Novel Chromosome 18 Polymorphism Identified through NIPT: A Case Report

Technical Summary: Novel Chromosome 18 Polymorphism Identified through NIPT

Problem Statement
Non-invasive prenatal testing (NIPT) using cell-free fetal DNA (cfDNA) has become a standard screening tool for common autosomal aneuploidies, including Trisomy 18 (Edwards syndrome). However, cfDNA is a screening modality with a known false-positive rate and cannot definitively confirm or characterize the nature of chromosomal abnormalities. This case report addresses a specific clinical scenario where a patient received a "high-risk" NIPT result for Trisomy 18, which was complicated by an inability of the screening algorithm to complete the analysis due to an interfering chromosomal data pattern. The core problem involves the potential for misinterpretation of such screening results, leading to unnecessary anxiety and potentially irreversible pregnancy management decisions (such as termination) without confirmatory diagnostic testing. Furthermore, the case highlights the challenge of interpreting novel copy number variants (CNVs) that do not fit established phenotypic patterns.

Methodology
The study utilizes a single-case report design involving a 25-year-old G1P0 patient presenting at 15 weeks and 3 days gestation. The methodology followed a multi-tiered diagnostic approach:

1. Initial Screening: Review of an external cfDNA report indicating high risk for Trisomy 18, though the report noted the test could not be completed due to data interference.
2. Diagnostic Confirmation: The patient underwent amniocentesis at 15w3d.
3. Genetic Analysis: The amniotic fluid sample was subjected to three distinct analyses:
   • Fluorescence in situ hybridization (FISH): Performed on uncultured amniocytes to rule out standard Trisomy 18.
   • Chromosome Analysis (Karyotyping): Performed to identify banding patterns.
   • Chromosomal Microarray Analysis (CMA): Specifically Single Nucleotide Polymorphism (SNP) microarray, to characterize the specific nature and size of the variant.
4. Maternal Correlation: The patient's blood was analyzed via CMA to determine the inheritance pattern of the identified variant.
5. Literature and Database Review: The identified variant was cross-referenced against the Online Mendelian Inheritance in Man (OMIM) catalog, the Clinical Genome Resource (ClinGen), the DECIPHER database, the UCSC Genome Browser, and the Database of Genomic Variants (DGV) to assess pathogenicity and frequency.

Key Results

• Variant Identification: While FISH was normal for Trisomy 18, chromosome analysis revealed an abnormal banding pattern on the long arm of chromosome 18 (18q). SNP microarray confirmed a 5.2 Mb triplication (resulting in four total copies) of the region chr18:36,723,898–41,924,037 (GRCh37).
• Inheritance: The triplication was found to be maternally inherited; the mother and fetus shared the identical variant.
• Classification: Due to the lack of prior reports in healthy populations or disease databases, the variant was classified as a Variant of Uncertain Significance (VUS) according to American College of Medical Genetics and Genomics (ACMG) standards. The authors noted that while inheritance from an unaffected parent suggests a benign familial variant, variable expressivity could not be ruled out.
• Phenotypic Correlation:
  • Maternal: The mother is phenotypically normal with no physical malformations or developmental abnormalities.
  • Fetal: Serial anatomy ultrasounds (at 15w and 20w) showed an anatomically normal fetus with no markers of Trisomy 18 (e.g., no hypoplastic nasal bone, micrognathia, or thickened nuchal fold).
  • Outcome: The pregnancy ended in intrauterine fetal demise at 21 weeks due to preterm premature rupture of membranes. Post-mortem autopsy of the fetus, placenta, and umbilical cord revealed no findings characteristic of Trisomy 18 or other chromosomal syndromes.
• NIPT Interference: Retrospective analysis by a QNatal geneticist confirmed that the specific chromosomal data pattern associated with this triplication interfered with the standard cfDNA algorithm's ability to detect gain or loss, leading to an inconclusive or "unable to be completed" report rather than a definitive positive.

Key Contributions

• Novel Variant Description: The paper reports the first known instance of a specific 5.2 Mb triplication in the 18q12.2q12.3 region (containing genes PIK3C3, RIT2, and SYT4) that presents without phenotypic abnormalities in either the carrier mother or the fetus.
• Genomic Characterization: The authors detail that the triplicated region lies largely within the heterochromatic 18q12.3 band, which is unlikely to undergo frequent transcription, potentially explaining the lack of pathogenicity despite the copy number increase.
• Clinical Workflow Demonstration: The case serves as a practical demonstration of the necessity of invasive diagnostic testing (amniocentesis with CMA) following abnormal or inconclusive NIPT results, particularly when the screening report indicates technical interference.

Significance and Claims
The paper modestly claims that this case underscores the critical importance of confirmatory testing when prenatal screens return abnormal or inconclusive results. The authors emphasize that:

1. NIPT Limitations: cfDNA is a screening tool, not a diagnostic one, and specific copy number variants can interfere with screening algorithms, leading to false alarms or technical failures.
2. Counseling Implications: Obstetricians must communicate the limitations of NIPT, specifically the positive predictive value (PPV) which can be as low as 15% in certain stratifications, to prevent patients from making irreversible decisions based solely on screening data.
3. Variant Interpretation: The identification of a novel triplication with no associated phenotype expands the known spectrum of chromosome 18 abnormalities and suggests that not all copy number gains in this region are pathogenic.
4. Need for Continued Characterization: The authors call for continued molecular characterization of chromosomal abnormalities to better determine the clinical significance of specific genotypes, noting that this specific triplication appears to be a rare, possibly benign familial variant.

The paper concludes that effective communication and the offering of diagnostic confirmation are essential to guide counseling, particularly in cases where screening results are ambiguous or where novel variants are detected.