1. Karyotyping
   • What it is: Analysis of metaphase chromosomes under a microscope to detect large chromosomal abnormalities (e.g., trisomies, large deletions/duplications).
   • Limitations: Resolution is limited to changes of ~5–10 megabases; smaller variants go undetected. Turnaround time is typically 10–14 days [1].
2. Fluorescence In Situ Hybridization (FISH)
   • What it is: Uses fluorescent probes to target specific DNA sequences on chromosomes, enabling the detection of microdeletions or duplications not visible via karyotype.
   • Limitations: Requires a priori suspicion of a particular chromosomal region; cannot screen the entire genome.
3. Targeted Single-Gene Testing
   • What it is: Sequencing or mutation analysis of one gene known to cause a patient’s phenotype (e.g., CFTR for cystic fibrosis).
   • Limitations: Inefficient when multiple genes could underlie the condition; negative results often prompt a lengthy search for the correct gene.

Chromosomal Microarray (CMA)

• Overview: CMA platforms (e.g., array comparative genomic hybridization [aCGH] or single nucleotide polymorphism [SNP] arrays) detect copy number variations (CNVs), submicroscopic gains and losses of DNA, across the genome [2].
• Advantages:
  • Higher resolution (~50–100 kilobases) compared to karyotyping.
  • Detects unbalanced rearrangements (microdeletions/duplications) that can cause developmental delays, autism spectrum disorders, and congenital anomalies.
• Clinical Impact:
  • Diagnostic yield in children with developmental delay/intellectual disability: ~15–20% [3].
  • Often serves as a first-tier test for unexplained neurodevelopmental disorders.

Next-Generation Sequencing (NGS)

NGS refers to high-throughput sequencing technologies that allow millions of DNA fragments to be read in parallel. Key NGS applications include:

• Panel Testing
  • • What it is: Simultaneous sequencing of dozens to hundreds of genes known to be associated with a specific phenotype (e.g., epilepsy panel, cardiomyopathy panel).
    • Advantages:
      • More cost-effective than sequential single-gene testing.
      • Higher diagnostic yield for heterogeneous conditions.
    • Clinical Impact:
      • Epilepsy gene panels can identify a molecular diagnosis in ~20–30% of patients with early-onset seizures [4].
      • Cardiomyopathy panels elucidate pathogenic variants in ~30–50% of familial cases [5].
• Whole Exome Sequencing (WES)
  • • What it is: Sequencing of all protein-coding regions (~1–2% of the genome) where approximately 85% of known disease-causing variants reside [6].
    • Advantages:
      • Broad coverage of ~20,000 genes.
      • Particularly useful when the phenotype is unclear or multiple genes could be implicated.
    • Clinical Impact:
      • Diagnostic yield in cohorts of undiagnosed rare disease patients: ~25–40% [7].
      • Can uncover novel gene-disease associations, advancing scientific knowledge and patient care.
• Whole Genome Sequencing (WGS)
  • • What it is: Sequencing of the entire genome, including coding and non-coding regions.
    • Advantages:
      • Identifies CNVs, single-nucleotide variants (SNVs), small insertions/deletions, structural variants (SVs), and variants in regulatory regions.
      • Does not require prior knowledge of candidate genes.
    • Clinical Impact:
      • Compared to WES, WGS can increase diagnostic yield by an additional 5–10% in rare disease cohorts [8].
      • Particularly valuable for detecting non-coding variants (e.g., intronic splice changes) or complex structural rearrangements.
• RNA Sequencing (RNA-Seq)
  • • What it is: Sequencing of transcriptomes (all RNA transcripts) to assess gene expression levels, alternative splicing events, and allele-specific expression [9].
    • Clinical Utility:
      • In cases where DNA sequencing (WES/WGS) is inconclusive, RNA-Seq from patient-derived tissues (e.g., blood, fibroblasts) can reveal splicing abnormalities, gene-fusion events, or expression outliers that explain disease [10].
    • Limitations:
      • Requires access to relevant tissue; blood may not reflect gene expression in affected tissue (e.g., brain for neurological disorders).
      • Interpretation of RNA data demands specialized bioinformatics pipelines.
• Methylation Analysis & Epigenetic Testing
  • • What it is: Assessment of DNA methylation patterns to diagnose imprinting disorders (e.g., Prader–Willi syndrome, Angelman syndrome) and multilocus imprinting disturbances [11].
    • Clinical Impact:
      • Identifies conditions invisible to sequence-based methods, such as epimutations or differential methylation.
      • Diagnostic yield of ~10–20% in patients with growth and developmental anomalies suggestive of imprinting defects [12].

Non-Invasive Prenatal Testing (NIPT)

• • What it is: Analysis of cell-free fetal DNA in maternal blood to screen for common aneuploidies (trisomy 21, 18, 13) and select microdeletion syndromes [13].
  • Advantages:
    • High sensitivity and specificity (>99% for trisomy 21).
    • Low risk: no invasive procedure required.
  • Limitations:
    • Screening, not diagnostic, positive results require confirmatory CVS or amniocentesis.
    • Can yield false positives/negatives in rare scenarios (e.g., confined placental mosaicism, vanishing twin).

Technological advances in genetic testing have tangible benefits for patient care:

1. Increased Diagnostic Yield
   • NGS-based approaches elevate diagnostic rates in complex disorders. In a large cohort, combining WES and CMA resulted in a molecular diagnosis in ~45% of cases with intellectual disability [14].
   • Earlier diagnosis facilitates targeted management, reducing morbidity and improving outcomes (e.g., early intervention for metabolic disorders).
2. Reduced Diagnostic Odysseys
   • Before NGS, patients often endured years of testing across multiple specialties. Now, trio-WES (sequencing of the patient and both parents) can yield diagnoses in as little as 3 months, compared to an average of 7 years historically [15].
3. Precision Medicine & Targeted Therapies
   • Identifying actionable variants enables personalized treatments (e.g., MECP2 mutations in Rett syndrome guiding targeted therapies; CFTR modulators for specific cystic fibrosis genotypes) [16][17].

While transformative, advanced genetic tests come with challenges:

1. Variants of Uncertain Significance (VUS)
   • NGS often uncovers VUS, genetic changes whose clinical relevance is unclear. VUS rates in WES can be ~30–50% [19].
   • Resolving VUS requires functional studies, segregation analysis, and reference to evolving databases.
2. Need for Confirmatory Testing
   • Microarray findings may need FISH or quantitative PCR for confirmation.
   • WES/WGS findings sometimes require Sanger sequencing or targeted assays to validate variants, especially in repetitive regions.
3. Ethical Considerations
   • Incidental Findings: WES/WGS can reveal unrelated actionable variants (e.g., BRCA1 pathogenic variant). It is like when performing an abdominal ultrasound to look at the stomach, the kidneys can also be screened, and these are called incidental and secondary findings. Guidelines from the American College of Medical Genetics and Genomics recommend offering to return certain actionable findings [21].

Privacy and Data Storage: Genome data is sensitive; therefore, secure storage and clear consent for data use and sharing are essential.

Genetic counselors bridge the gap between cutting-edge technology and patient needs:

1. Education & Informed Consent
   • Explaining test scope, possible outcomes (diagnostic, VUS, incidental), and limitations.
   • Ensuring patients understand turnaround times and follow-up requirements.
2. Risk Communication
   • Translating complex statistical probabilities into concrete implications for patients and families.
   • Providing context: for example, explaining that a VUS does not confirm or rule out a diagnosis but may require future re-evaluation.
3. Emotional and Psychosocial Support
   • Helping patients cope with uncertainty, anxiety, and potential guilt or blame.
   • Facilitating family discussions when hereditary findings may affect relatives.
4. Post-Test Guidance
   • Interpreting results and recommending appropriate referrals (e.g., neurology, metabolic specialists).
   • Discussing reproductive options if variants have reproductive implications (e.g., carrier status, risk to offspring).

For a comprehensive overview of the genetic counseling process, see our blog: Understanding the Genetic Counseling Process: A Comprehensive Guide.

Technological breakthroughs have made genetic testing more powerful, precise, and accessible than ever before. From high-resolution microarrays to whole-genome sequencing, these tools have shortened diagnostic journeys, informed targeted therapies, and advanced precision medicine.

Yet, the complexity of interpreting vast genomic data underscores the indispensability of genetic counseling.

By combining state-of-the-art technology with empathetic guidance, genetic counselors ensure patients receive both the scientific insights and emotional support they need to make informed health decisions.

Not everyone who comes in for counseling will require a genetic test, and not everyone who undergoes testing has received proper counseling. But combining both is what makes this process truly valuable.