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).
How are nucleotides numbered in a gene?
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)
What does c.83G>A mean?
c = coding reference sequence
The G which is normally present at position 83 of the reference sequence is now mutated to an A
What does p.V312A mean?
p = protein reference squence
The valine which is normally present at position 312 has been replaced with an alanine
What are the five categories of sequence variants? What is this for?
For describing the impactfulness of genetic mutation
- Pathogenic
- Likely pathogenic
- Unknown signifiance
- Likely benign
- Benign
What is an example of a large and small dosage change?
Large: Trisomy 21
Small: F508del = deletion of phenylalanine 508, as in cystic fibrosis
What is a silent mutation and how can it be pathogenic?
A mutation of the wobble nucleotide which causes no change in amino acid, but affects synthesis rate due to requirement of a different tRNA
What is the significance of a single nucleotide polymorphism?
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.
What can SNP arrays identify? How do they work?
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
What is uniparental disomy?
You are diploid for a chromosome, but both of those chromosomes came from the same parent (may or may not be homologous)
What is targeted mutation analysis?
Testing for a specific genetic condition - i.e. CF due to F508del
What is comprehensive gene sequencing and what are its limitations?
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
What do you use multiplex ligation dependent probe amplification (MLDPA) for?
Small dosage changes, and deletions and duplications which can be very large (Sanger sequencing will not pick this up)
What are the three types of next generation sequencing?
- Targeted gene panels - probe for all genes which cause a specific disease
- Whole Exome sequencing - 85% of mutations occur in exon region, finds most of these via exons which make up 1% of genome
- Whole genome sequencing, can find all mutations
What factors should be considered when determining if you should carrier screen?
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
What type of risk remains if you screen negative for a carrier?
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)
What technology does expanded carrier testing use, and what does a negative result mean?
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
What is presymptomatic testing and what is the model disease?
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
What is the molecular mechanism of Huntington’s disease, and what does a higher copy number mean?
CAG repeats in Huntington gene. More CAG repeats = earlier age of onset of Striatal degradation. Fully penetrant at >40 repeats
What is predisposition (susceptibility) genetic testing?
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.
