CopywriteR: DNA copy number detection from off-target sequence data
T Kuilman, A Velds, K Kemper, M Ranzani… - Genome biology, 2015 - Springer
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from
targeted sequencing data are based on the depth of coverage of captured exons. Accurate …
targeted sequencing data are based on the depth of coverage of captured exons. Accurate …
Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment
HF van Thuijl, T Mazor, BE Johnson, SD Fouse… - Acta …, 2015 - Springer
Temozolomide (TMZ) increases the overall survival of patients with glioblastoma (GBM), but
its role in the clinical management of diffuse low-grade gliomas (LGG) is still being defined …
its role in the clinical management of diffuse low-grade gliomas (LGG) is still being defined …
Fixing formalin: a method to recover genomic-scale DNA sequence data from formalin-fixed museum specimens using high-throughput sequencing
SM Hykin, K Bi, JA McGuire - PloS one, 2015 - journals.plos.org
For 150 years or more, specimens were routinely collected and deposited in natural history
collections without preserving fresh tissue samples for genetic analysis. In the case of most …
collections without preserving fresh tissue samples for genetic analysis. In the case of most …
Uncovering the genomic heterogeneity of multifocal breast cancer
C Desmedt, D Fumagalli, E Pietri… - The Journal of …, 2015 - Wiley Online Library
Multifocal breast cancer (MFBC), defined as multiple synchronous unilateral lesions of
invasive breast cancer, is relatively frequent and has been associated with more aggressive …
invasive breast cancer, is relatively frequent and has been associated with more aggressive …
[HTML][HTML] Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics
S Munchel, Y Hoang, Y Zhao, J Cottrell, B Klotzle… - Oncotarget, 2015 - ncbi.nlm.nih.gov
Current genomic studies are limited by the poor availability of fresh-frozen tissue samples.
Although formalin-fixed diagnostic samples are in abundance, they are seldom used in …
Although formalin-fixed diagnostic samples are in abundance, they are seldom used in …
Characterization of patient-derived tumor xenograft models of endometrial cancer for preclinical evaluation of targeted therapies
J Depreeuw, E Hermans, S Schrauwen, D Annibali… - Gynecologic …, 2015 - Elsevier
Objective Endometrial carcinoma (EC) is the sixth most common cancer in women and
therapies are limited for advanced and recurrent disease. Patient-derived tumor xenograft …
therapies are limited for advanced and recurrent disease. Patient-derived tumor xenograft …
Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method
L Deleye, DD Coninck, C Christodoulou, T Sante… - Scientific Reports, 2015 - nature.com
Current whole genome amplification (WGA) methods lead to amplification bias resulting in
over-and under-represented regions in the genome. Nevertheless, certain WGA methods …
over-and under-represented regions in the genome. Nevertheless, certain WGA methods …
[HTML][HTML] Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts
L Deleye, A Dheedene, D De Coninck, T Sante… - Fertility and sterility, 2015 - Elsevier
Objective To add evidence that massive parallel sequencing (MPS) is a valuable substitute
for array comparative genomic hybridization (arrayCGH) with a resolution that is more …
for array comparative genomic hybridization (arrayCGH) with a resolution that is more …
[HTML][HTML] Molecular characterization of 7 new established cell lines from high grade serous ovarian cancer
C Kreuzinger, M Gamperl, A Wolf, G Heinze… - Cancer letters, 2015 - Elsevier
Cancer cell lines are good in vitro models to study molecular mechanisms underlying
chemoresistance and cancer recurrence. Recent works have demonstrated that most of the …
chemoresistance and cancer recurrence. Recent works have demonstrated that most of the …
Modeling the next generation sequencing read count data for DNA copy number variant study
As one of the most recent advanced technologies developed for biomedical research, the
next generation sequencing (NGS) technology has opened more opportunities for scientific …
next generation sequencing (NGS) technology has opened more opportunities for scientific …