Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

Evaluating the performance of fibrillar collagen films formed at polystyrene surfaces as cell culture substrates.

While it is well-appreciated that the extracellular matrix plays a critical role in influencing cell responses, well-defined and reproducible presentation of extracellular matrix proteins poses a challenge for in vitro experiments. Films of type 1 collagen fibrils assembled on alkanethiolate monolayers formed at gold-coated surfaces have been shown to elicit a cellular response comparable to collagen gels, but with the advantages of excellent optical properties, and high reproducibility and robustness. To make this collagen matrix more accessible to laboratories that do not have access to gold film deposition the authors have examined the use of untreated polystyrene as a substrate for forming fibrillar collagen films. Direct comparison of films of fibrillar collagen fibrils formed at polystyrene with those formed at alkanethiolate monolayers indicates that films of collagen formed on these two surfaces compare very favorably to one another, both in their supramolecular structural characteristics as well as in the cell response that they elicit. Both substrates exhibit a dense covering of fibrils approximately 200 nm in diameter. The spreading of fibroblasts and activation of the tenascin-C gene promoter are statistically equivalent as determined by a metric derived from the D-statistic normally used in the Kolmogorov-Smirnov statistical test. The results of this study suggest that biologically relevant, robust thin films of collagen fibrils can be formed in any laboratory in untreated polystyrene dishes and multi-well polystyrene plates.

Tools for quantitative and validated measurements of cells.

In this chapter, we describe the preparation of thin films of collagen that can serve as reference materials for assuring reproducible and predictable cell responses. Subtle differences in the molecular-scale characteristics of extracellular matrix proteins, including the supramolecular structure of type 1 collagen, can have tremendous influences on cell state and cell-signaling pathways; therefore the careful control and analysis of the culture surface is critical to assure a relevant and consistent response in cell-based assays. We also describe how cell-phenotypic parameters such as morphology, proliferation, and green fluorescent protein expression can be unambiguously quantified in adherent cells by automated fluorescence microscopy or high content screening. Careful consideration of protocols, and the use of fluorescent reference materials, are essential to assure day-to-day and instrument-to-instrument interoperability. The ability to collect quantitative data on large numbers of cells in homogeneous matrix environments allows assessment of the range of phenotypes that are reproducibly expressed in clonal cell populations. The inherent distribution of responses in a cell population will determine how many cells must be measured to reach an accurate determination of cellular response.

Gradient substrate assembly for quantifying cellular response to biomaterials.

Using quantitative fluorescence microscopy in conjunction with a method of gradient substrate assembly established in their group, the authors were able to introduce and measure reproducible changes in cellular morphology and cell density by manipulating polymer grafting density. The mechanism behind this change in cellular behavior was explained by a semiempirical, geometric model that describes the effect of the spatial distribution of the polymer on protein attachment. A 10-fold increase in graft density of poly(2-hydroxyethyl methacrylate) [PHEMA] along the surface of a gradient sample, preexposed to bovine fibronectin, caused a change in the size of fibroblasts on the surface (i.e., cell spreading) from (1238 +/- 704) to (377 +/- 216) microm(2). The results were in quantitative agreement with those obtained on three separate gradient samples. Both cellular response and fibronectin adsorption (as measured via ellipsometry) were found to vary sigmoidally with graft density of PHEMA, demonstrating the high degree of correlation between the two phenomena. A simple, rigid-disk model accounting for the surface coverage of PHEMA was able to predict the amount of adsorbed fibronectin with a correlation coefficient of 0.97. Maximal cell adhesion and cell spreading were found to occur at fibronectin surface densities of 50 and 100 ng/cm(2), respectively. The results demonstrate the role of gradient substrate assembly as a method for quantifying the relationship between protein and cellular response to technologically relevant polymeric materials.

Thin films of Type 1 collagen for cell by cell analysis of morphology and tenascin-C promoter activity.

BACKGROUND: The use of highly reproducible and spatiallyhomogeneous thin film matrices permits automated microscopy and quantitative determination of the response of hundreds of cells in a population. Using thin films of extracellular matrix proteins, we have quantified, on a cell-by-cell basis, phenotypic parameters of cells on different extracellular matrices. We have quantitatively examined the relationship between fibroblast morphology and activation of the promoter for the extracellular matrix protein tenascin-C using a tenascin-C promoter-based GFP reporter construct. RESULTS: We find that when considering the average response from the population of cells, cell area correlates with tenascin-C promoter activity as has been previously suggested; however cell-by-cell analysis suggests that cell area and promoter activity are not tightly correlated within individual cells. CONCLUSION: This study demonstrates how quantitative cell-by-cell analysis, facilitated by the use of thin films of extracellular matrix proteins, can provide insight into the relationship between phenotypic parameters.

Tuning cell adhesion on gradient poly(2-hydroxyethyl methacrylate)-grafted surfaces.

A simple yet versatile method was developed to prepare a low-density polymerization initiator gradient, which was combined with surface-initiated atom transfer radical polymerization (ATRP) to produce a well-defined poly(2-hydroxyethyl methacrylate) (HEMA) gradient substrate. A smooth variation in film thickness was measured across the gradient, ranging from 20 A to over 80 A, but we observed a nonmonotonic variation in water contact angle. Fits of X-ray reflectivity profiles suggested that at the low graft density end, the polymer chain structure was in a "mushroom" regime, while the polymer chains at high graft density were in a "brush" regime. It was found that the "mushroom" region of the gradient could be made adhesive to cells by adsorbing adhesion proteins, and cell adhesion could be tuned by controlling the density of the polymer grafts. Fibroblasts were seeded on gradients precoated with fibronectin to test cellular responses to this novel substrate, but it was found that cell adhesion did not follow the expected trend; instead, saturated cell adhesion and spreading was found at the low grafting density region.

Vascular smooth muscle cell response on thin films of collagen.

Vascular smooth muscle cells (vSMC) cultured on gels of fibrillar type I collagen or denatured collagen (gelatin) comprise a model system that has been widely used for studying the role of the extracellular matrix in vascular diseases such as hypertension, restenosis and athrosclerosis. Despite the wide use of this model system, there are several disadvantages to using collagen gels for cellular studies. These include poor optical characteristics for microscopy, difficulty in verifying that the properties of the preparations are identical from experiment to experiment, heterogeneity within the gels, and difficulty in handling the gels because they are fragile. Previously, we developed an alternative collagen matrix by forming thin films of native fibrillar collagen or denatured collagen on self-assembled monolayers of alkanethiols [Elliott, J.T., Tona, A., Woodward, J., Jones,P., Plant, A., 2003a. Thin films of collagen affect smooth muscle cell morphology. Langmuir 19, 1506-1514.]. These substrates are robust and can be characterized by surface analytical techniques that allow both verification of the reproducibility of the preparation and high-resolution analysis of collagen structure. In addition, they have excellent optical properties that allow more details of the cell-matrix interactions to be observed by microscopy. In this study, we performed a side-by-side structural and functional comparison of collagen gels with thin films of collagen. Our results indicate that vSMC on thin films of collagen are nearly identical to vSMC on thick gels as determined by morphology, proliferation rate, integrin ligation, tenascin-C expression and intracellular signaling events. These results suggest that the features of collagen gels that direct the observed vSMC responses are adequately reconstituted in the thin films of collagen. These thin films will be useful for elucidating the features of the collagen matrix that regulate vSMC response and may be applicable to high content screening.