Kai Wang, PhD
Professor of Pathology and Laboratory MedicinePerelman School of Medicine at the University of Pennsylvania
Contact Information3501 Civic Center Blvd, CTRB 5004
Children's Hospital of Philadelphia
Philadelphia, PA, 19104
Office: 267-425-9573
Fax: 215-590-3660
Research Expertise
The research in our laboratory aims to develop novel genomics and bioinformatics methods to improve the diagnosis, treatment, and prognosis of rare diseases, to ultimately facilitate the implementation genomic medicine on scale. A detailed description of our research and rotation projects can be found on our lab website (https://wglab.org). In summary, our research can be divided into several areas.
First, we are developing analytical pipelines for whole genome and whole exome sequencing data, all the way from FASTQ/FAST5 files to biological insights. Some examples of computational tools used in the lab include SeqMule, ANNOVAR, Phenolyzer, SeqHBase, and InterVar. These approaches facilitate a better understanding of the functional content and clinical insights from sequencing data.
Furthermore, we are also developing genomic assays and methods to analyze long-read data, such as those generated from linked-read sequencing, optical mapping, PacBio, and Nanopore long-read sequencing. These methods help identify causal genetic variants on cases that failed to be diagnosed by traditional whole genome/exome sequencing approaches, and help map aberrant DNA modifications such as methylations in tissues from patients in comparison to controls. Some examples of computational tools developed by our lab include RepeatHMM, NextSV, LongSV, LinkedSV, NanoMod, and DeepMod.
Finally, we are developing data mining approaches from clinical phenotypic information in Electronic Health Records (EHR) to correlate genotype and phenotype together, and better understand the phenotypic heterogeneity of inherited diseases. Some examples of computational tools that we developed include EHR-Phenolyzer, SparkText, Doc2HPO, and Phen2Gene, which use natural language processing on clinical notes to predict possible genetic syndromes and candidate genes.
Itmat Expertise
Development and application of genomic approaches to study the genetic basis of human diseases.
Education
B.S. (Biochemistry & Molecular Biology), Peking University, 2000
M.S. (Tumor Biology), Mayo Clinic, 2002
Ph.D. (Microbiology & Computational Biology), University of Washington, 2005
Specialty Certification
Postgraduate Training
Postdoctoral Fellow, University of Pennsylvania, 2006-2008
Postdoctoral Fellow, The Children's Hospital of Philadelphia, 2008-2010
Awards and Honors
ISMB 2005 Travel Fellowship, International Society of Computational Biology, 2005
Alavi-Dabiri Postdoctoral Award, Mental Retardation and Developmental Disability Research Center, The Children's Hospital of Philadelphia, 2008
WCPG 2009 Travel Award, International Society of Psychiatric Genetics, 2009
Trainee Research Award Semi-finalist, American Society of Human Genetics, 2009
Top 10 Medical Breakthroughs, Time Magazine, 2009
Best Paper Award, International Conference on Intelligent Biology and Medicine, 2018
Distinguished Service Award, International Association for Intelligent Biology and Medicine, 2019
Penn Undergraduate Research Mentorship Award, 2020-2020
Penn Undergraduate Research Mentorship Award, 2022-2022
Memberships and Professional Organizations
International Society of Computational Biology, 2005 - Present
American Society of Human Genetics, 2006 - Present
Netherlands Organization for Scientific Research, 2010 - 2010
Ontario Research Fund - Research Excellence (ORF-RE), 2011 - 2011
SC-CTSI Pilot Award, 2012 - 2013
The Government of the Hong Kong SAR-Health and Medical Research Fund (HMRF), 2013 - 2013
American Cancer Society - Institutional Research Grant (ACS-IRG), 2013 - 2015
Medical Research Council (MRC), UK, 2013 - 2015
The National Science Centre Poland, 2014 - 2014
USC Chinese Student Career Assistant Group, 2014 - 2016
A*STAR Singapore, 2014 - 2014
National Institute of Health (NIH) GCAT Study Section, 2014 - 2014
Genome British Columbia, 2015 - 2015
School of Biomedical Sciences, University of Hong Kong, Hong Kong, 2015 - 2015
Association of Chinese Geneticists in America, 2015 - Present
Wellcome Trust UK, 2015 - 2015
Department of Biochemistry and Microbiology, Rhodes University, South Africa, 2017 - 2017
University of Southern California, 2017 - 2017
University of South Florida, 2017 - 2017
Cancer Research UK, 2017 - 2017
Simons Foundation, 2018 - 2018
CHOP K-readiness Grant Application, 2018 - Present
NIH Kids First Special Emphasis Panel ZHG1 HGR-T, 2018 - 2018
International Association for Intelligent Biology and Medicine, 2018 - Present
Israeli Ministry of Science & Technology, Israel, 2018 - 2018
CHOP Roberts Collaborative Forefront Application, 2018 - 2018
Fudan-Zhongzhi Science Award, 2019 - 2019
VITAL Somatic Working Group, Association for Molecular Pathology, 2019 - Present
University of Manitoba, 2019 - 2019
NIH BILDS Study Section, 2019 - 2019
Association for Molecular Pathology, 2019 - Present
International Association for Intelligent Biology and Medicine, 2019 - Present
NIH GCAT Study Section, 2020 - 2020
NIH BCHI Study Section, 2020 - 2020
Medical Research Council (MRC), UK, 2020 - 2020
University of Chicago, 2020 - 2020
Peking University, 2020 - 2020
IDDRC New Program Development, 2020 - Present
NIH New Innovator Awards panel, 2020 - 2020
CHOP Cell and Gene Therapy Grant, 2020 - Present
CHOP Junior Faculty Pilot Grant panel, 2020 - Present
European Science Foundation, 2020 - 2020
NIH Genes Genomes and Genetics SEP, 2021 - Present
NIH Transformative Research Awards panel, 2021 - Present
Tsinghua University, 2021 - 2021
NIH BILDS Study Section, 2021 - Present
CHOP Omics Maximizing Grant, 2022 - Present
Association for Molecular Pathology (AMP) ISV Working group, 2022 - Present
Yale University, 2022 - Present
Mount Sinai School of Medicine, 2022 - 2022
Mayo Clinic, 2022 - Present
CHOP next-generation sequencing grant, 2022 - Present
CHOP Add-An-Aim Thematic Accelerator Grant Program, 2022 - Present
NIH ZRG1 HSS-Z Special Emphasis Panel, 2023 - Present
NIH CDMA study section, 2023 - Present
University of Michigan, 2023 - Present
University of Virginia, 2023 - Present
NIH ZRG1 HSS-N (90) study section, 2024 - Present
Web Links
Selected Publications
Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing
Georgieva D, Liu Q, Wang K*, Egli D*, Nucleic Acids Res 48(15): e88, 2020, PMID:32710620
Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants
He MM, Li Q, Yan M, Cao H, Hu Y, He KY, Cao K, Li MM, Wang K, Genome Med 11(1): 53, 2019, PMID:31443733
Doc2Hpo: a web application for efficient and accurate HPO concept curation
Liu C, Fabricio K, Li Z, Ta C, Wang K*, Weng C*, Nucleic Acids Res 47(W1): W566-W570, 2019, PMID:31106327
The proteome and its dynamics: A missing piece for integrative multi-omics in schizophrenia
Borgmann-Winter KE, Wang K, Bandyopadhyay S, Doostparast Torshizi A, Blair I, Hahn CY, Schizophr Res 217(): 148-161, 2020, PMID:31416743
Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)
Dai Y, Li P, Wang Z, Liang F, Yang F, Fang L, Huang Y, Huang S, Zhou J, Wang D, Cui L, Wang K, J Med Genet pii(): jmedgenet-2019-106078, 2019, PMID:31506324
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data
Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K, Nat Commun 10(1): 2449, 2019, PMID:31164644
GDP: Group lasso regularized Deep learning for cancer Prognosis from multi-omics and clinical features
Xie G, Dong C, Kong Y, Zhong JF, Li M, Wang K, Genes 10(3): 240, 2019
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data
Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino R, Li M, Wenzel S, Wimmer K, Hakonarson H, Wang K, Nat Commun 10(1): 5585, 2019, PMID:31811119
Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy
Zeng S, Zhang MY, Wang XJ, Hu ZM, Li JC, Li N, Wang JL, Liang F, Yang Q, Liu Q, Fang L, Hao JW, Shi FD, Ding XB, Teng JF, Yin XM, Jiang H, Liao WP, Liu JY, Wang K*, Xia K*, Tang BS*, J Med Genet 56(4): 265-270, 2019, PMID:30194086
Deconvolution of Transcriptional Networks Identified TCF4 as a Master Regulator in Schizophrenia
Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J*, Wang K*, Sci Adv 5(9): eaau4139, 2019
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
Liu Q, Georgieva DC, Egli D, Wang K, BMC Genomics 20(Suppl 1): 78, 2019, PMID:30712508
A semi-supervised approach for predicting cell-type specific functional consequences of non-coding variation using MPRAs
He Z, Liu L, Wang K, Ionita-Laza I, Nat Commun 9(1): 5199, 2018, PMID:30518757
Deep phenotyping on electronic health records facilitates genetic diagnosis by clinical exomes
Hoon Son J, Xie G, Yuan C, Ena L, Li Z, Goldstein A, Huang L, Wang L, Shen F, Liu H, Mehl K, Groopman EE, Marasa M, Kiryluk K, Gharavi AG, Chung WK, Hripcsak G, Friedman C, Weng C*, Wang K*, Am J Hum Genet 103(1): 58-73, 2018, PMID:29961570
N6-methyladenine DNA modification in human genome
Xiao CL, Zhu S, He M, Chen D, Zhang Q, Chen Y, Yu GL, Liu J, Xie SQ, Luo F, Liang Z, Wang DP, Bo XC, Gu X-F*, Wang K*, Yan GR*, Mol Cell 71(2): 306-318, 2018, PMID:30017583
Next Generation Sequencing in Drug Development: Target Identification and Genetically Stratified Clinical Trials
Doostparast Torshizi A, Wang K, Drug Discovery Today 23(10): 1776-1783, 2018, PMID:29758342
