Family Testing: When and Why Is It Necessary?

Why family studies matter after Exome or Genome sequencing

1. From “a variant” to “a diagnosis”

Exome and genome sequencing can identify thousands of genetic variants in a single test. However, once results are returned, clinicians and families often face the same fundamental question:

“Is this variant truly responsible for my child’s symptoms?”

Answering this question almost always requires family testing, also known as a family study. Family testing is not a simple add-on test—it is a critical interpretive step that helps complete the genomic diagnosis.

2. Genomic testing is not only about finding variants, but about interpreting them

Exome and genome sequencing detect tens of thousands of variants per individual. The vast majority of these variants are also found in the general population and are clinically benign.

Therefore, the essence of genomic diagnosis is not whether a variant exists, but whether that variant can reasonably be interpreted as the cause of disease.

One of the most important pieces of evidence in this interpretation is whether the same variant is present in other family members.

3. Two distinct roles of family testing

Although family testing may appear to be a single procedure, it actually addresses two different and sequential questions.

[1] Where did this variant come from?

Determining the origin of the variant

The first question is straightforward:
Was this variant inherited from a parent, or did it arise newly in the patient?

De novo variants

• Not present in either parent
• Strongly increase the likelihood of pathogenicity, especially in pediatric-onset neurologic disorders, developmental delay, and congenital anomalies

Inherited variants

• Present in one or both parents
• By itself, inheritance does not confirm or exclude causality

At this stage, the goal is fact-finding. This step does not yet determine whether the variant is disease-causing.

[2] Is this variant truly the cause of disease?

Filtering out incidental findings

The second question is whether the variant can plausibly explain the patient’s clinical features—or whether it is an incidental finding.

For example, if a parent carries the same variant, is clinically healthy, and there is no relevant family history, the variant is more likely to be interpreted as unlikely to be causative, even though it was detected.

In other words:

• Step 1 asks “Where did the variant come from?”
• Step 2 asks “Does this variant actually matter?”

4. Why family testing is particularly important

▪ Reclassification of VUS (Variants of Uncertain Significance)

Segregation analysis—examining whether a variant is present only in affected individuals, absent in unaffected relatives, or shared by healthy family members—provides critical evidence for reclassifying VUS toward Likely Pathogenic or Benign.

▪ Validation of inheritance patterns

Family testing helps confirm whether a variant fits the expected mode of inheritance:

• Autosomal recessive disorders
  → Are both parents carriers?
• Autosomal dominant disorders
  → Is incomplete penetrance possible in an unaffected parent?
• X-linked disorders
  → Is the mother a carrier?

These questions cannot be reliably answered without family data.

▪ Recurrence risk and family planning counseling

Family testing results directly inform recurrence risk counseling, which is a key component of discussions with parents:

• De novo variants → Low recurrence risk
• Autosomal recessive disorders → 25% recurrence risk
• Autosomal dominant disorders → 50% recurrence risk

This information is essential for future pregnancy planning.

5. Summary

Exome and genome sequencing are powerful starting points for genomic analysis, but in many cases, the clinical significance of a detected variant cannot be determined from the proband’s data alone.

Family testing plays a crucial role not in discovering new variants, but in determining how already identified variants should be interpreted.

If exome and genome sequencing broaden the diagnostic possibilities, family testing is the step that allows those possibilities to be translated into a clinically meaningful conclusion.

6. A common clinical question

In practice, clinicians are often asked:

“We would like to proceed with family testing—can this variant be confirmed using Sanger sequencing?”

The answer is that not all variants can be reliably assessed using Sanger sequencing.

In the next article, we will explore which types of variants cannot be confirmed by Sanger sequencing, and why these limitations exist—based on real-world testing workflows.