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Comprehensive Guide to Genetic Testing: Prenatal Screening and Molecular Diagnostics, Exams of Advanced Education

Princeton UniversityAdvanced Education

A comprehensive overview of genetic testing, focusing on prenatal screening methods and molecular diagnostic tests. It covers various procedures such as nipt, microarray analysis, karyotyping, amniocentesis, and chorionic villus sampling, detailing their accuracy, suitable timing, and limitations. Additionally, it explores molecular diagnostic tests for conditions like fap, map, lynch syndrome, and breast cancer, including techniques like sanger sequencing, msi, and ihc. The document also discusses factors in developing next-generation sequencing tests and key concepts like clinical sensitivity and specificity, offering a detailed guide for understanding genetic testing methodologies and their applications.

Typology: Exams

2024/2025

Available from 07/13/2025

Prof-Cornel
Prof-Cornel 🇺🇸

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MGY250 Unit 9 - Genetic Testing With
Complete Solution
Goals of prenatal testing - Answer - Inform parents of risk of birth defects
- Provide couples with info for pregnancy decision making and delivery planning
- Ensure optimal of affected infants through diagnosis
- Reassure and reduce level of anxiety for parents
- Determine recurrence risk of future pregnancies
A priori risks - Answer Maternal age
Family History
Ethnic background
Environmental exposures
Maternal diseases
Describe NIPT - Answer Observe fetal DNA circulating maternal blood
Advantages of NIPT - Answer No risk to pregnancy
NIPT looks for - Answer Chromosomal abnormalities between fetus and mother
NIPT assigned risk comes from... - Answer Maternal age, fetal fraction and gestational
age
NIPT suitable time for usage - Answer As early as 10 weeks
NIPT accuracy - Answer 99%
What a microarray is able to determine - Answer Can detect
microdeletions/microduplications
Microarray procedure - Answer 1. Sample from patient and control and fluorescent label
with different colors
2. Break DNA into pieces and allow pieces to bind to platform (hybridisation)
3. Patient and control DNA compete to hybridise to platform
3. Count if there is an equal amount of patient DNA and control DNA hybridised
Microarray hybridisation outcomes - Answer Hybridisation levels between control and
patient
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Download Comprehensive Guide to Genetic Testing: Prenatal Screening and Molecular Diagnostics and more Exams Advanced Education in PDF only on Docsity!

MGY250 Unit 9 - Genetic Testing With

Complete Solution

Goals of prenatal testing - Answer - Inform parents of risk of birth defects

  • Provide couples with info for pregnancy decision making and delivery planning
  • Ensure optimal of affected infants through diagnosis
  • Reassure and reduce level of anxiety for parents
  • Determine recurrence risk of future pregnancies A priori risks - Answer Maternal age Family History Ethnic background Environmental exposures Maternal diseases Describe NIPT - Answer Observe fetal DNA circulating maternal blood Advantages of NIPT - Answer No risk to pregnancy NIPT looks for - Answer Chromosomal abnormalities between fetus and mother NIPT assigned risk comes from... - Answer Maternal age, fetal fraction and gestational age NIPT suitable time for usage - Answer As early as 10 weeks NIPT accuracy - Answer 99% What a microarray is able to determine - Answer Can detect microdeletions/microduplications Microarray procedure - Answer 1. Sample from patient and control and fluorescent label with different colors
  1. Break DNA into pieces and allow pieces to bind to platform (hybridisation)
  2. Patient and control DNA compete to hybridise to platform
  3. Count if there is an equal amount of patient DNA and control DNA hybridised Microarray hybridisation outcomes - Answer Hybridisation levels between control and patient
  • Equal: Equal amount of DNA in patient and control
  • If control > patient, maybe missing DNA from patient
  • If patient > control, maybe duplication or gain of DNA Advantages of microarray - Answer - Can identify smaller genetic imbalances than karyotype eg. CNV's
  • Improved diagnostic yield
  • Automated test can simultaneously analyse thousands of regions Limitations of microarray - Answer Cannot detect
  • Balanced rearrangements
  • Polyploidy
  • SNP
  • Imbalances below array resolution level
  • Low level mosaicism Microarray possible results - Answer 1. Benign - may be inherited
  1. Pathogenic - Previously reported important genes
  2. Unclear
  3. Secondary/Unexpected - adult onset conditions, carrier status Define karyotype - Answer Graph showing number and appearance of chromosomes in nucleus of cell Define embryogenesis - Answer Complex interaction between genome and environment Major genetic/environmental insult in first 2 weeks - Answer Early miscarriage Major genetic/environmental insult in Week 3-8 - Answer Major birth defects and malformations: most vulnerable time Major genetic/environmental insult after Week 8 - Answer Affect growth, function and/or physiological aspect Amniocentesis procedure - Answer Ultrasound guided and tiny needle is inserted into withdraw fluid, fluid contains cells whose chromosomes can be visualised Amniocentesis accuracy - Answer 99.9% Amniocentesis risk of pregnancy loss - Answer 0.5%

Molecular diagnostic tests used for FAP - Answer Sanger sequencing with MLPA (del/dup assay) FAP (Familial Adenomatous Polyposis) - Answer Dominant mutation in APC gene: tumor suppressor gene involved in Wnt signalling MAP (MUTYH Associated Polyposis) - Answer Recessive mutation in MUTYH gene: used for base excision repair Molecular diagnostic tests used for MAP - Answer Sanger sequencing with MLPA (del/dup assay), usually done after FAP tests Lynch Syndrome - Answer Dominant germline defect in mismatch repair pathway Molecular diagnostic tests used for Lynch syndrome - Answer 1. MSI

  1. IHC
  2. Germline mutation test (Sanger of 5 important genes + MLPA)

Important genes for Sanger sequencing in Lynch Syndrome - Answer MSH6 and MSH2, MLH1 and PMS2, EPCAM

Microsatellite Instability (MSI) - Answer Use 5 markers + 2 ID markers to look for expansion of repeats in genome NORMAL: Remains consistent TUMOR: Expansion of sites - MSI HIGH

Immunohistochemistry (IHC) - Answer Detect proteins in tissue using antibody stains and reporters MLH1 mutation = loss of MLH1 and PMS MSH2 mutation = loss of MSH2 and MSH

Molecular diagnostic tests used for breast cancer - Answer Sanger sequencing of BRCA1/

Clinical sensitivity - Answer Ability of a test to correctly identify patients WITH disease

TP/(TP+FN)

Clinical specificity - Answer Ability of a test to correctly identify patients WITHOUT disease TN/(TN+FP)

Positive predictive value - Answer How likely is patient to have disease if test is positive TP/(TP+FP)

Negative predictive value - Answer How likely is patient to have disease if test is negative TN/(TN+FN)

Factors taken into account when developing next generation sequencing test - Answer

  1. Design
  2. Optimisation
  3. Analysis
  4. Reporting
  5. SOP (Standard operation procedures)
  6. Validation
  7. Regulatory
  8. Update requisition

NGS Development: Design - Answer 1. NGS Platform

  1. Library Prep
  2. Genes targetted

NGS Development: Optimisation - Answer Improve conditions and coverage