Molecular Flashcards
4 benifits of MLPA for Duchenne Muscular Dystrophy testing
- Specific allele detection
- Copy number detection (deletion/duplication)
- Methylation status
- Carrier screening
Percentage risk for gonadal mosaicism in Duchenne Muscular Dystrophy
Risk of gonadal mosaism is 15%
Risk of germline mosaisism and recurrance risk in after a woman who has an afected child, is not found to have a DMD variant
Risk of gonadal mosaism X chance of transmitting
15% X 1/2 = 7% Recurrance risk
The majority of cases of achondroplasia are caused by this variant
- FGFR3*
p. Gly380Arg
99% G>A transistion
1% G>C transversion
80% de novo (paternal)
Juvanille repeats in Huntington Disease >60 repeats: an increase of > 7 repeats in the next generation is usually inherited from which parent
Paternal
WHat is the benifit of using linked markers to determine an at risk grandchild for Huntington’s disease
Linked markers look at “at risk” alleles and this does not change the parental risk with an at risk grandchild.
What is the smallest number of repeats that have been documented to expand in a Fragile X carrier?
56 CGG repeats
What number of repeats in a Fragile X carrier is amost 100% likly to expand in the next generation
100 CGG repeats
Modality used to identify Fragile X carriers and those affected
Triple primed PCR with methylation (extra step)
What is the signifigance of the poly T tract in CF mutation carriers
The poly T tract in intron 8 results in skipping of exon 9
resulting in a dysfuctional CFTR transcript or no transcript
the 5T allele results in 90% of transcripts without exon 9
p.Phe508del is a LD with the 9T Allele
What are the limitation of Sanger Sequencing
Can only analyze one sample at a time
cannot detect large deletions and duplications
not good for large repeat expansions
Allelic dropout
missed low level mosaicism
Most individuals who are RhD negative have a complete ______ of the gene
Deletion
Why is the mother sample needed for genetic testing for hemolytic Disease of the newborn
No maternal sample–> hard to interprate
could represent a true Rh positive fetus
could also represent Rh neg fetus with intact D gene or at least some portion of the D gene
Therefore the maternal sample is needed
Chromosomal microarrays are limited and cannot detect
Balanced translocations
Inversions
Polyploidy
UPD with fully parental heterodisomy
What is the benifits of using SNP genotyping with CGH array
Can be used to detect
- Consangunity
- Uniparental Disomy
- Long continuous stretches of homozygosity (>5Mb)
What are the 4 possible genetypes detected by SNP array in a sample that shows a duplication?
- BBBB
- BBBA
- AAAB
- AAAA
What is the Log2Ratio found for a duplication on aCGH
+0.6
ACMG recommends array based technology as the first tier for?
- Developmental delay and/or cognitive impairment DD/DI)
- Autism Spectrum Disorder (ASD/PDD)
- Multiple congenital anomalies
- Epilepsy
What are advantages of using microarray vs karyotype to analyze products of conception
CMA adds 10% sensitivity for miscariages
Finds pathogenic microdeletions and duplications
No need for culture–> faster TAT
In general, microscopically visable CNVs > ____ are reportable
>3-5Mb
Uncle-neice union
coefficient of consanguinity ((F)
1/4
Uncle-neice union coefficient of inbreeding
1/8
First cousins
coefficient of consanguinity (F)
1/8
First cousins coeeficient of inbreeding
1/16
First cousins once removed coefficient of consanguinity (F)
1/16
First cousins once removed
coefficient of inbreeding
1/32
What type of responders to codeine may get the drug to fast leading to respiratory distress
Ultrarapid-responders
CYP2D6
Codeine–>active form of morphine
N.Africans, Ethiopians, Saudi Arabians (16-28%)
CYPC19 poor responders to this medication cannot prevent clots, may need to take another drug
Clopidogrel (Plavix)
Poor metabolizers to Warfarin with these two mutations may be at risk for bleeding
- CYP2C9*
- VKORC1*
poor metabolizer- need to reduce dose
ultrarapid metabolizer- need to increase dose
Specific amino acid substitions in these genes may interfere with binding of this drug to kinase
used to treat CML and GIST (KIT mutations)
Imatinib Mesylate
CYP3A4 and CYP3A5
T3151I
HLA-B*5701 variants and Abacavir may put patient at increase risk for life threatening condition
Steven-Johnson Syndrome
The FDA recommends TPMT genotyping or phenotyping before starting this medications
Azathioprine
This allows patients who are at increased risk for toxicity to be identified and for the starting dose of azathioprine to be reduced, or for an alternative therapy to be used
Azathioprine is a prodrug that must first be activated to form thioguanine nucleotides (TGNs), the major active metabolites. Thiopurine S-methyltransferase (TPMT) inactivates azathioprine, leaving less parent drug available to form TGNs.
An adverse effect of azathioprine therapy is bone marrow suppression, which can occur in any patient, is dose-dependent, and may be reversed by reducing the dose of azathioprine
About what percentage of carriers of DMD have clinically signifigant cardiomyopathy
about 8%
What are the various ways a female with features of DMD can arise? (5)
- Skewed X- inactivation
- Turner syndrome 45, X
- Balanced X-autosome translocation (non-translated X is inactivated and DMD variant is on translocated active X)
- Uniparental disomy X
- Compound heterozygosity
What is the residual risk of a mother with negative genetic analysis for DMD having second son with DMD?
Residual Risk of 7%
Germline mosaisim up to 10-15% in mothers with negative genetic analysis
Acoording to the DMD practice guildines what is the first test that should be ordered if one is considering a diagnosis of DMD?
CPK
If not elevated DMD is not likly and should consider an alternative diagnosis
Order of evaluation
CPK–>DMD CNV analysis–>DMD sequence–>Muscle biopsy
what are the limitations of CNV by MLPA for DMD?
Allelic dropout
False positives: single exon deletion due to SNV under probe–>should confirm by sequencing
Limited by the amount of probes per reaxn.
Eteplirsen induces skipping of what exon for DMD tx.
exon 51
These repeats within the CGG repeats of FMRP result in less liklihood of CGG repeating in the next generation
AGG repeats
