@article{7096f0356103481cae8c9ec0bacf265b,
title = "A biological-computational human cell lineage discovery platform based on duplex molecular inversion probes",
abstract = "Short Tandem Repeats (STRs) are highly mutable genomic elements composed of repetitive short motifs, widely distributed within the human genome, and as such are the most promising source for somatic genomic variations. We present an affordable and scalable cell lineage reconstruction platform that combines customizable duplex Molecular Inversion Probes (MIPs), high throughput targeted sequencing and tailored analysis, all integrated in a bioinformatics Database Management System (DBMS). By applying this platform to a benchmark of ex vivo lineage samples, we demonstrate efficient acquisition of tens of thousands of targets in single-cell whole-genome amplified DNA and the discovery of lineage relations among these cells with superior accuracy. We then reconstruct a cell lineage tree of healthy and metastatic cells from a melanoma patient, supporting the hypothesis of clonal metastases and demonstrating that a na{\"i}ve panel targeting STR somatic mutations in single cells can outperform a cancer specific SNP panel in reconstruction accuracy.",
author = "Liming Tao and Ofir Raz and Zipora Marx and Tamir Biezuner and Shiran Amir and Lilach Milo and Rivka Adar and Amos Onn and Noa Chapal-Ilani and Veronika Berman and Ron Levy and Barak Oron and Ruth Halaban and Ehud Shapiro",
note = "Liming Tao is partially supported by VATAT postdoctoral fellowship from Israel{\textquoteright}s Council for Higher Education Planning and Budgeting Committee. Ehud Shapiro is the incumbent of The Harry Weinrebe Professorial Chair of Computer Science and Biology. This research was supported by the following foundations: the European Union FP7-ERC-AdG (European Research Council, 233047); The EU-H2020-ERC-AdG (European Research Council, 670535); the Deutsche Forschungsgemeinschaft (DFG, 611042); the Israeli Science Foundation (ISF, P14587); the Israeli Science Foundation-BROAD (ISF, P15439); the National Institutes of Health (VUMC 38347); the National Cancer Institute Fund (P50 CA121974, R. Halaban, PI); and the Kenneth and Sally Leafman Appelbaum Discovery Fund.",
year = "2018",
month = mar,
day = "18",
doi = "https://doi.org/10.1101/191296",
language = "الإنجليزيّة",
}