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 …

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 …

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 …

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 …

[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 …

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 …

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 …

[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 …

[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 …

Modeling the next generation sequencing read count data for DNA copy number variant study

T Ji, J Chen - Statistical applications in genetics and molecular …, 2015 - degruyter.com
As one of the most recent advanced technologies developed for biomedical research, the
next generation sequencing (NGS) technology has opened more opportunities for scientific …