Genetics Flashcards
Acrocentric chromosomes have STALKS and SATELLITES
Stalks: ribosomal RNA, nucleolar organizing region, NORs
Satellites: repetitive, non-encoding, satellite DNA
metacentric, submetacentric, acrocentric
what is position of centromere?
medial, distal, terminal!
what is the telomere sequence?
TTAGGG
Phases of prophase 1 in meiosis?
Lazy zebras perform dastardly deeds
Leptotene
Zygotene
Pachtytene
Diplotene
Diakinesis
Leptotene
Thin DNA threads in nucleus, start looking for homologous chromosomes
Zygotene
Chromosomes are pulled more tightly together
Begin to form synaptonemal complex, important for recombination
DSBs form, recombination/cross-over begin
telomere bouquet - see telomeres anchored towards outside of cell
Pachtytene
Most condensed chromosomes
Synaptonemal complexes= close together
Cross over has occurred, see bivalents or tetrads
GENETIC RECOMBINATION OCCURS AT THIS STEP
Diplotene
Loosening up of synamptonemal complex,
stay adhered at chiasma/chiasmata = points where crossover has occured
Diakineses
Nuclear envelope starts to disintegrate
= proceed to regular steps
Why is meiosis much longer?
Can be months to years
Time for crossover to occur= genetic diversity
Meiosis 1 is the ______ division
Reductional
Meiosis 2 is the ______ division
Equational
What is constitutional mosaicism?
at least 2 cell lines with different chromosomal complement in a fetoplacental unit derived from a single zygote
amount of mosaicism - % of cells with each karyotype depends and the tissue distribution is dependent on timing of event and cell selection
What are the three trisomies associated with survival and the name of their syndrome?
Trisomy 21 (Down’s syndrome)
Trisomy 18 (Edward Syndrome)
Trisomy 13 (Patau Syndrome)
*survival with 13 and 18 is not long
Etiological factor for DS
Advanced maternal age is the only etiological factor for which a link with aneuploidy is unequivocally recognized.
95% of a DS cases have a free 21.
4% of DS cases have…
A robertsonian translocation.
an additional 21 is translocated to chromosome 14, and two normal 21s.
(Parental karyotype shows father is a balanced carrier of the robertsonian translocation – have an increased risk of having conceptus with DS)
3 types of balanced structural rearrangements
reciprocal translocation
inversion
robertsonian translocation
normal amount of DNA = likely normal phenotype. carrier is at risk of having unbalanced conception. 4% of couples who have experienced 3 or more pregnancy losses have one member who is a carrier of a translocation or an inversion.
CML
Chronic myelogenous leukemia
Translocation between chromosome 9 and 22.
Fusion gene between 5’ regulatory region of BCR of 22 and ABL1 (tyrosine kinase) of 9
patients receive a targeted therapy: TK inhibitor (Imatinib/Gleevec)
what is PKU
Autosomal Recessive
Phenylketonuria = buildup of phenylalanine and lack of tyrosine as a result of deficiencies in the PAH (phenylalanine hydroxylase gene), which is normally responsible for transforming phe into tyrosine
Symptoms of PKU
Treatment?
Phenylalanine is neurotoxic
Intellectual disabilities
Fair Skin
Seizures
Rash
Symptoms do not start immediately at birth, a buildup of Phe is required.
Don’t eat Phe!
Allelic heterogeneity
More than 1 mutation in the same gene that can cause the same phenotype
If someone has this, we call them a compound heterozygote
Same mutation: homozygote, likely if there is founder effect or consanguinity (increasing frequency of same variant)
Locus/Genetic Heterogeneity
One disorder/phenotype is caused by changes in more than 1 gene
Marfan Syndrome, inheritance
Autosomal Dominant
Allelic Heterogeneity (Mutations in FBN1 gene)
Pleiotropy (defects in one gene causing multiple clinical manifestations)
Full penetrance
Variable expressivity
25% of mutations occur de novo
Clinical Features of Marfan
- Tall, thin, arm span that exceeds height,
- lens dislocation,
- dilation of aorta,
- pectus excavated/carinatum,
- arachnodactyly
Duchenne muscular dystrophy, inheritance?
Mutations in DMD gene, one of largest genes
Lethal, boys will not live to reproductive age
1/3 of mutations occur de novo
X linked recessive
MELAS
mitochondrial encephalopathy, lactic acidosis and stroke-like episodes
mitochondrial gene encoding tRNALeu are affected
Prader-Willi
Angelman syndrome
Genomic imprinting on chromosome 15
Prader: father’s copy is normally expressed
Angelman: mother’s copy is normally expressed
Cases: Deletion of relevant parent DNA, UPD of other parent, imprinting defects, UBE3A mutation for Angelman only
3 epigenetic mechanisms
Determine which parts of genome should be available for transcription and which parts should be compact and inaccessible.
- DNA methylation at CPG nucleotides
- covalent modifications of histone proteins
- regulation by noncoding RNAs
Complex disorders
Threshold for clinical expression
Polygenic and environmental/lifestyle factors
PRS - polygenic risk score
Incomplete Penetrance and Variable Expressivity
Laboratory Methods:
SNVs and Small indels
- genotyping methods (for known variants)
- Sanger sequencing
- Next-generation sequencing (NGS)
Laboratory methods
Structural variants
1.Karyotyping > 5 Mb
- Chromosomal microarray (5-10kb)
- MLPA (intragenic copy number variant) - Multiplex ligation dependent probe amplification
- NGS
Two ways to filter found variants
- genotype driven: find a variant, determine its frequency, call it clinically suspicious (helpful when identifying/considering a new gene)
- phenotype driven - only consider genes associated to primary phenotype
DNA sequencing in Clinical Diagnostics
- Preconception
- Prenatal
- Newborn screening and pediatric care (hearing loss, Cystic fibrosis)
- Adult medicine (cancer predisposition, cardiac evaluation)
- cancer- somatic testing
- Elderly health (Alzheimer testing)
When should you do a single-gene test?
- Minimal locus heterogeneity (CFTR for CF)
- Distinctive clinical findings clearly pointing to a specific gene (PAH for PKU)
- Limitations of NGS sequencing tech to detect trinucleotide repeat disorders and disorders with epigenetic abnormalities (Prader-Willi, Angelman, Huntington)
When should you do a gene panel?
- Heterogeneity
- Disorders with overlapping phenotype-differential diagnosis
- Disorders share one manifestation but may have completely different overall presentation
- diseases associated with genes from a common pathway or structure
When should you do ES/GS?
- Extreme heterogeneity and de novo mutations are the major mutations
- Two or more likely unrelated phenotypes in a patient
- No key phenotypic feature is present at the time when the test is ordered
- Phenotype is indistinct, and the real underlying cause is not easy to identify
Challenges remaining in Genetic testing
- Infrastructure and expertise
- Technological & Knowledge limitations
- Ethical legal and social implications (accidental findings, test reimbursement, inequality and genetic discrimination)
