Xiaowu Gai, PhD

Professor of Clinical Pathology

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Publications

  • An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors J Mol Diagn. 2024 Feb; 26(2):127-139. . View in PubMed
  • MSeqDR Quick-Mitome (QM): Combining Phenotype-Guided Variant Interpretation and Machine Learning Classifiers to Aid Primary Mitochondrial Disease Genetic Diagnosis Curr Protoc. 2024 Jan; 4(1):e955. . View in PubMed
  • Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors NPJ Precis Oncol. 2023 Feb 20; 7(1):21. . View in PubMed
  • Expert Panel Curation of 113 Primary Mitochondrial Disease Genes for the Leigh Syndrome Spectrum Ann Neurol. 2023 10; 94(4):696-712. . View in PubMed
  • Resilience to autosomal dominant Alzheimer’s disease in a Reelin-COLBOS heterozygous man Nat Med. 2023 05; 29(5):1243-1252. . View in PubMed
  • Low-pass whole-genome and targeted sequencing of cell-free DNA from cerebrospinal fluid in pediatric patients with central nervous system tumors Neurooncol Adv. 2023 Jan-Dec; 5(1):vdad077. . View in PubMed
  • Potential of Aqueous Humor as a Liquid Biopsy for Uveal Melanoma Int J Mol Sci. 2022 Jun 02; 23(11). . View in PubMed
  • Mitochondrial DNA haplogroup, genetic ancestry, and susceptibility to Ewing sarcoma Mitochondrion. 2022 11; 67:6-14. . View in PubMed
  • Utility of viral whole-genome sequencing for institutional infection surveillance during the coronavirus disease 2019 (COVID-19) pandemic Infect Control Hosp Epidemiol. 2022 08; 43(8):1086-1088. . View in PubMed
  • m3685T > C is a novel mitochondrial DNA variant that causes Leigh syndrome. Cold Spring Harb Mol Case Stud. 2022 02; 8(2). . View in PubMed
  • Implementation of a Streamlined SARS-CoV-2 Whole-Genome Sequencing Assay for Expeditious Surveillance during the Emergence of the Omicron Variant J Clin Microbiol. 2022 04 20; 60(4):e0256921. . View in PubMed
  • Mitochondrial 1555 G>A variant as a potential risk factor for childhood glioblastoma Neurooncol Adv. 2022 Jan-Dec; 4(1):vdac045. . View in PubMed
  • Rapidly emerging SARS-CoV-2 B1. 1. 7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Emerg Microbes Infect. 2021 Dec; 10(1):1293-1299. . View in PubMed
  • Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications Emerg Microbes Infect. 2021 Dec; 10(1):885-893. . View in PubMed
  • Inter-eye genomic heterogeneity in bilateral retinoblastoma via aqueous humor liquid biopsy NPJ Precis Oncol. 2021 Jul 27; 5(1):73. . View in PubMed
  • High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19 Open Forum Infect Dis. 2021 Jun; 8(6):ofaa551. . View in PubMed
  • Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: A consecutive case series EBioMedicine. 2021 May; 67:103355. . View in PubMed
  • Establishing the Clinical Utility of ctDNA Analysis for Diagnosis, Prognosis, and Treatment Monitoring of Retinoblastoma: The Aqueous Humor Liquid Biopsy Cancers (Basel). 2021 Mar 13; 13(6). . View in PubMed
  • Persistent SARS-CoV-2 infection and increasing viral variants in children and young adults with impaired humoral immunity medRxiv. 2021 Mar 02. . View in PubMed
  • Early pandemic molecular diversity of SARS-CoV-2 in children medRxiv. 2021 Feb 19. . View in PubMed
  • Am J Bioeth. 2021 12; 21(12):67-70. . View in PubMed
  • The spectrum of mitochondrial DNA (mtDNA) mutations in pediatric CNS tumors Neurooncol Adv. 2021 Jan-Dec; 3(1):vdab074. . View in PubMed
  • Aqueous Humor as a Liquid Biopsy for Retinoblastoma: Clear Corneal Paracentesis and Genomic Analysis J Vis Exp. 2021 09 07; (175). . View in PubMed
  • Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation Hum Mutat. 2020 12; 41(12):2028-2057. . View in PubMed
  • Simultaneous identification of clinically relevant RB1 mutations and copy number alterations in aqueous humor of retinoblastoma eyes Ophthalmic Genet. 2020 12; 41(6):526-532. . View in PubMed
  • Variability in retinoblastoma genome stability is driven by age and not heritability Genes Chromosomes Cancer. 2020 10; 59(10):584-590. . View in PubMed
  • Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease Clin Lab Med. 2020 06; 40(2):149-161. . View in PubMed
  • Detection of mitochondrial DNA variants at low level heteroplasmy in pediatric CNS and extra-CNS solid tumors with three different enrichment methods Mitochondrion. 2020 03; 51:97-103. . View in PubMed
  • Bilateral Choroidal Neovascularization and Chorioretinal Anastomosis in Autosomal Recessive Bestrophinopathy J Vitreoretin Dis. 2020 Jan-Feb; 4(1):69-74. . View in PubMed
  • Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country Front Microbiol. 2020; 11:573430. . View in PubMed
  • Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report Nat Med. 2019 11; 25(11):1680-1683. . View in PubMed
  • A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants Cold Spring Harb Mol Case Stud. 2019 04; 5(2). . View in PubMed
  • Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies Cancer Res. 2019 04 01; 79(7):1318-1330. . View in PubMed
  • OncoKids: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies J Mol Diagn. 2018 11; 20(6):765-776. . View in PubMed
  • MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion Hum Mutat. 2018 06; 39(6):806-810. . View in PubMed
  • USMG5 Ashkenazi Jewish founder mutation impairs mitochondrial complex V dimerization and ATP synthesis Hum Mol Genet. 2018 10 01; 27(19):3305-3312. . View in PubMed
  • Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma Am J Med Genet A. 2017 May; 173(5):1390-1395. . View in PubMed
  • Whole exome sequencing identification of novel candidate genes in patients with proliferative diabetic retinopathy Vision Res. 2017 10; 139:168-176. . View in PubMed
  • Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis Diabetes. 2017 07; 66(7):1950-1956. . View in PubMed
  • Copy-number variation is an important contributor to the genetic causality of inherited retinal degenerations Genet Med. 2017 06; 19(6):643-651. . View in PubMed
  • Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory BMC Med Genomics. 2017 10 06; 10(1):57. . View in PubMed
  • NOD2 genetic variants and sarcoidosis-associated uveitis Am J Ophthalmol Case Rep. 2016 Oct; 3:39-42. . View in PubMed
  • From case studies to community knowledge base: MSeqDR provides a platform for the curation and genomic analysis of mitochondrial diseases Cold Spring Harb Mol Case Stud. 2016 May; 2(3):a001065. . View in PubMed
  • MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease Hum Mutat. 2016 06; 37(6):540-548. . View in PubMed
  • A novel HSD17B10 mutation impairing the activities of the mitochondrial RNase P complex causes X-linked intractable epilepsy and neurodevelopmental regression RNA Biol. 2016 05 03; 13(5):477-85. . View in PubMed
  • Innovative genomic collaboration using the GENESIS (GEMapp) platform. Hum Mutat. 2015 Oct; 36(10):950-6. . View in PubMed
  • Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier Bioinformatics. 2015 Apr 15; 31(8):1310-2. . View in PubMed
  • Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing Genet Med. 2015 Apr; 17(4):253-261. . View in PubMed
  • Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities Mol Genet Metab. 2015 Mar; 114(3):388-96. . View in PubMed
  • Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome Hum Mol Genet. 2015 Jan 01; 24(1):230-42. . View in PubMed
  • Targeted exon sequencing in Usher syndrome type I Invest Ophthalmol Vis Sci. 2014 Dec 02; 55(12):8488-96. . View in PubMed
  • Mitochondrial DNA variant in COX1 subunit significantly alters energy metabolism of geographically divergent wild isolates in Caenorhabditis elegans J Mol Biol. 2014 May 29; 426(11):2199-216. . View in PubMed
  • Effect of low intensity pulsed ultrasound on repairing the periodontal bone of Beagle canines Asian Pac J Trop Med. 2014 Apr; 7(4):325-8. . View in PubMed
  • AGC1 Deficiency Causes Infantile Epilepsy, Abnormal Myelination, and Reduced N-Acetylaspartate JIMD Rep. 2014; 14:77-85. . View in PubMed
  • Single nucleotide polymorphism array analysis of bone marrow failure patients reveals characteristic patterns of genetic changes Br J Haematol. 2014 Jan; 164(1):73-82. . View in PubMed
  • Erratum to: AGC1 Deficiency Causes Infantile Epilepsy, Abnormal Myelination, and Reduced N-Acetylaspartate JIMD Rep. 2014; 14:119. . View in PubMed
  • Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders J Med Genet. 2013 Oct; 50(10):704-14. . View in PubMed
  • Mutations in FBXL4, encoding a mitochondrial protein, cause early-onset mitochondrial encephalomyopathy Am J Hum Genet. 2013 Sep 05; 93(3):482-95. . View in PubMed
  • Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome Discov Med. 2012 Dec; 14(79):389-99. . View in PubMed
  • NMNAT1 mutations cause Leber congenital amaurosis Nat Genet. 2012 Sep; 44(9):1040-5. . View in PubMed
  • Microdeletions and microduplications in patients with congenital heart disease and multiple congenital anomalies Congenit Heart Dis. 2011 Nov-Dec; 6(6):592-602. . View in PubMed
  • Mitochondrial genome sequence analysis: a custom bioinformatics pipeline substantially improves Affymetrix MitoChip v20 call rate and accuracy. BMC Bioinformatics. 2011 Oct 19; 12:402. . View in PubMed
  • Implementation of high resolution single nucleotide polymorphism array analysis as a clinical test for patients with hematologic malignancies Cancer Genet. 2011 Jan; 204(1):26-38. . View in PubMed
  • Genomic alterations in biliary atresia suggest region of potential disease susceptibility in 2q373. Am J Med Genet A. 2010 Apr; 152A(4):886-95. . View in PubMed
  • High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications Genome Res. 2009 Sep; 19(9):1682-90. . View in PubMed
  • Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene Brain Pathol. 2009 Jul; 19(3):449-58. . View in PubMed
  • A 31-Mb microdeletion of 3p21. 31 associated with cortical blindness, cleft lip, CNS abnormalities, and developmental delay. Eur J Med Genet. 2009 Jul-Aug; 52(4):265-8. . View in PubMed
  • Genomic analysis using high-density single nucleotide polymorphism-based oligonucleotide arrays and multiplex ligation-dependent probe amplification provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors Clin Cancer Res. 2009 Mar 15; 15(6):1923-30. . View in PubMed
  • SNP array mapping of chromosome 20p deletions: genotypes, phenotypes, and copy number variation Hum Mutat. 2009 Mar; 30(3):371-8. . View in PubMed
  • Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies PLoS One. 2008; 3(10):e3583. . View in PubMed