Wei, Angela, Richard Border, Boyang Fu, Sinéad Cullina, Nadav Brandes, Sriram Sankararaman, Eimear E. Kenny, Vasillis Ntranos, Noah Zaitlen, Valerie A. Arboleda. 2023. “The Genetic Underpinnings of Variable Penetrance and Expressivity of Pathogenic Mutations in Cardiometabolic Traits.” bioRxiv. https://doi.org/10.1101/2023.09.14.23295564.
Singh M., Spendlove S., Wei A., Nava A. A., Bondhus L., Vitorino F.N.L., Gomez D., Lee J., Echeverria G., Amano S., Garcia B., Arboleda V.A.. KAT6A mutations in Arboleda-Tham syndrome drive epigenetic regulation of posterior HOXC cluster. bioRxiv 2023.08.03.550595; doi: https://doi.org/10.1101/2023.08.03.550595
Nava, A.A., Jops, C.T., Vuong, C. K., Niles-Jensen, S., Bondhus, L., Ong, C. J., de la Torre-Ubieta, L., Gandal, M. J., Arboleda, V. A.. KAT6A mutations drive transcriptional dysregulation of cell cycle and Autism risk genes in an Arboleda-Tham Syndrome cerebral organoid model. bioRxiv 2023.06.17.545322; doi: https://doi.org/10.1101/2023.06.17.545322.
Nava AA, Arboleda VA. The omics era: a nexus of untapped potential for Mendelian chromatinopathies. Hum Genet. 2023 Apr 28. doi: 10.1007/s00439-023-02560-2. Epub ahead of print. PMID: 37115317.
Lin I, Wei A, Awamleh Z, Singh M, Ning A, Herrera A; REACH Biobank and Registry; Russell BE, Weksberg R, Arboleda VA. Multiomics of Bohring-Opitz syndrome truncating ASXL1 mutations identify canonical and noncanonical Wnt signaling dysregulation. JCI Insight. 2023 May 22;8(10):e167744. doi: https://doi.org/10.1172/jci.insight.167744 . PMID: 37053013.
Sathe LM, Khan NN, Williams JM, Saul R, Jajieh K, Sartippour MR, Young R, Xie J, Marquette DM, Duncan T, Eskin E, Arboleda VA. 3D Printing as an Effective Quality Assurance Implementation in Massive-Scale SARS-CoV-2 Testing at a SwabSeq Next-Generation Sequencing Laboratory. Lab Med. 2023 Feb 22:lmac161. doi: 10.1093/labmed/lmac161. Epub ahead of print. PMID: 36810591.
Isabella Lin, Zain Awamleh, Angela Wei, Bianca Russell, Rosanna Weksberg, Valerie A. Arboleda. ASXL1 mutations that cause Bohring Opitz Syndrome (BOS) or acute myeloid leukemia share epigenomic and transcriptomic signatures. bioRxiv 2022.12.15.519823; doi: https://doi.org/10.1101/2022.12.15.519823
Johnson R, Ding Y, Venkateswaran V, Bhattacharya A, Boulier K, Chiu A, Knyazev S, Schwarz T, Freund M, Zhan L, Burch KS, Caggiano C, Hill B, Rakocz N, Balliu B, Denny CT, Sul JH, Zaitlen N, Arboleda VA, Halperin E, Sankararaman S, Butte MJ; UCLA Precision Health Data Discovery Repository Working Group, UCLA Precision Health ATLAS Working Group; Lajonchere C, Geschwind DH, Pasaniuc B. Leveraging genomic diversity for discovery in an electronic health record linked biobank: the UCLA ATLAS Community Health Initiative. Genome Med. 2022 Sep 9;14(1):104. doi: 10.1186/s13073-022-01106-x.
Spendlove S, Bondhus L, Lluri G, Sul JH, Arboleda VA. Polygenic Risk Scores of Endo-phenotypes Identify the Effect of Genetic Background in Congenital Heart Disease. 2022 May. April 25, 2022. Human Genetics and Genomics. PMID: 35599848. PMCID: PMC9118152. DOI: 10.1016/j.xhgg.2022.100112
Bondhus L, Varma R, Hernandez Y, Arboleda VA. “Balancing the Transcriptome: Leveraging Sample Similarity to Improve Measures of Gene Specificity”. Briefings in Bioinformatics. bbac158. doi: 10.1093/bib/bbac15. PMID: 35534150
Longhua Guo, James Boocock, Evann E. Hilt, Sukantha Chandrasekaran, Yi Zhang, Chetan Munugala, Laila Sathe, Noah Alexander, Valerie A. Arboleda, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Shangxin Yang, Omai B. Garner, Yi Yin, Joshua S. Bloom, Leonid Kruglyak. Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA. April 4 2022 PMCID: PMC8978495, DOI: 10.1186/s12864-022-08488-7
Awamleh Z, Charter-Diehl E, Choufani S, Wei E, Kianmahd RR, Yu A, Tan W, Scherer SW, Arboleda VA, Russell BE, Weksberg R. DNA methylation signature of ASXL1 variants causing Bohring-Opitz syndrome (BOS). European Journal of Human Genetics. 2022 Apr 1. doi: 10.1038/s41431-022-01083-0. PMID: 35361921.
Adamson PC, Pfeffer MA, Arboleda VA, Garner OB, de St. Maurice A, von Bredow B; Flint J, Kruglyak L, Currier JS. SARS-CoV-2 cycle threshold values among healthcare workers in Los Angeles, California following implementation of a COVID-19 vaccination program. Open Forum Infectious Diseases. Open Forum Infect Dis. 2021 Nov 18;8(11):ofab526. doi: 10.1093/ofid/ofab526. eCollection 2021 Nov. PMID: 35005055.
Yabumoto M, Kianmahd J, Singh M, Palafox MF, Wei A, Elliott K, Goodloe DH, Dean SJ, Gooch C, Murray BK, Swartz E, Schrier Vergano SA, Towne MC, Nugent K, Roeder ER, Kresge C, Pletcher BA, Grand K, Graham JM Jr, Gates R, Gomez-Ospina N, Ramanathan S, Clark RD, Glaser K, Benke PJ, Cohen JS, Fatemi A, Mu W, Baranano KW, Madden JA, Gubbels CS, Yu TW, Agrawal PB, Chambers MK, Phornphutkul C, Pugh JA, Tauber KA, Azova S, Smith JR, O'Donnell-Luria A, Medsker H, Srivastava S, Krakow D, Schweitzer DN, Arboleda VA. Mol Genet Genomic Med. 2021 Sep 14:e1809. doi: 10.1002/mgg3.1809. PMID: 34519438
Bloom JS#, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S#, Kruglyak L#, Arboleda VA#. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat Biomed Eng. 2021 Jul;5(7):657-665. doi: 10.1038/s41551-021-00754-5. Epub 2021 Jul 1.PMID: 34211145; # co-corresponding authors.
Janae Jones*, Rosita Saul*, Laila Sathe, Joanna Xie, Dawn Marquette, Valerie A. Arboleda. LEAN Principles to Improve Quality in high throughput COVID-19 Testing using SwabSeq: A Barcoded Sequencing-Based testing platform. Lab Med. 2021 Aug 26:lmab069. doi: 10.1093/labmed/lmab069. PMID: 34436601
Hilt EE, Boocock J, Trejo M, Le CQ, Guo L, Zhang Y, Sathe L, Arboleda VA, Yin Y, Bloom JS, Wang J, Elmore JG, Kruglyak L, Shrestha L, Mohamed Bakhash SA, Lin M, Xie H, Huang M, Roychoudhury P, Greninger A, Chandrasekaran S, Yang S, Garner OB. Retrospective Detection of SARS-CoV-2 in Symptomatic Patients prior to Widespread Diagnostic Testing in Southern California. Clinical Infectious Disease. 2021 May 3:ciab360. doi: 10.1093/cid/ciab360. Online ahead of print, PMID: 33939799.
Bondhus L, Wei A, Arboleda VA. DMRscaler: A Scale-Aware Method to Identify Regions of Differential DNA Methylation Spanning Basepair to Multi-Megabase Features. https://www.biorxiv.org/content/10.1101/2021.02.03.428187v2 ; in Review.
Li S, Ma F, Yokota T, Garcia G Jr, Palermo A, Wang Y, Farrell C, Wang YC, Wu R, Zhou Z, Pan C, Morselli M, Teitell MA, Ryazantsev S, Fishbein GA, Hoeve JT, Arboleda VA, Bloom J, Dillon B, Pellegrini M, Lusis AJ, Graeber TG, Arumugaswami V, Deb A. Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity. JCI Insight. 2021 Jan 25;6(2):145027. doi: 10.1172/jci.insight.145027.
Longhua Guo, James Boocock, Jacob M. Tome, Sukantha Chandrasekaran , Evann E. Hilt, Yi Zhang, Laila Sathe, Xinmin Lig, Chongyuan Luo, Sriram Kosuri, Jay A. Shendure, Valerie A. Arboleda, Jonathan Flint, Eleazar Eskin, Omai B. Garner, Shangxin Yang, Joshua S. Bloom, Leonid Kruglyak, Yi Yin Rapid cost-effective viral genome sequencing by V-seq. Available from:
https://www.biorxiv.org/content/10.1101/2020.08.15.252510v1; in revision, G3
Bloom JS, Jones EM, Gasperini M, Lubock NB, Sathe L, Munugala C, Booeshaghi AS, Brandenberg OF, Guo L, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S*, Kruglyak L*, Arboleda VA*. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. medRxiv; 2020. Available from: https://www.medrxiv.org/content/10.1101/2020.08.04.20167874v1.abstract
Palafox MF, Desai H, Arboleda VA*, Backus KM*. From Chemoproteomic-Detected Amino Acids to Genomic Coordinates: Insights into Precise Multi-omic Data Integration [Internet]. 2020p. 2020.07.03.186007. *co-corresponding, these authors jointly supervised the work. Available from: https://www.embopress.org/doi/full/10.15252/msb.20209840
Freund MK, Burch KS, Shi H, Mancuso N, Kichaev G, Garske KM, Pan DZ, Miao Z, Mohlke KL, Laakso M, Pajukanta P, Pasaniuc B*, and Arboleda VA*. Phenotype-specific enrichment of Mendelian disorder genes near GWAS regions across 62 complex traits. * These authors jointly supervised the work. American Journal of Human Genetics. 2018 Oct 4. https://doi.org/10.1016/j.ajhg.2018.08.017.
Datkhaeva I, Arboleda VA, Senaratne N, Nikpour G, Meyerson C, Geng Y, Afshar Y, Scibetta E, Goldstein J, Quintero-Rivera F, Crandall B, Grody W, Deignan J, Janzen C. Prenatal Exome Sequencing for Hydrops Fetalis: A case report and review of the literature. American Journal of Medical Genetics,Part A. 2018 Sep 23. doi: 10.1002/ajmg.a.40533. PMID: 30244526
Kennedy J, Goudie D, Blair E , Chandler K, Joss S, McKay V, Green A, Armstrong R, Lees M, Kamien B, Hopper B, Tan TY, Yap P, Stark Z, Okamoto Z, Miyake N, Matsumoto N, Macnamara E, Murphy JL, McCormick E, Hakonarson H, Falk MJ, Li D, Blackburn P, Klee E, Babovic-Vuksanovic D, Schelley S, Hudgins L, Kant S, Isidor B, Cogne B, Bradbury K, Williams M, Patel C, Heussler H, Duff-Farrier C, Lakeman P, Scurr I, Kini U, Elting M, Reijnders M, Schuurs-Hoeijmakers J, Wafik M, Blomhoff A, Ruivenkamp CAL, Nibbeling E, Dingemans AJM, Douine ED, Nelson SF, The DDD Study, Arboleda VA*, Newbury-Ecob R*. KAT6A Syndrome: Genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants. Genetics in Medicine. 2018 Sep 24. doi: 10.1038/s41436-018-0259-2. PMID: 30245513.*These authors contributed equally, co-corresponding authors.
Barseghyan H, Symon A, Zadikyan M, Almalvez M, Segura EE, Eskin A, Bramble MS, Arboleda VA, Baxter R, Nelson SF, Délot EC, Harley V, Vilain E. Identification of novel candidate genes for 46,XY disorders of sex development (DSD) using a C57BL/6J-YPOS mouse model. Biol Sex Differ. 2018 Jan 30;9(1):8. doi: 10.1186/s13293-018-0167-9. PMID: 29378665.
Yoon WH, Sandoval H, Jaiswal SN, Jaiswal M, Yamamoto S, Haelterman NA, Putluri N, Putluri V, Sreekumar A, Tos T, Aksoy A, Donti A, Graham B, Ohno M, Nishi E, Hunter J, Muzny DM, Carmichael J, Shen J, Arboleda VA, Nelson SF, Wangler MF, Karaca E, Lupski JR, and Bellen HJ. Nardilysin Chaperones Mitochondrial Oxoglutarate Dehydrogenase and Protects against the Demise of Neurons in Flies and Human. Neuron. 2016 Dec 18. PMID: 28017472.
Bramble MS, Roach L, Lipson A, Eskin A, Vashist N, Ngun T, Gosschalk JE, Klein S, Barseghyan H, Arboleda VA, Vilain E. Sex-Specific Effects of Testosterone on the Sexually Dimorphic Transcriptome and Epigenome of Embryonic Neural Stem/Progenitor Cells. Scientific Reports. PMID: 27845378.
Bramble MS, Goldstein EH, Lipson A, Ngun T, Eskin A, Gosschalk JE, Roach L, Vashist N, Barseghyan H; Lee E; Arboleda VA; Vaiman D; Yuksel Z; Fellous M; Vilain E. A novel follicle-stimulating hormone receptor mutation causing primary ovarian failure: a fertility application of whole exome sequencing. Human Reproduction. 2016. PMID: 27845378
Contreras JR, Palanichamy JK, Tran TM, Fernando TR, Rodriguez-Malave NI, Goswami N, Arboleda VA, Casero D, Rao DS. MicroRNA-146a modulates B-cell oncogenesis by regulating Egr1. Oncotarget. 2015 April 13. PMCID: PMC4484436
Borges KS, Arboleda VA*, Vilain E. Mutations in the PCNA-binding site of CDKN1C inhibit cell proliferation by impairing the entry into S phase. Cell Division. 2015 Mar 28. (*Corresponding Author) PMCID: PMC4389716
Arboleda VA, Lee H, Dorrani N, Zadeh N, Willis M, Macmurdo CF, Manning M, Kwan A, Hudgins L, Strom SP, Deignan JL, UCLA Clinical Genomics Center, Grody WW, Vilain E, Nelson SF. De novo nonsense variants in KAT6A, a Lysine Acetyl-Transferase gene, causes a syndrome including Microcephaly and Global Developmental Delay. American Journal of Human Genetics. 2015 Feb 26. PMCID: PMC4375619.
Baxter RM, Arboleda VA, Lee, H, Barseghyan H, Adam MP, Fechner PY, Bargman R, Keegan C, Travers S, Schelley S, Hudgins L, Mathew RP, Stalker HJ, Zori R, Gordon OK, Ramos-Platt L, Pawlikowska-Haddal A, Eskin A, Nelson SF, Délot E, Vilain E. Exome sequencing for the diagnosis of 46, XY disorders of sex development. The Journal of Clinical Endocrinology & Metabolism, 2014 Nov 10.
Arboleda VA, Fleming A, Barseghyan H, Delot EC, Sinsheimer JS, Vilain E. Regulation of Sex Determination in Mice by a Non-Coding Genomic Region. Genetics. 2014 May 2.
Caburet S*, Arboleda VA*, Llano E, Overbeek PA, Barbero JL, Oka K, Harrison W, Vaiman D, Ben-Neriah Z, García-Tuñón I, Fellous M, Pendás AM, Veitia RA, Vilain E. Homozygous deletion in the STAG3 cohesin gene leads to Premature Ovarian Failure. New England Journal of Medicine. 2014 March 7. PMCID: PMC4068824.
Arboleda VA, Lee H, Parnaik R, Banerjee A, Ferraz-de-Souza B, Braslavsky D, Bergadá I, Nelson SF, Martinez-Agosto JA, Achermann JC, Vilain E. Mutations in the PCNA-binding domain of CDKN1C cause IMAGe Syndrome. Nature Genetics. 2012 May 27. **Featured in News and Views 2012.
Arboleda VA, Lee H, Sanchez F, Delot EC, Sandberg DE, Grody W, Nelson SF, Vilain E. Targeted Massively Parallel Sequencing Provides Comprehensive Genetic Diagnosis for Patients with Disorders of Sex Development. Clinical Genetics. 2012 Mar 15. PMCID: PMC4068824
White S., Ohnesorg T., Notini A., Smith C., Hewitt J., Daggag H., Roeszler K., Turbitt E., Gustin S., van den Bergen J., Miles D., Western P., Arboleda, VA, Schumacher V., Gordon L., Bell K., Bengtsson H., Speed T., Hutson J., Warne G., Harley V., Koopman P., Vilain E., Sinclair A. Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis. PLOS One. 2011 Mar 7;6(3):e17793. PMCID: PMC3049794
Sutton E, Hughes J, White S, Sekido R, Tan J, Arboleda V, Rogers N, Knower K, Rowley L, Eyre H, Rizzoti K, McAninch D, Goncalves J, Slee J, Turbitt E, Bruno D, Bengtsson H, Harley V, Vilain E, Sinclair A, Lovell-Badge R, Thomas P. Identification of SOX3 as an XX male sex reversal gene in mice and humans. J. Clin Invest. 2011 Jan 4;121(1):328-41.3. PMCID: PMC3007141
Davidson TJ, Harel S, Arboleda VA, Shelanski ML, Greene LA, Troy CM. Highly efficient siRNA delivery to primary mammalian neurons induces microRNA- like effects before mRNA degradation. J. Neurosci. 24 (45):10040-6. 2004.
PUBLICATIONS: CLINICAL PATHOLOGY
Woo JS, Arboleda VA, Garner OB. Point-of-Care Testing in infectious disease. In press. Clinical Microbiology Newsletter. 2017
Arboleda VA, Garner OB. Reigning in the beast: Ensuring quality laboratory testing in the point of care testing in the Ambulatory Care Setting. American Journal of Clinical Pathology, October 2017.
Arboleda VA, Lee S. Lymphoma and gout coexisting in the same joint fluid. Blood Work. Blood. 2015 May 14. 125(20):3213. PMID: 26171482
Reviews/CHAPTERS
Arboleda VA, Xian RR. An Overview of DNA analytical methods. Chapter 20. Methods in Molecular Biology: Biobanking. Springer. In press.
Arboleda VA, Sandberg DE, Vilain E. DSDs: genetics, underlying pathologies and psychosexual differentiation. Nature Endocrinology Reviews. 2014 Aug 5. PMCID: PMC4096368
Arboleda VA, Vilain E. “Disorders of Sex Development”. Chapter 16. Yen and Jaffe's Reproductive Endocrinology: Physiology, Pathophysiology, and Clinical Management. 7th edition. Ed Stauss JF III, R.L.Barbieri. Elsevier. 2013.
Arboleda VA, Vilain E. The evolution of the search for novel genes in mammalian sex determination: from mice to men. Mol Genet Metab. 2011 Sep-Oct;104(1-2):67-71. PMCID: PMC3171521.
Arboleda VA,.Fleming A, Vilain E. “Disorders of Sex Development”. Genetic Diagnosis of Endocrine Disorders. Eds. R. Weiss and S. Refetoff. McGraw-Hill. 2010.
Prunell GF, Arboleda VA, Troy CM. Caspase Function in Neuronal Death: Delineation of the role of Caspases in Ischemia. Current drug targets - CNS and Neurological disorders. 4(1): 51-61. February 2005.