Pengfei Liu, Ph.D.
Picture
Pengfei Liu, Ph.D.
Director
Positions
- Director
-
ACGME/ABMGG Laboratory Genetics and Genomics Fellowship Program
Baylor College of Medicine
Houston, Texas United States
- Associate Clinical Director
-
NGS/Molecular
Baylor Genetics
- Associate Professor
-
Molecular and Human Genetics
Baylor College of Medicine
- Director
-
Medical Genetics and Multiomics Laboratory (MGML)
Education
- PhD from Baylor College of Medicine
- 01/2012 - Houston, TX
Certifications
- Clinical Molecular Genetics
- #2015130
- American Board of Medical Genetics and Genomics
- Laboratory Genetics and Genomics
- #2023143
- merican Board of Medical Genetics and Genomics
Honors & Awards
- C. W. Cotterman Award
- The American Society of Human Genetics (01/2012)
- The 10 most significant advances in genomic medicine for 2019, by NHGRI
- https://www.cell.com/ajhg/pdf/S0002-9297(19)30427-6.pdf
- Dr. Michael S. Watson Genetic and Genomic Medicine Innovation Award
- The ACMG Foundation for Genetic and Genomic Medicine (03/2022)
Professional Interests
- Clinical whole genome sequencing
- Medical genetics
- Genomic disorders
Professional Statement
Dr. Pengfei Liu has contributed extensively to the advancement of genomic medicine for rare diseases over the past two decades. His work spans a broad range of technologies that have shaped modern clinical genetics—from early investigations of genome rearrangements using array-based platforms to clinical reanalysis of exome sequencing, whole genome sequencing (WGS) implementation, and, more recently, clinical transcriptome sequencing. These efforts have helped expand the diagnostic landscape for Mendelian disorders and laid the foundation for future precision medicine approaches.Dr. Liu’s research includes a landmark study on clinical exome reanalysis published in The New England Journal of Medicine, which was named one of the Top 10 Genomic Advances of the Year by NHGRI. He also developed and validated the clinical WGS test for the NIH Undiagnosed Diseases Network (UDN), now a central diagnostic tool at Baylor Genetics and widely used for patients with rare and undiagnosed conditions.
As Director of the Medical Genetics and Multiomics Laboratory (MGML) at Baylor College of Medicine, Dr. Liu leads efforts to bring transcriptome sequencing into clinical practice. His lab has established protocols to generate disease-relevant tissues through patient-derived cell transdifferentiation, enabling detection of splicing disruptions and gene expression anomalies not captured by DNA sequencing alone. This approach not only enhances diagnostic yield, but also supports downstream RNA-guided therapeutic development, including screening of antisense oligonucleotides (ASOs).
In addition to his research, Dr. Liu directs the ACGME-accredited Laboratory Genetics and Genomics Fellowship Program at Baylor, where he mentors and trains future leaders in clinical molecular diagnostics. He plays an active role in national consortia such as the UDN, GREGoR, RADIANT, and PrenatalSEQ, contributing to collaborative efforts to improve the diagnosis and treatment of rare genetic conditions.
Websites
Selected Publications
- Yuan B, Neira J, Pehlivan D, [...], Xiao R, Liu, P. "Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies." Genet Med. 2018; Pubmed PMID: 30158690
- Liu P, Yuan B, Carvalho CM, [...], Hurles ME, Lupski JR. "An Organismal CNV Mutator Phenotype Restricted to Early Human Development." Cell. 2017;168:830. Pubmed PMID: 28235197
- Liu P, Erez A, Nagamani SC, [...], Lupski JR, Bi W. "Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements.." Cell. 2011;146:889. Pubmed PMID: 21925314
- Liu P, Meng L, Normand EA, [...], Lupski JR, Yang Y. "Reanalysis of Clinical Exome Sequencing Data.." N Engl J Med. 2019;380:2478. Pubmed PMID: 31216405
- Vetrini F, McKee S, Rosenfeld JA, [...], Lupski JR, Liu P. "De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome.." Genome Med. 2019;11:12. Pubmed PMID: 30819258
- Mao D, Liu C, Wang L, (…), Liu P, Liu Z. "AI-MARRVEL - A Knowledge-Driven AI System for Diagnosing Mendelian Disorders.." NEJM AI. 2024;1:10.1056/aioa2300009. Pubmed PMID: 38962029
- Zhao S, Macakova K, Sinson J, (…), Liu P. "Clinical validation of RNA sequencing for Mendelian disorder diagnostics." medRxiv. 2024;doi.org/10.1101/2024.08.15.24312057
- Yuan, B, Schulze, K, (...), Liu P "Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits.." Genome Med. 2022;14:113.
- Li S, Zhao S, Sinson JC, (…), Liu P. "The clinical utility and diagnostic implementation of human subject cell transdifferentiation followed by RNA sequencing." Am J Hum Genet. 2024;111:841-862. Pubmed PMID: 38593811
- Du H, Jolly A, Grochowski CM, (…), Liu P. "The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation." Genome Med. 2022;14:122. Pubmed PMID: 36303224
Funding
- Characterizing disease-causing variants using personal genomes with large recurrent deletions - #R35 HG011311
- ( 07/01/2021 - 06/30/2026 ) NHGRI
- PI: Pengfei Liu
- Clinical Sequencing Core Facility for the Undiagnosed Diseases Network (UDN) - #U01 HG007942
- ( 09/22/2014 - 06/30/2022 ) NHGRI
- PI: Christine Eng
Log In to edit your profile
