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The temporal order of genetic and pathway alterations in tumorigenesis
- PloS one
, 2011
"... Cancer evolves through the accumulation of mutations, but the order in which mutations occur is poorly understood. Inference of a temporal ordering on the level of genes is challenging because clinically and histologically identical tumors often have few mutated genes in common. This heterogeneity m ..."
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Cited by 5 (2 self)
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may at least in part be due to mutations in different genes having similar phenotypic effects by acting in the same functional pathway. We estimate the constraints on the order in which alterations accumulate during cancer progression from cross-sectional mutation data using a probabilistic graphical
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
"... Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and lo ..."
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Cited by 1 (1 self)
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is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating
doi:10.1155/2012/797812 Research Article Inference of Tumor Phylogenies from Genomic Assays on
, 2012
"... Copyright © 2012 Ayshwarya Subramanian et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Tumorigenesis can in principle result f ..."
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from many combinations of mutations, but only a few roughly equivalent sequences of mutations, or “progression pathways, ” seem to account for most human tumors. Phylogenetics provides a promising way to identify common progression pathways and markers of those pathways. This approach, however, can
SHARING INFORMATION TO RECONSTRUCT PATIENT-SPECIFIC PATHWAYS IN HETEROGENEOUS DISEASES
"... Advances in experimental techniques resulted in abundant genomic, transcriptomic, epigenomic, and proteomic data that have the potential to reveal critical drivers of human diseases. Complementary algorithmic developments enable researchers to map these data onto protein-protein interaction network ..."
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networks and infer which signaling pathways are perturbed by a disease. Despite this progress, integrating data across different biological samples or patients remains a substantial challenge because samples from the same disease can be extremely heterogeneous. Somatic mutations in cancer are an infamous
Learning oncogenetic networks by reducing to mixed integer linear programming
- PloS one
"... Cancer can be a result of accumulation of different types of genetic mutations such as copy number aberrations. The data from tumors are cross-sectional and do not contain the temporal order of the genetic events. Finding the order in which the genetic events have occurred and progression pathways a ..."
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Cited by 1 (0 self)
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Cancer can be a result of accumulation of different types of genetic mutations such as copy number aberrations. The data from tumors are cross-sectional and do not contain the temporal order of the genetic events. Finding the order in which the genetic events have occurred and progression pathways
DOI 10.1186/s13059-015-0700-7 METHOD Open Access CoMEt: a statistical approach to identify
"... combinations of mutually exclusive alterations in cancer Mark DM Leiserson1,2†, Hsin-Ta Wu1,2†, Fabio Vandin1,3 and Benjamin J. Raphael1,2* Cancer is a heterogeneous disease with different combinations of genetic alterations driving its development in different individuals. We introduce CoMEt, an al ..."
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mutations in thousands of tumors in dozens of cancer types. Interpreting this data requires one to distinguish the driver mutations that play a role in cancer development and progression from passenger mutations that have no consequence for cancer. Identify-ing driver mutations directly from sequencing data
BDRS PRICE DESCRIPTOR,
"... This report focuses on the evidence about the health.consequences of smoking for women, and is intended to serve.the public health and medical communities as 'a unified source of existing scientific research. The major issues about tobacco use and women's health are examined, including tre ..."
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trends in consumption, biomedical evidence, and determinants of smoking ititiation, maintenance, and cessation. The biomedical aspects ofsmoking are presented in terms of mortality, morbiplity, cardiovasculaidiseases, cancer, pregnancy and infant,health,, Teptic ulcer disease, drug reactions and