Publications

All publications are free and available by request

Microsatellites and Cancer

  • Samuel Rivero-Hinojosa, Nicholas Kinney, Harold R. Garner, Brian R. Rood, Germline Microsatellite Genotypes Differentiate Children with Medulloblastoma, Neuro-oncology, noz179, https://doi.org/10.1093/neuonc/noz179, 28 September 2019
  • Ramu Anandakrishnan, Robin Varghese, Nick Kinney, and Harold R. Garner, Estimating the number of genetic mutations (hits) required for tumorigenesis based on the distribution of somatic mutations, PLoS Comput Biol. 2019 Mar 7;15(3):e1006881. doi: 10.1371/journal.pcbi.1006881. PMID: 30845172
  • Dash S, Kinney NA, Varghese RT, Garner HR, Feng WC, Anandakrishnan R. Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations.  Sci Rep. 2019 Jan 30;9(1):1005. doi: 10.1038/s41598-018-37835-6. PMID: 30700767
  • Kinney N, Varghese RT, Anandakrishnan R, Garner HR, ZDHHC3 as a risk and mortality marker for breast cancer in African American Women, Cancer Informatics, Volume 16: 1–6, 2017, DOI: 10.1177/1176935117746644
  • Velmurugan KR, Varghese RT, Fonville NC, Garner HR, High-depth, high-accuracy microsatellite genotyping enables precision lung cancer risk classification, Oncogene. 2017 Nov 16;36(46):6383-6390. doi: 10.1038/onc.2017.256.
  • Patidar PL, Motea EA, Fattah FJ, Zhou Y, Morales JC, Xie Y, Garner HR, Boothman DA, The Kub5-Hera/RPRD1B interactome: a novel role in preserving genetic stability by regulating DNA mismatch repair. Nucleic Acids Res. 2016 Feb 29;44(4):1718-31. PMID: 26819409
  • Karunasena Enusha, Lauren J. McIver, Jasmin H. Bavarva, Xiaowei Wu, Hongxiao Zhu, Harold R. Garner, ‘Cut from the Same Cloth’: Shared Microsatellite Variants among Cancers Link Origins to the Neural Crest, Oncotarget, 2015
  • Zalman Vaksman, Harold R. Garner, Somatic microsatellite variability as a predictive marker for colorectal cancer and liver cancer progression, Oncotarget. 2015 Jan 21. PMID: 25691061
  • Natalie C. Fonville, Zalman Vaksman, Lauren J. McIver and Harold R. Garner, Population analysis of microsatellite genotypes reveals a signature associated with Ovarian Cancer, OncoTarget 2015 Mar 4. PMID: 25779658
  • Zalman Vaksman, Harold R. Garner, Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies, PLOS ONE, October, 2014, PMID:  25402475
  • E. Karunasena, L.J. McIver, B. R. Rood, X. Wu, H. Zhu, J.H. Bavarva and H.R. Garner, Somatic Microsatellite Loci Differentiate Glioblastoma Multiforme from Lower-Grade Gliomas, Oncotarget, 2014
  • L.J. McIver, N.C. Fonville, E. Karunasena, H.R. Garner, Microsatellite genotyping reveals a signature in breast cancer exomes, Breast Cancer Res Treat. 2014 Jun;145(3):791-8. 2014 May 17. PMID: 24838940
  • Jasmin H. Bavarva, Hongseok Tae, Lauren McIver and Harold R. Garner, Nicotine and oxidative stress induced exomic variations are concordant and overrepresented in cancer-associated genes, Oncotarget, 2014
  • Cristi L. Galindo, Lauren J. McIver, Hongseok Tae, John F. McCormick, Michael A. Skinner, Ina Hoeschele, Cheryl M. Lewis, John D. Minna, David A. Boothman, and Harold R. Garner, Sporadic breast cancer patients’ germline DNA exhibit an AT-rich microsatellite signature, Genes Chromosomes Cancer. 2011 Jan 14. PMID: 21240973
  • C. L. Galindo, J. F. McCormick, V. J. Bubb, D H. Abid Alkadem, L. Shan, L. J. McIver, A. C. George, D.A. Boothman, J. P Quinn, M. A. Skinner, H.R. Garner, A long AAAG repeat allele in the 5’ UTR of the ERR-y gene is correlated with breast cancer predisposition and drives promoter activity in MCF-7 breast cancer cells, Breast Cancer Res Treat. 2010 Dec 10. PMID: 21153485
  • Wagner M, Li L, Morales J, Galindo C, Garner H, Bornmann W, and Boothman D, Role of c-Abl kinase in MMR-dependent G2 cell cycle checkpoint arrest responses, JBC, 2008 May;  PMID 18480061
  • Forgacs, E., Wren, J., Kamibayashi, C., Kondo, M., Xu, L., Markowitz, S., Tomlinson, G., Muller, C., Gazdar, A., Garner, H., and Minna, J. Searching for microsatellite mutations in coding regions in lung, breast, ovarian, and colorectal cancers, Oncogene 20:1005-1009, 2001. PMID: 11314036
  • Wistuba II, Behrens C, Virmani AK, Mele G, Milchgrub S, Girard L, Fondon JW 3rd, Garner HR, McKay B, Latif F, Lerman MI, Lam S, Gazdar AF, Minna JD., High Resolution Chromosome 3p Allelotyping of Human Lung Cancer and Preneoplastic/Preinvasive Bronchial Epithelium Reveals Multiple, Discontinuous Sites of 3p Allele Loss and Frequent Breakpoints, Cancer Research 60, 1949-1960, April, 2000. PMID: 10766185

Microsatellites and Other Diseases

  • Velmurugan KR, Michalak P, Kang L, Fonville NC, Garner HR, Dysfunctional DNA repair pathway via defective FANCD2 gene engenders multifarious exomic and transcriptomic effects in Fanconi anemia, Mol Genet Genomic Med. 2018 Nov;6(6):1199-1208 PMID: 30450770
  • Kinney N, Larsen TR, Kim DM, Varghese RT, Poelzing S, Garner HR, AlMahameed ST. Whole Exome Sequencing Reveals Microsatellites DNA Markers for Response to Dofetilide Initiation in Patients with Persistent Atrial Fibrillation, A Pilot Study.  Clin Cardiol. 2018 Apr 19. doi: 10.1002/clc.22969. PMID: 29671888
  • Harold R. Garner, Michael B. Waitzkin, Jasmin H. Bavarva, What do the changes in the aging genome mean for pharmacogenomics?, Pharmacogenomics, 2014, 15(14) 725-1728, PMID: 25493565
  • Jasmin H. Bavarva, Hongseok Tae, Lauren McIver, Enusha Karunasena and Harold R. Garner, The Dynamic Exome:  acquired variants as an individual ages, Aging Journal, 2014
  • A.E. Wandstrat, C. Nguyen, N. Limaye, Y. Yim, A. Chan, A. Pertsemlidis, H. Garner, L. Morel, and E.K. Wakeland, Association of extensive polymorphisms in the SLAM/CD2 gene cluster with murine lupus, Immunity. 2004 Dec;21(6):769-80 PMID: 15589166

Microsatellite Genomics and Technology

  • S. Dash, Q. Al-Hajri, W. Feng, H. R. Garner and R. Anandakrishnan, “Scaling Out a Combinatorial Algorithm for Discovering Carcinogenic Gene Combinations to Thousands of GPUs,” 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2021, pp. 837-846, doi: 10.1109/IPDPS49936.2021.00093.
  • Qais Al Hajri, Sajal Dash, Wu-chun Feng, Harold R Garner and Ramu Anandakrishnan, Identifying multi-hit carcinogenic gene combinations: Scaling up a weighted set cover algorithm using compressed binary matrix representation on a GPU, Nature Scientific Reports, 2020, Feb 6;10(1):2022. doi: 10.1038/s41598-020-58785-y.
  • Ramu Anandakrishnan, Tiffany L. Carpenetti, Peter Samuel, Breezy Wasko, Craig Johnson, Christy Smith, Jessica Kim, Pawel Michalak, Lin Kang, Nick Kinney, Arben Santo, John Anstrom, Harold R. Garner and Robin T. Varghese, DNA sequencing of anatomy lab cadavers to provide hands-on precision medicine introduction to medical students, BMC Medical Education (2020) 20:437 https://doi.org/10.1186/s12909-020-02366-0
  • Nick Kinney PhD, Kyle Titus-Glover, Jonathan D. Wren PhD, Robin T. Varghese PhD, P. Michalak PhD, Han Liao, Ramu Anandakrishnan PhD, Arichanah Pulenthiran, Lin Kang PhD, Harold R. Garner PhD, CAGm: a Repository of Germline Microsatellite Variations in the 1000 Genomes Project, NAR Database Issue, 2019
  • Fonville NC, Velmurugan KR, Tae H, Vaksman Z, McIver LJ, Garner HR., Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome,  Nat. Sci Rep. 2016 Jun 9;6:27722. PMID: 2727866
  • Tae H, Kim DY, McCormick J, Settlage RE, Garner HR., Discretized Gaussian Mixture for Genotyping of microsatellite loci containing homopolymer runs, Bioinformatics. 2014 Mar 1;30(5):652-9. doi: 10.1093/bioinformatics/btt595. Epub 2013 Oct 17. PMID: 24135263
  • Hongseok Tae, K. Wyatt McMahon, Robert E. Settlage, Jasmin H. Bavarva, and Harold R. Garner, ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats, Bioinformatics. 2013 Jul 15;29(14):1734-41. PMID:  23677944
  • McIver LJ, McCormick JF, Martin A, Fondon JW 3rd, Garner HR., Population-scale analysis of human microsatellites reveals novel sources of exonic variation, Gene. 2013 Mar 10;516(2):328-34.. .PMID:     23274653
  • H. Tae, S. Shallom, R. Settlage, D. Preston, G. Hawkings, G. Adams, B. Jasminkumar, Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes, Genomics. 2012 Nov;100(5):271-6  PMID: 22967795
  • L. J. McIver, J. W. Fondon III, M. A. Skinner, and H.R. Garner, Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments, Genomics. 2011 Jan 9. PMID:  21223998
  • Tae H, Shallom S, Settlage R, Preston D, Adams LG, Garner HR., Revised genome sequence of Brucella suis 1330, J Bacteriol. 2011 Nov;193(22):6410. PMID:    22038969
  • C. L. Galindo, L. J. McIver, J. F. McCormick, M. A. Skinner, Y. Xie, R. A. Gelhausen, K. Ng, N. M. Kumar and H. R. Garner, Global microsatellite content potentially distinguishes humans, primates, animals, and plants, Molecular Biology and Evolution, Mol Biol Evol. 2009 Dec;26(12):2809-19.
  • Fondon III JW and Garner HR, Detection of length-dependent effects of tandem repeat alleles by 3-D geometric decomposition of craniofacial variation, Development, Genes and Evolution 217:79–85, 2007.  PMID: 17066275
  • Laidlaw J, Ng KW, Garner HR, Ranganathan R, Fondon III JW, Elevated basal slippage mutation rates among the Canidae, J Hered. 2007;98(5):452-60 PMID: 1747958
  • Fondon III JW, and Garner HR, Molecular origins of rapid and continuous morphological evolution, Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18058-63. Epub 2004 Dec 13. PMID: 15596718
  • Lian Y, Garner HR, Evidence for the regulation of alternative splicing via complementary DNA sequence repeats, Bioinformatics, 2005 Apr 15;21(8):1358-64. Epub 2005 Jan 26. PMID: 15673565
  • Wren JD, Forgacs Eva, Fondon JW 3rd, Pertsemlidis A, Cheng SY, Gallardo T, Williams RS, Shohet RV, Minna JD, Garner HR, Repeat Polymorphisms Within Gene Regions: Phenotypic and Evolutionary Implications, American  Journal of Human Genetics, Vol. 67, No. 2, 345-356, Aug. 2000.
  • Fondon JW 3rd, Mele GM, Brezinschek RI, Cummings D, Pande A, Wren J, O’Brien KM, Kupfer KC, Wei MH, Lerman M, Minna JD, Garner HR., Computerized polymorphic marker identification: experimental validation and a predicted human polymorphism catalog, Proc. Nat. Acad. Sci USA. 1998, Jun 23;95(13):7514-9  PMID: 9636181

Microsatellites and Biology

  • Kinney N, Kang L, Bains H, Lawson E, Husain M, et al. (2021) Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans. PLOS ONE 16(3): e0249148. https://doi.org/10.1371/journal.pone.0249148
  • Kinney N, Kang L, Eckstrand L, Pulenthiran A, Samuel P, et al. (2019) Abundance of ethnically biased microsatellites in human gene regions. PLOS ONE 14(12): e0225216. https://doi.org/10.1371/journal.pone.0225216
  • Kang L, Settlage R, McMahon W, Michalak K, Tae H, Garner HR, Stacy EA, Price DK, Michalak P. Genomic Signatures of Speciation in Sympatric and Allopatric Hawaiian Picture-Winged Drosophila. Genome Biol Evol. 2016 May 30;8(5):1482-8. doi: 10.1093/gbe/evw095.
  • Michalak K, Maciak S, Kim YB, Santopietro G, Oh JH, Kang L, Garner HR, Michalak P. Nucleolar dominance and maternal control of 45S rDNA expression. Proc Biol Sci. 2015 Dec 7;282(1820):20152201. PMID: 26645200
  • Young Bun Kim, Jung Hun Oh, Lauren J. McIver, Eugenia Rashkovetsky, Katarzyna Michalak, Harold R. Garner, Lin Kang, Eviatar Nevo, Abraham Korol, Pawel Michalak, Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in ‘Evolution Canyon’, Israel, PNAS, July, 2014