Techniques 3 And Genetic Testing Flashcards

Question

Linked marker analysis can be used for which diseases.

Answer 1

1. X-linked - duchenne/Becker muscular dystrophy -Haemophilia A/B 2. Autosomal recessive -infantile polycystic kidney disease -beta thalassaemia -cystic fibrosis 3. Uni paternal disomy -prader-willi/ Angelman syndrome

Answer 2

1. You cannot tell which allele is associated with the disease locus.

Answer 3

Genetic counselling is the process of helping people understand and adapt to the medical, psychological and familial implications of genetic contributions to disease.

Answer 4

1. Interpretation of family and medical histories to asses the chance of disease occurrence or recurrence. 2. Education about inheritance, testing, management, prevention, resources and research. 3. Counselling to promote informed choices and adaptation to the risk or condition.

Answer 5

1. Family history of a genetic condition 2. child with birth defect or development delay. 3. Families with a strong cancer history 4. Dysmorphic features 5. Multiple miscarriages 6. Abnormalities on fetal ultrasound 7. Teratogen exposure 8. Patient with a known genetic condition.

Answer 6

1. Genetic disorder that results from a defect in a single gene that codes for an enzyme involved n a metabolic pathway.

Answer 7

1. Catabolic: breakdown of energy containing sources such as protein, lipid and carbohydrates to produce energy. 2. Anabolic: energy used to create molecules from smaller components

Answer 8

1. Autosomal recessive: 50% of normal level of enzymes produced -generally More than sufficient to continue normal metabolism. 2. Some are X-linked

Answer 9

1. Increase in substrate (may be toxic) 2. Reduction in product (reduction of energy production) 3. Increase in alternative product ( may be toxic)

Answer 10

Child initially develops milestone normally, then gradually loses skills and deteriorates. Usually relentless course ending in encephalopathy and premature death.

Answer 11

1. It’s an accumulation of waste products in cell over time, reaches a threshold and eventually results in cell death. 2. It’s often due to a genetic defect in an enzyme that removes cellular waste. 3. Examples are lysosomal storage diseases such as Tay-sachs.

Answer 12

1. Appropriate clinical managements: some can be management with diet or enzyme replacement therapy or bone marrows transplants. 2. Managing recurrence risks using prenatal, carrier testing and cascade family screening. 3. Understanding the incidence in Local population. 4. Bringing closure to a family by explaining the underlying cause.

Answer 13

1. IEM are rare conditions with complicated testing algorithms 2. Incidence varies globally 3. Mostly physicians do not see IEM regularly. 4. Very long and expensive journey to get to a diagnosis

Answer 14

1. Biochemical assay 2. Enzyme assay 3. Molecular genetic testing

Answer 15

1. Basically an indirect test the consequence of the missing enzyme likely causes accumulation of various biochemical substances in blood or urine. 2. Simple, inexpensive, easily available and can guide emergency management. 3. Example: urea cycle disorders

Answer 16

1. More direct assay. 2. Detection of presence or absence of enzyme of interest in blood. 3. Useful for common IEM. 4. Not all IEM have enzyme assay

Answer 17

1. Sequencing the gene coding for enzyme of interest.

Answer 18

1. The conditions included in the screening program are common in population. 2. The screening program is sensitive in terms of detecting the conditions-limit false neg 3. Need to know the difference between screening and diagnosing a condition. If you are going to screen a patient, you have to follow it up with a diagnosis. 4. Effective treatment needs to exist 5. Cost/benefit ratio

Answer 19

1. Gametogenesis is the formation of gametes through meiosis. 2. Meiosis 1 happens when the oogonium matures and becomes the primary oocyte, this occurs in the 1st few months of intrauterine life. 3. At birth primary oocyte maturation arrests. 4. Meiosis 2 resumes at age +-15 to 50. 5. Delayed onset at puberty and completion at 50 leads to wear and tear of primary oocyte during arrest. 6. This causes spindle damage which lead to non-disjunction.

Answer 20

Primary- nondisjunction in meiosis 1 Secondary- nondisjunction in meiosis 2

Answer 21

1. Trisomy 21- Down syndrome 2. Trisomy 13 - Palau syndrome 3. Trisomy 18- Edward syndrome

Answer 22

1. Monosomy x or do -Turner syndrome 2. XXY- klinegelter syndrome 3. XXX- Triple X syndrome 4. XYY-Jacob’s syndrome

Answer 23

1. Uses fluorescently labelled primers, specific to STRs of interest. 2. Each targeted STR marker is specific to the chromosome on which it is located. 3. The copy number of the STR marker can be diagnostic of the copy number of the chromosome. 4. PCR products are separated by capillary electrophoresis based on number of repeat units.

Answer 24

1. Amelogenin: amplifies chromosome X and Y 2. SRY: chromosome Y 3. TAF9L: sequences both chromosome 3 and X

Answer 25

1. Relatively quick test 2. High sensitivity for common trisomies 3. Can be used to infer likely maternal cell contamination 4. Rapid for XX/XY sexing 5. Works on DNA from old/degraded samples-different types. 6. Low DNA concentrations 7. Diagnostic test and alternative to karyotyping.

Answer 26

1. Mosaicism not always detected 2. No coverage of other chromosomes 3. Translocations of tested chromosomes may not be detected 3. Low concentration DNA may affect interpretation 4. Maternal cell contamination, incl only” CVS result “maternal 5. Confined placental mosaicism (abnormal CVS finding, but AFs or blood in normal ranges) 6. Null alleles/primer binding mutations

Answer 27

Techniques used for the quantification of copy number variants (CNVs) -deletions and duplications.

Answer 28

1. Sample DNA denature 2. Probe hybridisation 3. Probe ligation 4. Amplification of lighted probes 5. Fragment separation 6. data analysis

Answer 29

1. One probe consists of two oligonucleotides 2. Hybridised probe Oligos are connected by ligation 3. The lighted probes are amplified in a multiplex PCR. MLPA probes are amplified. 4. PCR reaction is very reproducible, as only one pair of PCR primers is used for all the reactions. 5. Each probe generates an amplification product of unique length 6. Amplification products are analysed by capillary electrophoresis. 7. Differences in relative amount of probe target sequences in the sample results in different relative peak heights between the patient sample and the reference sample.

Answer 30

1. DiGeorgesyndrome (22q11.2 microdeletion) 2. Williams-Beurensyndrome (7q11 microdeletion) 3. Neurofibromatosis type 1 (17q11 microdeletion) 4. Smith-Magenissyndrome (17p microdeletion)

Answer 31

1. The probemixeshas a limited number of probes for each specific chromosomal region and will therefore not detect all possible causes of the syndromes included. 2. MLPA cannot detect any changes that lie outside the target sequence of the probes. Even when MLPA did not detect any aberrations, the possibility remains that biological changes in that gene or chromosomal region do exist but remain undetected. 3. Sequence changes (e.g. SNPs, point mutations, small indels) in the target sequence detected by a probe can cause false positive results.

Answer 32

Methylation- sensitive MPLA has been developed to characterised imprinted regions in addition to the quantification of copy number variants.

Answer 33

1. Unable to detect balanced translocations- only karyotyping can 2. Limited to the kit design. Probes are specific to target regions. only karyotyping can 3. Comparative genomic hybridization ( aCGH )/ micro array is better at characterizing more regions. However this technique is not applicable for single gene disorders.

Answer 34

1. Limited resource lab: 1.1 driven on basis of clinical phenotype of patient 1.2 valuable in certain classic monogenic syndrome and families with previously attributed molecular cause. 2. New advanced technology (WES,WGS,NGS) impractical for routine testing.

Answer 35

1. Robust 2. Simple 3. Cost effective 4. Affordable 5. Validity

Answer 36

1. Analytical validity 2. Clinical validity 3. Clinical utility

Answer 37

1. Does test work in the lab? 2. Measure of ability of molecule test to detect genetic variant/mutation. 3. Analytical sensitivity (false-neg rate) 4. Analytical specificity (false-positive Rate)

Answer 38

1. Does test work in the talent population of interest? 2. Ability to correctly classify individuals to disease status or risk. 3. Test may be clinically valid when applied to individuals from high risk population, but not so when applied to general population.

Answer 39

1. Analytical validity 2. Clinical validity 3. Clinical utility 4. Ethical, legal and social issues (ELSI) It ensures that genetic diagnostic tests are fit for clinical use.

Answer 40

1. Preanalytical: Taking, labelling, transporting and receiving sample 2. Analytic: lab test 3. Post-analytical: reporting, within a specified turnaround time (TAT)

Answer 41

1. Standard operating procedures (SOPs) for each Step, ranging from specimen handling to instrument performance validation. 2. Defines administrative requirements eg record keeping 3. Specifies corrective actions, documentation, and the persons responsible for carrying out corrective actions when problems and identified. 4. Sustains high-quality employee performance

Answer 42

1. Sensivity 2. Specificity 3. Accuracy 4. Positive predictive value (PPV) 5. Negative predictive value (NPV)

Answer 43

1. Sensitivity describes how well a test can detect a specific disease or condition in people who actually have the disease or condition. 2. Sensitivity = true positive / true positive + false negative

Answer 44

1. Analytical sensitivity: genetic test is high vs slightly lower for genomic test. 2. Clinical sensitivity: genetic test is limited vs genomic test which is higher not 100%

Answer 45

1. Specificity refers to the percentage of people who test neg for a specific disease among a group of people who do not have disease. 2. True negative/ false positive + true negative

Answer 46

1. Accuracy is the ability of a test to correctly differentiate patients and healthy people. 2. (True positive +true negative)/(true positive + false positive + true negative + false negative)

Answer 47

1. The likelihood that a person with a positive test result does have the gene mutation or the disease. 2. PPV = true positive / true positive + false positive .

Answer 48

1. The likelihood that a person with a negative test exult does not have the disease, or the gene mutation. 2. NPV = true negative / false negative + true negative

Answer 49

(True positive + false negative ) /(true positive +true negative + false positive + false negative )

Answer 50

Usefulness (clinical utility) includes other considerations, specifically: 1. What’s are the benefits and risk of test? This includes consideration of cost . 2. This should be considered in comparison with alternatives

Answer 51

1. Genetic variants are present from conception (before the disease onset) thus genetic testing can therefore be used in different contexts: 1. Prenatal diagnosis 2. Carrier testing 3. Early pre-symptomatic testing

Answer 52

1. Not subject to clinical validation; clinical sensitivity and specificity are often not known. 2. Done when research funds allow thus there is no set turnaround time. 3. Not subject to strict quality control.

Answer 53

1. May allow people to be more proactive about their health. 2. Patients often report a sense of satisfaction, empowerment. 3. Raises public awareness of genetics

Answer 54

1. Especially regarding health related tests, concern about: - whether the tests have proven validity and utility - lack of genetic counselling at the feedback of results 2. DTC companies often claim test validity and utility for their products (often false) 3. Results may be misleading, and cause anxiety or confusion inappropriate modification to diet. 4. Cost of test is likely unjustified.

Answer 55

1. Done for a particular condition 2. In individuals, groups or populations 3. Without family history of the condition 4. Alters risk, may not be definitive 5. Positive results require further follow up.

Answer 56

1. MLPA analysis (micro deletion/duplication ) 2. Micro—array analysis 3. Whole genome sequencing 4. Karyotyping 5. FISH. 6. QF- PCR 7. Array CGH

Answer 57

1. Sequencing panels 2. Exome sequencing 3. Whole genome sequencing

Answer 58

1. When we want to confirmation/exclusion of diagnosis for known chromosomal syndromes. 2. Unexplained developmental delay 3. Multiple congenital abnormalities 4. Abnormal of sexual differentiation and development 5. Infertility/sub fertility 6. Recurrent miscarriages 7. Family history of abnormalities 8. Pregnancies at increased risk because of prenatal screening 9. Neoplastic conditions for which chromosome abnormality ID will help diagnosis and/ or management.

Answer 59

1. Enzyme activity 2. Amount of substrate 3. Amount of product 4. Alternative product

Answer 60

1. Testing for specific sequences changes such as southern blot, RFLP based on: 1.1 Family specific 1.2 common mutations 1.3 population specific 1.4 common mechanism 2. Sanger sequencing 3: next generation sequencing

Answer 61

1. Clinical diagnosis 2. Pre-clinical diagnosis 3. Carrier testing 4. Prenatal testing 5. Phenotype prediction 6. Directing therapy

Answer 62

1. Identify ‘at-risk” individuals prior to onset of symptoms - for mutation neg individuals we can say no follow-up unnecessary - mutation positive individuals can be given early intervention, appropriate monitoring and improved management. (Note: positive test does not always indicate patient will develop disease)

Answer 63

1. Family specific: known genetic disease in family therefore we Test for specific mutation. 2. Broad carrier screens -NGS panels 3. Population specific testing for common disorders.

Answer 64

To detect those at risk for genetic disease for themselves or their offspring so that they can make informed choices regarding their Reproductive options (Enhance autonomy)

Answer 65

1. Beta-thalassaemia: mediterraneans and Indians 2. Sickle cell anaemia: Sub-Saharan Africans and Indians 3. Cystic fibrosis: north-west European 4. Tay-Sachs: Ashkenazi Jews.

Answer 66

1. Detection of disease in utero/ preimplantation. -reproductive options -early management

Answer 67

1. DNA analysis not always most appropriate test 2. For many gene disorder there are no common mutations. 3. Each patient has unique mutations therefore there is a need individual testing and even if ‘’ problem’’ genes are known testing is not quick. 4. Mutation may be missed or multiple techniques required to detect different types of mutations. 5. Variants with unknown effect (VUS). 6. Unintended/secondary findings (What do we do???) 7. Tests May be expensive 8. Genetic complexity needs to be taken into account because it can cause misinterpretation. 9. Potential for inappropriate testing for profit rather than science. Can cause false reassurance or incorrect risk.

Answer 68

1. The purpose of screening is to identify people in an apparently healthy population who are at higher risk of a health problem or a condition, so that an early treatment or intervention can be offered. This may lead to better health outcomes for some of the screens individuals. 2. In some cases, such as antenatal screening , the purpose of screening is to give people information about an increased risk or condition to help them make an informed decision about their care or treatment . 3. Screening is not the same as early diagnosis.

Answer 69

1. To reduce mortality by early detection and early treatment of a condition. 2. To reduce the incidence of a condition by identifying and treatment is precursors. 3. To reduce the severity of a condition by identifying people with the condition and offering effective treatment. 4. To increase choice by identifying conditions or risk factors at an early stage in a life course when more option are available.

Answer 70

1. The condition should be an important health problem. 2. There should be an accepted treatment for patients with recognised disease. 3. Facilities for diagnosis and treatment should be available. 4. There should be a recognisable latent or early symptomatic phase. 5. There should be a suitable test or examination. 6. The test should be acceptable to the population. 7. The natural history of the condition, including development from latent to declared disease, should be adequately understood. 8. There should be an agreed policy on whom to treat as patients. 9. The cost of case-finding should be economically balanced in relation to possible expenditure on medical care as a whole 10. Case- finding should be a continuous process and not a ‘once’ and for all’ project .

Answer 71

1. Identify the population eligible for screening. 2. Invitation and information 3. Testing 4. Referral of screen positives and reporting of screen negative 5. Diagnosis 6. Intervention, treatment and follow up

Answer 72

When a Condition is less common in a country (low prevalence ), the positive predictive value is lower. This means that there will be more false positive than in a country with a higher prevalence of the condition, even though the sensitivity and specificity are the same.

Answer 73

1. Reduction in the incidence and mortality. 2. Early intervention for newborns 3. Providing parents with information in the antenatal period.

Answer 74

1. Because most people who are screened do not have the condition, more people can be exposed to the harm of screening than may be able to benefit from it. 2. Because screening tests are not 100% sensitive or specific, there will always be false positives and negatives. 3. Earlier detection of condition can lead to over diagnosis: detecting conditions that would never cause that individual harm in their life.

Answer 75

1. High-resolution technologies such as sensitive biomarkers or imaging technologies, which can detect very small occurrences of a condition, lower the detection threshold of the screening test, leading to detection of smaller, and often more benign, instances of a condition.