Published in BMC Cancer, 2020
This paper develops a Bayesian hierarchical model for copy number estimation and association in a large-scale study of germline risk factors of pancreatic cancer
Recommended citation: Cristiano S et al. (2020). "Bayesian copy number detection and association in large-scale studies." BMC Cancer. 20(1). http://rscharpf.github.io/files/Cristiano_et_al_BMCcancer_2020.pdf
Published in Nature Communications, 2020
Liquid biopsies may be confounded by alterations arising from clonal hematopoeisis. This study uses targeted sequencing of matched cfDNA and white blood cells to distinguish cfDNA from other cfDNA alterations and highlights the utility of ctDNA as a predictive biomarker of patient outcome to perioperative cancer therapy and surgical resection in patients with gastric cancer.
Recommended citation: Leal A et al. (2020). "White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer" Nature Communications 11(1). http://rscharpf.github.io/files/leal_naturecomm_2020.pdf
Published in Nature, 2019
This paper describes an approach called DELFI to identify features of cell-free DNA fragmentation from shallow whole genome sequencing for early cancer detection.
Recommended citation: Cristiano S et al. (2019). "Genome-wide cell-free DNA fragmentation in patients with cancer." Nature. 570(7761). http://rscharpf.github.io/files/Cristiano_et_al_Nature_2019.pdf
Published in Cell Reports, 2018
Integrated genomic analyses of ovarian cancer cell lines.
Recommended citation: Papp E et al. (2018). "Integrated genomic, epigenomic, and expression analyses of ovarian cancer cell lines." Cell Reports. 25(9). http://rscharpf.github.io/files/Papp_et_al_CellReports_2018.pdf
Published in Nature Genetics Reviews, 2010
We argue that batch effects are widespread and critical to address. We review experimental and computational approaches for doing so.
Recommended citation: Leek et al. (2010). "Tackling the widespread and critical impact of batch effects in high-throughput data." Nature Genetics Reviews. 11(10). http://rscharpf.github.io/files/leek_et_al_ngr_2010.pdf