Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project

BACKGROUND

Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications.

MATERIALS AND METHODS

Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values.

RESULTS

Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples.

CONCLUSIONS

Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.

Plant growth regulator-mediated anti-herbivore responses of cabbage (Brassica oleracea) against cabbage looper Trichoplusia ni Hübner (Lepidoptera: Noctuidae)

Plant elicitors can be biological or chemical-derived stimulators of jasmonic acid (JA) or salicylic acid (SA) pathways shown to prime the defenses in many crops. Examples of chemical elicitors of the JA and SA pathways include methyl-jasmonate and 1,2,3-benzothiadiazole-7-carbothioate (BTH or the commercial plant activator Actigard 50WG, respectively). The use of specific elicitors has been observed to affect the normal interaction between JA and SA pathways causing one to be upregulated and the other to be suppressed, often, but not always, at the expense of the plant's herbivore or pathogen defenses. The objective of this study was to determine whether insects feeding on Brassica crops might be negatively affected by SA inducible defenses combined with an inhibitor of detoxification and anti-oxidant enzymes that regulate the insect response to the plant's defenses. The relative growth rate of cabbage looper Trichoplusia ni Hübner (Lepidoptera: Noctuidae) fed induced cabbage Brassica oleraceae leaves with the inhibitor, quercetin, was significantly less than those fed control cabbage with and without the inhibitor. The reduced growth was related to the reduction of glutathione S-transferases (GSTs) by the combination of quercetin and increased levels of indole glucosinolates in the cabbage treated with BTH at 2.6× the recommended application rate. These findings may offer a novel combination of elicitor and synergist that can provide protection from plant disease and herbivores in cabbage and other Brassica crops.

Carcinoembryonic antigen promotes tumor cell survival in liver through an IL-10-dependent pathway

Most circulating tumor cells die within 24 h of entering the hepatic microvasculature because their arrest initiates an ischemia-reperfusion (I/R) injury that is cytotoxic. Human colorectal carcinomas (CRC) produce the glycoprotein Carcinoembryonic Antigen (CEA) that increases experimental liver metastasis in nude mice. Since CEA induces release of IL-6 and IL-10, we hypothesized that CEA inhibits the I/R injury through a Kupffer cell-mediated cytokine-dependent pathway. We assessed cytokine effects in CRC co-cultured with liver and in vivo. Human CRC prelabeled with fluorescent dyes were incubated with a reoxygenated suspension of ischemic nude mouse liver fragments in a bioreactor. CEA, rhIL-6 or rhIL-10 were either administered to the donor mice prior to hepatic ischemia or during co-culture. Liver donors were athymic nude or iNOS, IL-6 or IL-10 knock out mice. Ischemic-reoxygenated liver kills Clone A CRC through production of nitric oxide (NO) and superoxide anion. Treatment of liver donors with CEA prior to hepatic ischemia inhibited this in vitro cytotoxicity through an IL-10 and Kupffer cell dependent pathway that inhibited NF-kappaB activation, NO production and iNOS upregulation. IL-10 but not IL-6 enhanced CRC survival in nude mouse liver in vivo. Thus, CEA enhanced metastasis by inducing IL-10 to inhibit iNOS upregulation in host liver.

Palatal discrepancies and postdams

To investigate the variation in post-cure palatal discrepancy of dentures, 20 complete maxillary replica dentures were prepared on models with high and low palates and processed by conventional compression moulding and injection moulding. Measurements were made by travelling microscope of the sagittal midline discrepancies between palate and model on three occasions; after processing; after removal of part of the investing plaster; and after immersion in water for 1 month at 37 degrees C. The magnitudes of discrepancies were greatest distally, diminishing with distance anteriorly from the postdam. They increased with partial removal of plaster, and decreased slightly after immersion.

Poly(ADP-ribosyl)ation of p53 in vitro and in vivo modulates binding to its DNA consensus sequence

The tumor-suppressor p53 undergoes extensive poly(ADP-ribosyl)ation early during apoptosis in human osteosarcoma cells, and degradation of poly(ADP-ribose) (PAR) attached to p53 coincides with poly(ADP-ribose)polymerase-1, (PARP-1) cleavage, and expression of p53 target genes. The mechanism by which poly(ADP-ribosyl)ation may regulate p53 function has now been investigated. Purified wild-type PARP-1 catalyzed the poly(ADP-ribosyl) of full-length p53 in vitro. In gel supershift assays, poly(ADP-ribosyl)ation suppressed p53 binding to its DNA consensus sequence; however, when p53 remained unmodified in the presence of inactive mutant PARP-1, it retained sequence-specific DNA binding activity. Poly(ADP-ribosyl)ation of p53 by PARP-1 during early apoptosis in osteosarcoma cells also inhibited p53 interaction with its DNA consensus sequence; thus, poly(ADP-ribosyl)ation may represent a novel means for regulating transcriptional activation by p53 in vivo.

Progressive multifocal leukoencephalopathy in a patient with hypogammaglobulinemia

We describe a child with congenital hypogammaglobulinemia that was diagnosed at 13 months of age. When he was 4 years old, gait disturbances began. The main neurological manifestations were progressive spastic tetraparesis and intellectual and speech deterioration. No infectious agent was identified. A magnetic resonance imaging scan of the central nervous system revealed periventricular demyelinating areas in the frontal, temporal, and parietal lobes with cortical atrophy. Stereotactic brain biopsy confirmed the diagnosis of progressive multifocal leukoencephalopathy caused by JC virus. He was treated with intravenous and intraventricular cytarabine and interferon-alpha, and there was clinical improvement. We emphasize the need for brain biopsy as soon as a neurological complication is suspected in patients with congenital hypogammaglobulinemia for whom cerebrospinal cultures or polymerase chain reaction analyses are negative.

Impact of publicly funded contraceptive services on unintended pregnancies and implications for Medicaid expenditures

Of U.S. women who use a reversible method of contraception, 24% each year obtain family planning services from a publicly funded clinic or a private doctor reimbursed by Medicaid. If these subsidized contraceptive services were not available, women who currently use them would have an estimated 1.3 million additional unplanned pregnancies annually, of which 29% would involve women aged 15-19, 67% would involve never-married women and 61% would involve women with a household income below 200% of the federal poverty level. An estimated 632,300 of these pregnancies would end in induced abortion, an increase of 40% over the current national level. Another 533,800 pregnancies would result in unintended births. Some 76,400 of these would be births to families already receiving public assistance, and 64,100 would be to families that would become eligible for public assistance because of the birth; another 197,000 would be to women whose families would not receive public assistance, but would be eligible for Medicaid coverage of pregnancy, delivery and newborn care. In FY 1987, public-sector expenditures for contraceptive services totaled an estimated $412 million. If subsidized services had not been available, the federal and state governments would have spent an additional $1.2 billion through their Medicaid programs for expenses associated with unplanned births and abortions. Thus, for every dollar spent to provide publicly funded contraceptive services, an average of $3.00 was saved in Medical costs for pregnancy-related health care and medical care for newborns.

Using parity-progression ratios to estimate the effect of female sterilization on fertility

In this article, a new methodology that employs parity-progression ratios to estimate the effect of female sterilization on fertility is described, and results using data from Ecuador are compared to those obtained using a previously existing approach that classifies women by marital duration. The methods differ in how they disaggregate marital fertility and in the assumption they make about what the subsequent fertility of sterilized women would have been if they had not been sterilized. The analysis of the Ecuadoran data shows that the estimate of births averted by sterilization has diminished over time, even as sterilization prevalence has been increasing. This situation is attributed to a decline in the fertility of nonsterilized women resulting from increased use of reversible methods of contraception.