Genetics 2 Flashcards
p
Short arm.
Up.
q
Long arm.
Down.
aneuploidies compatible with life
Trisomy 13, 18, 21.
+X
+Y
Loss of a sex chromosome
All other trisomies associated with infertility or pregnancy loss.
prenatal testing
Serum screen.
Ultrasound (look at nuchal translucency).
Amniocentesis (cells take 7 days to grow for analysis).
FISH probe-mix: looks for frequent trisomies in cells that aren’t growing; helps with mother’s anxiety for waiting for 7 days for cells to grow.
trisomy 18
Edwards Syndrome.
1 in 6,000.
Small size, small head circumference, low weight.
Overlapping fingers.
Rockerbottom feet.
Congenital heart defects.
Very poor prognosis (only 5% live past 1 year).
trisomy 21
Down Syndrome. 1 in 700. Flat facial profile, upslanted palpebral fissures. Anomalous auricles. Nuchal skin fold. Single palmar crease, clinodactyly. Hypotonia. Hyperflexibility of joints. Life expectancy: 60 years.
Associated findings: intellectual disability, congenital heart disease, gastrointestinal abnormalities, atlantoaxial instability, strabismus, thyroid abnormalities, leukemia.
trisomy 13
Patau Syndrome.
1 in 10,000.
Scalp defects, microcephaly, micropthalmia, holoprosencephaly, cleft lip/palate.
CHD.
Polydactyly.
Renal anomalies.
Very poor prognosis (only 5% survive 6 months).
Turner Syndrome
1 in 2,000 females.
Too few X genes.
Lymphedema.
Bicuspid aortic valve, coarctation of aorta.
Short stature.
Gonadal regression.
Low posterior hairline, webbed neck, widely spaced hypoplastic nipples.
Horseshoe kidney.
Cubitus valgus of elbow.
Karyotypes: 45, X (most common, 50%)/ 46,X, abnormal X/ mosaicism
Klinefelter Syndrome
1 in 500 males. Extra X in males. Tall stature, long limbs. Learning differences. Gynecomastia (breast development). Small testicles. Infertility due to hypogonadism with oligospermia or azoospermia. Karyotype: 47,XXY
47, XXX
1 in 1,000 females.
Speech delay, lower IQ than siblings.
Increased risk for infertility.
Most offspring are chromosomally normal.
X-inactivation
Compensates for dosage difference between males and females.
Steps: counting, choice, cis inactivation.
Counting - assesses how many X chromosomes are present; must be at least 1 active X chromosome.
Choice - random if both are normal; abnormal X inactivated if has XIST; Normal X is inactivated if there’s a translocation between X and an autosome; abnormal X inactivated if an unbalanced translocation.
Cis activation - XIST locus in Xq13 is responsible.
meiosis I nondisjunction
gametes: heterodisomy (ABC)
Zygote: trisomy
meiosis II nondisjunction
gametes: isodisomy (AAC, BBC).
Zygotes: trisomy
uniparental disomy
2 chromosomes from 1 parent, 0 from other.
47, XYY
1 in 1,000 males.
Lower IQ than siblings.
Increased risk of behavior problems.
Most offspring are chromosomally normal.
microdeletion syndromes
Submicroscopic deletions of more than 1 gene.
Bigger deletion = more features.
Need FISH to diagnose.
Genes are physically contiguous on chromosomes.
Usually sporadic, sometimes dominant.
DiGeorge Syndrome
del(22)(q11.2)
Narrow face, narrow eye openings, flat cheeks, prominent nasal root.
Williams Syndrome
Deletion of elastin gene on chromosome 7.
Broad forehead, short palpebral fissures, supravulvar aortic stenosis.
Duplication 7q
Frontal bossing, abnormal ears, hydronephrosis.
Duplication with multiple deletions.
translocations
Exchange of material between 2 or more chromosomes.
Can be balanced/reciprocal or unbalanced.
Balanced translocations can survive but are often infertile (high chance offspring will not be balanced).
robertsonian translocation
Occur between acrocentric chromosomes (13, 14, 15, 21, 22).
Results in loss of non-critical genes in short arms of chromosomes.
Count is reduced to 45.
ex: 45, XY, der(15;22)(q10;q10)
pericentric inversion
Around the centromere.
p and q breakpoints.
paracentric inversion
Outside the centromere.
acquired changes
Not present at birth.
Only occur in the organ affected.
Trisomy origin: mitosis.
constitutional changes
Trisomy: 13, 18, 21.
Trisomy origin: meiosis.
Monosomy: X
Balanced translocation: no impact on phenotype.
Unbalanced translocation: abnormal phenotype.
Philadelphia translocation
90-95% of CML cases.
Balanced translocation: t(9;22) (q34,q11.2).
First cancer abnormality described.
cancer and translocations
Breakpoints occur at oncogenes.
Abnormal protein is produced and cannot be regulated.
Overproduction of a normal protein.
cancer and deletions
Result in loss of genes, typically tumor suppressors.
Loss of 1 gene and possible inactivation of the other removes cell cycle control.
types of deletions
Single base substitutions.
Deletions (single base & microdeletions).
Duplications (single base & microduplications).
Frameshift (insertion, deletion, duplication).
Regulatory (promoters, enhancers, UTR).
Tandem repeat expansions.
conservative missense mutations
new amino acid has the same properties.
nonconservative missense mutation
new amino acid has new properties
Charcot-Marie-Tooth
Duplication on chromosome 17.
Clawed hand, arched feet.
promoter mutations
Affect binding of RNAP to promoter.
Results in reduced production of mRNA and decreased protein production.
dyskeratosis
Promoter mutation.
Causes premature ageing and bone marrow disease.
null mutation
Loss of function mutation.
Classic autosomal recessive inheritance.
50% function is sufficient.
Carriers are healthy.
Ex: PKU
haploinsufficiency
Loss of function mutation. Autosomal dominant. Half of normal product is insufficient. Heterozygous = mild disease. Homozygous = severe disease. AKA incomplete dominance.
Ex: familial hypercholesterolemia
dominant negative
Loss of function mutation.
Autosomal dominant.
Mutant protein interferes with function of normal protein.
Ex: Marfan’s syndrome
gain of function
Usually due to a very particular change in gene.
Only 1 mutant gene necessary.
Autosomal dominant.
Ex: Achondroplasia
benefits of DNA based testing
Confirm clinical diagnosis.
Presymptomatic diagnosis.
Pre-implantation and prenatal diagnosis.
Genotype-phenotype correlation.
challenges of DNA based testing
Genetic heterogeneity. Allelic disorders. Variable expression. Non-paternity. Concerns regarding genetic discrimination. Mitochondria.
DNA sources
Blood (WBC). Saliva, buccal cells. Skin, hair, sperm. Amniocytes. Chorionic villus.
karyotype analysis
Visible chromosome abnormalities (>3 MB).
Deletions, duplications, translocations, inversions, insertions.
FISH
Fluorescent In-Situ Hybridization.
Known submicroscopic deletion/duplication syndromes.
Subtelomeric deletions/duplications.
Methylation Testing
Bisulfite treatment + MSP.
Shows methylation.
Determine if maternal or paternal.
Allele Specific Oligonucleotide Testing
Look for a panel of common mutations.
Short Tandem Repeat Polymorphisms (STRPs)
Polymorphic markers for indirect DNA testing.
Crime scenes, paternity testing, twin testing.
Multiple Ligation-Dependent Probe Amplification (MLPA)
Multiple exons at once.
Detect large deletions (many exons), small deletions (1 exon), single base change.
haplotype
SNPs observed in groups.
Inherited together from 1 parent.
Can be used for gene mapping.
comparative genomic hybridization (CGH) array
Compares patient DNA with control DNA.
Duplication: more patient DNA than control (red).
Deletion: more control DNA than patient DNA (green).
SNP array
Asks which SNPs are present.
If a duplication/deletion, it shows how many copies.
Provides more info than a CGH array.
Reports amount of DNA (deletions more easily recognized).
Can identify loss of heterozygosity.
importance of identifying loss of heterozygosity
(SNP array identifies loss of heterozygosity). For UDP (heterodisomy, not isodisomy). Imprinting. Consanguinity. AR conditions.
Expression array
Measures changes in gene regulation via gene expression level.
Used for tumor characterization.
Can use it to guide treatment based on response of cells.
use of arrays
When no clear, clinical picture.
Developmental delay, dysmorphic features.
Characterization of tumors.
Identification of genes (GWAS).
limitations of arrays
Might not detect low-level mosaicism.
Only look at quantity, not location.
Cannot detect translocations or inversions (but can be used to follow up an inversion: is there a small deletion as a result?)
Sanger sequencing
Slow. Expensive. Highly accurate. Gold standard for validation of NGS. Used in human genome project.
NGS (next generation sequencing)
Faster.
Cheaper.
Less accurate.
clinical uses of NGS
WGS (whole genome): research, now moving to clinical use.
WES (whole exome): loos for disease-causing mutations.
Panels: sequencing for a list of genes associated with a phenotype.
possible NGS results
Benign: does not affect gene function; not included in report.
VUS (variant of uncertain significance): not enough evidence for benign or pathogenic decision.
Pathogenic: disrupts gene function; potential to cause health effects.
secondary findings
Not what you were looking for, but has health implications.
Pathogenic mutations in medically actionable genes.
Have established interventions to reduce morbidity.
Limitations of NGS
Cannot detect trinucleotide repeat expansions, methylation/imprinting, structural rearrangements, or copy number variations.
Not a “one size fits all” test.
epigenetics
Modification of gene expression without alteration of DNA sequence.
Change over time.
Reversible.
3 types of epigenetic changes
1) Methylation: on DNA; reduces expression.
2) nucleosome positioning: move nucleosomes to expose an area for translation.
3) histone modifications: alteration of chromatin structure.
karyotypes can detect:
Large deletions.
2-3 mbs
FISH can detect:
120-400 kb
Arrays can detect:
500 bp
NGS can detect:
1 bp
% of cancers that are hereditary
5-10%
MOST are NOT hereditary.
Knudsen’s two-hit hypothesis
Sporadic cancer: requires 2 acquired mutations before tumor forms.
Have 2 genes, and loss of function is AR.
Hereditary cancer: only need 1 acquired mutation before tumor forms.
Already have 1 bad gene.
oncogenes
Promote excessive cell growth.
Mutated form of a gene involved in normal cell growth.
red flags for hereditary cancers
Early onset tumors (<50 years). Multiple/bilateral tumors. Rare/unusual tumors. Combinations of certain cancers. Multiple generations affected (AD inheritance). Lack of known contributing factor.
HBOC (hereditary breast and ovarian cancer)
Due to mutated BRCA1/2 gene.
Females: increased risk of breast/ovarian cancers, increased risk of having a 2nd breast tumor.
Males: increased risk of breast/prostate cancers.
colorectal tumors - genes affected
(in order)
APC
KRAS (increases size/dysplasia)
p53 (carcinomas)
Lynch Syndrome
Caused by mismatch repair genes.
Increased risk for colon cancer (also stomach, endometrial, uterine, ovary).
Prevention: increase screening, do surgical procedures.
risks/concerns of testing for cancers
Psychological stress.
Ethical concerns.
Life insurance discrimination.
Expensive.
objectives of prenatal diagnosis
Provide info to prospective parents regarding fetal diagnosis.
Counsel and support parents in personal reproductive decisions.
Offer fetal therapy / prevent postnatal medical implants.
screening tests (general, names)
PROBABILITY, not definitive.
Provides an individual risk assessment.
Ex: ultrasound, maternal serum marker screening, NIPT.
diagnostic tests (general, names)
Definitive.
Procedure-related risk of pregnancy loss.
Ex: CVS, amniocentesis, cordocentesis, PUBS
nuchal translucency ultrasound
11-13 weeks.
Measures fluid under skin behind fetal neck.
Increased nuchal translucency associated with increased risk for aneuploidies, heart defects.
Many false positives.
Fetal Anatomic Survey
18+ weeks.
Detects structural fetal anomalies, “soft marker” for aneuploidies.
Level II Ultrasound
After 18 weeks.
Detects open neural tube defects, congenital heart defects, trisomy 21, trisomy 18.
Maternal Serum Marker Screening
11-13 weeks (but can’t look at neural tube defects yet).
15-21 weeks (CAN look at neural tube defects).
Offered to all pregnant women.
Evaluates chances for trisomy 21/18, open neural tube defects.
Non-Invasive Prenatal Testing (NIPT)
10 weeks to delivery.
Offered to women at increased risk of aneuploidy.
Evaluates chances for trisomies 13/18/21, monosomy X.
Higher detection rate, lower false positive rate.
Chorionic Villus Sampling (CVS)
10-13 weeks.
Can NOT test for neural tube defects.
Testing includes FISH, karyotype analysis, microarray, targeted testing for single gene disorders.
1/300 to 1/500 chance of miscarriage.
Amniocentesis
15+ weeks.
Can detect neural tube defects.
Testing includes FISH, karyotype analysis, microarray, targeted testing for single gene disorders, neural tube defects.
1/300 to 1/500 chance of miscarriage.
Pre-implantation Genetic Testing
Embryos in IVF can be screened for aneuploidy or single gene disorders.
PGS or PGD.
PGS (pre-implantation genetic screening)
Microarray based.
Screens for aneuploidies.
PGD (pre-implantation genetic diagnosis)
NOT DIAGNOSTIC, still just a screening.
Uses a family-specific test.
Screens for single gene disorders.
Confirmed via CVS or amniocentesis.
indications for additional testing
Advanced maternal age (>35). Fetal ultrasound finding. Prior pregnancy with aneuploidy. Prenatal chromosome translocation. Positive maternal serum screen results. Positive non-invasive prenatal testing results.
