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Optimizing Cancer Genome Sequencing and Analysis

Malachi Griffith, Christopher A. Miller, Obi L. Griffith, Kilannin Krysiak, Zachary L. Skidmore, Avinash Ramu, Jason R. Walker, Ha X. Dang, Lee Trani, David E. Larson, Ryan T. Demeter, Michael C. Wendl (+15 others)
2015 Cell Systems  
Additional targeted sequencing provided over 10,000× coverage and ddPCR assays provided up to ~250,000× sampling of selected sites.  ...  We demonstrate that current sequencing paradigms are inadequate for tumors that are impure, aneuploid or clonally heterogeneous.  ...  Ley from the NCI (PO1CA101937) and to Richard K. Wilson from the NHGRI (U54HG003079).  ... 
doi:10.1016/j.cels.2015.08.015 pmid:26645048 pmcid:PMC4669575 fatcat:3sm5sn4tfncjrhmzdjrmucvqxi

Computational approaches for inferring tumor evolution from single-cell genomic data

Hamim Zafar, Nicholas Navin, Luay Nakhleh, Ken Chen
2018 Current Opinion in Systems Biology  
Genomic heterogeneity in tumors results from mutations and selection of high-fitness single cells, the operational components of evolution.  ...  Precise knowledge about mutational heterogeneity and evolutionary trajectory of a tumor can provide useful insights into predicting cancer progression and designing personalized treatment.  ...  Figure 3 Tumor 3 phylogeny inference from single-cell sequencing data. (a) Illustration of a heterogeneous tumor tissue that evolved according to the clonal expansion represented in (b).  ... 
doi:10.1016/j.coisb.2017.11.008 fatcat:ynw5xltnvndghbajgpmhnjpmhy

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M. Prentice, Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks, Justina Biele, Jiarui Ding (+9 others)
2014 Genome Research  
Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key  ...  We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient.  ...  of TITAN predictions using single-cell sequencing confirm the presence of multiple tumor populations We further validated the CNA predictions from DG1136g using single-cell sequencing of targeted positions  ... 
doi:10.1101/gr.180281.114 pmid:25060187 pmcid:PMC4216928 fatcat:77ddt6of3vbqrizara7ckukc6e

Sensitivity to sequencing depth in single-cell cancer genomics

João M. Alves, David Posada
2018 Genome Medicine  
structural and driver mutations, genotyping accuracy, clonal inference 10 and phylogenetic reconstruction, using recent tools specifically designed for 11 single-cell data. 12 Results: Altogether, our  ...  of clonal genotypes or 15 the estimation of phylogenies from single tumor cells. 16 Conclusions: We demonstrate that sequencing many individual tumor cells at a 17 modest depth represents an effective  ...  OncoNEM: inferring tumor evolution from single-cell 418 sequencing data. Genome Biol. 2016;17: 69. 419 25. Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.  ... 
doi:10.1186/s13073-018-0537-2 pmid:29661213 pmcid:PMC5901877 fatcat:paq4ckb67ngtfgsk7oqzcmkctm

Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

Xinping Fan, Guanghao Luo, Yu S. Huang
2021 BMC Bioinformatics  
Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task.  ...  Conclusions We describe Accucopy, a method that can predict both TCNs and ASCNs from low-coverage low-purity tumor sequencing data.  ...  infer CNAs from these tumor sequencing data [6] [7] [8] [9] [10] but few automated and efficient methods exist to infer CNAs by shallow-sequencing low-purity tumor samples.  ... 
doi:10.1186/s12859-020-03924-5 pmid:33451280 fatcat:qle7ra6tejgzhdnxsjsftb7xpq

Current Progresses of Single Cell DNA Sequencing in Breast Cancer Research

Jianlin Liu, Ragini Adhav, Xiaoling Xu
2017 International Journal of Biological Sciences  
Clonal evolution theory recapitulates that a tumor initially arises from a single cell, which then undergoes clonal expansion to a population of cancer cells.  ...  In recent years, single cell sequencing (SCS) technology developed rapidly, providing a powerful new way to better understand the heterogeneity, which may lay foundations to some new strategies for breast  ...  using single nucleus sequencing with low coverage (~6%), revealing three different subclones that might represent sequential clonal expansion.  ... 
doi:10.7150/ijbs.19627 pmid:28924377 pmcid:PMC5599901 fatcat:67yz3qyb2jc37gwitlxshltwq4

Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data

Leila Baghaarabani, Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Seyed Peyman Shariatpanahi, Bahram Goliaei
2021 BMC Bioinformatics  
Result In this study, a new method called Conifer (ClONal tree Inference For hEterogeneity of tumoR) is proposed which combines aggregated variant allele frequency from bulk sequencing data with branching  ...  However, the temporal order of mutations may be determined with ambiguities using only single-cell data, while variant allele frequencies from bulk sequencing data can provide beneficial information for  ...  B-SCITE [21] is the first computational approach that infers tumor phylogeny from combined single-cell and bulk sequencing data.  ... 
doi:10.1186/s12859-021-04338-7 pmid:34461827 fatcat:hgrod6swxvggfftjjj6iedvh6q

Sensitivity to sequencing depth in single-cell cancer genomics [article]

Joao M. Alves, David Posada
2017 bioRxiv   pre-print
structural and driver mutations, genotyping accuracy, clonal inference and phylogenetic reconstruction, using recent tools specifically designed for single-cell data.  ...  of clonal genotypes or the estimation of phylogenies from single tumor cells.  ...  OncoNEM: inferring tumor evolution from single-cell 418 sequencing data. Genome Biol. 2016;17: 69. 419 25. Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.  ... 
doi:10.1101/213744 fatcat:5jibl2rejrh3npwsrq6eqgyfbe

Advances for studying clonal evolution in cancer

Li Ding, Benjamin J. Raphael, Feng Chen, Michael C. Wendl
2013 Cancer Letters  
New methodological advancements, including deep digital sequencing of a mixed tumor population, single cell sequencing, and the development of more sophisticated computational tools, will continue to shape  ...  Recent studies have also shown that clonal evolution is highly heterogeneous: different individual tumors of the same type may undergo very different paths of clonal evolution.  ...  Acknowledgments The authors are supported by grants from the NIH (U01HG006517, U54HG003079, R01HG005690, R01DK081592, and R01DK087960).  ... 
doi:10.1016/j.canlet.2012.12.028 pmid:23353056 pmcid:PMC3783624 fatcat:u3723hwp4bayrf3njn4rp57piu

Parameter, noise, and tree topology effects in tumor phylogeny inference

Kiran Tomlinson, Layla Oesper
2019 BMC Medical Genomics  
While a number of methods have been proposed to reconstruct the evolutionary history of a tumor from DNA sequencing data, it is not clear how aspects of the sequencing data and tumor itself affect these  ...  Accurate inference of the evolutionary history of a tumor has important implications for understanding and potentially treating the disease.  ...  Many recent computational methods have been developed to infer tumor phylogenetic trees using multi-sample bulk sequencing data.  ... 
doi:10.1186/s12920-019-0626-0 pmid:31865909 pmcid:PMC6927103 fatcat:p5nomzes5jdwhkvr3b5tiawq34

Inferring Clonal Composition from Multiple Sections of a Breast Cancer

Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie Nickerson, ChaoZhong Song, Daniela Witten, C. Anthony Blau, William Stafford Noble, Amos Tanay
2014 PLoS Computational Biology  
Mutation counts and frequencies resulting from next-generation sequencing (NGS) potentially reflect a tumor's clonal composition; however, deconvolving NGS data to infer a tumor's clonal structure presents  ...  We propose a generative model for NGS data derived from multiple subsections of a single tumor, and we describe an expectation-maximization procedure for estimating the clonal genotypes and relative frequencies  ...  We collect, from several physical subsections of the tumor, shotgun sequencing reads. We also collect sequencing data from a non-tumor subsection from the same patient.  ... 
doi:10.1371/journal.pcbi.1003703 pmid:25010360 pmcid:PMC4091710 fatcat:c76nicayvnfsviybege3yxy2i4

Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing

Andrew E. O. Hughes, Vincent Magrini, Ryan Demeter, Christopher A. Miller, Robert Fulton, Lucinda L. Fulton, William C. Eades, Kevin Elliott, Sharon Heath, Peter Westervelt, Li Ding, Donald F. Conrad (+10 others)
2014 PLoS Genetics  
Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples.  ...  cells from three subjects diagnosed with secondary acute myeloid leukemia, each of whom had been previously characterized by whole genome sequencing of unfractionated tumor samples.  ...  In addition to multi-sampling strategies, we and others have reported clonal inference from deep sequencing of individual tumor samples [1, [13] [14] [15] .  ... 
doi:10.1371/journal.pgen.1004462 pmid:25010716 pmcid:PMC4091781 fatcat:xodczvuzrjhy5met3tu6yzycdq

Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST

Subhayan Chattopadhyay, Jenny Karlsson, Anders Valind, Natalie Andersson, David Gisselsson
2021 Briefings in Bioinformatics  
Using published and simulated tumor sequences, we reliably segregated clonal/subclonal variants even at a low sequencing depth (~50×).  ...  Absent à priori copy number data, it renders in silico copy number estimations from bulk sequences.  ...  A special thanks to Chris Miller and Malachi Griffith for their assistance in procuring data from community resources (dbGaP: phs000159).  ... 
doi:10.1093/bib/bbab292 pmid:34343239 pmcid:PMC8981300 fatcat:vgjspskpu5aj3and6dr4ynsboe

Characterizing the allele- and haplotype-specific copy number landscape of cancer genomes at single-cell resolution with CHISEL [article]

Simone Zaccaria, Benjamin J. Raphael
2019 bioRxiv   pre-print
These technologies provide the opportunity to characterize genomic heterogeneity at single-cell resolution, but their extremely low sequencing coverage (<0.05X per cell) has thus far restricted their use  ...  We applied CHISEL to 10 single-cell sequencing datasets from 2 breast cancer patients, each dataset containing ~2000 cells.  ...  Acknowledgments We thank Lance Hepler and Karthik Ganapathy from 10X Genomics for providing additional data for our study, for providing access to the published data of the total copy number analysis,  ... 
doi:10.1101/837195 fatcat:rrsb2qplvnb4tjlonct3dol5gy

Intratumor Heterogeneity: Novel Approaches for Resolving Genomic Architecture and Clonal Evolution

Ravi G. Gupta, Robert A. Somer
2017 Molecular Cancer Research  
This review focuses on novel approaches to mitigate these challenges using bulk tumor, liquid biopsies, single-cell analysis, and deep sequencing techniques.  ...  and clonal selection.  ...  Recurrent mutaƟons A C T A C T G A C T A C T G Inferring Clonal Evolution from Deep Sequencing Data As the sampling depth of sequencing techniques increases, so too will the multiplicity of genomic changes  ... 
doi:10.1158/1541-7786.mcr-17-0070 pmid:28596419 fatcat:nyfrmxfskzfj7pdhwjufjdmpdm
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