Modern Approaches to Rare Disease Testing

Many people living with rare diseases spend years searching for answers.^1,2 The path to a correct diagnosis is filled with repeated tests, specialist referrals, and long stretches of uncertainty. This experience is widely known as the diagnostic odyssey, and it can be deeply frustrating for families who can’t begin appropriate care until they understand the cause of their condition. Christine Eng, M.D., Chief Medical Officer and Chief Quality Officer at Baylor Genetics, is among those working to shorten this journey. Her background in pediatrics and medical genetics has shaped a career focused on bringing clarity to families facing uncertain diagnoses. “We know that behind every test is a patient and a family, and they're looking for the clearest possible answers that we can provide,” stated Eng.

The Diagnostic Challenge
Despite steady progress in genetic testing, diagnosing rare diseases remains a challenging task. There are thousands of known conditions, and with overlapping symptoms and limited available data, each case requires careful and individualized investigation.³ But diagnostic tools have improved considerably over the past several decades. The field has moved from karyotyping and Sanger sequencing to chromosomal microarrays, and more recently to next-generation sequencing (NGS).⁴ NGS now supports routine evaluation of suspected genetic disorders and is a central part of rare disease testing.

Drawing on more than 45 years of experience, Eng explained that Baylor Genetics has adapted to each major shift in genetic testing. Throughout these changes, the goal has stayed the same: to use every available tool to identify the cause of a patient’s symptoms. A key part of their current approach involves whole exome and whole genome sequencing. These methods enable clinicians to review thousands of genes at once and search for genetic changes that may explain a disorder. Eng noted that exome and genome sequencing are even beginning to move into frontline care. This shift is reflected in recent guidance from the American Academy of Pediatrics recommending these tests as first-tier options for children with intellectual disability or developmental delay, a change that helps clinicians apply them earlier in the diagnostic process.⁵

The wider use of exome and genome sequencing has also shown that some rare disease cases remain unresolved and require programs that can examine these histories in greater depth. Baylor Genetics supports this effort through its role in the Undiagnosed Diseases Network, a National Institutes of Health supported consortium that reviews some of the most complex and longstanding medical histories. The network brings together clinical and research experts nationwide to investigate medical mysteries that require in-depth analysis. Eng shared that Baylor Genetics serves as the sequencing core for this program, providing exome, genome, and now transcriptomic testing for families who continue to search for answers.

Turning to the Transcriptome
When DNA testing results are inconclusive, additional data can supply evidence needed to interpret ambiguous findings. One emerging approach is RNA sequencing (RNA-seq), which helps show the consequences of a variant at the transcription level.⁶ “While DNA tells us what variants are there, RNA-seq can reveal what those variants end up causing or how they actually affect gene function,” explained Eng. This is particularly valuable for variants of uncertain significance, genetic changes that cannot be confidently classified as harmful or benign.

Some of these variants can lead to abnormal expression or disrupted splice junctions that become visible using RNA sequencing. With this in mind, Baylor Genetics established RNA sequencing as a reflex test after genome or exome sequencing when a variant needs clearer interpretation. “We found that over 40 percent of the variants that qualify for RNA-seq are able to be reclassified,” noted Eng. “That is really helpful to the patient and the clinician.”

Expanding Tools in Rare Disease Diagnosis
While difficult cases continue to arise, scientists are developing tests that capture information beyond the genome. Eng explained that her team starts by identifying specific gaps in the field and determining where additional data could help clarify unresolved findings. Any new test must also demonstrate analytical and clinical validity and provide information that is meaningful in a clinical setting. Eng added that education is an essential part of the process, ensuring that providers understand the capabilities of each method and how to interpret the findings correctly.

Building on these approaches, the group has expanded its work to include metabolomics. Baylor Genetics’ Global MAPS (Metabolomic Assisted Pathway Screen) test examines small molecules in metabolic pathways as a stand-alone analysis and can pair those findings with genomic data when available. “We are trying to bring all of these different techniques to improve the diagnostic precision,” stated Eng. She noted that metabolomic data can help clarify variants of uncertain significance by identifying pathway abnormalities that support or refute a suspected genetic effect.

Across the field, other emerging tools are contributing to rare disease testing. Methylation profiling can identify characteristic signatures linked to imprinting conditions or syndromes tied to disruptions in epigenetic machinery.⁷ In some cases, these patterns help support or rule out variants in genes associated with methylation. Long-read sequencing is being applied to capture regions that are difficult to evaluate with short-read approaches, including repeat expansions and complex rearrangements.⁸ Optical genome mapping can detect large structural changes, such as inversions or sizable deletions, that standard sequencing may miss.⁹ Proteomics may also play a valuable role by examining protein levels and protein modifications.¹⁰ These patterns can clarify the effect of genetic variants on downstream pathways and support diagnoses in conditions that affect protein stability or cellular signaling.

Looking Ahead in Rare Disease Diagnosis
For the future, Eng described a field that will increasingly become more multiomic, where rare disease testing draws on genomic, transcriptomic, metabolic, and other data types to examine gene activity from several angles. She added that advances developed in research settings will continue to move into clinical practice as evidence grows and workflows mature. As more of these approaches become part of routine evaluation, Baylor Genetics plans to help clinicians understand how to apply them and how to interpret the findings in a clear and dependable way. Ultimately, Eng emphasized that the group remains committed to supporting patients and their families and helping bring the diagnostic odyssey to a close. “We see ourselves as partners in this journey and taking really complex work and trying to make it as accessible and clear as possible,” Eng stated.

References

1. Faye F, Crocione C, Anido de Peña R, et al. Time to diagnosis and determinants of diagnostic delays of people living with a rare disease: results of a Rare Barometer retrospective patient survey. Eur J Hum Genet. 2024;32:1116-1126. doi:10.1038/s41431-024-01604-z
2. The Lancet Global Health. The landscape for rare diseases in 2024. Lancet Glob Health. 2024;12(3):e341. doi:10.1016/S2214-109X(24)00056-1
3. Haendel M, Vasilevsky N, Unni D, et al. How many rare diseases are there? Nat Rev Drug Discov. 2020;19(2):77-78. doi:10.1038/d41573-019-00180-y
4. Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New diagnostic approaches for undiagnosed rare genetic diseases. Annu Rev Genom Hum Genet. 2020;21:351-372. doi:10.1146/annurev-genom-083118-015345
5. Rodan LH, Stoler J, Chen E, Geleske T, Council on Genetics. Genetic evaluation of the child with intellectual disability or global developmental delay, clinical report. Pediatrics. 2025;156(1):e2025072219. doi:10.1542/peds.2025-072219
6. Zhao S, Macakova K, Sinson JC, et al. Clinical validation of RNA sequencing for Mendelian disorder diagnostics. Am J Hum Genet. 2025;112(4):779-792. doi:10.1016/j.ajhg.2025.02.006
7. Tan JW, Blake EJ, Farris JD, Klee EW. Expanding upon genomics in rare diseases, epigenomic insights. Int J Mol Sci. 2024;26(1):135. doi:10.3390/ijms26010135
8. Steyaert W, Sagath L, Demidov G, et al. Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing. Genome Res. 2024;35(4), 755-768. doi:10.1101/gr.279414.124
9. van der Sanden B, Neveling K, Shukor S, et al. Optical genome mapping enables accurate testing of large repeat expansions. Genome Res. 2025;35(4):810-823. doi:10.1101/gr.279491.124
10. McCormick EM. The case for including proteomics in routine diagnostic practice for rare disease. Genome Med. 2025;17(1):61. doi:10.1186/s13073-025-01491-z