Circulating tumor DNA sequencing provides comprehensive mutation profiling for pediatric central nervous system tumors.

Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to the sensitive tumor location. We developed a targeted deep sequencing platform to detect tumor driver mutations, copy number variations, and heterogeneity in the liquid biome. Here, we present the sensitivity, specificity, and clinical relevance of our minimally invasive platform for tumor mutation profiling in children diagnosed with CNS cancer.

Use of Biosynthetic Controls as Performance Standards for Next-Generation Sequencing Assays of Somatic Tumors: A Multilaboratory Study.

BACKGROUND: Next-generation sequencing (NGS) assays are highly complex tests that can vary substantially in both their design and intended application. Despite their innumerous advantages, NGS assays present some unique challenges associated with the preanalytical process, library preparation, data analysis, and reporting. According to a number of professional laboratory organization, control materials should be included both during the analytical validation phase and in routine clinical use to guarantee highly accurate results. The SeraseqTM Solid Tumor Mutation Mix AF10 and AF20 control materials consist of 26 biosynthetic DNA constructs in a genomic DNA background, each containing a specific variant or mutation of interest and an internal quality marker at 2 distinct allelic frequencies of 10% and 20%, respectively. The goal of this interlaboratory study was to evaluate the Seraseq AF10 and AF20 control materials by verifying their performance as control materials and by evaluating their ability to measure quality metrics essential to a clinical test. METHODS: Performance characteristics were assessed within and between 6 CLIA-accredited laboratories and 1 research laboratory. RESULTS: Most laboratories detected all 26 mutations of interest; however, some discrepancies involving the internal quality markers were observed. CONCLUSION: This interlaboratory study showed that the Seraseq AF10 and AF20 control materials have high quality, stability, and genomic complexity in variant types that are well suited for assisting in NGS assay analytical validation and monitoring routine clinical applications.

Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial: Molecular Analysis for Therapy Choice Clinical Trial.

The National Cancer Institute-Molecular Analysis for Therapy Choice (NCI-MATCH) trial is a national signal-finding precision medicine study that relies on genomic assays to screen and enroll patients with relapsed or refractory cancer after standard treatments. We report the analytical validation processes for the next-generation sequencing (NGS) assay that was tailored for regulatory compliant use in the trial. The Oncomine Cancer Panel assay and the Personal Genome Machine were used in four networked laboratories accredited for the Clinical Laboratory Improvement Amendments. Using formalin-fixed paraffin-embedded clinical specimens and cell lines, we found that the assay achieved overall sensitivity of 96.98% for 265 known mutations and 99.99% specificity. High reproducibility in detecting all reportable variants was observed, with a 99.99% mean interoperator pairwise concordance across the four laboratories. The limit of detection for each variant type was 2.8% for single-nucleotide variants, 10.5% for insertion/deletions, 6.8% for large insertion/deletions (gap ≥4 bp), and four copies for gene amplification. The assay system from biopsy collection through reporting was tested and found to be fully fit for purpose. Our results indicate that the NCI-MATCH NGS assay met the criteria for the intended clinical use and that high reproducibility of a complex NGS assay is achievable across multiple clinical laboratories. Our validation approaches can serve as a template for development and validation of other NGS assays for precision medicine.

Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods.

The National Institute of Standards and Technology (NIST) Standard Reference Materials 2373 is a set of genomic DNA samples prepared from five breast cancer cell lines with certified values for the ratio of the HER2 gene copy number to the copy numbers of reference genes determined by real-time quantitative PCR and digital PCR. Targeted-amplicon, whole-exome, and whole-genome sequencing measurements were used with the reference material to compare the performance of both the laboratory steps and the bioinformatic approaches of the different methods using a range of amplification ratios. Although good reproducibility was observed in each next-generation sequencing method, slightly different HER2 copy numbers associated with platform-specific biases were obtained. This study clearly demonstrates the value of Standard Reference Materials 2373 as reference material and as a calibrator for evaluating assay performance as well as for increasing confidence in reporting HER2 amplification for clinical applications.

Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays.

Although next-generation sequencing technologies have been widely adapted for clinical diagnostic applications, an urgent need exists for multianalyte calibrator materials and controls to evaluate the performance of these assays. Control materials will also play a major role in the assessment, development, and selection of appropriate alignment and variant calling pipelines. We report an approach to provide effective multianalyte controls for next-generation sequencing assays, referred to as the control plasmid spiked-in genome (CPSG). Control plasmids that contain approximately 1000 bases of human genomic sequence with a specific mutation of interest positioned near the middle of the insert and a nearby 6-bp molecular barcode were synthesized, linearized, quantitated, and spiked into genomic DNA derived from formalin-fixed, paraffin-embedded-prepared hapmap cell lines at defined copy number ratios. Serial titration experiments demonstrated the CPSGs performed with similar efficiency of variant detection as formalin-fixed, paraffin-embedded cell line genomic DNA. Repetitive analyses of one lot of CPSGs 90 times during 18 months revealed that the reagents were stable with consistent detection of each of the plasmids at similar variant allele frequencies. CPSGs are designed to work across most next-generation sequencing methods, platforms, and data analysis pipelines. CPSGs are robust controls and can be used to evaluate the performance of different next-generation sequencing diagnostic assays, assess data analysis pipelines, and ensure robust assay performance metrics.

Analytical Validation and Application of a Targeted Next-Generation Sequencing Mutation-Detection Assay for Use in Treatment Assignment in the NCI-MPACT Trial.

Robust and analytically validated assays are essential for clinical studies. We outline an analytical validation study of a targeted next-generation sequencing mutation-detection assay used for patient selection in the National Cancer Institute Molecular Profiling-Based Assignment of Cancer Therapy (NCI-MPACT) trial (NCT01827384). Using DNA samples from normal or tumor cell lines and xenografts with known variants, we assessed the sensitivity, specificity, and reproducibility of the NCI-MPACT assay in five variant types: single-nucleotide variants (SNVs), SNVs at homopolymeric (HP) regions (≥3 identical bases), small insertions/deletions (indels), large indels (gap ≥4 bp), and indels at HP regions. The assay achieved sensitivities of 100% for 64 SNVs, nine SNVs at HP regions, and 11 large indels, 83.33% for six indels, and 93.33% for 15 indels at HP regions. Zero false positives (100% specificity) were found in 380 actionable mutation loci in 96 runs of haplotype map cells. Reproducibility analysis showed 96.3% to 100% intraoperator and 98.1% to 100% interoperator mean concordance in detected variants and 100% reproducibility in treatment selection. To date, 38 tumors have been screened, 34 passed preanalytical quality control, and 18 had actionable mutations for treatment assignment. The NCI-MPACT assay is well suited for its intended investigational use and can serve as a template for developing next-generation sequencing assays for other cancer clinical trial applications.

Ecophysiology of exotic and native shrubs in Southern Wisconsin : I. Relationship of leaf characteristics, resource availability, and phenology to seasonal patterns of carbon gain.

We compared seasonal trends in photosynthesis of two naturalized exotic shrubs (Rhamnus cathartica and Lonicera X bella) and two native shrubs (Cornus racemosa and Prunus serotina) in open and understory habitats in southern Wisconsin. We examined the relationships between resource availability and leaf photosynthetic performance in these four species. All four species had similar relationships between leaf nitrogen (N) content and photosynthetic rate, but the species differed in absolute leaf N content and therefore in photosynthetic rates. Maximum daily photosynthetic rates of all species were significantly correlated with leaf N content in the open habitat, but not in the understory, where low light availability was the major limitation to photosynthesis. Extended leaf longevity was important in the forest understory because it allowed shrubs to take advantage of high light availability at times when the overstory canopy was leafless. Early leaf emergence was more important than late senescence: from 27% to 35% of the annual carbon gain of P. serotina, R. cathartica, and L. X bella occurred prior to leaf emergence of C. racemosa, the species with the shortest leaf life span. Extended leaf longevity of exotic shrubs may help explain their persistence in the understory habitat, but it contributed relatively less to their annual carbon gain in the open habitat.

Forest growth along a rainfall gradient in Hawaii: Acacia koa stand structure, productivity, foliar nutrients, and water- and nutrient-use efficiencies.

We tested whether variation in growth of native koa (Acacia koa) forest along a rainfall gradient was attributable to differences in leaf area index (LAI) or to differences in physiological performance per unit of leaf area. Koa stands were studied on western Kauai prior to Hurricane Iniki, and ranged from 500 to 1130 m elevation and from 850 to 1800 mm annual precipitation. Koa stands along the gradient had basal area ranging from 8 to 42 m2/ha, LAI ranging from 1.4 to 5.4, and wood increment ranging from 0.7 to 7.1 tonnes/ha/year. N, P, and K contents by weight of sun leaves (phyllodes) were negatively correlated with specific leaf mass (SLM, g m-2) across sites; on a leaf area basis, N increased whereas P and K decreased with SLM. LAI, aboveground woody biomass increment, and production per unit leaf area (E) increased as phyllode δ13C became more negative. The δ13C data suggested that intrinsic water-use efficiency (ratio of assimilation to conductance) increased as water availability decreased. In five of the six sites, phyllode P contents increased as LAI increased, but biomass increment and E were not correlated with phyllode nutrient contents, suggesting that productivity was limited more by water than by nutrient availability. Because vapor pressure deficits increased with decreasing elevation, actual water-use efficiency (ratio of assimilation to transpiration) was lower at drier, low-elevation sites. There was a trade-off between intrinsic water-use efficiency and production per unit of canopy N or P across the gradient. In summary, koa responds to water limitation both by reducing stand LAI and by adjusting gas exchange, which results in increased intrinsic water-use efficiency but decreased E.

Ecophysiology of exotic and native shrubs in Southern Wisconsin : II. Annual growth and carbon gain.

In this study we compared the aboveground growth rates of two exotic shrubs (Rhamnus cathartica and Lonicera X bella) and two native shrubs (Cornus racemosa and Prunus serotina) that are important in southern Wisconsin hardwood forests. For all species except P. serotina, aboveground growth rates in an open habitat were greater than in an understory environment. Growth rates differed among species in the open habitat and were significantly correlated with woody production per unit leaf area. All species had greater leaf area per unit wood biomass in the understory than in the open habitat. A comparison of above-ground growth and annual carbon gain suggests much greater respiratory costs in the open habitat, especially for P. serotina. The data from this study were used to examine mechanisms of species response to different light availabilities. We found that the species that increased their production per unit leaf area in response to increased light did not increase their leaf area per unit wood biomass in response to low light, and vice versa. Production of proportionately high leaf area may be important for the growth of C. racemosa in low light.

Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.

The Bacillus anthracis Carbosap genome, which includes the pXO1 and pXO2 plasmids, has been shown to encode the major B. anthracis virulence factors, yet this strain's attenuation has not yet been explained. Here we report the draft genome sequence of this strain, and a comparison to fully virulent B. anthracis.

Lentivirus-mediated gene transfer to human epidermis.

For long-term cutaneous gene therapy, the therapeutic gene must be targeted to stem cells and be stably transmitted to and expressed in descendant cells. Retroviral vectors are highly efficient in gene transfer to human keratinocyte stem cells in culture; however, they cannot transduce quiescent stem cells in vivo. As lentiviral vectors (LVV) transduce non-proliferating cells, their ability to target human epidermal stem cells was evaluated. LVV were highly efficient in gene transfer to clonogenic keratinocytes in vitro. Despite higher transgene DNA content and comparable levels of transgene mRNA, levels of transgene product directed by lentivectors were 3-folds lower than that of retrovectors. When transduced keratinocytes were grafted onto mice, transgene expression persisted for at least 20 wk; however, transgene product was detected primarily in the uppermost layers of epidermis. Inclusion of an element that is known to facilitate nuclear export of intron-less transcripts, resulted in enhanced transgene expression in keratinocytes. In vivo transduction of xenografted human skin with these vectors resulted in efficient gene transfer to epidermal progenitor cells. These results demonstrate stem cell transduction by LVV and point out the utility of using these vectors for direct gene transfer to and sustained expression in human epidermis.