Publications

2017

• Vossen R.H.A.M and White S.J. (2017) Quantitative DNA analysis with Digital PCR. Methods in Molecular Biology, 1492:167-77

• Hottentot Q., et al (2017) Targeted Locus Amplification and Next Generation Sequencing. Methods in Molecular Biology, 1492:185-196

• De Boer C.M. and White S.J. (2017) Genotyping Multiallelic Copy Number Variation with Multiplex Ligation-Dependent Probe Amplification. Methods in Molecular Biology, 1492:147-53

• Buermans H.P.J. et al., (2017) Flexible, scalable and cost efficient full-length CYP2D6 long amplicon PacBio sequencing. Human Mutation - e-pub Jan 3

• Vossen R.H.A.M and Buermans H.P.J. (2017) Full-Length Mitochondrial-DNA Sequencing on the PacBio RSII. Methods in Molecular Biology, 1492:179-184

• Vossen R.H.A.M. (2017) Genotyping DNA Variants with High-Resolution Melting Analysis. Methods in Molecular Biology, 1492:17-28

• Borras D.M. et al., (2017) Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing. Human Mutation - e-pub Apr 4



2016

• Cantsilieris S., et al (2016) Multiallelic copy-number variation in the complement component 4A (C4A) gene is associated with late stage age-related macular degeneration (AMD). J Neuroinflamm 13:81 

• Juniarto Z., et al (2016) Hormonal evaluation in relation to phenotype and genotype in 286 patients with a Disorder of Sex Development from Indonesia. Clinical Endocrinology 85:247-57 

• Johnson J., et al (2016) Deletion of the complex I subunit NDUFS4 adversely modulates cellular differentiation. Stem Cells Dev, 25:239-50.

• Jones S.A., et al (2016) Glucocorticoid-induced leucine zipper (GILZ) inhibits B cell activation in systemic lupus erythematosus. Ann Rheum Dis. 75:739-47

• Kolder I.C.R.M. et al. (2016) A full-body transcriptome and proteome resource for the European common carp. BMC Genomics. 17:701

• Torres-Espanol M. et al. (2016) Variations in the genome: detection, genome sequencing and interpretation. Human Mutation. 37:1106-9

• Kraaijeveld K. et al. (2016) Decay of sexual trait genes in an asexual parasitoid wasp. Genome Biology and Evolution. Epub online

• Faddeeva-Vakhrusheva A. et al (2016) Gene family evolution reflects adaptation to soil environmental stressors in the genome of the collembolan Orchesella cincta. Genome Biology and Evolution. 8:2106-17



2015

• Punt S, et al. Whole-transcriptome analysis of flow-sorted cervical cancer samples reveals that B cell expressed TCL1A is correlated with improved survival. Oncotarget. 2015 Nov 17;6(36):38681-94

• Roost MS, et al. KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas. Stem Cell Reports. 2015 Jun 9;4(6):1112-24. 

• Rivas MA, et al. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 2015 May 8;348(6235):666-9. 

• White SJ. Counting copy number and calories. Nat Genet. 2015 Aug;47(8):852-3. 

• Romanelli Tavares VL, et al. Novel variants in GNAI3 associated with auriculocondylar syndrome strengthen a common dominant negative effect. Eur J Hum Genet. 2015 Apr;23(4):481-5. 

• Goossens-Beumer IJ, et al. MicroRNA classifier and nomogram for metastasis prediction in colon cancer. Cancer Epidemiol Biomarkers Prev. 2015 Jan;24(1):187-97. 

• Pulyakhina I, et al. SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing. Nucleic Acids Res. 2015 Jul 13;43(12):e80. 

• den Dunnen JT. The DNA Bank: High-Security Bank Accounts to Protect and Share Your Genetic Identity. Hum Mutat. 2015 Jul;36(7):657-9. 

• Sun Y, et al. Next-generation diagnostics: gene panel, exome, or whole genome? Hum Mutat. 2015 Jun;36(6):648-55. 

• de Klerk E, et al. Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res. 2015 May 19;43(9):4408-28. 

• Faddeeva A, et al. Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life. PLoS One. 2015 Jun 15;10(6):e0130600. 

• Kraaijeveld K, et al. Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing. Mol Ecol Resour. 2015 Jan;15(1):8-16. 

• Mastrokolias A, et al. Huntington’s disease biomarker progression profile identified by transcriptome sequencing in peripheral blood. Eur J Hum Genet. 2015 Oct;23(10):1349-56. 


2014

• Rong J, et al. New insights into domestication of carrot from root transcriptome analyses. BMC Genomics. 2014 Oct 14;15:895. 

• Anvar SY, et al. Determining the quality and complexity of next-generation sequencing data without a reference genome. Genome Biol. 2014;15(12):555. 

• Buermans HP, den Dunnen JT. Next generation sequencing technology: Advances and applications. Biochim Biophys Acta. 2014 Oct;1842(10):1932-1941. 

• Dambrot C, et al. Strategies for rapidly mapping proviral integration sites and assessing cardiogenic potential of nascent human induced pluripotent stem cell clones. Exp Cell Res. 2014 Oct 1;327(2):297-306. 

• den Dunnen J. Redefining mutational spectra via updated locus-specific databases. Hum Mutat. 2014 Oct;35(10):v. 

• de Vree PJ, et al. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat Biotechnol. 2014 Oct;32(10):1019-25.

• Hassan SM, et al. Molecular diagnostics of the HBB gene in an Omani cohort using bench-top DNA Ion Torrent PGM technology. Blood Cells Mol Dis. 2014 Sep;53(3):133-7. 

• de Klerk E, et al. RNA sequencing: from tag-based profiling to resolving complete transcript structure. Cell Mol Life Sci. 2014 Sep;71(18):3537-51. 

• den Dunnen JT. Pathogenic: light or dark skin? Hum Mutat. 2014 May;35(5):520. 

• Liang C, et al. Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing. Anal Bioanal Chem. 2014 Apr;406(11):2603-11. 

• Anvar SY, et al. TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes. Bioinformatics. 2014 Jun 15;30(12):1651-9. 

• Greger L, et al. Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.  PLoS One. 2014 Aug 18;9(8):e104567.