Publication Archive | Frazer Lab

2024

Malka S, Biswas P, Berry AM, Sangermano R, Ullah M, Lin S, D’Antonio M, Jestin A, Jiao X, Quinodoz M, Sullivan L, Gardner JC, Place EM, Michaelides M, Kaminska K, Mahroo OA, Schiff E, Wright G, Cancellieri F, Vaclavik F, Santos C, Rehman AU, Mehrotra S, Baig HMA, Iqbal M, Ansar M, Santos LC, Sousa AB, Tran VH, Matsui H, Bhatia A, Naeem MA, Akram SJ, Akram J, Riazuddin S, Ayuso C, Pierce EA, Hardcastle AJ, Riazuddin SA, Frazer KA, Hejtmancik JF, Rivolta C, Bujakowska KM, Arno G, Webster AR, Ayyagari R. Substitution of a single non-coding nucleotide upstream of TMEM216 causes non-syndromic retinitis pigmentosa and is associated with reduced TMEM216 expression. American Journal of Human Genetics. 2024 September 5. doi: 10.1016/j.ajhg.2024.07.020. PMID: 39191256
Tan MCB, Isom CA, Liu Y, Trégouët DA, Lindstrom S, Wang L, Smith EN, Gordon W, van Hylckama Vlieg A, de Andrade M, Brody JA, Pattee JW, Haessler J, Brumpton BM, Chasman DI, Suchon P, Chen MH, Turman C, Germain M, Wiggins KL, MacDonald J, Braekkan SK, Armasu SM, Pankratz N, Jackson RD, Nielsen JB, Giulianini F, Puurunen MK, Ibrahim M, Heckbert SR, Damrauer SM, Natarajan P, Klarin D, de Vries PS, Sabater-Lleal M, Huffman JE, Bammler TK, Frazer KA, McCauley BM, Taylor K, Pankow JS, Reiner AP, Gabrielsen ME, Deleuze JF, O'Donnell CJ, Kim J, McKnight B, Kraft P, Hansen JB, Rosendaal FR, Heit JA, Psaty BM, Tang W, Kooperberg C, Hveem K, Ridker PM, Morange PE, Johnson AD, Kabrhel C, Smith N, Wu L, Zhou D, Gamazon ER. Transcriptome-wide association study and Mendelian randomization in pancreatic cancer identifies susceptibility genes and causal relationships with type 2 diabetes and venous thromboembolism. eBioMedicine. 2024 August. doi: 10.1016/j.ebiom.2024.105233. PMID: 39002386
Schmidt TT, Tyer C, Rughani P, Haggblom C, Jones JR, Dai X, Frazer KA, Gage FH, Juul S, Hickey S, Karlseder J. High resolution long-read telomere sequencing reveals dynamic mechanisms in aging and cancer. Nature Communications. 2024 June 18. doi: 10.1038/s41467-024-48917-7 PMID: 38890299
Arthur TA, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva N, Joshua IN, iPSCORE Consortium, Young Greenwald WW, D'Antonia M, Pera MF, Frazer KA. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. Nature Communications. 2024 February 23. doi: 10.1101/2023.05.20.541447. PMID: 38395976

2023

Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D’Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, and Farley EK. Single-nucleotide variants within heart enhancers increase binding affinity. Developmental Cell. 2023 November 6. doi: 10.1016/j.devcel.2023.09.005. PMID: 37848026
Nguyen JP, Arthur TD, Fujita K, Salgado BM, Donovan MKR, iPSCORE Consortium, Matsui M, Kim JH, D'Antonio-Chronowska A, D'Antonio D, Frazer KA. eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk. Nature Communications. 2023 October 30. doi: 10.1038/s41467-023-42560-4. PMID: 37903777
Frazer KA & Schork N. The human pangenome reference anticipates equitable and fundamental genomic insights. Cell Genomics. 2023 July 12. doi: 10.1016/j.xgen.2023.100360. PMID: 37492100
Costanzo MC, von Grotthuss M, Massung J, Jang D, Caulkins L….Frazer KA,…. Wholley D, Yuksel K, Zaghloul NA, Fauman EB, Kamphaus TN, Abecasis GR. The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. Cell Metabolism. 2023 April 4. doi: 10.1016/j.cmet.2023.03.001. PMID: 36963395
D'Antonio M, Nguyen JP, Arthur TD, iPSCORE Consortium, Matsui M, D'Antonio-Chronowska A, Frazer KA. Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. Nature Communications. 2023 February 28. doi: 10.1038/s41467-023-36638-2. PMID: 36854752

2022

Benaglio P, Zhu H, Okino ML, Yan J, Elgamal R, Nariai N, Beebe E, Korgaonkar K, Qiu, Donovan MKR, Chiou J, Wang G, Newsome J, Kaur J, Miller M, Preissl S, Corban S, Aylward A, Taipale J, Ren B, Frazer KA, Sander M, Gaulton KJ. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines. Cell Genomics. 2022 December 14. doi: 10.1016/j.xgen.2022.100214. PMID: 36778047.
den Hollander AI, Mullins RF, D Orozco L, Voigt AP, Chen HH, Strunz T, Grassmann F, Haines JL, Kuiper JJW, Tumminia SJ, Allikmets R, Hageman GS, Stambolian D, Klaver CCW, Boeke JD, Chen H, Honigberg L, Katti S, Frazer KA, Weber BHF, Gorin MB. Systems genomics in age-related macular degeneration. Experimental Eye Research. 2022 September 13. doi: 10.1016/j.exer.2022.109248. PMID: 36108770.
Temprano-Sagrera G, Sitlani CM, Bone WP, ... Frazer KA, ... Amouyel P, Ay H. Multi-phenotype analyses of hemostatic traits with cardiovascular events reveal novel genetic associations. Journal of Thrombosis and Haemostasis. 2022 June. doi: 10.1111/jth.15698.
D'Antonio M, Nguyen JP, Arthur TD, Matsui M, Donovan, MKR, Antonio-Chronowska A, Frazer KA. In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. PLOS Computational Biology. 2022 February 28; doi: 10.1371/journal.pcbi.1009918. PMID: 35226669.
Liu R, Lee J, Tchoe, Y, Pre, D, Bourhis, A M, D'Antonio-Chronowska, A, Robin, G, Lee, S H, Ro, Y G, Vatsyayan, R, Tonsfeldt, K J, Hossain, L A, Phipps, M L, Yoo, J, Nogan, J, Martinez, J S, Frazer, K A, Bang, A G, Dayeh, S A. Ultra-Sharp Nanowire Arrays Natively Permeate, Record, and Stimulate Intracellular Activity in Neuronal and Cardiac Networks. Advanced Functional Material. 2022 February 16. doi: doi:10.1002/adfm.202108378.

2021

D’Antonio M, Nguyen JP, Arthur TD, Matsui H, The COVID-19 Host Genetics Initiative, D’Antonio-Chronowska A, Frazer KA. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a wide variety of tissues. Cell Reports. 2021 November 16. doi: I10.1016/j.celrep.2021.110020. PMID: 34762851
Nguyen JP, D’Antonio-Chronowska A, Fujita K, Salgado BM, Matsui H, Arthur TD, iPSCORE Consortium, Donovan MK, D’Antonio M, Frazer KA. Regulatory variants active in iPSC-derived pancreatic progenitor cells are associated with Type 2 Diabetes in adults. bioRxiv. 2021 October 21. https://doi.org/10.1101/2021.10.20.465206
Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kumarov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhao J, Devalaraja S, Huynh A, Alapati A Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genetics. 2021 October 18. 10.1371/journal.pgen.1009848. PMID: 34662339.
Rawat P, Brummel SS, Singh KK, Kim J, Frazer KA, Nichols S, Seage GR III, Williams PL, Van Dyke RB, Harismendy O, Trout RN, Spector SA. Genomics Links Inflammation with Neurocognitive Impairment in Children Living with Human Immunodeficiency Virus type-1. The Journal of Infectious Diseases. 2021 September 1. doi.org/10.1093/infdis/jiaa792. PMID: 33373444.
Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG. Enhancer release and retargeting activates disease-susceptibility genes. Nature. 2021 May 26. doi: 10.1038/s41586-021-03577-1. PMID: 34040254.
Bonder MJ, Smai, C, Gloudemans MJ, Fresard L, Jakubosky D, D’Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE, HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nature Genetics. 2021 March 4. doi: 10.1038/s41588-021-00800-7. PMID: 33664507.
Yan J, Qui Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Ram A, Li X, Fan S, Chiou J, Chen F, Frazer KA, Gaulton KJ, Sander M, Taipale J, Ren B. Systematic analysis of binding of transcription factors to noncoding variants. Nature. 2021 March. doi: 10.1038/s41586-021-03211-0. PMID: 33505025.
Biswas P, Borooah A, Matsui H, Voronchikhina M, Zhou J, Raghavendra PB, Riazuddin SA, Wahlin K, Frazer KA, Ayyagari R. Detection and validation of novel mutations in MERTK in a simplex case of retinal degeneration using WGS and hiPSC‐RPEs model. Human Mutation. 2021 February. doi: 10.1002/humu.24146. PMID: 33252167.

2020

D’Antonio-Chronowska A, D’Antonio M, Frazer KA (2020). In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs). Bio-protocol 10(18): e3755. DOI: 10.21769/BioProtoc.3755.
D'Antonio M, D'Antonio-Chronowska A, Frazer KA. Revealing Instability: Genetic Variation Underlies Variability in mESC Pluripotency. Cell Stem Cell. 2020 Sept. 3. doi.org/10.1016/j.stem.2020.08.012. https://authors.elsevier.com/a/1bgxm6tu0CboNI
Paulsen B, Skille H, Smith EN, Hveem K, Gabrielsen ME, Brækkan SK, Rosendaal FR, Frazer KA, Gran OV, Hansen JB. Fibrinogen gamma gene rs2066865 and risk of cancer-related venous thromboembolism. Haematologica. 2020 July 1. doi: 10.3324/haematol.2019.224279. PMID: 31582554.
Jakubosky D, Smith EN, D'Antonio M, Jan Bonder M, Young Greenwald WW, D'Antonio-Chronowska A, Matsui H; i2QTL Consortium, Stegle O, Montgomery SB, DeBoever C, Frazer KA. Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats. Nat Commun. 2020 Jun 10. doi: 10.1038/s41467-020-16481-5. PMID: 32522985.
Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H; i2QTL Consortium, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. Properties of structural variants and short tandem repeats associated with gene expression and complex traits. Nat Commun. 2020 Jun 10. doi: 10.1038/s41467-020-16482-4. PMID: 32522982.
Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA. Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. Stem Cell Research. 2020 July. doi: 10.1016/j.scr.2020.101803.
Donovan MKR, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants. Nature Communication. 2020 Feb 19. doi: 10.1038/s41467-020-14561-0. PMID: 32075962.
Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D'Antonio M, Nguyen ND, Saberi S, Ma J, Miki S, Boyer AD, Ravits J, Frazer KA, Bafna V, Chen CC, Mischel PS, Yeo GW, Furnari FB. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat Commun. 2020 Jan 28. doi: 10.1038/s41467-020-14312-1. PMID: 31992716.

2019

D’Antonio-Chronowska A, D’Antonio M, Frazer, KA. In vitro Differentiation of Human iPSC-derived Retinal Pigment Epithelium Cells (iPSC-RPE). Bio-protocol. 2019 December 20. doi: 10.21769/BioProtoc.3469.
D'Antonio M, Reyna J, Jakubosky D, Donovan MKR, Bonder MJ, Matsui M, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. eLife. 2019 November 20. doi: 10.7554/eLife.48476.
Jin W, Mulas F, Gaertner B, Sui Y, Wang J, Matta I, Zeng C, Vinckier N, Wang A, Nguyen-Ngoc KV, Chiou J, Kaestner KH, Frazer KA, Carrano AC, Shih HP, Sander M. A Network of microRNAs Acts to Promote Cell Cycle Exit and Differentiation of Human Pancreatic Endocrine Cells. iScience. 2019 Nov 1. doi: 10.1016/j.isci.2019.10.063. PMID: 31733514.
D’Antonio-Chronowska A, Donovan MKR, Young Greenwald WW, Nguyen JP, Fujita K, Hashem S, Matsui H, Soncin F, Parast M, Ward MC, Coulet F, Smith EN, Adler E, D’Antonio M, Frazer KA. Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories. Stem Cell Reports. 2019 October 24. doi: 10.1016/j.stemcr.2019.09.011. PMID: 31668852.
Benaglio P, D'Antonio-Chronowska A, Ma W, Yang F, Young Greenwald WW, Donovan MKR, DeBoever C, Li H, Drees F, Singhal S, Matsui H, van Setten J, Sotoodehnia N, Gaulton KJ, Smith EN, D'Antonio M, Rosenfeld MG, Frazer KA. Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. Nature Genetics. 2019 Sept 30. doi: 10.1038/s41588-019-0499-3. PMID: 31570892.
Lindstrom S, Wang L, Smith EN, Gordon W, van Hylckama Vlieg A, de Andrade M, Brody JA, Pattee JW, Haessler J, Brumpton BM, Chasman DI, Suchon P, Chen MH, Turman C, Germain M, Wiggins KL, MacDonald J, Braekkan SK, Armasu SM, Pankratz N, Jackson RD, Nielsen JB, Giulianini F, Puurunen MK, Ibrahim M, Heckbert SR, Damrauer SM, Natarajan P, Klarin D, de Vries PS, Sabater-Lleal M, Huffman JE, Bammler TK, Frazer KA, McCauley BM, Taylor K, Pankow JS, Reiner AP, Gabrielsen ME, Deleuze JF, O'Donnell CJ, Kim J, McKnight B, Kraft P, Hansen JB, Rosendaal FR, Heit JA, Psaty BM, Tang W, Kooperberg C, Hveem K, Ridker PM, Morange PE, Johnson AD, Kabrhel C, Trégouët DA, Smith NL. Genomic and Transcriptomic Association Studies Identify 16 Novel Susceptibility Loci for Venous Thromboembolism. Blood. 2019 Aug 16. doi: 10.1182/blood.2019000435. PMID: 31420334.
Broderick L, Yost S, Li D, McGeough MD, Booshehri LM, Guaderrama M, Brydges SD, Kucharova K, Pate NC, Harr M, Hakonarson H, Zackai E, Cowell IG, Austin CA, Hügle B, Gebauer C, Zhang J, Xu X, Wang J, Croker BA, Frazer KA, Putnam CD, Hoffman HM. Mutations in topoisomerase IIβ result in a B cell immunodeficiency. Nat Commun. 2019 Aug 13. doi: 10.1038/s41467-019-11570-6. PMID: 31409799.
Greenwald WW, Chiou J, Yan J, Qiu Y, Dai N, Wang A, Nariai N, Aylward A, Han JY, Kadakia N, Regue L, Okino ML, Drees F, Kramer D, Vinckier N, Minichiello L, Gorkin D, Avruch J, Frazer KA, Sander M, Ren B, Gaulton KJ. Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. Nat Commun. 2019 May 7. doi: 10.1038/s41467-019-09975-4. PMID: 31064983.
Smith EN, D'Antonio-Chronowska A, Greenwald WW, Borja V, Aguiar LR, Pogue R, Matsui H, Benaglio P, Borooah S, D'Antonio M, Ayyagari R, Frazer KA. Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci. Stem Cell Reports. 2019 Apr 25. doi: 10.1016/j.stemcr.2019.04.012. PMID: 31080113.
Ghia EM, Rassenti LZ, Neuberg DS, Blanco A, Yousif F, Smith EN, McPherson JD, Hudson TJ, Harismendy O, Frazer KA, Kipps TJ. Activation of Hedgehog signaling associates with early disease progression in chronic lymphocytic leukemia. Blood. 2019 Mar 28. doi: 10.1182/blood-2018-09-873695. PMID: 30923040.
Greenwald WW, Li H, Benaglio P, Jakubosky D, Matsui H, Schmitt A, Selvaraj S, D'Antonio M, D'Antonio-Chronowska A, Smith EN, Frazer KA. Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression. Nat Commun. 2019 Mar 5. doi: 10.1038/s41467-019-08940-5. PubMed PMID: 30837461.
Rinde LB, Morelli VM, Småbrekke B, Mathiesen EB, Løchen M, Njølstad I, Wilsgaard T, Smith E, Rosendaal FR, Frazer KA, Brækkan SK and Hansen J. Effect of prothrombotic genotypes on the risk of venous thromboembolism in patients with and without ischemic stroke: The TromsØ Study. J Thromb Haemost. 2019 Feb 18. doi:10.1111/jth.14410. PMID:30773804.
Lindström S, Brody JA, Turman C, Germain M, Bartz TM, Smith EN, Chen MH, Puurunen M, Chasman D, Hassler J, Pankratz N, Basu S, Guan W, Gyorgy B, Ibrahim M, Empana JP, Olaso R, Jackson R, Braekkan SK, McKnight B, Deleuze JF, O'Donnell CJ, Jouven X, Frazer KA, Psaty BM, Wiggins KL, Taylor K, Reiner AP, Heckbert SR, Kooperberg C, Ridker P, Hansen JB, Tang W, Johnson AD, Morange PE, Trégouët DA, Kraft P, Smith NL, Kabrhel C; INVENT Consortium. A large-scale exome array analysis of venous thromboembolism. Genet Epidemiol. 2019 Jan 19. doi: 10.1002/gepi.22187. PMID: 30659681.

2018

Solomon T, Lapek JD, Jensen SB, Greenwald WW, Hindberg Kristian, Matsui H, Latysheva N, Braekken SK, Gonzalez DJ, Frazer KA, Smith EN, Hansen JB. Identification of common and rare genetic variation associated with plasma protein levels using whole-exome sequencing and mass spectrometry. Circulation: Genomic and Precision Medicine. 2018 December 11. DOI: 10.1161/CIRCGEN.118.002170. PMID: 30562114.
Veevers J, Farah EN, Mirko C, Witty AD, Palomares K, Vidal JG, Emre N, Carson CT, Ouyang K, Liu C, Van Vliet, P, Zhu M, Hegarty JM, Deacon DC, Grinstein JD, Dirschinger RJ, Frazer KA, Adler ED, Evans SM. Cell-surface marker signature for enrichment of ventricular cardiomyocytes derived from human embryonic stem cells. Stem Cell Reports. 2018 September 11. Doi: 10.1016/j.stemcr.2018.07.007 PMID: 30122443
Jensen SB, Hindberg K, Solomon T, Smith EN, Lapek Jr JD, Gonzalez DJ, Latysheva N, Frazer KA, Braekkan SK, Hansen JB. Discovery of novel plasma biomarkers for future incident venous thromboembolism by untargeted synchronous precursor selection mass spectrometry proteomics. Journal of Thrombosis and Haemostasis. 2018 July 2. doi: 10.1111/jth.14220. PMID: 29964323
D’Antonio M, Benaglio P, Jakubosky DA, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D’Antonio-Chronowska A, Frazer KA. Insights into the mutational burden of human induced pluripotent stem cells using an integrative multi-omics approach. Cell Reports. 2018 July 24. doi: 10.1016/j.celrep.2018.06.091. PMID: 30044985.
Chekuri A, Guru AA, Biswas P, Branham K, Borooah S, Soto-Hermida A, Hicks M, Khan NW, Matsui H, Alapati A, Raghavendra PB, Roosing S, Sarangapani S, Mathavan S, Telenti A, Heckenlively JR, Riazuddin SA, Frazer KA, Sieving PA, Ayyagari R. IFT88 mutations identified in individuals with non-syndromic recessive retinal degeneration result in abnormal ciliogenesis. Human Genetics. 2018 July 5. doi: 10.1007/s00439-018-1897-9. PMID: 29978320.
Horvei LD, Braekkan SK, Smith EN, Solomon T, Hindberg K, Frazer KA, Rosendaal FR, Hansen JB. Joint effects of prothrombotic genotypes and body weight on the risk of venous thromboembolism: The Tromsø Study. Journal of Thrombosis and Haemostasis. 2018 Jan 16. doi: 1111/jth.13892. PMID: 29094466.

2017

Koga T, Benitez J, Markmiller S, D’Antonio M, Parisian A, Saberi S, Turner K, Hessenauer MF, Thorne AH, Mischel CZP, Frazer KA, Yeo G, Cavenee W, Furnari F. TMOD-42. CRISPER/Cas9-Edited human neural stem cells give rise to brain tumors resembling glioblastomas. Neuro-Oncology. 2017 Nov 6. DOI: 10.1093/neuonc/nox168.1078
Nariai N, Greenwald WW, DeBoever C, Li H, Frazer KA. Efficient prioritization of multiple causal eQTL variants via sparse polygenic modeling. Genetics. 2017 Dec. Epub 2017 Oct 26. DOI: 10.1534/genetics.117.300435. PMID:29074555
Biswas P, Duncan JL, Ali M, Matsui H, Naeem MA, Raghavendra PB, Frazer KA, Arts HH, Riazuddin S, Akram J, Hejtmancik JF, Riazuddin SA, Ayyagari R. A mutation in IFT43 causes non-syndromic recessive retinal degeneration. Human Molecular Genetics. 2017 Sept 18. DOI: 10.1093/hmg/ddx356. PMID: 28973684
D’Antonio M, Weghorn D, D’Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer KA. Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. Nature Communications. 2017 Sept 5. DOI: 10.1038/s41467-017-00100x. PMID: 28874753
Gustafson K, Duncan JL, Biswas P, Soto-Hermida A, Matsui H, Jakubosky D, Suk J, Telenti A, Frazer KA, Ayyagari R. Whole genome sequencing revealed mutations in two independent genes as the underlying cause of retinal degeneration in an ashkenazi jewish pedigree. Genes. 2017 Aug 24. DOI: 10.3390/genes8090210. PMID: 28837078
Zanca, C, Villa GR, Benitez JA, Thhorne AH, Koga T, D’Antonio M, Ikegami S, Ma J, Boyer AD, Banisadr A, Jameson NM, Parisian AD, Eliseeva OV, Barnabe GF, Liu F, Wu S, Yang H, Wykosky J, Frazer KA, Verkusha VV, Isaguliants MG, Weiss WA, Gahman TC, Shiau AK, Chen CC, Mischel PS, Cavanee WK, Furnari FB. Glioblastoma cellular cross-talk converges on NF-κB to attenuate EGFR inhibitor sensitivity. Genes Dev. 2017 Jul 19. Doi: 10.1101/gad.300079.117. PMID: 28724615
Benitez JA, Ma J, D’Antonio M, Boyer A, Camargo MF, Zanca C, Kelly S, Khodadadi-Jamayran A, Jameson NM, Andersen M, Miletic H, Saberi S, Frazer KA, Cavenee WK, Furnari FB. Nature Communications. PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. 2017 May 12. Doi:10.1038/ncomms15223. PMID: 28497778
Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA. Pgltools:a genomic arithmetic tool suite for maipulation of Hi-C peak and other chromatin interaction data. BMC Bioinformatics. 2017 Apr 7. DOI: 10.1186/s12859-017-1621-0. PMC: 5384132. PMID: 28388874
Panopoulos AD, D’Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O’Connor DT, Yeo, GW, Evans SM, Chi NC, Jepsen K, Nariai N, Muller F, Goldstein LSB, Belmonte JCI, Adler E, Loring JF, Berggren WT, D’Antonio-Chronowska A, Smith EN, Frazer KA. iPSCORE: A resource of 222 iPSC lines enabling functional characterization of genetic variation across a variety of cell types. Stem Cell Reports. 2017 Apr 6. DOI: 10.1016/j.stemcr.2017.03.012. PMC: 5390244. PMID: 28410642
Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C, Biggs W, Sandoval E, D’Antonio-Chronowska A, Berggren WT, Belmonte JCI, Frazer KA. Aberrant iPSC methylation is associated with motif enrichment and gene expression changes in a clone-specific manner independent of genetics. Cell Stem Cell. 2017 Apr 6. DOI: 10.1016/j.stem.2017.03.010. PMID: 28388429
DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D’Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D’Antonio-Chronowska A, Farley EK, Frazer KA. Large-scale profiling reveals the influence of genetic variation on gene expression in human induced pluripotent stem cells. Cell Stem Cell. 2017 Apr 6. DOI: 10.1016/j.stem. 2017.03.009. PMID: 28388430
D’Antonio M, Woodruff G, Nathanson JL, D’Antonio-Chronowska A, Arias A, Matsui H, Williams R, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos A, Frazer KA. High-throughput and cost-effective characterization of induced pluripotent stem cells. Stem Cell Reports. 2017 Apr 6. DOI: 10.1016/j.stemcr. 2017.03.011. PMC: 5390243. PMID: 28410643

2016

Cui B, Ghia EM, Chen L, Rassenti LZ, DeBoever C, Widhopf GF 2nd, Yu J, Neuberg DS, Wierda WG, Rai KR, Kay NE, Brown JR, Jones JA, Gribben JG, Frazer KA, Kipps TJ. High Level ROR1 associates with accelerated disease progression in chronic lymphocytic leukemia. Blood. 2016 Dec 22. Doi. 10.1182/blood-2016-04-712562. Epub 2016 Nov 4. PMID: 27815263
Branham K, Matsui H, Biswas P, Guru AA, Hicks M, Suk JJ, Li H, Jakubosky D, Long T, Nariai N, Heckenlively JR, Frazer KA, Sieving PA, Ayyagari R. Establishing the involvement of the novel gene AGBL5 in retinitis pigmentosa by whole genome sequencing. Physiol Genomics. 2016 October 7. doi: 10.1152/physiolgenomics.00101.2016. PMID: 27764769
Kaneda, MM, Messer KS, Ralainirina N, Li H, Leem C, Gorjestani S, Woo G, Nguyen AV, Figueiredo CC, Foubert P, Schmid MC, Pink M, Winkler DG, Rausch M, Palombella VJ, Kutok J, McGovern K, Frazer KA, Wu X, Karin M, Sasik R, Cohen EEW, Varner JA. P13K is a molecular switch that controls immune suppression. Nature. 2016 September 19. http://dx.doi.org/10.1038/nature19834.
D’Antonio M, Tamayo P, Mesirov JP, Frazer KA. Kataegis expression signature in breast cancer is associated with late onset, better prognosis, and higher HER2 levels. Cell Reports. 2016 July 19; 1-12. Cell Reports: S2211-1247(16)30766-5 PMID:27373164
Solomon T, Smith EN, Matsui H, Braekkan SK, Wilsgaard T, Njølstad I, Mathiesen EB, Hansen JB, Frazer KA. Associations between common and rare exonic genetic variants and serum levels of twenty cardiovascular-related proteins. The Tromsø Study. 2016 June 21; doi:10.1161/CIRCGENETICS.115.001327. Circ Cardiovasc Genet:CIRCGENETICS.115.001327 PMID:27329291
- Accompanying editorial: McGarrah RW and Shah SH. Exomes, Proteins, and Cardiovascular Disease: Making Sense of the Signals. 2016; 9. doi: 10.1161/CIRCGENETICS.116.001549 PMID:27531916
Gran O, Smith EN, Braekkan SK, Jensvoll H, Solomon T, Hindberg K, Wilsgaard T, Rosendaal FR, Frazer KA, Hansen JB. Joint effects of cancer and variants in the factor 5 gene on the risk of venous thromboembolism. Haematologica. 2016 June 10. Haematol.2016.147405; Doi:10.3324/haematol.2016.147405. Haematologica:haematol.2016.147405
Zipeto MA, Court AC, Sadarangani A, Delos Santos NP, Balaian L, Chun HJ, Pineda G, Morris SR, Mason CN, Geron I, Barrett C, Goff DJ, Wall R, Pellecchia M, Minden M, Frazer KA, Marra MA, Crews LA, Jiang Q, Jamieson CH. ADAR1 activation drives leukemia stem cell self-renewal by impairing let-7 biogenesis. Cell Stem Cell. 2016 Jun 7. pii: S1934-5909(16)30088-1. doi: 10.1016/j.stem.2016.05.004. PubMed PMID:27292188

2015

Holm F, Hellqvist E, Mason CN, Ali SA, Delos-Santos N, Barrett CL, Chun HJ, Minden MD, Moore RA, Marra MA, Runza V, Frazer KA, Sadarangani A, Jamieson CHM. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal. Proc Natl Acad Sci USA. 2015 Dec 15; 112(50). doi: 10.1073/pnas. 1506943112. Epub 2015 Nov 30. PMID:26621726
Bao L, Messer K, Schwab R, Harismendy O, Pu M, Crain B, Yost S, Frazer KA, Rana B, Hasteh F, Wallace A, Parker BA. Mutational profiling can establish clonal or independent origin in synchronous bilateral breast and other tumors. PLoS One. 2015 Nov 10: 10(11), e0142487. Doi: 10.1371/journal.pone.0142487. PMID:26554380
Barrett CL, DeBoever C, Jepsen K, Saenz CC, Carson DA, Frazer KA. Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy. Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):E3050-7. doi: 10.1073/pnas. 1508057112. Epub 2015 May 26. PMID:26015570
Alakus H, Yost SE, Woo B, French R, Lin GY, Jepsen K, Frazer KA, Lowy AM, Harismendy O. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. J Transl Med 2015 Apr 16;13(1):122. PMID:25889843
Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CH, Carson DA, Kipps TJ, Frazer KA. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J. 2015 Apr 10;5:e303. doi: 10.1038/bcj.2015.14. PMID:25860294
Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED. Oxidative stress mediates cardiomyocyte apoptosis in a human model of danon disease and heart failure. Stem Cells. 2015 Mar 31. doi: 10.1002/stem.2015. PMID:25826782
DeBoever C, Ghia EM, Shepard PJ, Rassenti L, Barrett CL, Jepsen K, Jamieson CH, Carson D, Kipps TJ, Frazer KA. Transcriptome sequencing reveals potential mechanism of cryptic 3’splice site selection in SF3B1-mutated cancers. PLoS Computational Biology 2015 Mar 13: 11 (3), e1004105-e1004105. PMID:25768983
Crews LA, Jiang Q, Zipeto MA, Lazzari E, Court AC, Ali S, Barrett CL, Frazer KA, Jamieson CH. An RNA editing fingerprint of cancer stem cell reprogramming. J Transl Med. 2015 Feb 12;13(1):52. doi:10.1186/s12967-014-0370-3. PMID:25889244

2014

Shepard PJ, Barshop BA, Baumgartner MR, Hansen JB, Jepsen K, Smith EN, Frazer KA. Consanguinity and rare mutations outside of MCCC genes underlie nonspecific phenotypes of MCCD. Genetics in Medicine. 2014 Nov 6. 10.1038/gim.2014.157. PMID:25356967
Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biology. 2014 Aug 7;15(8):420. PMID:25103687
Cheng CP, Kuo IY, Alakus H, Frazer KA, Harismendy O, Wang YC, Tseng VS. Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. Bioinformatics. 2014 Jul 10. pii: btu433. PMID:25015989
Alakus H, Bollschweiler E, Hölscher AH, Warnecke-Eberz U, Frazer KA, Harismendy O, Lowy AM, Monig SP, Eberz PM, Maus M, Drebber U, Siffert W, Metzger R. Homozygous GNAS 393C-allele carriers with locally advanced esophageal cancer fail to benefit from platinum-based preoperative chemoradiotherapy. Ann Surg Oncol. 2014 Jul 2. PMID:24986238
Cheng CP, DeBoever C, Frazer KA, Liu YC, Tseng VS. MiningABs: mining associated biomarkers across multi-connected gene expression datasets. BMC Bioinformatics. 2014 Jun 8;15(1):173. doi:10.1186/1471-2105-15-173. PMID:24909518
Alakus H, Babicky ML, Ghosh P, Yost S, Jepsen K, Dai Y, Arias A, Samuels ML, Mose ES, Schwab RB, Peterson MR, Lowy AM, Frazer KA, Harismendy O. Genome-wide mutational landscape of mucinous carcinomatosis peritonei of appendiceal origin. Genome Med. 2014 May 29;6(5):43. doi: 10.1186/gm559. PMID:24944587
Carson AR, Smith EN, Matsui H, Brækkan SK, Jepsen K, Hansen JB, Frazer KA. Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. BMC Bioinformatics. 2014 May 2, 15 (125): 1471-2105. doi:10.1186/1471-2105-15-125. PMID:24884706
Mraz M, Chen L, Rassenti LZ, Ghia EM, Li H, Jepsen K, Smith EN, Messer K, Frazer KA, Kipps TJ. MicroRNA-150 contributes to the proficiency of B-cell receptor signaling in chronic lymphocytic leukemia by regulating expression of GAB1 and FOXP1 genes. Blood. 2014 May 1; doi: 10.1182/blood-2013-09-527234. PMID:24787006
Shlush L, Zandi S, Mitchell A, Chen WC, Brandwein JM, Gupta V, Kennedy JA, Schimmer AD, Schuh AC, Yee KW, McLeod JL, Doedens M, Medeiros JJ, Marke R, Kim HJ, Lee K, McPherson JD, Hudson TJ, HALT Pan-Leukemia Gene Panel Consortium, Brown AM, Yousif F, Trinh QM, Stein LD, Minden MD, Wang JC, Dick JE. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature. 2014 Feb 20; 506(7488):328-33. doi: 10.1038/nature13038. PMID:24522528
Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biology. 2014 Feb 20; 15 :R36, doi:10.1186/gb-2014-15-2-r36. PMID:24555826
Smith EN, Jepsen K, Arias AD, Shepard PJ, Chambers CD, Frazer KA. Genetic ancestry of participants in the National Children's Study. Genome Biology. 2014 Feb 3;15(2):R22. doi:10.1186/gb-2014-15-2-r22. PMID:24490717

2013

Harismendy O, Schwab RB, Alakus H, Yost SE, Matsui H, Hasteh F, Wallace AM, Park HL, Madlensky L, Parker B, Carpenter PM, Jepsen K, Anton-Culver H, Frazer KA. Evaluation of ultra-deep targeted sequencing for personalized breast cancer care. Breast Cancer Research. 2013 Dec 10’ 15(6):R115, doi:10.1186/bcr3584. PMID:24326041
He G, Dhar D, Nakagawa H, Font-Burgada J, Ogata H, Jiang Y, Shalapour S, Seki E, Yost SE, Jepsen K, Frazer KA, Harismendy O, Hatziapostolou M, Illiopoulus D, Suetsugu A, Hoffman RM, Tateishi R, Koike K, Karin M. Idendification of liver cancer progenitors whose malignant progression depends on autocrine IL-6 signaling. Cell. 2013 Oct 10; 155(2): 384-396, doi: 10.1016/j.cell.2013.09.031. Epub 2013 Oct 11. PMID:24120137
Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in andean highlanders. American Journal of Human Genetics. 2013 Sep 5;93(3):452-62. doi: 10.1016/j.ajhg.2013.07.011. Epub 2013 Aug 15. PMID:23954164
DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS ONE. 2013 Sept 4: 8(9): e73956. doi:10.1371/journal.pone.0073956. PMID:24023918
Yost SE, Alakus H, Matsui H, Schwab R, Jepsen K, Frazer KA, Harismendy O. Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing. Bioinformatics. 2013 May 27: 29(15) 1908–1909. doi: 10.1093/bioinformatics/btt305. Epub 2013 May 27. PMID:23712659
Barrett CL, Schwab RB, Jung H, Crain B, Goff DJ, Jamieson CH, Thistlethwaite PA, Harismendy O, Carson DA, Frazer KA. (2013) Transcriptome sequencing of tumor Ssbpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer. 2013 Mar 20. PLoS ONE 8(3): e58714. doi:10.1371/journal.pone.0058714 PMID:23527012
Goff DJ, Recart AC, Sadarangani A, Chun HJ, Barrett CL, Krajewska M, Leu H, Low-Marchelli J, Ma W, Shih Ay, Wei J, Zhai D, Geron I, Pu M, Bao L, Chuang R, Balaian L, Gotlib J, Minden M, Martinelli G, Rusert J, Dao KH, Shazard K, Wentworth P, Smith KM, Jamieson CA, Morris SR, Messer K, Goldstein LS, Hudson TJ, Marra M, Frazer KA, Pellecchia M, Reed JC, Jamieson CH. A Pan-BCL2 inhibitor renders bone-marrow-resident human leukemia stem cells sensitive to tyrosine kinase inhibition. Cell Stem Cell. 2013 Mar 7;12(3):316-328. PMID:23333150
Yost SE, Pastorino S, Rozenzhak S, Smith EN, Chao YS, Jiang P, Kesari, Frazer KA, Harismendy O. High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models. 2013. PLoS ONE 8(2): e56185. doi:10.1371/journal.pone.0056185. PMID:23441165
Jiang Q, Crews LA, Barrett CL, Chun HJ, Court AC, Isquith JM, Zipeto MA, Goff DJ, Minden M, Sadarangani A, Rusert JM, Dao KH, Morris SR, Goldstein LS, Marra MA, Frazer KA, Jamieson CH. ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia. Proceedings of the National Academy of Sciences. 2013 Jan 15;110(3):1041-1046. PMID:23275297
Manolio TA, Chisholm RL, Ozenberger B, Roden DM, Williams MS, Wilson R, Bick D, Bottinger EP, Brilliant MH, Eng C, Frazer KA, Korf B, Ledbetter, DH, Lupski JR, Marsh C, Mrazek D, Murray MF, O’Donnell PH, Rader DJ, Relling MV, Shuldiner AR, Valle D, Weinshilboum R, Green ED, Ginsburg G. Implementing genomic medicine in the clinic: the future is here. Genetics in Medicine. 2013 Jan 10;15:258-267. Genetics in Medicine:gim2012157

2012

Yost SE, Smith EN, Schwab RB, Bao L, Jung H, Wang X, Voest E, Pierce JP, Messer K, Parker BA, Harismendy O, Frazer KA. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res. 2012 Aug;40(14):e107. Epub 2012 Apr 6. PMID: 22492626
Frazer, K. A. Decoding the human genome. Genome Research 22, 1599–1601 (2012). PMID: 22955971

2011

Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulos SK, Pond S, Crain B, Chee MS, Messer K, Link DR, Frazer KA. Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol. 2011 Dec 20;12(12):R124. PMID:22185227
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-seq read pairs. Bioinformatics. 2011 Apr 15;27(8):1068-1075. Epub 2011 Feb 16. PubMed PMID:21330288
Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA. 9p21 DNA variants associated with coronary artery disease impair interferon-? signalling response. Nature. 2011 Feb 10;470(7333):264-8.PubMed PMID:21307941
Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2349-54. Epub 2011 Jan 24. PubMed PMID:21262834

2010

Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang XC, Dib C, Turlotte E, Sipe JC, Murray SS, Deleuze JF, Bafna V, Topol EJ, Frazer KA. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol. 2010 Nov 30;11(11):R118. PubMed PMID: 21118518
Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010 Oct 14;6(10):e1000954. PubMed PMID: 20976246.
Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer KA, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics. 2010 Jul;185(3):1081-95. Epub 2010 May 3. PubMed PMID: 20439770.
Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010 Apr;20(4):537-45. Epub 2010 Feb 11. PubMed PMID: 20150320.

2009

Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol. 2009 Nov;27(11):1025-31. Epub 2009 Nov 1. PubMed PMID: 19881494.
Tewhey R, Nakano M, Wang X, Pabón-Peña C, Novak B, Giuffre A, Lin E, Happe S, Roberts DN, Leproust EM, Topol EJ, Harismendy O, Frazer KA. Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol. 2009 Oct 16;10(10):R116. PubMed PMID: 19835619.
Harismendy O, Frazer KA. Elucidating the role of 8q24 in colorectal cancer. Nat Genet. 2009 Aug;41(8):868-9. Erratum in: Nat Genet. 2009 Oct;41(10):1156. PubMed PMID: 19639026.
McNally KL, et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8. Epub 2009 Jul 13. PubMed PMID: 19597147; PubMed Central PMCID: PMC2718348.
Schork NJ, Murray SS, Frazer KA, Topol EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev. 2009 Jun;19(3):212-9. Epub 2009 May 28. Review. PubMed PMID: 19481926.
Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet. 2009 Apr;10(4):241-51. Review. PubMed PMID: 19293820.
Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009;10(3):R32. Epub 2009 Mar 27. PubMed PMID: 19327155; PubMed Central PMCID: PMC2691003.
Harismendy O, Frazer K. Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques. 2009 Mar;46(3):229-31.PMID: 19317667.

2008

Rahim NG, Harismendy O, Topol EJ, Frazer KA. Genetic determinants of phenotypic diversity in humans. Genome Biol. 2008 Apr 24;9(4):215. [Epub ahead of print] PubMed PMID: 18439327; PubMed Central PMCID: PMC2643926.
Kooner JS, Chambers JC, Aguilar-Salinas CA, Hinds DA, Hyde CL, Warnes GR, Gómez Pérez FJ, Frazer KA, Elliott P, Scott J, Milos PM, Cox DR, Thompson JF. Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat Genet. 2008 Feb;40(2):149-51. Epub 2008 Jan 13. PubMed PMID: 18193046.
Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. A genome-wide approach to identifying novel-imprinted genes. Hum Genet. 2008 Jan;122(6):625-34. Epub 2007 Oct 23.

2007

Sabeti PC, et al. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18;449(7164):913-8. PubMed PMID: 17943131; PubMed Central PMCID: PMC2687721.
International HapMap Consortium, Frazer KA, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61. PubMed PMID: 17943122; PubMed Central PMCID: PMC2689609.
GAIN Collaborative Research Group, Manolio TA, Rodriguez LL, Brooks L, Abecasis G; Collaborative Association Study of Psoriasis, Ballinger D, Daly M, Donnelly P, Faraone SV; International Multi-Center ADHD Genetics Project, Frazer K, Gabriel S, Gejman P; Molecular Genetics of Schizophrenia Collaboration, Guttmacher A, Harris EL, Insel T, Kelsoe JR; Bipolar Genome Study, Lander E, McCowin N, Mailman MD, Nabel E, Ostell J, Pugh E, Sherry S, Sullivan PF; Major Depression Stage 1 Genomewide Association in Population-Based Samples Study, Thompson JF, Warram J; Genetics of Kidneys in Diabetes (GoKinD) Study, Wholley D, Milos PM, Collins FS. New models of collaboration in genome-wide association studies: the Genetic Association Information Network. Nat Genet. 2007 Sep;39(9):1045-51. PubMed PMID: 17728769.
Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature. 2007 Aug 30;448(7157):1050-3. Epub 2007 Jul 29. PubMed PMID: 17660834.
Tao H, Berno AJ, Cox DR, Frazer KA. In vitro human keratinocyte migration rates are associated with SNPs in the KRT1 interval. PLoS One. 2007 Aug 1;2(1):e697. PubMed PMID: 17668073; PubMed Central PMCID: PMC1933256.
Clark RM, et al. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science. 2007 Jul 20;317(5836):338-42. PubMed PMID: 17641193.
Topol EJ, Murray SS, Frazer KA. The genomics gold rush. JAMA. 2007 Jul 11;298(2):218-21. PubMed PMID: 17622604.
Johansson A, Vavruch-Nilsson V, Cox DR, Frazer KA, Gyllensten U. Evaluation of the SNP tagging approach in an independent population sample--array-based SNP discovery in Sami. Hum Genet. 2007 Sep;122(2):141-50. Epub 2007 Jun 7. PubMed PMID: 17554563.
Topol EJ, Frazer KA. The resequencing imperative. Nat Genet. 2007 Apr;39(4):439-40. PubMed PMID: 17392801.

2006

Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat Genet. 2006 Jan 01. PubMed PMID: 16327809.
Tao H, Cox DR, Frazer KA. Allele-specific KRT1 expression is a complex trait. PLoS Genet. 2006 Jun;2(6):e93. Epub 2006 Jun 9. PubMed PMID: 16789827; PubMed Central PMCID: PMC1475705.
Pant PV, Tao H, Beilharz EJ, Ballinger DG, Cox DR, Frazer KA. Analysis of allelic differential expression in human white blood cells. Genome Res. 2006 Mar;16(3):331-9. Epub 2006 Feb 8. PubMed PMID: 16467561; PubMed Central PMCID: PMC1415206.

2005

Donfack J, Schneider DH, Tan Z, Kurz T, Dubchak I, Frazer KA, Ober C. Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy. Respir Res. 2005 Dec 10;6:145. PubMed PMID: 16336695; PubMed Central PMCID: PMC1325232.
Maraganore DM, de Andrade M, Lesnick TG, Strain KJ, Farrer MJ, Rocca WA, Pant PV, Frazer KA, Cox DR, Ballinger DG. High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet. 2005 Nov;77(5):685-93. Epub 2005 Sep 9. PubMed PMID: 16252231; PubMed Central PMCID: PMC1271381.
Ptak SE, Hinds DA, Koehler K, Nickel B, Patil N, Ballinger DG, Przeworski M, Frazer KA, Pääbo S. Fine-scale recombination patterns differ between chimpanzees and humans. Nat Genet. 2005 Apr;37(4):429-34. Epub 2005 Feb 18. Erratum in: Nat Genet. 2005 Apr;37(4):445. PubMed PMID: 15723063.
Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR. Whole-genome patterns of common DNA variation in three human populations. Science. 2005 Feb 18;307(5712):1072-9. PubMed PMID: 15718463.

2004

Hinds DA, Seymour AB, Durham LK, Banerjee P, Ballinger DG, Milos PM, Cox DR, Thompson JF, Frazer KA. Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels. Hum Genomics. 2004 Nov;1(6):421-34. PubMed PMID: 15606997.
Frazer KA, Wade CM, Hinds DA, Patil N, Cox DR, Daly MJ. Segmental phylogenetic relationships of inbred mouse strains revealed by fine-scale analysis of sequence variation across 4.6 mb of mouse genome. Genome Res. 2004 Aug;14(8):1493-500. PubMed PMID: 15289472; PubMed Central PMCID: PMC509258.
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. PubMed PMID: 15215394; PubMed Central PMCID: PMC441596.
Frazer KA, Tao H, Osoegawa K, de Jong PJ, Chen X, Doherty MF, Cox DR. Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 2004 Mar;14(3):367-72. Epub 2004 Feb 12. PubMed PMID: 14962988; PubMed Central PMCID: PMC353216.
Eichler EE, Frazer KA. The nature, pattern and function of human sequence variation. Genome Biol. 2004;5(4):318. Epub 2004 Mar 12. PubMed PMID: 15059253; PubMed Central PMCID: PMC395779.

2003

Dubchak I, Frazer K. Multi-species sequence comparison: the next frontier in genome annotation. Genome Biol. 2003;4(12):122. Epub 2003 Nov 27. PubMed PMID: 14659006; PubMed Central PMCID: PMC329408.
Frazer KA, Chen X, Hinds DA, Pant PV, Patil N, Cox DR. Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Res. 2003 Mar;13(3):341-6. PubMed PMID: 12618364; PubMed Central PMCID: PMC430260.
Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC. Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 2003 Jan;13(1):1-12. Review. PubMed PMID: 12529301; PubMed Central PMCID: PMC430969.

2001

Patil N, et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science. 2001 Nov 23;294(5547):1719-23. PubMed PMID: 11721056.
Frazer KA, Sheehan JB, Stokowski RP, Chen X, Hosseini R, Cheng JF, Fodor SP, Cox DR, Patil N. Evolutionarily conserved sequences on human chromosome 21. Genome Res. 2001 Oct;11(10):1651-9. PubMed PMID: 11591642; PubMed Central PMCID: PMC311124.

2000

Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I. VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2000 Nov;16(11):1046-7. PubMed PMID: 11159318.
Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 2000 Sep;10(9):1304-6. PubMed PMID: 10984448; PubMed Central PMCID: PMC310906.
Murphy K, Frazer KA, Loots G, Rubin EM. Database Searches for Binding Sites. Science. 2000 Jun 30;288(5475):2319a. PubMed PMID: 17769838.
Lacy DA, Wang ZE, Symula DJ, McArthur CJ, Rubin EM, Frazer KA, Locksley RM. Faithful expression of the human 5q31 cytokine cluster in transgenic mice. J Immunol. 2000 May 1;164(9):4569-74. PubMed PMID: 10779759.
Loots GG, Locksley RM, Blankespoor CM, Wang ZE, Miller W, Rubin EM, Frazer KA. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science. 2000 Apr 7;288(5463):136-40. PubMed PMID: 10753117.
Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W. PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000 Apr;10(4):577-86. PubMed PMID: 10779500; PubMed Central PMCID: PMC310868.
Zhu Y, Jong MC, Frazer KA, Gong E, Krauss RM, Cheng JF, Boffelli D, Rubin EM. Genomic interval engineering of mice identifies a novel modulator of triglyceride production. Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1137-42. PubMed PMID: 10655497; PubMed Central PMCID: PMC15548.

1999

Whitehead JL, Wang SY, Bost-Usinger L, Hoang E, Frazer KA, Burnside B. Photoreceptor localization of the KIF3A and KIF3B subunits of the heterotrimeric microtubule motor kinesin II in vertebrate retina. Exp Eye Res. 1999 Nov;69(5):491-503. PubMed PMID: 10548469.
Symula DJ, Frazer KA, Ueda Y, Denefle P, Stevens ME, Wang ZE, Locksley R, Rubin EM. Functional screening of an asthma QTL in YAC transgenic mice. Nat Genet. 1999 Oct;23(2):241-4. PubMed PMID: 10508526.

1997

Frazer KA, Ueda Y, Zhu Y, Gifford VR, Garofalo MR, Mohandas N, Martin CH, Palazzolo MJ, Cheng JF, Rubin EM. Computational and biological analysis of 680 kb of DNA sequence from the human 5q31 cytokine gene cluster region. Genome Res. 1997 May;7(5):495-512. PubMed PMID: 9149945.

1995

Frazer KA, Narla G, Zhang JL, Rubin EM. The apolipoprotein(a) gene is regulated by sex hormones and acute-phase inducers in YAC transgenic mice. Nat Genet. 1995 Apr;9(4):424-31. PubMed PMID: 7795650.

1992

Frazer KA, Boehnke M, Budarf ML, Wolff RK, Emanuel BS, Myers RM, Cox DR. A radiation hybrid map of the region on human chromosome 22 containing the neurofibromatosis type 2 locus. Genomics. 1992 Nov;14(3):574-84. PubMed PMID: 1427886.
Wolff RK, Frazer KA, Jackler RK, Lanser MJ, Pitts LH, Cox DR. Analysis of chromosome 22 deletions in neurofibromatosis type 2-related tumors. Am J Hum Genet. 1992 Sep;51(3):478-85. PubMed PMID: 1496981; PubMed Central PMCID: PMC1682717.
Lanser MJ, Sussman SA, Frazer K. Epidemiology, pathogenesis, and genetics of acoustic tumors. Otolaryngol Clin North Am. 1992 Jun;25(3):499-520. Review. PubMed PMID: 1625863.

1991

Patel K, Cox R, Shipley J, Kiely F, Frazer K, Cox DR, Lehrach H, Sheer D. A novel and rapid method for isolating sequences adjacent to rare cutting sites and their use in physical mapping. Nucleic Acids Res. 1991 Aug 25;19(16):4371-5. PubMed PMID: 1886764; PubMed Central PMCID: PMC328622.

1988

Hall DE, Frazer KA, Hann BC, Reichardt LF. Isolation and characterization of a laminin-binding protein from rat and chick muscle. J Cell Biol. 1988 Aug;107(2):687-97. PubMed PMID: 3417768; PubMed Central PMCID: PMC2115226.

1985

Brown CR, Higgins KW, Frazer K, Schoelz LK, Dyminski JW, Marinkovich VA, Miller SP, Burd JF. Simultaneous determination of total IgE and allergen-specific IgE in serum by the MAST chemiluminescent assay system. Clin Chem. 1985 Sep;31(9):1500-5. PubMed PMID: 4028399.