Expanded Chromosome Screening of Products of Conception (POCs) Using Next-Generation Sequencing (NGS)

PATHCHAT Edition No. 48
July 2018
Please contact your local Ampath pathologist for more information.

Author: Dr. Jaysen Knezovich, PhD

Introduction to POC Testing Using NGS

🔹 Why Use Next-Generation Sequencing (NGS) for POCs?

• NGS allows comprehensive screening of all chromosomes (1–22, X, and Y).
• Significantly higher detection rates of chromosomal abnormalities compared to conventional techniques.
• Faster turnaround time and improved accuracy.

📌 Ampath Genetics now offers NGS-based POC testing to replace conventional methods like karyotyping and QF-PCR.

Background: Chromosome Abnormalities in Pregnancy Loss

✅ Human Genome Overview:

• A normal diploid genome consists of 46 chromosomes (23 pairs).
• Gametes (sperm & egg) are haploid, carrying 23 chromosomes.
• Fertilization results in a diploid conceptus (zygote) with 46 chromosomes.

🔹 Meiotic Errors Leading to Chromosomal Abnormalities:

• Non-disjunction during meiosis can result in:
  • Trisomy (extra chromosome).
  • Monosomy (missing chromosome).
  • Polyploidy (extra sets of chromosomes, e.g., triploidy, tetraploidy).
• Chromosomal abnormalities are a major cause of spontaneous abortions and congenital disorders.

📌 Up to 50% of first-trimester miscarriages are due to chromosomal abnormalities.

Chromosomal Abnormalities & Pregnancy Loss

✅ Key Statistics on Pregnancy Loss:

• 15–20% of clinically recognized pregnancies end in miscarriage.
• 1% of couples experience recurrent pregnancy loss (two or more miscarriages).
• 65–75% of early pregnancy losses are due to chromosomal abnormalities.

🔹 Common Chromosomal Abnormalities in POCs:

1. Trisomy (most common, accounting for ~60% of aneuploidies).
2. Monosomy X (Turner syndrome, 45,X) (~13% of cases).
3. Triploidy (11%).
4. Tetraploidy (4%).
5. Structural chromosomal abnormalities (4%).
6. Mosaic trisomy (2%).
7. Double trisomy (3%).

📌 Trisomy 16 is the most frequently observed aneuploidy in POCs (~30% of cases).

Aneuploidy & Maternal Age

✅ Maternal age increases the risk of aneuploidies due to errors in meiosis.

• Older oocytes have a higher probability of chromosomal missegregation.
• Women over 35 have an increased risk of trisomic conceptions.

📌 Genetic counseling is advised for women with recurrent pregnancy loss or advanced maternal age.

POC Testing Techniques: NGS vs. Traditional Methods

✅ 1. Karyotyping (Traditional Method):

• Analyzes all chromosomes using stained metaphase spreads.
• Requires viable cells for culturing.
• 40% of cases fail due to poor tissue viability.
• Maternal cell contamination may mask fetal abnormalities.

✅ 2. Quantitative Fluorescent PCR (QF-PCR):

• Molecular technique that does not require viable cells.
• Screens only selected chromosomes (13, 15, 16, 18, 21, 22, X, Y).
• Misses ~28% of chromosomal abnormalities.

✅ 3. Next-Generation Sequencing (NGS) (New Ampath Protocol):

• Screens all chromosomes (1–22, X, Y).
• Requires DNA (does not need viable cells).
• Detects:
  • Trisomies.
  • Monosomies.
  • Polyploidies (triploidy, tetraploidy).
  • Large chromosomal deletions/duplications (>10 Mb).
• >95% detection rate, >99% success rate.

📌 NGS is now the preferred method at Ampath due to its superior accuracy and ability to analyze non-viable tissue.

Expanded Chromosome Screening Using NGS at Ampath

✅ Advantages of NGS-Based POC Testing:

• Covers all chromosomes, unlike QF-PCR.
• No need for cell culture (reducing failure rates).
• Higher accuracy and detection rates.
• Detects large deletions and duplications.

✅ Sample Collection & Transport:

• Tissue should be collected in saline and transported at room temperature.

✅ Turnaround Time:

• 7 working days.

📌 The cost of NGS-based POC testing remains the same as QF-PCR testing previously offered by Ampath.

Key Takeaways for Clinicians

✅ NGS is now the preferred method for POC testing, replacing QF-PCR.
✅ Trisomy is the most common chromosomal abnormality in pregnancy loss (~60% of aneuploidies).
✅ NGS detects aneuploidies, polyploidies, and large deletions/duplications with >95% accuracy.
✅ Maternal age is a key risk factor for chromosomal abnormalities in pregnancy.
✅ POC samples can be collected in saline and transported at room temperature.

📌 Ampath Genetics provides NGS-based expanded chromosome screening for POCs, offering faster and more comprehensive results than traditional methods.