Molecular and Cytogenetics Flashcards
What protein complexes are associated with the following phases of the cell cycle?
1) S phase
2) G1 phase
3) G2 phase
4) M phase
1) S phase
cyclin E and CDK2
2) G1 phase
cyclin D and CDK4
3) G2 phase
cyclin A and CDK2
4) M phase
cyclin B and CDK1
What molecular alterations occur in the following stages of the adenoma-carcinoma sequence in colorectal cancer?
1) normal epithelium to dysplastic foci
2) early adenoma to intermediate adenoma
3) intermediate adenoma to late adenoma
4) late adenoma to carcinoma
1) normal epithelium to dysplastic foci
loss or mutation of the APC locus on chr 5q
2) early adenoma to intermediate adenoma
mutation of RAS gene on chr 12p
3) intermediate adenoma to late adenoma
loss of tumor suppressor on chr 18q
4) late adenoma to carcinoma
loss of p53 gene on chr 17
What percentage of Down’s is due to a Robertsonian translocation?
4% of DS due to Robertsonian translocation
Mostly der(14;21)
Uniparental disomy (imprinting) of the following chromosomes can result in what disorder?
1) Chr 15
2) Chr 6
3) Chr 11
1) Prader-Willi or Angelman
2) Neonatal diabetes
3) Beckwith-Weideman
*idea behind the imprinting disorders is that you need a copy from each parent of the gene for it to function properly so if you inherit two copies from only one parent, you are going to have disorders
What is the method of PCR?
► Amplifies DNA up to ~35 kb
► Primers, specific design, universal or degenerative
►DNA polymerase enzyme, Mg2+ buffer, dNTPs
► Denature, anneal, extension, repeat ~ 30-35 cycles, yields thousands of copies of original DNA template
Describe the process of sequencing.
► ‘Gold standard’ of DNA testing
► Uses 4 mixes of dNTP’s and dye-attached dideoxy nucleotides (ddATP, ddCTP, ddGTP, ddTTP)
► Each time nucleotide incorporated into chain, if dideoxynucleotide, extension of chain will be terminated
► DNA pulled through capillary by electrophoresis, separated by bases into the ladder patterns
► Ladder ‘read’ automatically using computer algorithm with each base a different color
CYP2D6 affects metabolism of what two drugs?
Codeine to its metabolite morphine
TCAs (ie nortryptyline)
What drugs metabolism is affected by:
1) CYP2C9
2) CYP2C19
3) N-acetyltransferase
1) Warfarin and phenytoin
2) Omeprazole, phenytoin and diazepam
3) N-acetyltransferase is central to the metabolism of isoniazid, some polymorphisms result in increased or decreased activity
What disease is caused by mutations in the COL4A5 gene on Xp22.3 which encodes the alpha 5 chain of type IV collagen and how is it diagnosed on skin or renal biopsy?
Alport’s syndrome
X-linked recessive disorder
Diagnosis by skin or renal biopsies that show absence of IHC staining for alpha5 chain of type IV collagen
What inherited nephrotic syndrome:
caused by mutation of NPHS1 (19q13.1) gene which encodes nephrin which is a key component in the glomerular slit diaphragm
affected children born with markedly enlarged placenta
EM shows abnormal variation in the size of the slit pores and rarefaction of the slit diaphragms
Congenital nephrotic syndrome of the Finnish type
What inherited nephrotic syndrome:
caused by mutation of the LAMB2 (3p21) gene which encodes ß2 laminin which is a component of the glomerular basement membrane
associated with microcoria (fixed narrow pupils), death within several months and renal biopsy shows mesangial sclerosis and crescents
Pierson syndrome
What inherited nephrotic syndrome:
caused by mutation in LMX1B (9q34.1) gene which encodes a transcription factor that regulates transcription of COL4A3
Autosomal dominant disorder with skeletal and ocular anomalies
Renal biopsy shows basement membrane expansion by fibrillary collagen deposits
Nail-patella syndrome
What inherited nephrotic syndrome:
caused by mutation in WT1 gene (11p13)
causes Wilms tumor, male pseudohermaphroditism and rapidly progressive renal failure
Renal biopsy shows mesangial sclerosis
Denys-Drash syndrome
*Frasier syndrome is similar but less severe and is associated with gonadoblastoma
What inherited nephrotic syndrome:
caused by mutation in ACTN4 gene which encodes alpha-actinin or a mutation in TRPC6 gene which encodes transient receptor potential cation channel 6
patients get onset of nephrotic syndrome in adolescence or young adulthood
Familial autosomal dominant focal segmental glomerulosclerosis
What inherited nephrotic syndrome:
caused by mutation in NPHS2 gene which encodes podocin
patients get onset of proteinuria in early childhood
renal biopsy initially resembles minimal change disease but transforms into FSGS
Familial autosomal recessive corticosteroid-resistant nephrotic syndrome
What is an X-linked recessive disorder in the CLCN5 gene encoding a chloride channel that causes proximal tubular dysfunction?
Dent disease
What is the mutation in autosomal recessive PCKD? autosomal dominant PCKD?
PKHD1 gene on chromosome 6p for AR
PKD1 on chromosome 16p13 in 85% for AD
What syndrome has cystic renal dysplasia, polydactyly and occipital encephalocele?
Meckel-Gruber syndrome
What disease is a form of arrhythmogenic right ventricular dysplasia with cutaneous manifestations and woolly hair?
Naxos disease
What is the most common gene mutated in the inherited long QT syndrome?
LQT1 (KCNQ1)
exercise (especially swimming) triggered arrhythmias
What gene is mutated in the form of inherited long QT syndrome that is triggered by auditory stimulus or emotional stimulus and it is the second most common mutated gene in these syndromes?
LQT2 (KCNH2, HERG)
What gene is mutated in the inherited long QT syndrome that is triggered by sleep?
LQT3 (SCN5A)
What gene is mutated in the inherited long QT syndrome that encodes portions of a channel shared with skeletal muscle and it causes Anderson-Tawil syndrome which is a triad of episodic paralysis, long QT interval and dysmorphic features?
LQT7 (KCNJ2)
What gene is mutated in the X linked form of dilated cardiomyopathy? What about the AD form?
X linked: Dystrophin (same as Duchenne and Becker MD)
AD: lots of mutations but most commonly MYH7 gene encoding ß myosin heavy chain
What is the most commonly affected gene in HOCM?
MYH7 (most common mutation R403Q)
Autosomal dominant
What gene is responsible for Holt-Oram syndrome (heart-hand syndrome)?
TBX-5
AD disorder with heart and upper limb abnormalities
Heart defects are usually septal defects
What syndrome is caused by a PTPN11 mutation and consists of right sided heart defects, most commonly pulmonic stenosis and HOCM is the 2nd most common finding, lymphatic malformations are also common?
Noonan syndrome
What is the mutation in Alagille syndrome and what is this syndrome?
JAG1
AD condition causing paucity of bile ducts but it also causing disease of blood vessels and the heart and most commonly affects pulmonary circulation in the form of pulmonary artery stenosis
What gene is responsible for the cardiac anomalies seen in DiGeorge syndrome?
TBX1
What syndrome is due to deletion of the elasin gene and has a characteristic supravalvular aortic stenosis (hourglass stenosis)?
Willams syndrome
What gene is involved in 21 hydroxylase deficiency?
The gene encoding 21 hydroxylase is CYP21 located at 6p21 within the HLA locus
What can be the 1st sign of steroid sulfatase deficiency?
(in compendium and seems like good board fodder)
Prolonged or nonprogressive labor, unresponive to oxytocin
After birth cholesterol sulfate begins to deposit in blood and tissues
High incidence of cryptorchidism and germ cell tumors
Gene for steroid sulfatase (STS) located at Xp22.3
What syndrome is characterized by gain of function mutation in GNAS1, all patients at somatic mosaics because germline mutations are incompatible with life and the severity is highly variable?
The syndrome is characterized by cafe au lait spots, polyostotic fibrous dysplasia, precocious pubery and other endocrine abnormalities
McCune-Albright syndrome
What is the mutation in Osler-Weber-Rendu syndrome?
ENG gene or the ACVRL1 gene
What congenital malformation is strongly associated with DECREASED maternal age?
Gastroschisis
*very high maternal serum AFP
Why would hemochromatosis patients get hypogonadotrophic hypogonadism and infertility?
PITUITARY iron deposition
What is the mutation in Wilson’s disease?
ATP7B gene which encodes an ATPase utilized in copper binding to ceruloplasmin
It is AR inheritance
What are the mutations associated with Gilbert’s and Crigler-Najjar syndrome?
*can’t conjugate bilirubin so increased UNCONJUGATED bilirubin
Gilberts: mutations in the 5’ TATA box of the promoter for UGTA1
CN: mutations in the coding sequence of UGTA1
What is the mutation in Dubin Johnson and Rotor syndrome?
*can’t secrete conjugated bilirubin so increased CONJUGATED bilirubin
MRP2
pretty much the same except Rotor doesn’t have the pigmentation
What is the most common CFTR gene mutation in cystic fibrosis?
F508 (66%)
What is the autosomal dominant chromosomal breakage syndrome affecting the mitochondrial DNA and it causes pancreatitis and marrow failure with sideroblastic anemia and vacuolization of precursors?
Pearson syndrome
molecular defect is a microdeletion within the mitochondrial DNA
What syndrome causes marrow failure and pancreatic exocrine insufficiency and so the pancreas demonstrates fatty metamorphosis with islet preservation and its caused by mutation in SBDS gene?
Shwachman-Diamond syndrome
What syndrome shows hypoplasia fo the nasal alae, pancreatic exocrine insufficiency with pancreatic lipomatosis, hypothyroidism and deafness?
Johanson-Blizzard syndrome
What is the mutation in late (usual) onset Alzheimer’s?
E4 allele at the APOE gene
What is the mutation in familial Pick disease?
MAPT gene that encodes the microtubule associated protein tau
What is the gene that has the trinucleotide repeats in Huntington disease?
HTT gene on 4p
What is the mutation in CADASIL and what does this stand for?
NOTCH3
cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy
What is the mutation in Charcot-Marie-Tooth disease?
Duplication of a 1.5 Mb region of DNA on 17p12 containing the PMP22 gene
What gene is mutated in spinal muscular atrophy?
SMN1 gene
What gene mutation is responsible for malignant hyperthermia?
Defective RYR1 calcium channel due to RYR1 gene mutation
What syndromes have increased risk of pancreatic ductal adenoCA?
- Peutz Jeghers (100 fold increased risk)
- Familial atypical mole melanoma (FAMM) syndrome (50 fold increased risk)
- Hereditary pancreatitis (50 fold increased risk)
- FAP, BRCA2, ataxia-telangectasia and Lynch all associated with increased risk ranging from 2-10 fold
What mutation is seen in familial papillary RCC?
c-MET on chromosome 7q31
What is the mutation in MEN1? MEN2?
MEN1: MEN1 gene mutation on 11q13
*parathyroid adenoma, pancreatic endocrine tumors and pituitary adenomas
MEN2: mutations in the RET protooncogene on chr 10q (MEN2a exon 10 & 11, MEN2b exon 16)
*MEN2a pheo, medullary thyroid CA and parathyroid adenomas
*MEN2b pheo, med thyroid CA and mucosal neuromas
What mutation seems to be the sole inciting event for most cases of pilocytic astrocytoma?
BRAF (80% of PA)
What are the mutations and location of gene in NF1 and NF2?
1) NF1 gene on chr 17q11.2, neurofibromin
2) NF2 gene on chr 22q; merlin
What gene OTHER than WT1 is associated with WAGR syndrome and why?
PAX6
WAGR syndrome is a large germline deletion in chr 11p13 which spans the coding region for both WT1 AND PAX6. PAX6 is what is responsible for the aniridia seen in this syndrome.
SImilar mutations of WT1 can also lead to Denys-Drash syndrome, which is characterized by Wilms tumor, nephropathy and either true or pseudo hermaphroditism
What is the CLSI recommended minimum for testing samples when establishing a reference intervals?
20 healthy individuals and at least 18 must fall within the established reference range
*reference intervals are usually chosen such that 5% of results from healthy individuals are abnormal, thus a large number of “abnormal” lab tests are a consequence of statistical necessity
Patients with paraproteinemia can have hypercalcemia as a result of three situations, what are they?
1) Factitious hypercalcemia caused by the turbidity of the paraprotein
2) True total hypercalcemia with normal ionized calcium caused by increased calcium transport by paraprotein
3) True total and ionized calcium caused by the myeloma itself
Patients with high leukemic counts and those with thrombocytosis may have factitious hyperkalemia. How do you tell this apart from TRUE hyperkalemia
These patients will usually have a more pronounced hyperkalemia in the SERUM whereas true hyperkalemia should be roughly equal in both serum and plasma
CML is notorious for causing spuriously high vitamin ____?
Vitamin B12 levels
What mutation is found in approximately 20% of ALS?
SOD1 located on chrom 21 and encodes a copper/zinc superoxide dismutase
*incidence is 1-2 per 100,000 but is much higher in Guam and Japan possibly due to consumption of environmental toxin, ß-methylamino-L-alanine
What is the most commonly maternally inherited mitochondrial disorder?
MELAS
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes
*in this disorder, the ragged red fibers in muscle biopsise are COX positive which is in contrast to the other mitochondrial disorders. Also, RRF are most noticeable in the vasculature where they have strong staining for succinate dehydrogenase
~2-5% of Angelman syndrome is caused by mutation in what gene?
UBE3A in a maternal allele
Loss of function in what gene appears to be associated with higher rates of recurrent cardiovascular events in patients receiving clopidogrel?
CYP2C19
Name four recurrent chromosome aberrations in CLL.
1) Trisomy 12
2) Deletion 13q14.3 (a likely target of microRNA genes miR-16-1 and miR-15a)
3) Deletion 11q22 (likely target of ATM gene)
4) Deletion 17p13 (likely target of the TP53 gene)
What percentage of spontaneous abortions are due to chromosome abnormalities?
60-70%
What essential amino acid needs to be added to cell culture just prior to use?
L-Glutamine
*L-Glutamine is unstable and breaks down on storage to D-Glutamine, a form that can’t be used by cells. L-Glutamine may be kept frozen to retain its stability and should only be added to culture medium just prior to use
What translocation can serve as a diagnostic cytogenetic marker in multiple myeloma?
t(14;20)
This abnormality ONLY occurs recurrently in multiple myeloma
In myeloma, the following IGH translocations are associated with short progression-free survive and decreased overall survival: t(4;14), t(14;16), t(14;20)
GOOD prognosis: hyperdiploidy, t(11;14)
What cytogenetic abnormality is seen in up to 80% of T-cell prolymphocytic leukemia?
inv(14)(q11.2q32)
What tumors are associated with NF1 other than neurofibromas?
optic nerve pilocytic astrocytomas, ampullary somatostatinoma, duodenal gangliocytic paraganglioma, GIST, pheochromocytoma, juvenile xanthogranuloma
Name 4 tumors that have the identical translocation t(12;15) ETV6-NTRK3.
Infantile fibrosarcoma
Congenital mesoblastic nephroma
Secretory carcinoma of the breast
Mammary analogue secretory carcinoma of salivary glands
DEFINITE BOARD Q!!!
Be able to interpret a gel from a patient with Fragile X!!
Here is an example gel–lane 7 is pt with FragX
Fragile X syndrome is associated with the expansion of the CGG trinucleotide repeat affecting the Fragile X mental retardation 1 (FMR1) gene on the X chromosome, resulting in a failure to express the fragile X mental retardation protein (FMRP), which is required for normal neural development. Depending on the length of the CGG repeat, an allele may be classified as normal (unaffected by the syndrome), a premutation (at risk of fragile X associated disorders), or full mutation (usually affected by the syndrome)
Defects in the MMR proteins allow mutations to go unchecked and in this pathway, what are the three major oncogenes?
BRAF
KRAS
p16INK4a
What marker is performed to test for possible targeted therapy in both breast and gastric/GE jxn cancers and what does its expression mean at each site?
HER2neu
In breast (20-30%), positive HER2 usually means worse response but these pts can be treated with Herceptin
In gastric/GE jxn cancers (20-30%), Her2 overexpression is evidence of LIKELY response
What molecular alteration can be found in meningioma?
monosomy chr22
