Mendelian Flashcards
Explain the approach to finding Mendelian gene via the protein
— Worked backwards from the amino acid sequence of a protein to the DNA sequence of the gene that encoded it.
- A DNA probe could then be synthesised to isolate the gene in genomic DNA
Explain the approach to finding Mendelian gene via chromosomal abnormality
- sometimes a patient has a de novo dominant or X-linked condition, together with a de novo chromosome deletion, translocation or inversion
- The CNV might affect the relevant gene, or one of the breakpoint of a chromosomal rearrangement might disrupt it.
Explain the approach to finding Mendelian gene via an animal model
- Most human genes have an exact counterpart in mice and other animals, and it is easier to identify genes in laboratory animals
- controlled breeding means genes can be mapped far mor easily and techniques like mutagenesis can be used.
Explain the approach to finding Mendelian gene via positional cloning
- Collect multi cases families -> perform linkage analysis
- Results in Candidate chromosomal location -> identify all genes in the candidate region
- Results in a shortlist of candidate genes -> sequence candidate genes in a set of unrelated cases
- Results identify causative gene
What are the basic linkage analysis
- Find a suitable family and obtained DNA from as many family members as possible - both affected and unaffected
- Type the family members for a large panel of DNA markers, looking for a marker that exactly tracks the unknown disease gene through the family
- If this happens to a degree that is too significant to be just coincidental, the unknown disease locus must lie close to the marker locus on the same chromosome.
First disease gene to be mapped via linkage
Huntington’s HTT gene
Explain the approach to finding Mendelian gene via autozygosity mapping
- used in consanguineous family
-The autosomal recessive disease in a pedigree is rare. It is therefore highly likely that three affected children all inherited both their disease alleles from one or other of their great grandparent in generation. - therefore we are looking for alleles that are identical
Finding disease genes, what is the benefits
- Connects genes to phenotype
- Connects phenotypes to a biological system
- Unravel locus heterogeneity
- Enables precise diagnosis, and counseling
- Allows for informed treatment regimes
- Research stimulus - taking knowledge from the bench to the bedsides
- Phenotype expansion - new technology allows addition of features to a classical phenotype
What is the research question of DDD-project
Does systematic phenotyping and detailed genomic analysis improve the prospect of identifying likely pathogenic mutations in African patients with Developmental delay.
Define genotype -phenotype correlation
Correlating the presence of a particular disease -causing variant , with the specific features seen in a persons with the genetic disorder.
Clinical utility of genotype phenotype correlation
- can provide provision of information on clinical features (type/severity), complications & prognosis
-Allows for access to novel therapies ( example; duchenne exon skipping therapies) - allows for better medical management (better treatment and surveillance
List genetic factors that may affect genotype to phenotype correlation
- allelic heterogeneity
- modifier genes
-epigenetic factors
-dynamic mutations - X-chromosome inactivation
- mosaicism
- heteroplasmy
- environmental factors
-penetrance; proportion of individuals with the mutation that exhibit clinical symptoms among all individuals with such mutation
-Variable expressivity ; shared genotype exhibit varying phenotypes
Using phenylketonuria as a example, what are non-genetic factors that coul affect genotype phenotype correlation
If phenylaline is consistent between people then this must be considered;
1. Brain related factors (differences in the function of the blood-brain-barrier)
2. Metabolic -related factors (differences in the absorption uptake and disposal )
3. Other protein & enzyme relationships
What percentage of the current GRCh8 reference genome is missing . And which parts of the chromosome make up the missing genome.
-8% is missing
Missing parts:
-centromeres
-segmental duplications
-tandem satellite arrays
-acrocentric p-arms
- missing regions can span several Mbps
Why is it a problem that there are parts of the genome missing
- missing variation may contain important functional regions
- centromeres involved in cell division
-rDNA encode for RNA of ribosomes
-Telomeres
Other than the missing 8% what are additional shortcomings of the current linear reference
- Reference bias- sequence diversity not accurately represented - 70% of reference based on European genome
- Observational bias - only examine places in the current reference sequence
- Representational bias - linear and haploid (single sequence ) - human have two copies of each chromosome
How have we improved on the missing 8 %
Recent major advances in long read sequencing technologies and algorithms has allowed for the resolution of the missing complex genomic regions with high quality data
T2T used what cell line and what are the characteristics of this cell line
- Hydra-tidi-form mole (CHM13) cell line
- Diploid 46, XX karyotype
- Ancestry - European with some Asian or American
Improvements made by the T2T genome (6)
- Millions of new variants identified (SNV and SV)
- 240Mbp and 189Mbp of non-syntenic and novel sequences added
- Eliminates several false variants and incorrect genotypes
- Improved mapping of reads
- Improved genotyping reduced false positives / negatives
- More comprehensive SV calling
Limitations of T2T
- It is based on a human cell lines that is haploid -CHM13
- Does not represent true human diversity
- May contain errors in some regions
4 is haploid and linear
What is a pangenome
Instead of a linear haploid reference sequence we generate a collection of high -quality phased genomes from a diverse set of individuals
Applications of pangenome
- Definite improvement in variants called in challenging regions and medically relevant loci.
- Improved structural variant calling based on polymorphic SVs represented in graph -based pangenome reference
- Recalled SVs in 1000 genomes using pangenome
- 104% gained in SVs called using pangenome
Define mosaicism
Mosaicism refers to the presence of two or more genetically different cell lines in one individual who has developed From a single fertilised egg.
Define chimerasim
The presence of two or more genetically different cell lines in one individual who has developed From a two or more fertilised eggs
Cause of aneuploidy mosaicism
- A nondisjunction event during an early cell division in a normal embryo leads to a fraction of the cell with a trisomy
- A Trisomic embryo undergoes nondisjunction and some boy the cells in th embryo revert to the normal chromosomal arrangement
Practical & Ethical consideration of performing NGS
- Permanence of a germline genetic results
- Familial and reproductive implications of genetic results
- Unexpected results
-secondary findings
-non paternity - Impact on insurance, employment
- Predictive testing and testing of minors informed consent
- Cost and accessibility
- Clinical utility and analytical validity
- Turnaround time
- Variant interpretation- VUS
10 data storage - Potential for inappropriate testing (based on profit, not science)
