Short answer questions submitted by Tate

Short answer questions on genetics and molecular pathology.

These are some questions I came up with that are plausible to me... let me know if they are out to lunch.

Molecular Genetic Diagnosis

List three basic molecular diagnostic techniques
a. Karyotyping, b. Southern blot, c. Sanger DNA sequencing, d. Polymerase chain reaction

CAP Molecular Diagnosis of Lung Cancer

List 5 treatment defining molecular transformation, the neoplasm, and the genetic alteration
1. 100% of CML: BRR-ABL > Imatinib, 2. 20% of Lung Adenocarcinoma: EGFR > Erlotinib/Gefitinib, 3. 25% Infiltrative ductal carcinoma of breast HER2>Trastuzumab, 4. 50% of Melanoma, BRAF v600E > PLX4032, 5. 4% of Lung Adenocarcinoma: ALK > Crizotinib

List and describe 5 areas of Genetic characaterization of tumours for personalized medicine
DNA mutations, DNA chromosomal alterations, mRNA and MiRNA profiling, Proteomics, DNA epigenetics

What fraction of Lung adenocarcinomas have no known detactable mutations
42%

What are the three most common molecular alterations of Lung Adenocarcinoma
KRAS 23%, EGFR 15%, TP53 5%

What is the two most common molecular alteration makes patients with EGFR mutations resistant to targetted therapies?
KRAS (primary) and T790M (primary and acquired)

List two EGFR kinase inhibitors.
Gefitinib/Iressa, Erlotinib/Tarceva

What are the three most common cancers associated with KRAS mutations?
Pancreatic 90%, Colon 50%, Lung NSCLC 30%

Why don't KRAS + tumours respond to Anti EGFR therapies?
KRAS is downstream from EGFR, so changing the function of EFGR would not have any effect on mutated KRAS

Explain the cost effectiveness of genetic testing for targetted therapies?
Most molecular tests cost $200-1000, vs one month of targetted therapy $2000-10000/month

What are the three most common cancers associated with BRAF mutations?
Melanoma 70%, Papillary Thyroid Carcinoma 50%, Ovarian serious carcinoma 30%, Colon cancer 10%, Hint Papillary architecture

Beta catenin/CTNNB1 expression is found with which histological pattern of lung adenocarcinoma?
Low grade adenocarcinoma of fetal type, poor px, <40yo, and has glycogen rich glandular formations, may occur in FAP patients

What is the most common ALK rearrangement found in NSCLC?
EML4-ALK (90% of the 13% of lung cancers found to due to ALK fusions)

List some pros and cons of ALK FISH.
Pros: commercial FDA approved probes available, not too expensive, moderately easy to disseminate screening, clinically validated, and failed tests on poorly preserved tissues are not reported as negative. Cons: need fish lab expertise (including pathologist and PhD), can be tricky if genes are close

List some pros and cons of ALK IHC.
Pros: fast, cheap, easy to disseminate screening, Cons: commercial antibodies sub-optimal, poorly preserved tissues (esp bx) may give false negative results due to loss of antigenicity, no internal control

What is a positive count in the ALK-FISH?
Signal split >2 probe diameters

CAP Molecular Diagnosis of AML

List 6 genes associated with Acute Myeloid Leukemia that have been identified by cloning translocation break points
RUNX1, RUNX1T1, PML, CBFB, ETV6, MLL

List the 5 main categories of classification of Acute Myeloid Leukemia
1. AML with recurrent genetic abnormalities, 2. AML with myelodysplasia-related changes, 3. Therapy related myeloid neoplasms, 4. AML, NOS, 5. Myeloid sarcoma

Give any three translocations identified in AML.
t(8,21), inv (16), t(15,17), t(9,11), t(6,9), inv(3), t(1,22), mutated NPM1, mutated CEBPA

What entities are fall under the AML, NOS classification?
AML with minimal differentiation, AML without maturation, AML with maturation, Acute myelomonocytic leukemia, Acute monoblastic/monocytic leukemia, Acute erythroid leukemias (pure erythroid, erythroleukemia, erythroid/myeloid), Acute Megakaryoblastic leukemia, Acute basophilic leukemia, Acte panmyelosis with myelofibrosis

List 2 genes which confer a poor prognostic impact vs 2 which confer a good prognostic impact.
Poor: KIT, FLT3, Good: NPM1, CEBPA

CAP Breast Cancer and Molecular

List 3 patient and 4 tumour features that affect Prognosis and treatment.
Patient: age, menstual status, comorbidities; Tumour factors: N status, LVI, size, grade

Describe the histological grading system used for breast cancer.
Nuclear pleomorphism, mitoses, and mitotic index (each scored 1-3), with cumulative grade 1(score 3-5), grade 2(score 6-7), and grade 3 (score 8-9)

Describe the genomic grading system used for breast cancer.
Low grade path (+1q, -16q), High grade (17q12, 11q13, nad 1p21-p25)

What defines a positive ER by IHC for the purpose of determining Tamoxifen therapy?
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what defines a positive HER2 for the purpose of treatment with Herceptin?
HER2 IHC >30% with complete membranous staining OR HER2/CEP17 >2.2

What are the indications for chemotherapy for breast cancer patients?
Low expression of ER/PR, Grade 3 histology, Ki67>20%, 4+ nodes positive, +LVI, and tumour >5cm]

What are the indications for hormonal therapy alone?
high expression of ER, Grade 1, Ki67>40%, Node negative, LVI not identified, and tumour 1-2cm

What are the four categories of breast cancer using the molecular classification of gene expression?
Luminal A, Luminal B, Basal, and Her2 OverExpression

What is the difference between unsupervised and supervised molecular classification of tumours?
Supervised is based on seperating patients by clinical features (e.g. progression) and trying to identify common molecular characteristics within those groups. Unsupervised is the opposite, tumours are grouped by common molecular features and their behaviour examined based on these groups.

What are the four groups and list one gene for each used in the Oncotype Dx 21 Gene prognostic model.
Invasion (Cathespin L2, Stromolysin), HER2 (Her2, GRB7), ER (BCL2, SCUBE2, ER, PR), Proliferation (Cyclin D1, Ki67, MYBL2, STK15, Survivin)

What are the features of Luminal A breast cancer?
High ER/PR expression, low histological grade, low levels of proliferative genes, HER2neg, indolent clinical course, better prognosis, Tamoxifen responders, low recurrence score Oncotype Dx, minimal benefits of adjuvant chemotherapy.

What are the features of Luminal B breast cancer?
low ER/PR expression (may be PR neg), over expression GFR(Her2 & EGFR), higher histological grade, more aggressive clinical course, worse prognosis, more likely positive lymph nodes, and high expression of proliferative genes (Ki67)

What are the features of Luminal B HER2
ER+, HER2+, agressive clinical course, decrease response to tamoxifen, may benefit from chemo and tamoxifen, increased recurrence risk Oncotype Dx Score, some may benefit form Herceptin+Chemo+Tamoxifen

What are the features of Her2 Enriched breast cancers?
GEP are ER neg, over expression of other genes in HER2 aplification, high proliferative index, increased probability of P53 mutation, high histological grade, younger age, agressive clinical course, Poor Px, good response to herceptin in combination with chemo, pathological complete response to chemo+herceptin

What are the features of Basal breast cancer?