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Supplementary Table 2 from Cell Lineage Analysis of a Mouse Tumor

Supplementary Text 1 from Cell Lineage Analysis of a Mouse Tumor

Supplementary Figure 1 from Cell Lineage Analysis of a Mouse Tumor

Supplementary Text 3 from Cell Lineage Analysis of a Mouse Tumor

Supplementary Text 4 from Cell Lineage Analysis of a Mouse Tumor

Supplementary Text 5 from Cell Lineage Analysis of a Mouse Tumor

Revealing the lineage relations among cancer cells can shed light on tumor growth patterns and metastasis formation, yet cell lineages have been difficult to come by in the absence of a suitable method. We previously developed a method for reconstructing cell lineage trees from genomic variability caused by somatic mutations. Here, we apply the method to cancer and reconstruct, for the first time, a lineage tree of neoplastic and adjacent normal cells obtained by laser microdissection from tissue sections of a mouse lymphoma. Analysis of the reconstructed tree reveals that the tumor initiated from a single founder cell, ∼5 months before diagnosis, that the tumor grew in a physically coherent manner, and that the average number of cell divisions accumulated in cancerous cells was almost twice than in adjacent normal lung epithelial cells but slightly less than the expected figure for normal B lymphocytes. The cells were also genotyped at the TP53 locus, and neoplastic cells were found to share a common mutation, which was most likely present in a heterozygous state. Our work shows that the ability to obtain data regarding the physical appearance, precise anatomic position, genotypic profile, and lineage position of single cells may be useful for investigating cancer development, progression, and interaction with the microenvironment. [Cancer Res 2008;68(14):5924–31]

Summary Short tandem repeats (STRs) are highly abundant in the human genome, but existing approaches for accurate genotyping of STRs are limited. Here, we describe a protocol for duplex molecular inversion probes for high-throughput and cost-effective STR enrichment. We have successfully tested panels targeting as many as 50K STRs in several thousands of genomic samples (e.g., HeLa cells, Du145 cells, leukemia cells, melanoma cells). However, because the protocol is plate based, the sample size is limited to a few thousand. For complete details on the use and execution of this protocol, please refer to Tao et al. (2021)., Graphical abstract, Highlights • This protocol enable us to enrich tens of thousands of STR from single-cell WGA • The protocol can easily deployed in any labs with generic equipment • The highly mutable STR panel is generic across human samples • The panels are highly customizable to include SNV targets like cancer hotspots and flexible from dozens of targets to over 50K targets; probes for different panels can be combined in one reaction, Short tandem repeats (STRs) are highly abundant in the human genome, but existing approaches for accurate genotyping of STRs are limited. Here, we describe a protocol for duplex molecular inversion probes for high-throughput and cost-effective STR enrichment. We have successfully tested panels targeting as many as 50K STRs in several thousands of genomic samples (e.g., HeLa cells, Du145 cells, leukemia cells, melanoma cells). However, because the protocol is plate based, the sample size is limited to a few thousand.

Advances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the needfor a dedicated kit selection depending on the desired single cell assay.

Consider n agents forming an egalitarian, self-governed community. Their first task is to decide on a decision rule to make further decisions. We start from a rather general initial agreement on the decision-making process based upon a set of intuitive and self-evident axioms, as well as simplifying assumptions about the preferences of the agents. From these humble beginnings we derive a decision rule. Crucially, the decision rule also specifies how it can be changed, or amended, and thus acts as a de facto constitution. Our main contribution is in providing an example of an initial agreement that is simple and intuitive, and a constitution that logically follows from it. The naive agreement is on the basic process of decision making – that agents approve or disapprove proposals; that their vote determines either the acceptance or rejection of each proposal; and on the axioms, which are requirements regarding a constitution that engenders a self-updating decision making process.