Frazer Lab Department of Pediatrics, Genome Information Sciences

Publications

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
  • 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, 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

  • 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.
  • 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;38(1):82-5. Epub 2005 Dec 4. PubMed PMID: 16327809.

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.

Page 'Breadcrumb' Navigation:

External Resources: