Pengfei Liu
PhD
Associate Clinical Director, NGS/Molecular
Dr. Pengfei Liu graduated with his BS from the College of Life Science at Nankai University. He later earned his PhD at Baylor College of Medicine, where he also went on to complete his fellowship in clinical molecular genetics. Currently, Dr. Liu is the Associate Clinical Director of NGS/Molecular at Baylor Genetics, and specializes in the clinical implementation of whole genome and exome sequencing. In addition, Dr. Liu is an investigator of the NIH Undiagnosed Diseases Network (UDN).
Position
Assistant Professor
Molecular and Human Genetics
Baylor College of Medicine
Houston, TX, United States
Director
Laboratory Genetics and Genomics Training Program
Baylor College of Medicine
Houston, TX, United States
Associate Clinical Director
NGS/Molecular
Baylor Genetics
Houston, TX, United States
Education
PhD from Baylor College of Medicine
Houston, TX, United States
BS from Nankai University
Tianjin, China
Certifications
Clinical Molecular Genetics
American Board of Medical Genetics
Publications
Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits
Yuan, B., Schulze, K. V., Assia Batzir, N., Sinson, J., Dai, H., Zhu, W., Bocanegra, F., Fong, C. T., Holder, J., Nguyen, J., Schaaf, C. P., Yang, Y., Bi, W., Eng, C., Shaw, C., Lupski, J. R., & Liu, P. (2022). Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. Genome Medicine, 14(1), 113. PMID: 36180924.
Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis
Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis. Chen, C. A., Lattier, J., Kumar, R. D., Meng, L., Liu, P., Miyake, C. Y., Worley, K. C., Bi, W., & Lalani, S. R. American Journal of Medical Genetics. 2022 Sep 6. https://doi.org/10.1002/ajmg.a.62967.
Contribution of uniparental disomy in a clinical trio exome cohort of 2,675 patients
Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. Wang L, Liu P, Bi W, Sim T, Wang X, Walkiewicz M, Leduc MS, Meng L, Xia F, Eng CM, Yang Y, Yuan B, Dai H. Mol Genet Genomic Med. 2021 Sep 29; e1792. PMID: 34587367.
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny D, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SW, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. Genet Med. 2020 Jun 24. PMID: 32576985
Reanalysis of Clinical Exome Sequencing Data
Reanalysis of Clinical Exome Sequencing Data. Liu P, Meng L, Normand EA, Xia F, Song X, Ghazi A, Rosenfeld J, Magoulas PL, Braxton A, Ward P, Dai H, Yuan B, Bi W, Xiao R, Wang X, Chiang T, Vetrini F, He W, Cheng H, Dong J, Gijavanekar C, Benke PJ, Bernstein JA, Eble T, Eroglu Y, Erwin D, Escobar L, Gibson JB, Gripp K, Kleppe S, Koenig MK, Lewis AM, Natowicz M, Mancias P, Minor L, Scaglia F, Schaaf CP, Streff H, Vernon H, Uhles CL, Zackai EH, Wu N, Sutton VR, Beaudet AL, Muzny D, Gibbs RA, Posey JE, Lalani S, Shaw C, Eng CM, Lupski JR, Yang Y. N Engl J Med. 2019 Jun 20; 380(25):2478-2480. PMID: 31216405
Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected mendelian disorder
Normand, E. A., Braxton, A., Nassef, S., Ward, P. A., Vetrini, F., He, W., Patel, V., Qu, C., Westerfield, L. E., Stover, S., Dharmadhikari, A. V., Muzny, D. M., Gibbs, R. A., Dai, H., Meng, L., Wang, X., Xiao, R., Liu, P., Bi, W., Xia, F., … Yang, Y. (2018). Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Medicine, 10(1), 74. https://doi.org/10.1186/s13073-018-0582-x. PMID: 30266093.
Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing
Liu, P., & Vossaert, L. (2022). Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenatal diagnosis, 42(6), 686–696.PMID: 35416301.
An Organismal CNV Mutator Phenotype Restricted to Early Human Development
An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. Cell. 2017. Feb 23;168(5):830-842.e7. PMID: 28235197
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencingx
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Ye Cao, Mari J Tokita, Edward S Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M Eng, Yaping Yang, Tomasz Gambin, Chad Shaw, Pengfei Liu, Pawel Stankiewicz. Genome Med. 2019 Jul 26;11(1):48. PMID: 31349857
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Avinash V Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E Posey, Allen H Jiang, Weimin He, Francesco Vetrini, Alicia A Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu, Chad A Shaw, Janice L Smith, Seema Lalani, Pawel Stankiewicz, Sau-Wai Cheung, Carlos A Bacino, Ankita Patel, Amy M Breman, Xia Wang, Linyan Meng, Rui Xiao, Fan Xia, Donna Muzny, Richard A Gibbs, Arthur L Beaudet, Christine M Eng, James R Lupski, Yaping Yang, Weimin Bi. Genome Med. 2019 May 17;11(1):30. PMID: 31101064
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. Claudia MB Carvalho, Zeynep Coban-Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J Turner, Rupa S Kanchi, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Pawel Stankiewicz, John W Belmont, Chad A Shaw, Sau Wai Cheung, Neil A Hanchard, V Reid Sutton, Patricia I Bader, James R Lupski. Genome Med. 2019 Apr 23;11(1):25. . PMID: 31014393
Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies
Clinical exome sequencing reveals the locus heterogeneity and phenotypic variability of cohesinopathies. Yuan B, Neira J, Pehlivan, D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, DDD Study, Abid F, Bertuch A, Grange D, Immken L, Schaaf CP, Esch HV, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P. Genet Med. 2019 Mar; 21(3):663-675. PMID: 30158690
De novo missense variant in the GTPase effector domain (GED) of DNM1L leads to static encephalopathy and seizures
Nurit Assia Batzir, Christine M. Eng, Alica M. Goldman, Pranjali K. Bhagwat, Tanya N. Eble, Pengfei Liu, Laurie A. Robak, Fernando Scaglia, Sarah H. Elsea, Shweta U. Dhar, and Michael F. Wangler. De novo missense variant in the GTPase effector domain (GED) of DNM1L leads to static encephalopathy and seizures. Genome Med 11, 12. Jun 2019 PMID: 30850373
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing
Ye Cao, Mari J. Tokita, Edward S. Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A. Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M. Eng, Yaping Yang, Tomasz Gambin, Chad Shaw, Pengfei Liu & Pawel Stankiewicz (2019). A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Genome Med 11, 12. PMID: 31349857
De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith–Magenis syndrome
Vetrini, F., McKee, S., Rosenfeld, J.A., Suri, M., Lewis, A.M., Nugent, K.M., Roeder, E., Littlejohn, R.O., Holder, S., Zhu, W., Alaimo, J.T., Graham, B., Harris, J.M., Gibson, J.B., Pastore, M., McBride, K.L., Komara, M., Al-Gazali, L., Al Shamsi, A., Fanning, E.A., Wierenga, K.J., Scott, D.A., Ben-Neriah, Z., Meiner, V., Cassuto, H., Elpeleg, O., Holder, J.L., Jr., Burrage, L.C., Seaver, L.H., Van Maldergem, L., Mahida, S., Soul, J.S., Marlatt, M., Matyakhina, L., Vogt, J., Gold, J.A., Park, S.M., Varghese, V., Lampe, A.K., Kumar, A., Lees, M., Holder-Espinasse, M., McConnell, V., Bernhard, B., Blair, E., Harrison, V., study, D.D.D., Muzny, D.M., Gibbs, R.A., Elsea, S.H., Posey, J.E., Bi, W., Lalani, S., Xia, F., Yang, Y., Eng, C.M., Lupski, J.R., and Liu, P. (2019). 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 11, 12. PMID: 30819258
Passage number is a major contributor to genomic structural variations in mouse iPSCs
Liu, P., Kaplan, A., Yuan, B., Hanna, J.H., Lupski, J.R., and Reiner, O*. (2014). Passage number is a major contributor to genomic structural variations in mouse iPSCs. Passage number is a major contributor to genomic structural variations in mouse iPSCs. Stem Cells 32, 2657-2667. PMID: 24965231
Mechanism, Prevalence, and More Severe Neuropathy Phenotype of the Charcot-Marie-Tooth Type 1A Triplication
Liu, P., Gelowani, V., Zhang, F., Drory, V.E., Ben-Shachar, S., Roney, E., Medeiros, A.C., Moore, R.J., Divincenzo, C., Burnette, W.B., Higgins, J.J., Li, J., Orr-Urtreger, A., and Lupski, J.R. (2014). Mechanism, Prevalence, and More Severe Neuropathy Phenotype of the Charcot-Marie-Tooth Type 1A Triplication. Am J Hum Genet 94, 462-469. PMID: 24530202
Mechanisms for recurrent and complex human genomic rearrangements
Liu, P., Carvalho, C.M., Hastings, P., and Lupski, J.R. (2012). Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22, 211-220. PMID: 22440479
Frequency of Nonallelic Homologous Recombination Is Correlated with Length of Homology: Evidence that Ectopic Synapsis Precedes Ectopic Crossing-Over
Liu, P., Lacaria, M., Zhang, F., Withers, M., Hastings, P.J., and Lupski, J.R. (2011). Frequency of Nonallelic Homologous Recombination Is Correlated with Length of Homology: Evidence that Ectopic Synapsis Precedes Ectopic Crossing-Over. Am J Hum Genet 89, 580-588. PMID: 21981782
Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements
Liu, P., Erez, A., Nagamani, S.C., Dhar, S.U., Kolodziejska, K.E., Dharmadhikari, A.V., Cooper, M.L., Wiszniewska, J., Zhang, F., Withers, M.A., Bacino, C.A., Campos-Acevedo, L.D., Delgado, M.R., Freedenberg, D., Garnica, A., Grebe, T.A., Hernandez-Almaguer, D., Immken, L., Lalani, S.R., McLean, S.D., Northrup, H., Scaglia, F., Strathearn, L., Trapane, P., Kang, S.H., Patel, A., Cheung, S.W., Hastings, P.J., Stankiewicz, P., Lupski, J.R., and Bi, W. (2011). Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146, 889-903. PMID: 21925314
Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications
Liu, P., Erez, A., Nagamani, S.C., Bi, W., Carvalho, C.M., Simmons, A.D., Wiszniewska, J., Fang, P., Eng, P.A., Cooper, M.L., Sutton, V.R., Roeder, E.R., Bodensteiner, J.B., Delgado, M.R., Prakash, S.K., Belmont, J.W., Stankiewicz, P., Berg, J.S., Shinawi, M., Patel, A., Cheung, S.W., and Lupski, J.R. (2011). Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications. Hum Mol Genet 20, 1975-1988. PMID: 21355048
Pengfei Liu
PhD
Associate Clinical Director, NGS/Molecular
Dr. Pengfei Liu graduated with his BS from the College of Life Science at Nankai University. He later earned his PhD at Baylor College of Medicine, where he also went on to complete his fellowship in clinical molecular genetics. Currently, Dr. Liu is the Associate Clinical Director of NGS/Molecular at Baylor Genetics, and specializes in the clinical implementation of whole genome and exome sequencing. In addition, Dr. Liu is an investigator of the NIH Undiagnosed Diseases Network (UDN).
Position
Assistant Professor
Molecular and Human Genetics
Baylor College of Medicine
Houston, TX, United States
Director
Laboratory Genetics and Genomics Training Program
Baylor College of Medicine
Houston, TX, United States
Associate Clinical Director
NGS/Molecular
Baylor Genetics
Houston, TX, United States
Education
PhD from Baylor College of Medicine
Houston, TX, United States
BS from Nankai University
Tianjin, China
Certifications
Clinical Molecular Genetics
American Board of Medical Genetics
Publications
Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits
Yuan, B., Schulze, K. V., Assia Batzir, N., Sinson, J., Dai, H., Zhu, W., Bocanegra, F., Fong, C. T., Holder, J., Nguyen, J., Schaaf, C. P., Yang, Y., Bi, W., Eng, C., Shaw, C., Lupski, J. R., & Liu, P. (2022). Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. Genome Medicine, 14(1), 113. PMID: 36180924.
Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis
Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis. Chen, C. A., Lattier, J., Kumar, R. D., Meng, L., Liu, P., Miyake, C. Y., Worley, K. C., Bi, W., & Lalani, S. R. American Journal of Medical Genetics. 2022 Sep 6. https://doi.org/10.1002/ajmg.a.62967.
Contribution of uniparental disomy in a clinical trio exome cohort of 2,675 patients
Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. Wang L, Liu P, Bi W, Sim T, Wang X, Walkiewicz M, Leduc MS, Meng L, Xia F, Eng CM, Yang Y, Yuan B, Dai H. Mol Genet Genomic Med. 2021 Sep 29; e1792. PMID: 34587367.
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny D, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SW, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. Genet Med. 2020 Jun 24. PMID: 32576985
Reanalysis of Clinical Exome Sequencing Data
Reanalysis of Clinical Exome Sequencing Data. Liu P, Meng L, Normand EA, Xia F, Song X, Ghazi A, Rosenfeld J, Magoulas PL, Braxton A, Ward P, Dai H, Yuan B, Bi W, Xiao R, Wang X, Chiang T, Vetrini F, He W, Cheng H, Dong J, Gijavanekar C, Benke PJ, Bernstein JA, Eble T, Eroglu Y, Erwin D, Escobar L, Gibson JB, Gripp K, Kleppe S, Koenig MK, Lewis AM, Natowicz M, Mancias P, Minor L, Scaglia F, Schaaf CP, Streff H, Vernon H, Uhles CL, Zackai EH, Wu N, Sutton VR, Beaudet AL, Muzny D, Gibbs RA, Posey JE, Lalani S, Shaw C, Eng CM, Lupski JR, Yang Y. N Engl J Med. 2019 Jun 20; 380(25):2478-2480. PMID: 31216405
Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected mendelian disorder
Normand, E. A., Braxton, A., Nassef, S., Ward, P. A., Vetrini, F., He, W., Patel, V., Qu, C., Westerfield, L. E., Stover, S., Dharmadhikari, A. V., Muzny, D. M., Gibbs, R. A., Dai, H., Meng, L., Wang, X., Xiao, R., Liu, P., Bi, W., Xia, F., … Yang, Y. (2018). Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Medicine, 10(1), 74. https://doi.org/10.1186/s13073-018-0582-x. PMID: 30266093.
Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing
Liu, P., & Vossaert, L. (2022). Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenatal diagnosis, 42(6), 686–696.PMID: 35416301.
An Organismal CNV Mutator Phenotype Restricted to Early Human Development
An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. Cell. 2017. Feb 23;168(5):830-842.e7. PMID: 28235197
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencingx
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Ye Cao, Mari J Tokita, Edward S Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M Eng, Yaping Yang, Tomasz Gambin, Chad Shaw, Pengfei Liu, Pawel Stankiewicz. Genome Med. 2019 Jul 26;11(1):48. PMID: 31349857
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Avinash V Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E Posey, Allen H Jiang, Weimin He, Francesco Vetrini, Alicia A Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu, Chad A Shaw, Janice L Smith, Seema Lalani, Pawel Stankiewicz, Sau-Wai Cheung, Carlos A Bacino, Ankita Patel, Amy M Breman, Xia Wang, Linyan Meng, Rui Xiao, Fan Xia, Donna Muzny, Richard A Gibbs, Arthur L Beaudet, Christine M Eng, James R Lupski, Yaping Yang, Weimin Bi. Genome Med. 2019 May 17;11(1):30. PMID: 31101064
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. Claudia MB Carvalho, Zeynep Coban-Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J Turner, Rupa S Kanchi, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Pawel Stankiewicz, John W Belmont, Chad A Shaw, Sau Wai Cheung, Neil A Hanchard, V Reid Sutton, Patricia I Bader, James R Lupski. Genome Med. 2019 Apr 23;11(1):25. . PMID: 31014393
Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies
Clinical exome sequencing reveals the locus heterogeneity and phenotypic variability of cohesinopathies. Yuan B, Neira J, Pehlivan, D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, DDD Study, Abid F, Bertuch A, Grange D, Immken L, Schaaf CP, Esch HV, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P. Genet Med. 2019 Mar; 21(3):663-675. PMID: 30158690
De novo missense variant in the GTPase effector domain (GED) of DNM1L leads to static encephalopathy and seizures
Nurit Assia Batzir, Christine M. Eng, Alica M. Goldman, Pranjali K. Bhagwat, Tanya N. Eble, Pengfei Liu, Laurie A. Robak, Fernando Scaglia, Sarah H. Elsea, Shweta U. Dhar, and Michael F. Wangler. De novo missense variant in the GTPase effector domain (GED) of DNM1L leads to static encephalopathy and seizures. Genome Med 11, 12. Jun 2019 PMID: 30850373
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing
Ye Cao, Mari J. Tokita, Edward S. Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A. Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M. Eng, Yaping Yang, Tomasz Gambin, Chad Shaw, Pengfei Liu & Pawel Stankiewicz (2019). A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Genome Med 11, 12. PMID: 31349857
De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith–Magenis syndrome
Vetrini, F., McKee, S., Rosenfeld, J.A., Suri, M., Lewis, A.M., Nugent, K.M., Roeder, E., Littlejohn, R.O., Holder, S., Zhu, W., Alaimo, J.T., Graham, B., Harris, J.M., Gibson, J.B., Pastore, M., McBride, K.L., Komara, M., Al-Gazali, L., Al Shamsi, A., Fanning, E.A., Wierenga, K.J., Scott, D.A., Ben-Neriah, Z., Meiner, V., Cassuto, H., Elpeleg, O., Holder, J.L., Jr., Burrage, L.C., Seaver, L.H., Van Maldergem, L., Mahida, S., Soul, J.S., Marlatt, M., Matyakhina, L., Vogt, J., Gold, J.A., Park, S.M., Varghese, V., Lampe, A.K., Kumar, A., Lees, M., Holder-Espinasse, M., McConnell, V., Bernhard, B., Blair, E., Harrison, V., study, D.D.D., Muzny, D.M., Gibbs, R.A., Elsea, S.H., Posey, J.E., Bi, W., Lalani, S., Xia, F., Yang, Y., Eng, C.M., Lupski, J.R., and Liu, P. (2019). 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 11, 12. PMID: 30819258
Passage number is a major contributor to genomic structural variations in mouse iPSCs
Liu, P., Kaplan, A., Yuan, B., Hanna, J.H., Lupski, J.R., and Reiner, O*. (2014). Passage number is a major contributor to genomic structural variations in mouse iPSCs. Passage number is a major contributor to genomic structural variations in mouse iPSCs. Stem Cells 32, 2657-2667. PMID: 24965231
Mechanism, Prevalence, and More Severe Neuropathy Phenotype of the Charcot-Marie-Tooth Type 1A Triplication
Liu, P., Gelowani, V., Zhang, F., Drory, V.E., Ben-Shachar, S., Roney, E., Medeiros, A.C., Moore, R.J., Divincenzo, C., Burnette, W.B., Higgins, J.J., Li, J., Orr-Urtreger, A., and Lupski, J.R. (2014). Mechanism, Prevalence, and More Severe Neuropathy Phenotype of the Charcot-Marie-Tooth Type 1A Triplication. Am J Hum Genet 94, 462-469. PMID: 24530202
Mechanisms for recurrent and complex human genomic rearrangements
Liu, P., Carvalho, C.M., Hastings, P., and Lupski, J.R. (2012). Mechanisms for recurrent and complex human genomic rearrangements. Curr Opin Genet Dev 22, 211-220. PMID: 22440479
Frequency of Nonallelic Homologous Recombination Is Correlated with Length of Homology: Evidence that Ectopic Synapsis Precedes Ectopic Crossing-Over
Liu, P., Lacaria, M., Zhang, F., Withers, M., Hastings, P.J., and Lupski, J.R. (2011). Frequency of Nonallelic Homologous Recombination Is Correlated with Length of Homology: Evidence that Ectopic Synapsis Precedes Ectopic Crossing-Over. Am J Hum Genet 89, 580-588. PMID: 21981782
Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements
Liu, P., Erez, A., Nagamani, S.C., Dhar, S.U., Kolodziejska, K.E., Dharmadhikari, A.V., Cooper, M.L., Wiszniewska, J., Zhang, F., Withers, M.A., Bacino, C.A., Campos-Acevedo, L.D., Delgado, M.R., Freedenberg, D., Garnica, A., Grebe, T.A., Hernandez-Almaguer, D., Immken, L., Lalani, S.R., McLean, S.D., Northrup, H., Scaglia, F., Strathearn, L., Trapane, P., Kang, S.H., Patel, A., Cheung, S.W., Hastings, P.J., Stankiewicz, P., Lupski, J.R., and Bi, W. (2011). Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146, 889-903. PMID: 21925314
Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications
Liu, P., Erez, A., Nagamani, S.C., Bi, W., Carvalho, C.M., Simmons, A.D., Wiszniewska, J., Fang, P., Eng, P.A., Cooper, M.L., Sutton, V.R., Roeder, E.R., Bodensteiner, J.B., Delgado, M.R., Prakash, S.K., Belmont, J.W., Stankiewicz, P., Berg, J.S., Shinawi, M., Patel, A., Cheung, S.W., and Lupski, J.R. (2011). Copy number gain at Xp22.31 includes complex duplication rearrangements and recurrent triplications. Hum Mol Genet 20, 1975-1988. PMID: 21355048