Baylor College of Medicine








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Dr. Pengfei Liu is an Associate Professor at the Department of Molecular and Human Genetics in Baylor College of Medicine. He is the Director of the ACGME/ABMGG Laboratory Genetics and Genomics Fellowship Program. Dr. Liu also work in the Baylor Genetics diagnostic laboratories as a sign out lab director. The broad research interest of Dr. Liu's research laboratory is to improve the molecular diagnosis and clinical care of patients with Mendelian disorders.


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Coauthor's Affiliations

Our broad research interest is to improve the molecular diagnosis and clinical care of patients with Mendelian disorders. On the translational side, we aim to bring transformative technologies and concepts to clinical diagnostics. On the discovery side, we strive to empower diagnostic resources and clinical big data to stimulate research investigations. Below are several ongoing projects.

Diagnostic RNA-seq and cell trans-differentiation

A fundamental obstacle in the clinical application of diagnostic RNA-seq is that the genes of interest are not always adequately expressed in the clinically accessible tissues. We are developing protocols to activate the genes of interest by trans-differentiating available patient cells to the desired cell type. The goal is to optimize the protocols so that they are low cost, rapid, and can be applied at scale in a clinical workflow. We have successfully converted human fibroblasts into induced neurons to help the interpretation of variants associated with neurological disorders. This workflow is being applied to patients from the Undiagnosed Diseases Network (UDN) project to improve the molecular diagnostic yield.

Implementing a low-cost sequencing technology into clinical diagnostics

We are collaborating with a new biotechnology company, Ultima Genomics, to bring low-cost next generation sequencing to clinical diagnostics. The Ultima sequencer can deliver whole genome sequencing for a human specimen at a cost considerably lower than traditional methods. We are in the process of implementing and optimizing the wet lab set up, bioinformatics pipeline, and clinical interpretation processes for clinical diagnostics using whole genome sequencing and RNA-seq.

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

We seek to sequence a group of individuals with large recurrent heterozygous genomic deletions to elucidate the impact and mechanisms of genetic modifiers. These selected individuals present two unique features, which allow us to detect from their genomic analysis disease-risk modifying alleles, especially those that are clinically meaningful, at an enhanced power compared to conventional GWAS studies. First, these unrelated individuals share identical large heterozygous deletions; second, they present 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. Findings from this project are expected to bridge the gap between our understanding of highly penetrant, rare Mendelian variants and variants with higher population frequencies and association with complex diseases.

Screening of genetic elements using segmental haploid human cell lines

We are establishing human cell lines derived from individuals with constitutional large heterozygous genomic deletions as models. These models can be used to conduct genetic screens, for example, CRISPR screens. Screening results from these ‘segmental haploid’ cell lines are expected to be more sensitive and more likely to be clinically meaningful than screening results obtained from traditional diploid or cancerous cell lines.

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Pengfei Liu Ph.D.


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Associate Professor
Molecular and Human Genetics
Baylor College of Medicine
ACGME/ABMGG Laboratory Genetics and Genomics Fellowship Program
Baylor College of Medicine
Houston, Texas United States
Associate Clinical Director
Baylor Genetics
One Baylor Plaza
Room 223E
Mail Stop BCM 225
Houston, TX 77030

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