Access Array Publications

Successful targeted sequencing depends on quality library preparation, and successful prep depends on the Access Array™ system. Since its launch in 2009, Access Array has been an indispensible support tool for high-throughput sequencing, targeted enrichment and library preparation for some of the world’s leading laboratories.

Browse our catalog of related publications to learn how Access Array enables researchers around the globe to do more with much less when it comes to library prep.

• Overview

  Number of papers per research area as of May, 2021

  Number of cumulative papers as of May, 2021

• Recent

  • NSD1- and NSD2-damaging mutations define a subset of laryngeal tumors with favorable prognosis
    Peri, S., Izumchenko, E., Schubert, A.D. et al. Nature Communications (2017): 1,772
  • Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates
    Yablonovitch, A.L., Fu, J., Li, K. et al. Nature Communications (2017): 1,570
  • Characterization of a thermo-inducible chlorophyll-deficient mutant in barley
    Wang, R., Yang, F., Zhang, X.Q. et al. Frontiers in Plant Science (2017): 1,936
  • Inherited mutations in BRCA1 and BRCA2 in an unselected multiethnic cohort of Asian patients with breast cancer and healthy controls from Malaysia
    Wen, W.X., Allen, J., Lai, K.N. et al. Journal of Medical Genetics (2018): 97–103
  • A new perspective on polyploid Fragaria (strawberry) genome composition based on large-scale, multi-locus phylogenetic analysis
    Yang, Y., Davis, T.M. Genome Biology and Evolution (2017): 3,433–48

• Research Areas

  • Biomarker Screening

    • Mutation detection in cholestatic patients using microarray resequencing of ATP8B1 and ABCB11
      McKay, K.E., Bruce, C.K., Hartley, J.L. et al. F1000 Research (2013): 32
    • Methylomic analysis of salivary DNA in childhood ADHD identifies altered DNA methylation in VIPR2
      Wilmot, B., Fry, R., Smeester, L. et al. Journal of Child Psychology and Psychiatry (2016): 152–60
    • Rapid detection of monogenic causes of childhood-onset steroid-resistant nephrotic syndrome
      Lovric, S., Fang, H., Vega-Warner, V. et al. Clinical Journal of the American Society of Nephrology (2014): 1,109–16
    • ABCA4 gene screening by next-generation sequencing in a British cohort
      Fujinami, K., Zernant, J., Chana, R.K. et al. Investigative Opthalmology and Visual Science (2013): 6,662–74
    • Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing
      Stockenhuber, R., Zoller, S., Shimizu-Inatsugi, R. et al. PLoS One (2015): e0128181
    • Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease
      Johnson, M.D., Mueller, M., Adamowicz-Brice, M. et al. PLoS Genetics (2014): e1004813
    • A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome
      Sadowski, C.E., Lovric, S., Ashraf, S. et al. Journal of the American Society of Nephrology (2015): 1,279–89
    • CSN1 somatic mutations in penile squamous cell carcinoma
      Feber, A., Worth, D.C., Chakravarthy, A. et al. Cancer Research (2016): 4,720–7
    • Prevalence of monogenic causes in pediatric patients with nephrolithiasis or nephrocalcinosis
      Braun, D.A., Lawson, J.A., Gee, H.Y. et al. Clinical Journal of the American Society of Nephrology (2016): 664–72
    • A highly sensitive and quantitative test platform for detection of NSCLC EGFR mutations in urine and plasma
      Reckamp, K.L., Melnikova, V.O., Karlovich, C. et al. Journal of Thoracic Oncology (2016): 1,690–700
    • Targeted re-sequencing approach of candidate genes implicates rare potentially functional variants in Tourette Syndrome etiology
      Alexander, J., Potamianou, H., Xing, J. et al. Frontiers in Neuroscience (2016): 428
    • Characterization of a thermo-inducible chlorophyll-deficient mutant in barley
      Wang, R., Yang, F., Zhang, X.Q. et al. Frontiers in Plant Science (2017): 1,936
    • Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation
      Paliwal, A., Temkin, A.M., Kerkel, K. et al. PLOS Genetics (2013): e1003622
    • Physiological effects of stress related to helicopter travel in Federal Emergency Management Agency search-and-rescue canines
      Perry, E., Gulson, N., Liu Cross, T.W. et al. Journal of Nutritional Science (2017): e28
    • Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia
      Roche, O., Deguiz, M.L., Tiana, M. et al. Nucleic Acids Research (2016): 9,315–30
    • Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting
      Correll, M., Johnson, C.K., Ferrari, G. et al. Genomics (2013): 313–7
    • CTNS mutations in publicly-available human cystinosis cell lines
      Zykovich, A., Kinkade, R., Royal, G., Zankel, T. Molecular Genetics and Metabolism Reports (2015): 63–6
    • A lung cancer risk classifier comprising genome maintenance genes measured in normal bronchial epithelial cells
      Yeo, J., Crawford, E.L., Zhang, X. et al. BMC Cancer (2017): 301
    • Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event
      Diaz, J.M., Hansel, C.M., Apprill, A. et al. Nature Communications (2016): 13,801
    • Targeted sequencing identifies patients with preclinical MDS at high risk of disease progression
      Cargo, C.A., Rowbotham, N., Evans, P.A. et al. Blood (2015): 2,362–5
    • Deep sequencing reveals spatially distributed distinct hotspot mutations in DICER1-related multinodular goiter
      de Kock, L., Bah, I., Revil, T. et al. Journal of Clinical Endocrinology and Metabolism (2016): 3,637–45
    • Implementation of digital technology solutions for a lung health trial in rural Malawi
      Chisunkha, B., Banda, H., Thomson, R. et al. European Respiratory Journal (2016): 1,876–9
    • Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants
      Duan, J., Sanders, A.R., Moy, W. et al. Human Molecular Genetics (2015): 4,674–85
    • A modifier screen identifies DNAJB6 as a cardiomyopathy susceptibility gene
      Ding, Y., Long, P.A., Bos, J.M., et al. JCI Insight (2016): e88797
    • Prevalence of familial hypercholesterolemia among young north Karelian patients with coronary heart disease: a study based on diagnosis by polymerase chain reaction
      Koivisto, U.M., Hämäläinen, L., Taskinen, M.R. et al. Journal of Lipid Research (1993): 269–77
    • Fourteen monogenic genes account for 15% of nephrolithiasis/nephrocalcinosis
      Halbritter, J., Baum, M., Hynes, A.M. et al. Journal of the American Society of Nephrology (2015): 543–51
    • Mutations in nuclear pore genes NUP93, NUP205, and XPO5 cause steroid resistant nephrotic syndrome
      Braun, D.A., Sadowski, C.E., Kohl, S. et al. Nature Genetics (2016): 457–65
    • Visualizing the origins of selfish de novo mutations in individual seminiferous tubules of human testes
      Maher, G.J., McGowan, S.J., Giannoulatou, E. et al. Proceedings of the National Academy of Sciences of the United States of America (2016): 2,454–9
    • MDS-associated somatic mutations and clonal hematopoiesis are common in idiopathic cytopenias of undetermined significance
      Kwok, B., Hall, J.M., Witte, J.S. et al. Blood (2015): 2,355–61
    • Whole-exome sequencing in individuals with multiple cardiovascular risk factors and normal coronary arteries
      Abramowitz, Y., Roth, A., Keren, G., et al. Coronary Artery Disease (2016): 257–66

  • Carrier Screening

    • IFT81, encoding an IFT-B core protein, as a very rare cause of a ciliopathy phenotype
      Perrault, I., Halbritter, J., Porath, J.D. et al. Journal of Medical Genetics (2015): 657–65
    • Expanding preconception carrier screening for the Jewish population using high throughput microfluidics technology and next generation sequencing
      Gal, M., Khermesh, K., Barak, M. et al. BMC Medical Genomics (2016): 24

  • Data Analysis Methods

    • CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data
      Minoura, K., Abe, K., Maeda, Y. Bioinformatics (2020): DOI: 10.1093/bioinformatics/btaa873

  • Fingerprinting/Sample ID

    • Robust detection of individual forensic profiles in DNA mixtures
      Isaacson, J., Schwoebel, E., Shcherbina, A. et al. Forensic Science International: Genetics (2014): 31–7

  • HLA Typing

    • Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing
      Yamamoto, F., Höglund, B., Fernandez-Vina, M. et al. Human Immunology (2015): 910–16
    • Survey of major histocompatibility complex class II diversity in pig-tailed macaques
      Karl, J.A., Heimbruch, K.E., Vriezen, C.E. et al. Immunogenetics (2014): 613–23
    • Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing
      Lange, V., Böhme, I., Hofmann, J. et al. BMC Genomics (2014): 63
    • High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ system for simplified amplicon library preparation
      Moonsamy, P.V., Williams, T., Bonella, P. et al. Tissue Antigens (2013): 141–9
    • Prediction of spurious HLA class II typing results using probabilistic classification
      Schöfl, G., Schmidt, A.H., Lange, V. Human Immunology (2016): 264–72

  • Immunology

    • One million samples typed by NGS: lessons learned
      Lange, V., Boehme, I., Paul, P. et al. Human Immunology (2015): 210
    • Burn injury alters the intestinal microbiome and increases gut permeability and bacterial translocation
      Earley, Z.M., Akhtar, S., Green, S.J. et al. PLoS One (2015): e0129996
    • Discovery of invariant T cells by next generation sequencing of the human T cell receptor α chain repertoire
      van Schaik, B., Klarenbeek, P., Doorenspleet, M. et al. Journal of Immunology (2014): 5,338–44
    • Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals
      Boudinot, P., Mondot, S., Jouneau, L. et al. Proceedings of the National Academy of Sciences of the United States of America (2016): e2983–92

  • Inherited Disease

    • High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing
      Halbritter, J., Diaz, K., Chaki, M. et al. Journal of Medical Genetics (2012): 756–67
    • Towards clinical molecular diagnosis of inherited cardiac conditions: A comparison of bench-top genome DNA sequencers
      Li, X., Buckton, A.J., Wilkinson, S.L. et al. PLoS One (2013): e67744
    • Targeted genetic testing for familial hypercholesterolaemia using next generation sequencing: a population-based study
      Norsworthy, P.J., Vandrovcova, J., Thomas, E.R.A. et al. BMC Medical Genetics (2014): 70
    • Exome sequencing of 75 individuals from multiply affected coeliac families and large scale resequencing follow up
      Mistry, V., Bockett, N.A., Levine, A.P. et al. PLoS One (2015): e0116845
    • IGSF10 mutations dysregulate gonadotropin‐releasing hormone neuronal migration resulting in delayed puberty
      Howard, S.R., Guasti, L., Ruiz-Babot, G. et al. EMBO Molecular Medicine (2016): 626–42
    • Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
      Shamay-Ramot, A., Khermesh, K., Porath, H.T. et al. PLoS Genetics (2015): e1005702
    • Mutations in RASA1 and GDF2 identified in patients with clinical features of hereditary hemorrhagic telangiectasia
      Hernandez, F., Huether, R., Carter, L. et al. Human Genome Variation (2015): 15,040
    • Next generation diagnostics in inherited arrhythmia syndromes: A comparison of two approaches
      Ware, J.S., John, S., Roberts, A.M. et al. Journal of Cardiovascular Translational Research (2013): 94–103
    • Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6
      Rost, S., Bach, E., Neuner, C. et al. European Journal of Human Genetics (2014): 208–15
    • Detection of mutations in KLHL3 and CUL3 in families with FHHt (familial hyperkalaemic hypertension or Gordon's syndrome)
      Glover, M., Ware, J.S., Henry, A. et al. Clinical Science (2014): 721–6
    • Mutations in 12 known dominant disease-causing genes clarify many congenital anomalies of the kidney and urinary tract
      Hwang, D.Y., Dworschak, G.C., Kohl, S. et al. Kidney International (2014): 1,429–33
    • Haploinsufficiency of insulin gene enhancer protein 1 (ISL1) is associated with d-transposition of the great arteries
      Osoegawa, K., Schultz, K., Yun, K. et al. Molecular Genetics & Genomic Medicine (2014): 341–51
    • Mild recessive mutations in six Fraser syndrome–related genes cause isolated congenital anomalies of the kidney and urinary tract
      Kohl, S., Hwang, D.Y., Dworschak, G.C. et al. Journal of the American Society of Nephrology (2014): 1,917–22
    • Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation
      Kato, N., Loh, M., Takeuchi, F. et al. Nature Genetics (2015): 1,282–93
    • A recurrent mutation in CACNA1G alters Cav3.1 T-type calcium-channel conduction and causes autosomal-dominant cerebellar ataxia
      Coutelier, M., Blesneac, J., Monteil, A. et al. American Journal of Human Genetics (2015): 726–37
    • AP5Z1/SPG48 frequency in autosomal recessive and sporadic spastic paraplegia
      Schlipf, N.A., Schüle, R., Klimpe, S. et al. Molecular Genetics and Genomic Medicine (2014): 379–82
    • Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1
      Larsen, M., Rost, S., Hajj, N.E. et al. European Journal of Human Genetics (2015): 808–16
    • DCDC2 mutations cause a renal-hepatic ciliopathy by disrupting Wnt signaling
      Schueler, M., Braun, D.A., Chandrasekar, G. et al. The American Journal of Human Genetics (2015): 81–92
    • Mutations of the SLIT2-ROBO2 pathway genes SLIT2 and SRGAP1 confer risk for congenital anomalies of the kidney and urinary tract
      Hwang, D.Y., Kohl, S., Fan, X., et al. Human Genetics (2015): 905–16
    • AmpliVar: Mutation detection in high-throughput sequence from amplicon-based libraries
      Hsu, A.L., Kondrashova, O., Lunke, S. et al. Human Mutation (2015): 411–8
    • Microfluidic amplification as a tool for massive parallel sequencing of familial hypercholesterolemia genes
      Hollants, S., Redeker, E.J., Matthijs, G. American Association for Clinical Chemistry (2012): 717–24
    • Differential methylation is associated with non-syndromic cleft lip and palate and contributes to penetrance effects
      Alvizi, L., Ke, X., Brito, L.A. et al. Scientific Reports (2017): 2,441
    • Prevalence of DNA-confirmed familial hypercholesterolaemia in young patients with myocardial infarction
      Wald, D.S., Bangash, F.A., Bestwick, J.P. European Journal of Internal Medicine (2015): 127–30
    • Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies
      Schueler, M., Halbritter, J., Phelps, I.G. et al. Journal of Medical Genetics (2016): 208–14
    • High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome
      de Kock, L., Wang, Y.C., Revil, T. et al. Journal of Medical Genetics (2016): 43–52
    • Genetic epidemiology of motor neuron disease-associated variants in the Scottish population
      Black, H.A., Leighton, D.J., Cleary, E.M. et al. Neurobiology of Aging (2017): 51
    • Recessive nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum is caused by homozygous protein-truncating mutations of WDR73
      Jinks, R.N., Puffenberger, E.G., Baple, E., et al. Brain (2015): 2,173–90
    • Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy
      Halbritter, J., Porath, J., Diaz, K. et al. Human Genetics (2013): 865–84
    • Negligible impact of rare autoimmune locus coding-region variants on missing heritability
      Hunt, K.A., Mistry, V., Bockett, N.A. et al. Nature (2013): 232–5
    • Genetic and clinical characterization of Pakistani families with Bardet-Biedl syndrome extends the genetic and phenotypic spectrum
      Maria, M., Lamers, I.J.C., Schmidts, M. et al. Scientific Reports (2016): 34,764
    • Amplicon-based high-throughput pooled sequencing identifies mutations in CYP7B1 and SPG7 in sporadic spastic paraplegia patients
      Schlipf, N.A., Schüle, R., Klimpe, S. et al. Clinical Genetics (2011): 148–60
    • Targeted PCR-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation (CDG)
      Jones, M., Bhide, S., Chin, E. et al. Genetics in Medicine (2011): 921–32
    • Activating mutations affecting the Dbl homology domain of SOS2 cause Noonan syndrome
      Cordeddu, V., Yin, J.C., Gunnarsson, C., Virtanen, C., Drunat, S., Lepri, F., De Luca, A., Rossi, C., Ciolfi, A., Pugh, T.J., Bruselles, A., Priest, J.R., Pennacchio, L.A., Lu, Z., Danesh, A., Quevedo, R., Hamid, A., Martinelli, S., Pantaleoni, F., Gnazzo, M., Daniele, P., Lissewski, C., Bocchinfuso, G., Stella, L., Odent, S., Philip, N., Faivre, L., Vlckova, M., Seemanova, E., Digilio, C., Zenker, M., Zampino, G., Verloes, A., Dallapiccola, B., Roberts, A.E., Cavé, H., Gelb, B.D., Neel, B.G., Tartaglia, M. Human Mutation (2015): 1080–7
    • Heterozygous HTRA1 mutations are associated with autosomal dominant cerebral small vessel disease
      Verdura, E., Hervé, D., Scharrer, E., Amador, M.D., Guyant-Maréchal, L., Philippi, A., Corlobé, A., Bergametti, F., Gazal, S., Prieto-Morin, C., Beaufort, N., Le Bail, B., Viakhireva, I., Dichgans, M., Chabriat, H., Haffner, C., Tournier-Lasserve, E. Brain - A Journal of Neurology (2015): 2347–58
    • Alteration of ornithine metabolism leads to dominant and recessive hereditary spastic paraplegia
      Coutelier, M., Goizet, C., Durr, A., Habarou, F., Morais, S., Dionne-Laporte, A., Tao, F., Konop, J., Stoll, M., Charles, P., Jacoupy, M., Matusiak, R., Alonso, I., Tallaksen, C., Mairey, M., Kennerson, M., Gaussen, M., Schule, R., Janin, M., Morice-Picard, F., Durand, C.M., Depienne, C., Calvas, P., Coutinho, P., Saudubray, J.M., Rouleau, G., Brice, A., Nicholson, G., Darios, F., Loureiro, J.L., Zuchner, S., Ottolenghi, C., Mochel, F., Stevanin, G. Brain - A Journal of Neurology (2015): 2191–205
    • Ten new cases further delineate the syndromic intellectual disability phenotype caused by mutations in DYRK1A
      Bronicki, L.M., Redin, C., Drunat, S., Piton, A., Lyons, M., Passemard, S., Baumann, C., Faivre, L., Thevenon, J., Rivière, J.B., Isidor, B., Gan, G., Francannet, C., Willems, M., Gunel, M., Jones, J.R., Gleeson, J.G., Mandel, J.L., Stevenson, R.E., Friez, M.J., Aylsworth, A.S. European Journal of Human Genetics (2015): 1482–7

  • Liquid Biopsy

    • Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits
      Alcaide, M., Yu, S., Davidson, J. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-10269-2
    • Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients
      Madic, J., Kiialainen, A., Bidard, F.C. et al. International Journal of Cancer (2014): 2,158–65
    • Circulating tumour DNA reflects treatment response and clonal evolution in chronic lymphocytic leukaemia
      Yeh, P., Hunter, T., Sinha, D. et al. Nature Communications (2017): 14,756
    • PPM1D Mutations in Circulating White Blood Cells and the Risk for Ovarian Cancer
      Akbari, M.R., Lepage, P., Rosen, B. et al. Journal of the National Cancer Institute (2013): djt323
    • Circulating Cell Free Tumor DNA Detection as a Routine Tool for Lung Cancer Patient Management
      Vendrell, J.A., Mau-Them, F.T., Béganton, B. et al. International Journal of Molecular Sciences (2017): 264

  • Marker Assisted Breeding

    • Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2
      Curk, F., Ancillo, G., Garcia-Lor, A. et al. BMC Genetics (2014): 152
    • Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus
      Richards, J., Chao, S., Friesen, T., Brueggeman, R. G3 (2016): 1,809–18
    • Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture
      Johnson, T.A., Stedtfeld, R.D., Wang, Q., et al. mBio (2016): e02214–5
    • Multilocus Haplotyping by Parallel Sequencing to Decipher the Interspecific Mosaic Genome Structure of Cultivated Citrus
      Curk, F., Ancillo, G., Garcia-Lor, A. et al. International Society for Horticultural Science (2015): DOI: 10.17660/ActaHortic.2015.1065.11
    • Whole‐genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback
      Yoshida, K., Miyagi, R., Mori, S., Takahashi, A., Makino, T., Toyoda, A., Fujiyama, A., Kitano, J. Ecology and Evolution (2016): 2,190–204
    • Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties
      Curk, F., Ancillo, G., Ollitraut, F., Perrier, X., Jacquemoud-Collet, J.P., Garcia-Lor, A., Navarro, L., Ollitraut, P. PLoS One (2015): e0125628

  • Method Development

    • Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci
      Latvis, M., Jacobs, S.J., Mortimer, S.M.E. et al. Applications in Plant Sciences (2017): doi: 10.3732/apps.1700038
    • Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
      Leung, K., Klaus, A., Lin, B.K. et al. Proceedings of the National Academy of Sciences of the United States of America (2016): 8,484–9
    • Method for Dual Viral Vector Mediated CRISPR-Cas9 Gene Disruption in Primary Human Endothelial Cells
      Gong, H., Liu, M., Klomp, J. et al. Scientific Reports (2017): 42,127
    • MPD: multiplex primer design for next-generation targeted sequencing
      Wingo, T.S., Kotlar, A., Cutler, D.J. BMC Bioinformatics (2017): 14
    • Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research
      Menke, S., Gillingham, M.A.F., Wilhelm, K. et al. Frontiers in Microbiology (2017): 102
    • Targeted enrichment strategies for next-generation plant biology
      Cronn, R., Knaus, B.J., Liston, A., et al. American Journal of Botany (2012): 291–311
    • tarSVM: Improving the accuracy of variant calls derived from microfluidic PCR-based targeted next generation sequencing using a support vector machine
      Gillies, C.E., Otto, E.A., Vega-Warner, V. et al. BMC Bioinformatics (2016): 233
    • Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing
      Zhang, R., Li, X., Ramaswami, G. et al. Nature Methods (2014): 51–4
    • Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array.
      Brown, S.P., Ferrer, A., Dalling, J.W., Heath, K.D. Molecular Ecology Resources (2016): doi: 10.1111/1755-0998.12507
    • Next Generation Sequencing for Clinical Diagnostics-Principles and Application to Targeted Resequencing for Hypertrophic Cardiomyopathy
      Voelkerding, K.V., Dames, S., Durtschi, J.D. Journal of Molecular Diagnostics (2010): 539–51
    • A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps
      Tan, S.J., Phan, H., Gerry, B.M., Kuhn, A., Hong, L.Z., Ong, Y.M., Poon, P.S.Y., Unger, M.A., Jones, R.C., Quake, S.R., Burkholder, W.F. PLoS One (2013): e64084
    • A long PCR–based approach for DNA enrichment prior to next-generation sequencing for systematic studies
      Uribe-Convers, S., Duke, J.R., Moore, M.J., Tank, D.C. Applications in Plant Sciences (2014): 1,300,063
    • A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)
      Uribe-Convers, S., Settles, M.L., Tank, D.C. PLoS One (2016): e0148203
    • Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants
      Kuhn, A., Ong, Y.M., Quake, S.R., Burkholder, W.F. BMC Genomics (2015): 508
    • Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches
      Green, S.J., Venkatramanan, R., Naqib, A. PLoS One (2015): e0128122
    • Ion Torrent's Personal Genome Machine coupled with Fluidigm's Access Array Provides a Multiplexed Sample Approach to Rapid Evaluation of Novel Genomic Targets
      Myers, J., Rothberg, J., May, A., Roberson, D. Journal of Biomolecular Techniques (2011): S39
    • High-Throughput Microfluidic Preparation of Targeted Resequencing Libraries Using the Access Array System
      Anderson, M., Chen, P., Wang, J., Kaper, F., Lin, M., Pieprzyk, M., Jones. R. Journal of Biomolecular Techniques (2010): S26

  • Microbiology/Pathogen Detection (viral)

    • Great cormorants (Phalacrocorax carbo) as potential vectors for the dispersal of Vibrio cholerae
      Laviad-Shitrit, S. Lev-Ari, T., Katzir, G. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-08434-8
    • The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia
      Frontiers in Microbiology (2017): 1,221
    • Detection of cytomegalovirus drug resistance mutations by next-generation sequencing
      Sahoo, M.K., Lefterova, M.I., Yamamoto, F. et al. Journal of Clinical Microbiology (2013): 3,700–10
    • Microfluidic PCR combined with pyrosequencing for identification of allelic variants with phenotypic associations among targeted Salmonella genes
      Yue, M., Schmieder, R., Edwards, R.A. et al. Applied and Environmental Microbiology (2012): 7,480–2
    • Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattle
      Zeineldin, M.M., Lowe, J.F., Grimmer, E.D. et al. BMC Microbiology (2017): 138
    • The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate
      Popova, M., McGovern, E., McCabe, M.S. et al. Frontiers in Microbiology (2017): 937
    • The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition
      Heitlinger, E., Ferreira, S.C.M., Thierer, D. et al. Frontiers in Cellular and Infection Microbiology (2017): 262
    • Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections
      Mizrahi, H., Peretz, A., Lesnik, R. et al. Scientific Reports (2017): 40,114
    • Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields
      Rime, T., Hartmann, M., Stierli, B., Anesio, A.M., Frey, B. Soil Biology and Biochemistry (2016): 30–41
    • Love the one you’re with: replicate viral adaptations converge on the same phenotypic change
      Miller, C.R., Nagel, A.C., Scott, L. et al. PeerJ (2016): e2227
    • Microbial diversity in European alpine permafrost and active layers
      Frey, B., Rime, T., Phillips, M. et al. FEMS Microbiology Ecology (2016): fiw018
    • Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis
      Ofek-Lalzar, M., Gur, Y., Ben-Moshe, S. et al. FEMS Microbiology Ecology (2016): fiw152
    • Pyridine-type alkaloid composition affects bacterial community composition of floral nectar
      Aizenberg-Gershtein, Y., Izhaki, I. et al. Scientific Reports (2015): 11,536
    • Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis
      Byrne, A.Q., Rothstein, A.P., Poorten, T.J. et al. Molecular Ecology Resources (2017): DOI 10.1111/1755-0998.12675.
    • Histologic, Molecular, and Clinical Evaluation of Explanted Breast Prostheses, Capsules, and Acellular Dermal Matrices for Bacteria
      Poppler, L., Cohen, J., Dolen, U.C. et al. Aesthetic Surgery Journal (2015): 653–68
    • Population expansion and individual age affect endoparasite richness and diversity in a recolonising large carnivore population
      Lesniak, I., Heckmann, I., Heitlinger, E. et al. Scientific Reports (2017): 41,730
    • Stability of peatland carbon to rising temperatures
      Wilson, R.M., Hopple, A.M., Tfaily, M.M. et al. Nature Communications (2016): 13,723
    • Multi-Targeted Community Profiling: Leveraging the Fluidigm Access Array and Illumina MiSeq for Metagenomic Sequencing - Microorganisms
      Wright, C., Akraiko, T., Hernandez, A., Band, M. Plant & Animal Genome XXIII (2015):
    • The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity
      Hermann-Bank, M.L., Skovgaard, K., Stockmarr, A. et al. BMC Genomics (2013): 788
    • Improved Detection of Emerging Drug-Resistant Mutant Cytomegalovirus Subpopulations by Deep Sequencing
      Chou, S., Ercolani, R.J., Sahoo, M.K., Lefterova, M.I., Strasfeld, L.M., Pinsky, B.A. Antimicrobial Agents and Chemotherapy (2014): 4,697–702
    • Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique
      Applied and Environmental Microbiology (2016): 640–9
    • Metagenomic Evaluation of Bacterial and Archaeal Diversity in the Geothermal Hot Springs of Manikaran, India
      Bhatia, S., Batra, N., Pathak, A., Green, S.J., Joshi, A., Chauhan, A. Genome Announcements (2015): e01544-14
    • Impact of Dietary Lipids on Colonic Function and Microbiota: An Experimental Approach Involving Orlistat-Induced Fat Malabsorption in Human Volunteers
      Morales, P., Fujio, S., Navarrete, P., Ugalde, J.A., Magne, F., Carrasco-Pozo, C., Tralma, K., Quezada, M.P., Hurtado, C., Covarrubias, N., Brignardello, J., Henriquez, D., Gotteland, M. Clinical and Translational Gastroenterology (2016): e161
    • Identification of Associations between Bacterioplankton and Photosynthetic Picoeukaryotes in Coastal Waters
      Farnelid, H.M., Turk-Kubo, K.A., Zehr, J.P. Frontiers in Microbiology (2016): 339
    • Culex pipiens and Culex restuans mosquitoes harbor distinct microbiota dominated by few bacterial taxa
      Muturi, E.J., Kim, C.H., Bara, J., Bach, E.M., Siddappaji, M.H. Parasites and Vectors (2016): 18
    • Allelic variation contributes to bacterial host specificity
      Yue, M., Han, X., De Masi, L., Zhu, C., Ma, X., Zhang, J., Wu, R., Schmieder, R., Kaushik, R.S., Fraser, G.P., Zhao, S., McDermott, P.F., Weill, F.X., Mainil, J.G., Arze, C., Fricke, W.F., Edwards, R.A., Brisson, D., Zhang, N.R., Rankin, S.C., Schifferli, D.M. Nature Communications (2015): 8,754
    • Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea
      Hermann-Bank, M.L., Skovgaard, K., Stockmarr, A., Strube, M.L., Larsen, N., Kongsted, H., Ingerslev, H.V., Mølbak, L., Boye, M. BioMed Central Veterinary Research (2015): 139
    • Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level
      Menke, S., Wasimuddin, Meier, M., Melzheimer, J., Mfune, J.K.E., Heinrich, S., Thalwitzer, S., Wachter, B., Sommer, S. Frontiers in Microbiology (2014): 526
    • The Impact of Spatial Structure on Viral Genomic Diversity Generated during Adaptation to Thermal Stress
      Ally, D., Wiss, V.R., Deckert, G.E., Green, D., Roychoudhury, P., Wichman, H.A., Brown, C.J., Krone, S.M. PLoS One (2014): e88702

  • Neurology

    • Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
      Zhang, R., Deng, P., Jacobson, D. et al. PLoS Genetics (2017): e1006563
    • Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition
      Gal-Mark, N., Shalley, L., Sweetat, S. et al. Scientific Reports (2017): 43,421
    • Genetic and neurodevelopmental spectrum of SYNGAP1-associated intellectual disability and epilepsy
      Mignot, C., von Stülpnagel, C., Nava, C., Ville, D., Sanlaville, D., Lesca, G., Rastetter, A., Gachet, B., Marie, Y., Korenke, G.C., et al Journal of Medical Genetics (2016): 511-22
    • Mutations in JMJD1C are involved in Rett syndrome and intellectual disability
      Sáez, M.A., Fernández-Rodríguez, J., Moutinho, C., Sanchez-Mut, J.V., Gomez, A., Vidal, E., Petazzi, P., Szczesna, K., Lopez-Serra, P., Lucariello, M., Lorden, P., Delgado-Morales, R., de la Caridad, O.J., Huertas, D., Gelpí, J.L., Orozco, M., López-Doriga, A., Milà, M., Perez-Jurado, L.A., Pineda, M., Armstrong, J., Lázaro, C., Esteller, M. Genetics in Medicine (2016): 378–85
    • Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease
      Khermesh, K., D'Erchia, A.M., Barak, M., Annese, A., Wachtel, C., Levanon, E.Y., Picardi, E., Eisenberg, E. RNA (2016): 290–302
    • Meeting Report: Using Stem Cells for Biological and Therapeutics Discovery in Mental Illness, April 2012
      Panchision, D.M. Stem Cells Translational Medicine (2013): 217–22
    • CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia
      Williams, K.L., Topp, S., Yang, S., Smith, B., Fifita, J.A., Warraich, S.T., Zhang, K.Y., Farrawell, N., Vance, C., Hu, X., Chesi, A., Leblond, C.S., Lee, A., Rayner, S.L., Sundaramoorthy, V., Dobson-Stone, C., Molloy, M.P., van Blitterswijk, M., Dickson, D.W., Petersen, R.C., Graff-Radford, N.R., Boeve, B.F., Murray, M.E., Pottier, C., Don, E., Winnick, C., McCann, E.P., Hogan, A., Daoud, H., Levert, A., Dion, P.A., Mitsui, J., Ishiura, H., Takahashi, Y., Goto, J., Kost, J., Gellera, C., Gkazi, A.S., Miller, J., Stockton, J., Brooks, W.S., Boundy, K., Polak, M., Muñoz-Blanco, J.L., Esteban-Pérez, J., Rábano, A., Hardiman, O., Morrison, K.E., Ticozzi, N., Silani, V., de Belleroche, J., Glass, J.D., Kwok, J.B.J., Guillemin, G.J., Chung, R.S., Tsuji, S., Brown, Jr R.H., García-Redondo, A., Rademakers, R., Landers, J.E., Gitler, A.D., Rouleau, G.A., Cole, N.J., Yerbury, J.J., Atkin, J.D., Shaw, C.E., Nicholson, G.A., Blaira, I.P. Nature Communications (2016): 11,253
    • Genetic mapping uncovers cis-regulatory landscape of RNA editing
      Ramaswami, G., Deng, P., Zhang, R., Carbone, M.A., Mackay, T.F.C., Li, J.B. Nature Communications (2015): 8,194
    • αβ T-cell receptors from multiple sclerosis brain lesions show MAIT cell–related features
      Held, K., Bhonsle-Deeng, L., Siewert, K., Sato, W., Beltrán, E., Schmidt, S., Rühl, G., Ng, J.K.M., Engerer, P., Moser, M., Klinkert, W.E.F., Babbe, H., Misgeld, T., Wekerle, H., Laplaud, D.A., Hohlfeld, R., Dornmair, K. Neurology Neuroimmunology and Neuroinflammation (2015): e107
    • Loss of delta catenin function in severe autism
      Turner, T.N., Sharma, K., Oh, E.C., Liu, Y.P., Collins, R.L., Sosa, M.X., Auer, D.R., Brand, H., Sanders, S.J., Moreno-De-Luca, D., Pihur, V., Plona, T., Pike, K., Soppet, D.R., Smith, M.W., Cheung, S.W., Martin, C.L., State, M.W., Talkowski, M.E., Cook, E., Huganir, R., Katsanis, N., Chakravarti, A. Nature (2015): 51-6
    • Unusual multisystemic involvement and a novel BAG3 mutation revealed by NGS screening in a large cohort of myofibrillar myopathies
      Semmler, A.L., Sacconi, S., Bach, J.E., Liebe, C., Bürmann, J., Kley, R.A., Ferbert, A., Anderheiden, R., Van den Bergh, P., Martin, J.J., De Jonghe, P., Neuen-Jacob, E., Müller, O., Deschauer, M., Bergmann, M., Schröder, J.M., Vorgerd, M., Schulz, J.B., Weis, J., Kress, W., Claeys, K.G. Orphanet Journal of Rare Diseases (2014): 121

  • Oncology

    • Inherited mutations in BRCA1 and BRCA2 in an unselected multiethnic cohort of Asian patients with breast cancer and healthy controls from Malaysia
      Wen, W.X., Allen, J., Lai, K.N. et al. Journal of Medical Genetics (2018): 97–103
    • NSD1- and NSD2-damaging mutations define a subset of laryngeal tumors with favorable prognosis
      Peri, S., Izumchenko, E., Schubert, A.D. et al. Nature Communications (2017): 1,772
    • Comprehensive analyses of somatic TP53 mutation in tumors with variable mutant allele frequency
      Cole, A.J., Zhu, Y., Dwight, T. et al. Scientific Data (2017): doi: 10.1038/sdata.2017.120
    • Identification of critical steps involved in optimization of next generation sequencing (NGS) using a retrospective meta-analysis of a large clinical testing cohort
      Murphy, D.A., Scott, C., Fitzgerald, K et al. The Journal of Cancer Research (2014): 5,601
    • Prevalence of germline mutations in genes engaged in DNA damage repair by homologous recombination in patients with triple-negative and hereditary non-triple-negative breast cancers
      Domagala, P., Jakubowska, A., Jaworska-Bieniek, K. et al. PLoS One (2015): e0130393
    • Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing
      Wong, S.Q., Li, J., Tan, A.Y. et al. BMC Medical Genomics (2014): 23
    • RNF43 is frequently mutated in colorectal and endometrial cancers
      Giannakis, M., Hodis, E., Mu, X.J. et al. Nature Genetics (2014): 1,264–6
    • The contribution of deleterious germline mutations in BRCA1, BRCA2 and the mismatch repair genes to ovarian cancer in the population
      Song, H., Cicek, M.S., Dicks, E. et al. Human Molecular Genetics (2014): 4,703–9
    • High throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing
      Bourgon R., Lu, S., Yan, Y. et al. Clinical Cancer Research (2014): 2,080–91
    • Analysis of circulating tumor DNA to monitor metastatic breast cancer
      Dawson, S.J., Tsui, D.W.Y., Murtaza, M. et al. The New England Journal of Medicine (2013): 1,199–209
    • Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA
      Forshew, T., Murtaza, M., Parkinson, C. et al. Science Translational Medicine (2012): 136ra68
    • Molecular landscape of acute promyelocytic leukemia at diagnosis and relapse
      Fasan, A., Haferlach, C., Perglerovà, K. et al. Haematologica (2017): e222–4
    • Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study
      Parkinson, C.A., Gale, D., Piskorz, A.M. et al. PLoS One (2017): e1002198
    • BRCA1/2 mutations associated with progression-free survival in ovarian cancer patients in the AGO-OVAR 16 study
      Harter, P., Johnson, T., Berton-Rigaud, D. et al. Gynecologic Oncology (2016): 443–9
    • Chromosomal microarray provides enhanced targetable gene aberration detection when paired with next generation sequencing panel in profiling lung and colorectal tumors
      Mukherjee, S., Ma, Z., Wheeler, S. et al. Cancer Genetics (2016): 119–29
    • Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing
      Imielinski, M., Berger, A.H., Hammerman, P.S. et al. Cell (2012): 1,107–20
    • Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software
      Poulet, A., Privat, M., Ponelle, F., et al. BioMed Research International (2016): 5,623,089
    • Next-generation sequencing with a myeloid gene panel in core-binding factor AML showed KIT activation loop and TET2 mutations predictive of outcome
      Cher, C.Y., Leung, G.M.K., Au, C.H. et al. Blood Cancer Journal (2016): e442
    • Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors
      Rivera, B., Gayden, T., Carrot-Zhang, J. et al. Acta Neuropathologica (2016): 847–63
    • Reduced Representation Bisulfite Sequencing Determination of Distinctive DNA Hypermethylated Genes in the Progression to Colon Cancer in African Americans
      Ashktorab, H., Shakoori, A., Zarnogi, S., et al. Gastroenterology Research and Practice (2016): 2,102,674
    • Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies
      Fisher, K.E., Zhang, L., Wang, J. et al. Journal of Molecular Diagnostics (2016): 299–315
    • Molecular classification of endometrial carcinoma on diagnostic specimens is highly concordant with final hysterectomy: Earlier prognostic information to guide treatment
      Talhouk, A., Hoang, L.N., McConechy, M.K. et al. Gynecologic Oncology (2016): 46–53
    • Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite
      Grünewald, T.G.P., Bernard, V., Gilardi-Hebenstreit, P. et al. Nature Genetics (2015): 1,073–8
    • NOTCH1 Mutations Occur Early during Cutaneous Squamous Cell Carcinogenesis
      South, A.P., Purdie, K.J., Watt, S.A. et al. Journal of Investigative Dermatology (2014): 2,630–8
    • Robustness of amplicon deep sequencing underlines its utility in clinical applications
      Grossmann, V., Roller, A., Klein, H.U. et al. Journal of Molecular Diagnostics (2013): 473–84
    • Rare ATAD5 missense variants in breast and ovarian cancer patients
      Maleva Kostovska, I., Wang, J., Bogdanova, N. et al. Cancer Letters (2016): 173–7
    • Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
      Perry, J.A., Kiezun, A., Tonzi, P. et al. Proceedings of the National Academy of Sciences of the United States of America (2014): e5564–73
    • Ovarian cancer familial relative risks by tumour subtypes and by known ovarian cancer genetic susceptibility variants
      Jervis, S., Song, H., Lee, A. et al. Journal of Medical Genetics (2014): 108–13
    • No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing
      Easton, D.F., Lesueur, F., Decker, B. et al. Journal of Medical Genetics (2016): 298–309
    • Genetically distinct leukemic stem cells in human CD34− acute myeloid leukemia are arrested at a hemopoietic precursor-like stage
      Quek, L., Otto, G.W., Garnett, C. et al. Journal of Experimental Medicine (2016): 1,513–35
    • MED12 protein expression in breast fibroepithelial lesions: correlation with mutation status and oestrogen receptor expression
      Tan, W.J., Chan, J.Y., Thike, A.A. et al. Journal of Clinical Pathology (2016): 858–65
    • Integrated analysis of promoter mutation, methylation and expression of AKT1 gene in Chinese breast cancer patients
      Heng, J., Guo, X., Wu, W. et al. PLoS One (2017): e0174022
    • Contribution of Germline Mutations in the RAD51B, RAD51C, and RAD51D Genes to Ovarian Cancer in the Population
      Ramus, S.J., Song, H., Dicks, E. et al. Journal of Clinical Oncology (2015): 2,901–7
    • Germline Mutations in the BRIP1, BARD1, PALB2, and NBN Genes in Women With Ovarian Cancer
      Ramus, S.J., Song, H., Dicks, E., T et al. Journal of the National Cancer Institute (2015): djv214
    • PPM1D Mosaic Truncating Variants in Ovarian Cancer Cases May Be Treatment-Related Somatic Mutations
      Pharoah, P.D., Song, H., Dicks et al. Journal of the National Cancer Institute (2016): djv347
    • SETD2 histone modifier loss in aggressive GI stromal tumours
      Huang, K.K., McPherson, J.R., Tay, S.T. et al. Gut (2015): 1,960–72
    • Somatic DICER1 mutations in adult-onset pulmonary blastoma
      de Kock, L., Bah, I., Brunet, J. et al. European Respiratory Journal (2016): 1,879–82
    • Rare inactivating PDE11A variants associated with testicular germ cell tumors
      Pathak, A., Stewart, D.R., Faucz, F.R. et al. Endocrine-Related Cancer (2015): 909–17
    • Upregulation of Periostin and Reactive Stroma Is Associated with Primary Chemoresistance and Predicts Clinical Outcomes in Epithelial Ovarian Cancer
      Ryner, L., Guan, Y., Firestein, R. et al. Clinical Cancer Research (2015): 2,941–51
    • Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor
      Karpathakis, A., Dibra, H., Pipinikas, C. et al. Clinical Cancer Research (2016): 250–8
    • Endometrial Carcinomas with POLE Exonuclease Domain Mutations Have a Favorable Prognosis
      McConechy, M.K., Talhouk, A., Leung, S. et al. Clinical Cancer Research (2016): 2,865–73
    • Spatial and Temporal Heterogeneity in High-Grade Serous Ovarian Cancer: A Phylogenetic Analysis
      Schwarz, R.F., Ng, C.K., Cooke, S.L. et al. PLoS One (2015): e1001789
    • Gauging NOTCH1 Activation in Cancer Using Immunohistochemistry
      Kluk, M.J., Ashworth, T., Wang, H., Knoechel, B., Mason, E.F., Morgan, E.A., Dorfman, D., Pinkus, G., Weigert, O., Hornick, J.L., et al PLoS One (2013): e67306
    • Up-Regulation of Periostin and Reactive Stroma is Associated with Primary Chemoresistance and Predicts Clinical Outcomes in Epithelial Ovarian Cancer
      Ryner, L., Guan, Y., Firestein, R. et al. Clinical Cancer Research (2015): 2941–51
    • Molecular profiling of chronic myelomonocytic leukemia reveals diverse mutations in >80% of patients with TET2 and EZH2 being of high prognostic relevance
      Grossmann, V., Kohlmann, A., Eder, C. et al. Leukemia (2011): 877–9
    • Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification
      Kamps, R., Brandão, R.D., van den Bosch, B.J. et al. International Journal of Molecular Sciences (2017): 308
    • A novel hierarchical prognostic model of AML solely based on molecular mutations
      Grossman, V., Schnittger, S., Kohlmann, A., et al. Blood (2012): 2,963–72
    • Exome and genome sequencing of nasopharynx cancer identifies NF-κB pathway activating mutations
      Li, Y.Y., Chung, G.T.Y., Lui, V.W.Y. et al. Nature Communications (2017): 14,121
    • Widespread sex differences in gene expression and splicing in the adult human brain
      Trabzuni, D., Ramasamy, A., Imran, S., et al. Nature Communications (2013): 2,771
    • Variable maternal methylation overlapping the nc886/vtRNA2-1 locus is locked between hypermethylated repeats and is frequently altered in cancer
      Romanelli, V., Nakabayashi, K., Vizoso, M., et al. Epigenetics (2014): 783–90
    • Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM mutations in chronic lymphocytic leukemia
      Nadeu, F., Delgado, J., Royo, C., et al. Blood (2016): 2,122–30
    • TCF12 is mutated in anaplastic oligodendroglioma
      Labreche, K., Simeonova, I., Kamoun, A., et al. Nature Communications (2015): 7,207
    • Germline mutation in BRCA1 or BRCA2 and ten-year survival for women diagnosed with epithelial ovarian cancer
      Candido-dos-Reis, F.J., Song, H., Goode, E.L., et al. Clinical Cancer Research (2015): 652–7
    • Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics
      Presneau, N., Baumhoer, D., Behjati, S. et al. The Journal of Pathology: Clinical Research (2015): 113–23
    • Notch1 mutations are drivers of oral tumorigenesis
      Izumchenko, E., Sun, K., Jones, S. et al. Cancer Prevention Research (2014): 277–86
    • Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma
      Gossage, L., Murtaza, M., Slatter, A.F. et al. Genes, Chromosomes and Cancer (2013): 38–51
    • Clinical application of amplicon-based next-generation sequencing in cancer
      Chang, F., Li, M.M. Cancer Genetics (2013): 413–9
    • Low frequency KRAS mutations in colorectal cancer patients and the presence of multiple mutations in oncogenic drivers in non-small cell lung cancer patients
      Jiang, L., Huang, J., Morehouse, C. et al. Cancer Genetics (2013): 330–9
    • Dramatic reduction of sequence artefacts from DNA isolated from formalin-fixed cancer biopsies by treatment with uracil-DNA glycosylase
      Do, H., Dobrovic, A. Oncotarget (2012): 546–58
    • Targeted next-generation sequencing of TP53 in oral tongue carcinoma from non-smokers
      Faden, D.L., Arron, S.T., Heaton, C.M. et al. Journal of Otolaryngology - Head & Neck Surgery (2016): 47
    • Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
      Lohr, J.G., Stojanov, P., Lawrence, M.S. et al. Proceedings of the National Academy of Sciences (2011): 3,879–84
    • EGFR promoter exhibits dynamic histone modifications and binding of ASH2L and P300 in human germinal matrix and gliomas
      Erfani, P., Tome-Garcia, J., Canoll, P., Doetsch, F., Tsankova, N.M. Epigenetics (2015): 496–507
    • BRCA1 and BRCA2 Mutations in Ethnic Lebanese Arab Women With High Hereditary Risk Breast Cancer
      Saghir, N.S., Zgheib, N.K., Assi, H.A., Khoury, K.E., Bidet, Y., Jaber, S.M., Charara, R.N., Farhat, R.A., Kreidieh, F.Y., Decousus, S., Romero, P., Nemer, G.M., Salem, Z., Shamseddine, A., Tfayli, A., Abbas, J., Jamali, F., Seoud, M., Armstrong, D.K., Bignon, Y.J., Uhrhammer, N. The Oncologist (2015): 357–64
    • Novel CARD11 Mutations in Human Cutaneous Squamous Cell Carcinoma Lead to Aberrant NF-κB Regulation
      Watt, S.A., Purdie, K.J., den Breems, N.Y., Dimon, M., Arron, S.T., McHugh, A.T., Xue, D.J., Dayal, J.H.S., Proby, C.M., Harwood, C.A., Leigh, I.M., South, A.P. American Journal of Pathology (2015): 2,354–63
    • Mutations driving CLL and their evolution in progression and relapse
      Landau, D.A., Tausch, E., Taylor-Weiner, A.N., Stewart, C., Reiter, J.G., Bahlo, J., Kluth, S., Bozic, I., Lawrence, M., Böttcher, S., Carter, S.L., Cibulskis, K., Mertens, D., Sougnez, C., Rosenberg, M., Hess, J.M., Edelmann, J., Kless, S., Kneba, M., Ritgen, M., Fink, A., Fischer, K., Gabriel, S., Lander, E., Nowak, M.A., Döhner, H., Hallek, M., Neuberg, D., Getz, G., Stilgenbauer, S., Wu, C.J. Nature (2015): 525–30
    • An Investigator-Initiated Open-Label Trial of Sonidegib in Advanced Basal Cell Carcinoma Patients Resistant to Vismodegib
      Danial, C., Sarin, K.Y., Oro, A.E., Chang, A.L.S. Clinical Cancer Research (2016): 1,325–9
    • Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma
      Jessica Okosun, J., Wolfson, R.L., Wang, J., Araf, S., Wilkins, L., Castellano, B.M., Escudero-Ibarz, L., Al Seraihi, A.F., Richter, J., Bernhart, S.H., Efeyan, A., Iqbal, S., Matthews, J., Clear, A., Guerra-Assunção, J.A., Bödör, C., Quentmeier, H., Mansbridge, C., Johnson, P., Davies, A., Strefford, J.C., Packham, G., Barrans, S., Jack, A., Du, M.Q., Calaminici, M., Lister, T.A., Auer, R., Montoto, S., Gribben, J.G., Siebert, R., Chelala, C., Zoncu, R., Sabatini, D.M., Fitzgibbon, J. Nature Genetics (2016): 183–8
    • A risk prediction algorithm for ovarian cancer incorporating BRCA1, BRCA2, common alleles and other familial effects
      Jervis, S., Song, H., Lee, A., Dicks, E., Harrington, P., Baynes, C., Manchanda, R., Easton, D.F., Jacobs, I., Pharoah, P.P.D., Antoniou, A.C. Journal of Medical Genetics (2015): 465–75
    • Germ-line and somatic DICER1 mutations in pineoblastoma
      de Kock, L., Sabbaghian, N., Druker, H., Weber, E., Hamel, N., Miller, S., Choong, C.S., Gottardo, N.G., Kees, U.R., Rednam, S.P., van Hest, L.P., Jongmans, M.C., Jhangiani, S., Lupski, J.R., Zacharin, M., Bouron-Dal Soglio, D., Huang, A., Priest, J.R., Perry, A., Mueller, S., Albrecht, S., Malkin, D., Grundy, R.G., Foulkes, W.D. Acta Neuropathologica (2014): 583–95
    • Analysis of the Genetic Phylogeny of Multifocal Prostate Cancer Identifies Multiple Independent Clonal Expansions in Neoplastic and Morphologically Normal Prostate Tissue
      Cooper, C.S., Eeles, R., Wedge, D.C., Van Loo, P., Gundem, G., Alexandrov, L.B., Kremeyer, B., Butler, A., Lynch, A.G., Camacho, N., Massie, C.E., Kay, J., Luxton, H.J., Edwards, S., Kote-Jarai, Z., Dennis, N., Merson, S., Leongamornlert, D., Zamora, J., Corbishley, C., Thomas, S., Nik-Zainal, S., O’Meara, S., Matthews, L., Clark, J., Hurst, R., Mithen, R., Bristow, R.G., Boutros, P.C., Fraser, M., Cooke, S., Raine, K., Jones, D., Menzies, A., Stebbings, L., Hinton, J., Teague, J., McLaren, S., Mudie, L., Hardy, C., Anderson, E., Joseph, O., Goody, V., Robinson, B., Maddison, M., Gamble, S., Greenman, C., Berney, D., Hazell, S., Livni, N., The ICGC Prostate Group, Fisher, C., Ogden, C., Kumar, P., Thompson, A., Woodhouse, C., Nicol, D., Mayer, E., Dudderidge, T., Shah, N.C., Gnanapragasam, V., Voet, T., Campbell, P., Futreal, A., Easton, D., Warren, A.Y., Foster, C.S., Stratton, M.R., Whitaker, H.C., McDermott, U., Brewer, D.S., Neal, D.E. Nature Genetics (2015): 367–72
    • Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
      Kim, H., Zheng, S., Amini, S.S., Virk, S.M., Mikkelsen, T., Brat, D.J., Grimsby, J., Sougnez, C., Muller, F., Hu, J., et al Genome Research (2015): 316–27
    • Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma
      Van Allen, E.M., Mouw, K.W., Kim, P., Iyer, G., Wagle, N., Al-Ahmadie, H., Zhu, C., Ostrovnaya, I., Kryukov, G.V., O’Connor, K.W., Sfakianos, J., Garcia-Grossman, I., Kim, J., Guancial, E.A., Bambury, R., Bahl, S., Gupta, N., Farlow, D., Qu, A., Signoretti, S., Barletta, J.A., Reuter, V., Boehm, J., Lawrence, M., Getz, G., Kantoff, P., Bochner, B.H., Choueiri, T.K., Bajorin, D.F., Solit, D.B., Gabriel, S., D’Andrea, A., Garraway, L.A., Rosenberg, J.E. Cancer Discovery (2014): 1,140–53
    • Pituitary blastoma: a pathognomonic feature of germ-line DICER1 mutations
      Kock, L., Sabbaghian, N., Plourde, F., Srivastava, A., Weber, E., Bouron-Dal Soglio, D., Hamel, N., Choi, J.H., Park, S.H., Deal, C.L., Kelsey, M.M., Dishop, M.K., Esbenshade, A., Kuttesch, J.F., Jacques, T.S., Perry, A., Leichter, H., Maeder, P., Brundler, M.A., Warner, J., Neal, J., Zacharin, M., Korbonits, M., Cole, T., Traunecker, H., McLean, T.W., Rotondo, F., Lepage, P., Albrecht, S., Horvath, E., Kovacs, K., Priest, J.R., Foulkes, W.D. Acta Neuropathologica (2014): 111–22
    • DNA methylome profiling identifies novel methylated genes in African American patients with colorectal neoplasia
      Ashktorab, H., Daremipouran, M., Goel, A., Varma, S., Leavitt, R., Sun, X., Brim, H. Epigenetics (2014): 503–12
    • Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis
      Weaver, J.M.J., Ross-Innes, C.S., Shannon, N., Lynch, A.G., Forshew, T., Barbera, M., Murtaza, M., Ong, C.A.J., Lao-Sirieix, P., Dunning, M.J., Smith, L., Smith, M.L., Anderson, C.L., Carvalho, B., O’Donovan, M., Underwood, T.J., May, A.P., Grehan, N., Hardwick, R., Davies, J., Oloumi, A., Aparicio, S., Caldas, C., Eldridge, M.D., Edwards, P.A.W., Rosenfeld, N., Tavaré, S., Fitzgerald, R.C., OCCAMS consortium Nature Genetics (2015): 837–43
    • Genomic landscape of CD34+ hematopoietic cells in myelodysplastic syndrome and gene mutation profiles as prognostic markers
      Xu, L., Gu, Z.H., Zhang, J.L., Chang, C.K., Pan, C.M., Shi, J.Y., Shen, Y., Chen, B., Wang, Y.Y., Jiang, L., Lu, J., Xu, X., Tan, J.L., Chen, Y., Wang, S.Y., Li, X., Chen, Z., Chen, S.J. Proceedings of the National Academy of Sciences of the United States of America (2014): 8,589–94
    • Genetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing
      McFadden, D.G., Papagiannakopoulos, T., Taylor-Weiner, A., Stewart, C., Carter, S.L., Cibulskis, K., Bhutkar, A., McKenna, A., Dooley, A., Vernon, A., Sougnez, C., Malstrom, S., Heimann, M., Park, J., Chen, F., Farago, A.F., Dayton, T., Shefler, E., Gabriel, S., Getz, G., Jacks, T. Cell (2015): 1,298–311
    • Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas
      Palomero, T., Couronné, L., Khiabanian, H., Kim, M.Y., Ambesi-Impiombato, A., Perez-Garcia, A., Carpenter, Z., Abate, F., Allegretta, M., Haydu, J.E., Jiang, X., Lossos, I.S., Nicolas, C., Balbin, M., Bastard, C., Bhagat, G., Piris, M.A., Campo, E., Bernard, O., Rabadan, R., Ferrando, A. Nature Genetics (2014): 166–70
    • Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma
      Okosun, J., Bödör, C., Wang, J., Araf, S., Yang, C.Y., Pan, C., Boller, S., Cittaro, D., Bozek, M., Iqbal, S., Matthews, J., Wrench, D., Marzec, J., Tawana, K., Popov, N., O’Riain, C., O’Shea, D., Carlotti, E., Davies, A., Lawrie, C.H., Matolcsy, A., Calaminici, M., Norton, A., Byers, R.J., Mein, C., Stupka, E., Lister, T.A., Lenz, G., Montoto, S., Gribben, J.G., Fan, Y., Grosschedl, R., Chelala, C., Fitzgibbon, J. Nature Genetics (2014): 176–81
    • EZH2 mutations are frequent and represent an early event in follicular lymphoma
      Bödör, C., Grossmann, V., Popov, N., Okosun, J., O’Riain, C., Tan, K., Marzec, J., Araf, S., Wang, J., Lee, A.M., Clear, A., Montoto, S., Matthews, J., Iqbal, S., Rajnai, H., Rosenwald, A., Ott, G., Campo, E., Rimsza, L.M., Smeland, E.B., Chan, W.C., Braziel, R.M., Staudt, L.M., Wright, G., Lister, T.A., Elemento, O., Hills, R., Gribben, J.G., Chelala, C., Matolcsy, A., Kohlmann, A., Haferlach, T., Gascoyne, R.D., Fitzgibbon, J. Blood (2013): 3,165–8
    • DNA repair genes are selectively mutated in diffuse large B cell lymphomas
      FCC de Miranda, N., Peng, R., Georgiou, K., Wu, C., Sörqvist, E.F., Berglund, M., Chen, L., Gao, Z., Lagerstedt, K., Lisboa, S., Roos, F., van Wezel, T., Teixeira, M.R., Rosenquist, R., Sundström, C., Enblad, G., Nilsson, M., Zeng, Y., Kipling, D., Pan-Hammarström, Q. Journal of Experimental Medicine (2013): 1,729–42
    • Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas
      Fontebasso, A.M., Schwartzentruber, J., Khuong-Quang, D.A., Liu, X.Y., Sturm, D., Korshunov, A., Jones, D.T.W., Witt, H., Kool, M., Albrecht, S., Fleming, A., Hadjadj, D., Busche, S., Lepage, P., Montpetit, A., Staffa, A., Gerges, N., Zakrzewska, M., Zakrzewski, K., Liberski, P.P., Hauser, P., Garami, M., Klekner, A., Bognar, L., Zadeh, G., Faury, D., Pfister, S.M.Nada Jabado, Jacek Majewski Acta Neuropathologica (2013): 659–69
    • Medulloblastoma Exome Sequencing Uncovers Subtype-Specific Somatic Mutations
      Pugh, T.J., Weeraratne, S.D., Archer, T.C., Pomeranz Krummel, D.A., Auclair, D., Bochicchio, J., Carneiro, M.O., Carter, S.L., Cibulskis, K., Erlich, R.L., Greulich, H., Lawrence, M.S., Lennon, N.J., McKenna, A., Meldrim, J., Ramos, A.H., Ross, M.G., Russ, C., Shefler, E., Sivachenko, A., Sogoloff, B., Stojanov, P., Tamayo, P., Mesirov, J.P., Amani, V., Teider, N., Sengupta, S., Francois, J.P., Northcott, P.A., Taylor, M.D., Yu, F., Crabtree, G.R., Kautzman, A.G., Gabriel, S.B., Getz, G., Jäger, N., Jones, D.T.W., Lichter, P., Pfister, S.M., Roberts, T.M., Meyerson, M., Pomeroy, S.L., Cho, Y.J. Nature (2012): 106–10
    • Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing
      Wang, M., Escudero-Ibarz, L., Moody, S., Zeng, N., Clipson, A., Huang, Y., Xue, X., Grigoropoulos, N.F., Barrans, S., Worrillow, L., et al The Journal of Molecular Diagnostics (2015): 521–32
    • TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
      Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L.M., Melnyk, N., McPherson, A., Bashashati, A., Laks, E., Biele, J., Ding, J., Le, A., Rosner, J., Shumansky, K., Marra, M.O., Gilks, C.B., Huntsman, D.G., McAlpine, J.N., Aparicio, S., Shah, S.P. Genome Research (2014): 1,881–93
    • Assessing mutant p53 in primary high-grade serous ovarian cancer using immunohistochemistry and massively parallel sequencing
      Cole, A.J., Dwight, T., Gill, A.J., Dickson, K.A., Zhu, Y., Clarkson, A., Gard, G.B., Maidens, J., Valmadre, S., Clifton-Bligh, R., Marsh, D.J. Scientific Reports (2016): 26,191
    • Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition
      Burger, J.A., Landau, D.A., Taylor-Weiner, A., Bozic, I., Zhang, H., Sarosiek, K., Wang, L., Stewart, C., Fan, J., Hoellenriegel, J., Sivina, M., Dubuc, A.M., Fraser, C., Han, Y., Li, S., Livak, K.J., Zou, L., Wan, Y., Konoplev, S., Sougnez, C., Brown, J.R., Abruzzo, L.V., Carter, S.L., Keating, M.J., Davids, M.S., Wierda, W.G., Cibulskis, K., Zenz, T., Werner, L., Dal Cin, P., Kharchencko, P., Neuberg, D., Kantarjian, H., Lander, E., Gabriel, S., O'Brien, S., Letai, A., Weitz, D.A., Nowak, M.A., Getz, G., Wu, C.J. Nature Communications (2016): 11,589
    • Methylation profiling of 48 candidate genes in tumor and matched normal tissues from breast cancer patients
      Li, Z., Guo, X., Wu, Y., Li, S., Yan, J., Peng, L., Xiao, Z., Wang, S., Deng, Z., Dai, L., Yi, W., Xia, K., Tang, L., Wang, J. Breast Cancer Research and Treatment (2015): 767–79
    • Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses
      Aitken S.J., Presneau, N., Kalimuthu, S., Dileo, P., Berisha, F., Tirabosco, R., Amary, M.F., Flanagan, A.M. Virchows Archiv (2015): 203–10
    • Smoothened Variants Explain the Majority of Drug Resistance in Basal Cell Carcinoma
      Atwood, S.X., Sarin, K.Y., Whitson, R.J., Li, J.R., Kim, G., Rezaee, M., Ally, M.S., Kim, J., Yao, C., Chang, A.L., Oro, A.E., Tang, J.Y. Cancer Cell (2015): 342–353
    • Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer
      Ward, D.G., Baxter, L., Gordon, N.S., Ott, S., Savage, R.S., Beggs, A.D., James, J.D., Lickiss, J., Green, S., Wallis, Y., Wei, W., James, N.D., Zeegers, M.P., Cheng, K.K., Mathews, G.M., Patel, P., Griffiths, M., Bryan, R.T. PLoS One (2016): e0149756
    • FAT1 mutations cause a glomerulotubular nephropathy
      Gee, H.Y., Sadowski, C.E., Aggarwal, P.K., Porath, J.D., Yakulov, T.A., Schueler, M., Lovric, S., Ashraf, S., Braun, D.A., Halbritter, J., Fang, H., Airik, R., Vega-Warner, V., Cho, K.J., Chan, T.A., Morris, L.G.T., French-Constant, C., Allen, N., McNeill, H., Büscher, R., Kyrieleis, H., Wallot, M., Gaspert, A., Kistler, T., Milford, D.V., Saleem, M.A., Keng, W.T., Alexander, S.I., Valentini, R.P., Licht, C., Teh, J.C., Bogdanovic, R., Koziell, A., Bierzynska, A., Soliman, N.A., Otto, E.A., Lifton, R.P., Holzman, L.B., Sibinga, N.E.S., Walz, G., Tufro, A., Hildebrandta, F. Nature Communications (2016): 10,822
    • Farewell to GBM-O: Genomic and transcriptomic profiling of glioblastoma with oligodendroglioma component reveals distinct molecular subgroups
      Hinrichs, B.H., Newman, S., Appin, C.L., Dunn, W., Cooper, L., Pauly, R., Kowalski, J., Rossi, M.R., Brat, D.J. Acta Neuropathologica Communications (2016): 4
    • Towards a Next-Generation Sequencing Diagnostic Service for Tumour Genotyping: A Comparison of Panels and Platforms
      Burghel, G.J., Hurst, C.D., Watson, C.M., Chambers, P.A., Dickinson, H., Roberts, P., Knowles, M.A. BioMed Research International (2015): 478,017
    • DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer
      Stone, A., Zotenko, E., Locke, W.J., Korbie, D., Millar, E.K.A., Pidsley, R., Stirzaker, C., Graham, P., Trau, M., Musgrove, E.A., Nicholson, R.I., Gee, J.M.W., Clark, S.J. Nature Communications (2015): 7,758
    • Integrative epigenomic and genomic filtering for methylation markers in hepatocellular carcinomas
      Shen, J., LeFave, C., Sirosh, I., Siegel, A.B., Tycko, B., Santella, R.M. BMC Medical Genomics (2015): 28
    • Clinical Characteristics of Ovarian Cancer Classified by BRCA1, BRCA2, and RAD51C Status
      Cunningham, J.M., Cicek, M.S., Larson, N.B., Davila, J., Wang, C., Larson, M.C., Song, H., Dicks, E.M., Harrington, P., Wick, M., Winterhoff, B.J., Hamidi, H., Konecny, G.E., Chien, J., Bibikova, M., Fan, J.B., Kalli, K.R., Lindor, N.M., Fridley, B.L., Pharoah, P.P.D., Goode, E.L. Scientific Reports (2014): 4,026
    • Ovarian Cancer Cell Line Panel (OCCP): Clinical Importance of In Vitro Morphological Subtypes
      Beaufort, C.M., Helmijr, J.C.A., Piskorz, A.M., Hoogstraat, M., Ruigrok-Ritstier, K., Besselink, N., Murtaza, M., van IJcken, W.F.J., Heine, A.A.J., Smid, M., Koudijs, M.J., Brenton, J.D., Berns, E.M.J.J., Helleman, J. PLoS One (2014): e103988
    • Mutation and expression analysis in medulloblastoma yields prognostic variants and a putative mechanism of disease for i17q tumors
      Bien-Willner, G.A., Mitra, R.D. Acta Neuropathologica Communications (2014): 74
    • Mutations in epigenetic regulators including SETD2 are gained during relapse in pediatric acute lymphoblastic leukemia
      Mar, B.G., Bullinger, L.B., McLean, K.M., Grauman, P.V., Harris, M.H., Stevenson, K., Neuberg, D.S., Sinha, A.U., Sallan, S.E., Silverman, L.B., Kung, A.L., Lo Nigro, L., Ebert, B.L., Armstrong, S.A. Nature Communications (2014): 3,469
    • Acquired PIK3CA amplification causes resistance to selective phosphoinositide 3-kinase inhibitors in breast cancer
      Huw, L.Y., O'Brien, C., Pandita, A., Mohan, S., Spoerke, J.M., Lu, S., Hampton, G.M., Wilson, T.R., Lackner, M.R. Oncogenesis (2013): e83
    • Massively Parallel Sequencing Reveals an Accumulation of De Novo Mutations and an Activating Mutation of LPAR1 in a Patient with Metastatic Neuroblastoma
      Wei, J.S., Johansson, P., Chen, L., Song, Y.K., Tolman, C., Li, S., Hurd, L., Patidar, R., Wen, X., Badgett, T.C., Cheuk, A.T.C., Marshall, J.C., Steeg, P.S., Vaqué Díez, J.P., Yu, Y., Gutkind, J.S., Khan, J. PLoS One (2013): e77731
    • Mutation Analysis of BRCA1, BRCA2, PALB2 and BRD7 in a Hospital-Based Series of German Patients with Triple-Negative Breast Cancer
      Pern, F., Bogdanova, N., Schürmann, P., Lin, M., Ay, A., Länger, F., Hillemanns, P., Christiansen, H., Park-Simon, T.W., Dörk, T. PLoS One (2012): e47993
    • Molecular analysis of RAS-RAF tyrosine-kinase signaling pathway alterations in patients with plasma cell myeloma
      Grossmann, V., Bacher, U., Artusi, V., Kohlmann, A., Nadarajah, N., Kern, W., Schnittger, S., Haferlach, T., Haferlach, C. Blood Cancer Journal (2012): e85
    • Recurrent DICER1 hotspot mutations in endometrial tumours and their impact on microRNA biogenesis
      Chen, J., Wang, Y., McMonechy, M.K., Anglesio, M.S., Yang, W., Senz, J., Maines-Bandiera, S., Rosner, J., Trigo-Gonzalez, G., Cheng, S.W.G., Kim, J., Matzuk, M.M., Morin, G.B., Huntsman, D.G. The Journal of Pathology (2015): 215–25
    • Polymerase Epsilon Exonuclease Domain Mutations in Ovarian Endometrioid Carcinoma
      Hoang, L.N., McConechy, M.K., Köbel, M., Anglesio, M., Senz, J., Maassen, M., Kommoss, S., Meng, B., Postovit, L., Kelemen, L.E., Staebler, A., Brucker, S., Krämer, B., McAlpine, J.N., Gilks, C.B., Huntsman, D.G., Lee, C.H. International Journal of Gynecological Cancer (2015): 1187–93
    • Multiplex bisulfite PCR resequencing of clinical FFPE DNA
      Korbie, D., Lin, E., Wall, D., Nair, S.S., Stirzaker, C., Clark, S.J., Trau, M. Clinical Epigenetics (2015): 28
    • MED12 is frequently mutated in breast phyllodes tumours: a study of 112 cases
      Ng,C.C.Y., Tan, J., Ong, C.K., Lim, W.K., Rajasegaran, V., Nasir N.D.M., Lim, J.C.T., Thike, A.A., Salahuddin, S.A., Iqbal, J., Busmanis, I., Chong, A.P.Y., The, B.T., Tan, P.H. Journal of Clinical Pathology (2015):
    • In-depth molecular profiling of the biphasic components of uterine carcinosarcomas
      McConechy, M.K., Hoang, L.N., Chui, M.H., Senz, J., Yang, W., Rozenberg, N., Mackenzie, R., McAlpine, J.N., Huntsman, D.G., Clarke, B.A., Gilks, C.B., Cheng-Han Lee, C.H. Journal of Pathology: Clinical Research (2015): 173–185
    • Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas
      Tone, A.A., McConechy, M.K., Yang, W., Ding, J., Yip, S., Kong, E., Wong, K.K., Gershenson, D.M., Mackay, H., Shah, S., Gilks, B., Tinker, A.V., Clarke, B., McAlpine, J.N., Huntsman, D. BMC Cancer (2014): 982
    • The molecular spectrum and clinical impact of DIS3 mutations in multiple myeloma
      Weißbach, S., Langer, C., Puppe, B., Nedeva, T., Bach, E., Kull, M., Bargou, R., Einsele, H., Rosenwald, A., Knop, S., Leich, E. British Journal of Haematology (2014): 57–70
    • Flexible, Scalable and Efficient Targeted Resequencing on a Benchtop Sequencer for Variant Detection in Clinical Practice
      De Leeneer, K., Hellemans, J., Steyaert, W., Lefever, S., Vereecke, I., Debals, E., Crombez, B., Baetens, M., Van Heetvelde, M., Coppieters, F., Vandesompele, J., De Jaegher, A., De Baere, E., Coucke, P., Claes, K. Human Mutation (2015): 379–87

  • Parentage ID

    • A new perspective on polyploid Fragaria (strawberry) genome composition based on large-scale, multi-locus phylogenetic analysis
      Yang, Y., Davis, T.M. Genome Biology and Evolution (2017): 3,433–48

  • Population Screening

    • Allelic expression of deleterious protein-coding variants across human tissues
      Kukurba, K.R., Zhang, R., Li, X. et al. PLOS Genetics (2014): e1004304
    • Analysis of the ABCA4 gene by next-generation sequencing
      Zernant, J., Schubert, C., Im, K.M. et al. Investigative Ophthalmology & Visual Science (2011): 8479–87
    • Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes
      Bledsoe, J.W., Peterson, B.C., Swanson, K.S. et al. PLoS One (2016): e0166379
    • Targeted Capture in Evolutionary and Ecological Genomics
      Jones, M.R., Good, J.M. Molecular Ecology (2016): 185–202
    • Comparative analysis of gut microbiota of mosquito communities in central Illinois
      Muturi, E.J., Ramirez, J.L., Rooney, A.P. et al. PLoS Neglected Tropical Diseases (2017): e0005377
    • Effect of pesticides on microbial communities in container aquatic habitats
      Muturi, E., Donthu, R., Fields, C.J. et al. Scientific Reports (2017): 44,565
    • Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata; Asteraceae)
      Richardson, B.A., Page, J.T., Bajgain, P., et al. American Journal of Botany (2012): 1,962–75
    • Spotted phenotypes in horses lost attractiveness in the Middle Ages
      Wutke, S., Benecke, N., Sandoval-Castellanos, E. et al. Scientific Reports (2016): 38,548
    • Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India
      Panda, A.K., Bisht, S.S., Mandal, S.D. et al. AMB Express (2016): 111
    • ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing
      Lang, K., Wagner, I., Schöne, B., Schöfl, G., Birkner, K., Hofmann, J.A., Sauter, J., Pingel, J., Böhme, I., Schmidt, A.H., Lange, V. BMC Genomics (2016): 374
    • A Research Workflow for Development of Single-Copy Nuclear Loci and High-throughput Targeted Enrichment for Two or More Phylogenetic Studies.
      Jordon-Thaden, I., Uribe-Convers, S., Godden, G.T., Srikar, C., Tank, D.C., Martine, C.T. Botany Society of America (2014):

  • Stem Cell

    • Tumor-Derived Suppressor of Fused Mutations Reveal Hedgehog Pathway Interactions
      Urman, N.M., Mirza, A., Atwood, S.X. et al. PLoS One (2016): e0168031
    • Inactivation of TGFβ receptors in stem cells drives cutaneous squamous cell carcinoma
      Cammareri, P., Rose, A.M., Vincent, D.F. et al. Nature Communications (2016): 12,493

  • Other

    • Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates
      Yablonovitch, A.L., Fu, J., Li, K. et al. Nature Communications (2017): 1,570
    • Soy Improves Cardiometabolic Health and Cecal Microbiota in Female Low-Fit Rats
      Cross, T.W.L., Zidon, T.M., Welly, R.J. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-08965-0
    • Transcriptomic resources and marker validation for diploid and polyploid Veronica (Plantaginaceae) from New Zealand and Europe
      Mayland-Quellhorst, E., Meudt, H.M., Albach, D.C. Applications in Plant Sciences (2016): 1,600,091
    • Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
      Zhang, R., Deng, P., Jacobson, D. et al. PLoS Genetics (2017): e1006563
    • Quantification of global mitochondrial DNA methylation levels and inverse correlation with age at two CpG sites
      Mawlood, S.K., Dennany, L., Watson, N. et al. Aging (2016): 636–41
    • TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
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