Diagnostic RNA-seq Implementation

Our laboratory has launched clinical transcriptome sequencing as an innovative tool for molecular diagnosis, offering transcriptome-based analysis beyond DNA-based testing. Since 2024, we have been operating the RNA-seq diagnostic pipeline as part of the NIH Undiagnosed Diseases Network (UDN) sequencing core, supporting all clinical sites nationwide. Through this effort, we are generating clinical experience in the development, validation, and implementation of RNA-seq for routine diagnostics. Ongoing work focuses on defining clinical utility, refining analytical workflows, and expanding the interpretive value of transcriptome-based findings in rare disease diagnostics.

Enhancing Diagnostic Yield Through Cell Differentiation

A major limitation of diagnostic RNA-seq is that disease-relevant genes may be inadequately expressed in clinically accessible tissues such as blood or skin fibroblasts. To overcome this, we are developing scalable protocols to differentiate patient-derived cells into target cell types that better reflect tissue-specific gene expression. Our lab has successfully implemented transdifferentiation approaches to generate induced neurons from both fibroblasts and blood specimens, enabling functional assessment of variants associated with neurological disorders. These strategies are currently being applied in UDN cases to improve diagnostic sensitivity and expand the scope of RNA-seq–based variant interpretation.

Patient-derived differentiated cells as a platform for streamlining individualized therapies

We are exploring the potential of trans-differentiated, patient-specific cell lines for the design and validation of oligonucleotide therapies for Mendelian disorders. The successful development of such a patient-specific cell-based system holds the promise of enabling early intervention in genetic disorders. In one project, we are collaborating with families affected by SPTAN1 defects to develop antisense oligonucleotide (ASO) therapies. Our long-term goal is to establish a systematic framework for screening, validating, and recommending RNA-based therapies directly following molecular diagnostics.

Implementing a low-cost sequencing technology into clinical diagnostics

We are partnering with Ultima Genomics to explore the integration of high-throughput, low-cost next-generation sequencing technologies into clinical diagnostic applications, with the goal of expanding access to genomic testing. Our team is currently implementing and optimizing the entire workflow—including wet lab protocols, bioinformatics pipelines, and clinical interpretation processes—for both whole genome sequencing and RNA-seq in a diagnostic setting.

Characterization of clinically actionable genetic modifiers by sequencing individuals with large genomic deletions

In this project, we leverage our unique access to rare disease patient resources to conduct an “enhancer screen” using carefully selected patient samples. We aim to sequence a cohort of individuals with large, recurrent heterozygous genomic deletions to elucidate the impact and mechanisms of genetic modifiers. These selected individuals present two unique features that allow us to detect disease-risk modifying alleles with enhanced power compared to conventional GWAS studies: first, these unrelated individuals share identical large heterozygous deletions; second, they exhibit a wide range of incompletely penetrant clinical phenotypes. We are currently studying two disorders as proof-of-concepts: the 17q12 deletions associated with diabetes and kidney cysts, and the distal 1q21 deletions associated with neurodevelopmental disorders. The findings from this project are expected to bridge the gap between our understanding of highly penetrant, rare Mendelian variants and those with higher population frequencies that are associated with complex diseases.

Pengfei Liu Ph.D.

Email:

pengfeil@bcm.edu

By Phone:

(713)-798-7725

Molecular and Human Genetics

Baylor College of Medicine

ACGME/ABMGG Laboratory Genetics and Genomics Fellowship Program

Baylor College of Medicine

Houston, Texas United States

NGS/Molecular

Baylor Genetics

One Baylor Plaza

Room 223E

Mail Stop BCM 225

Houston, TX 77030

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