Managing Pandora's Box: Familial Expectations around the Return of (Future) Germline Results

BACKGROUND

Pediatric oncology patients are increasingly being offered germline testing to diagnose underlying cancer predispositions. Meanwhile, as understanding of variant pathogenicity evolves, planned reanalysis of genomic results has been suggested. Little is known regarding the types of genomic information that parents and their adolescent children with cancer prefer to receive at the time of testing or their expectations around the future return of genomic results.

METHODS

Parents and adolescent children with cancer eligible for genomic testing for cancer predisposition were surveyed regarding their attitudes and expectations for receiving current and future germline results (ClinicalTrials.gov Identifier: NCT02530658).

RESULTS

All parents (100%) desired to learn about results for treatable or preventable conditions, with 92.4% wanting results even when there is no treatment or prevention. Parents expressed less interest in receiving uncertain results for themselves (88.3%) than for their children (95.3%). Most parents (95.9%) and adolescents (87.9%) believed that providers have a responsibility to share new or updated germline results indefinitely or at any point during follow-up care. Fewer parents (67.5%) indicated that they would want results if their child was deceased: 10.3% would not want to be contacted, 19.3% were uncertain.

CONCLUSIONS

Expectations for return of new or updated genomic results are high among pediatric oncology families, although up to one third of parents have reservations about receiving such information in the event of their child's death. These results underscore the importance of high-quality pre-and post-test counseling, conducted by individuals trained in consenting around genomic testing to elicit family preferences and align expectations around the return of germline results.

Performance of the McGill Interactive Pediatric OncoGenetic Guidelines for Identifying Cancer Predisposition Syndromes

Importance

Prompt recognition of a child with a cancer predisposition syndrome (CPS) has implications for cancer management, surveillance, genetic counseling, and cascade testing of relatives. Diagnosis of CPS requires practitioner expertise, access to genetic testing, and test result interpretation. This diagnostic process is not accessible in all institutions worldwide, leading to missed CPS diagnoses. Advances in electronic health technology can facilitate CPS risk assessment.

Objective

To evaluate the diagnostic accuracy of a CPS prediction tool (McGill Interactive Pediatric OncoGenetic Guidelines [MIPOGG]) in identifying children with cancer who have a low or high likelihood of having a CPS.

Design, Setting, and Participants

In this international, multicenter diagnostic accuracy study, 1071 pediatric (<19 years of age) oncology patients who had a confirmed CPS (12 oncology referral centers) or who underwent germline DNA sequencing through precision medicine programs (6 centers) from January 1, 2000, to July 31, 2020, were studied.

Exposures

Exposures were MIPOGG application in patients with cancer and a confirmed CPS (diagnosed through routine clinical care; n = 413) in phase 1 and MIPOGG application in patients with cancer who underwent germline DNA sequencing (n = 658) in phase 2. Study phases did not overlap. Data analysts were blinded to genetic test results.

Main Outcomes and Measures

The performance of MIPOGG in CPS recognition was compared with that of routine clinical care, including identifying a CPS earlier than practitioners. The tool's test characteristics were calculated using next-generation germline DNA sequencing as the comparator.

Results

In phase 1, a total of 413 patients with cancer (median age, 3.0 years; range, 0-18 years) and a confirmed CPS were identified. MIPOGG correctly recognized 410 of 412 patients (99.5%) as requiring referral for CPS evaluation at the time of primary cancer diagnosis. Nine patients diagnosed with a CPS by a practitioner after their second malignant tumor were detected by MIPOGG using information available at the time of the first cancer. In phase 2, of 658 children with cancer (median age, 6.6 years; range, 0-18.8 years) who underwent comprehensive germline DNA sequencing, 636 had sufficient information for MIPOGG application. When compared with germline DNA sequencing for CPS detection, the MIPOGG test characteristics for pediatric-onset CPSs were as follows: sensitivity, 90.7%; specificity, 60.5%; positive predictive value, 17.6%; and negative predictive value, 98.6%. Tumor DNA sequencing data confirmed the MIPOGG recommendation for CPS evaluation in 20 of 22 patients with established cancer-CPS associations.

Conclusions and Relevance

In this diagnostic study, MIPOGG exhibited a favorable accuracy profile for CPS screening and reduced time to CPS recognition. These findings suggest that MIPOGG implementation could standardize and rationalize recommendations for CPS evaluation in children with cancer.

Genomes for Kids: The scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing

Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole genome (WGS), exome, and RNA sequencing, to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically-relevant (25%), and/or cancer predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors) and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers.

Abstract 642: Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer

Clinical genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. In the Genomes for Kids study (NCT02530658) we used a three-platform sequencing approach, including whole genome (WGS), whole exome (WES) and RNA sequencing, to examine tumor and paired germline genomes from prospectively identified children with cancer. The goal of the study was to assess the potential of comprehensive next generation sequencing to elucidate the molecular mechanisms underlying tumor formation and investigate the potential of this information to influence clinical decision-making.The cohort, with a median age of 6 yrs, range 0 - 26 yrs, included 301 patients with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type or stage. Patients with hematologic malignancies accounted for 41% of cases, 31% had CNS tumors, and 28% had other non-CNS solid tumors. This cohort also included 18 patients with very rare tumor types, defined here as occurring in less than 2 cases per million person per year.Two hundred fifty three patients (84%) had sufficient tumor for three-platform sequencing and all 301 had adequate paired germline samples. Following analysis, 86% of patients harbored diagnostic (53%), prognostic (57%), therapeutically relevant (25%), and/or cancer predisposing (18%) variants. The inclusion of WGS enabled detection of oncogenic gene fusions, as well as 22 cases in which oncogenes were activated through enhancer hijacking, a particularly frequent occurrence in hematologic malignancies. In addition, WGS effectively detected clinically relevant small intragenic deletions (15% of tumors) and a variety of mutational signatures, which were not detectable through analysis of whole exome data. Evaluation of 56 pathogenic germline variants in the context of paired tumor sequence data helped establish the disease relevance of several genes that are not typically associated with the cancer type in question, providing critical insights on a case-by-case basis. Examples include a pathogenic germline variant in MUTYH in a patient with retinoblastoma whose tumor exhibited a mutation signature associated with reactive oxygen species indicative of loss of MUTYH function; and conversely, a likely pathogenic variant in PMS2 in a rare brain cancer, which did not exhibit a mutation signature associated with microsatellite instability. This study successfully demonstrated the power of this three-platform approach to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers. As a result of these findings, we have incorporated this three-platform approach into our routine real-time clinical service at St. Jude Children's Hospital.

Citation Format: David A. Wheeler, Scott Newman, Joy Nakitandwe, Chimene A. Kesserwan, Elizabeth M. Azzato, Michael C. Rusch, Sheila Shurtleff, Armita Bahrami, Brent Orr, Jeffery M. Klco, Dale J. Hedges, Kayla V. Hamilton, Scott G. Foy, Michael N. Edmonson, Andrew Thrasher, Jiali Gu, Lynn W. Harrison, Lu Wang, Roya Mostafavi, Manish Kubal, Jamie Maciaszek, Michael Clay, Annastasia Ouma, Antonina Silkov, Yanling Liu, Zhaojie Zhang, Yu Liu, Samuel W. Brady, Xin Zhou, Mark Wilkinson, Delaram Rahbarinia, Jay Knight, Jian Wang, Charles G. Mullighan, Rose B. McGee, Emily A. Quinn, Elsie L. Gerhardt, Leslie M. Taylor, Regina Nuccio, Jessica M. Valdez, Stacy J. Hines-Dowell, Alberto Pappo, Giles Robinson, Liza-Marie Johnson, Ching-Hon Pui, David W. Ellison, James R. Downing, Jinghui Zhang, Kim E. Nichols. Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 642.

Development and DNA polymerase activities in cultured preimplantation mouse embryos: comparison with embryos developed in vivo

Embryos from superovulated female mice that developed in vitro from the two-cell stage were compared with in vivo embryos with respect to yield of blastocytes, number and types of cells, morphology in histologic section, and DNA polymerase activities. Significantly more embryos developed into blastocytes in vitro (93%) than in vivo (18%). Inner cell mass (ICM) cells comprised approximately 30% of total cells in late morula/early blastocyst stage embryos developed either in vitro or in vivo. However, the in vitro embryos developed approximately half the number of total cells as in vivo embryos, did not develop endoderm, and did not develop abembryonic trophoblast cells with morphologic characteristics of late preimplantation in vivo embryos. DNA-dependent DNA polymerase activities in in vitro embryos decreased in correspondence with the decrease in cell number resulting in per cell levels comparable to in vivo embryos. In contrast, the poly (A).oligo(dT)-dependent DNA polymerase activity was the same in embryos developing either in vitro or in vivo, indicating different regulatory mechanisms for the two enzyme activities. A variety of nutrients and growth factors in the culture medium did not increase cell numbers or DNA polymerase activities in embryos cultured for 3 days; extending the culture an additional 24 hours resulted in a loss of ICM cells and decreases in both DNA polymerase activities. These results show that the retarded growth of embryos in vitro is equally distributed between ICM and trophoblast, is not reversed by culture conditions that include serum growth factors, and is not due to decreased cellular levels of DNA polymerase activities.

Dietary factors and the incidence of cancer of the stomach

A case-control study of diet and stomach cancer was conducted during 1979-1982 in Toronto, Winnipeg, and St. John's Canada. Two hundred forty-six histologically verified cancer cases were individually matched by age, sex, and area of residence to 246 randomly selected population controls. Daily nutrient consumption values were calculated from quantitative diet history questionnaire data through use of the US Department of Agriculture Food Composition Data Bank, which was extended and modified for Canadian items. For the analysis, continuous conditional logistic regression methods were used. It was found that consumption of dietary fiber was associated with decreased risk of gastric cancer; the odds ratio estimate of trend was 0.40/10 g average daily intake of fiber (i.e., 0.40(1.5)/15 g, etc.) (p less than 10(-8)). Also, average daily consumption of nitrite, chocolate, and carbohydrate was associated with increasing trends in risk, with odds ratio estimates, respectively, 2.6/mg (p less than 10(-4)), 1.8/10 g (p less than 10(-4)), and 1.5/100 g (p = 0.015). While citrus fruit intake appeared to be somewhat protective (odds ratio = 0.75/100 g daily average, p = 0.0056), vitamin C intake was less so, and vitamin E not at all. Thus, a number of dietary components seem to be implicated in the pathogenesis of stomach cancer.

Kinetics of substrate and product interactions with arsanilazotyrosine-248 carboxypeptidase A

The chromophoric intramolecular azoTyr-248.Zn complex detects discrete kinetic steps in the interaction of azocarboxypeptidase with products or substrates that are hydrolyzed slowly. Temperature-jump experiments at 510 nm indicate that the rapid binding of such ligands is followed by a slower change in the conformation of the enzyme--ligand complex: that defines the initial binding, and the rate constants k2 and k-2 for the forward and reverse steps of this conversion, respectively. For each ligand, the kinetically determined dissociation constant is virtually identical to that obtained at equilibrium form circular dichroic titrations. Although there are small variations in k2 and k-2 for each substrate, all the rate processes are much faster than the rate-determining step for the hydrolysis of these substrates. The proposed model of the mechanism of peptide hydrolysis by carboxypeptidase incorporates the results of these temperature jump experiments.

Intramolecular arsanilazotyrosine-248-Zn complex of carboxypeptidase A: a monitor of multiple conformational states in solution

The red azoTyr-248-Zn complex of arnilazocarboxypeptidase, previously used to demonstrate differences in conformation of the enzyme in crystals and in solution, has now provided means to detect multiple conformations of the enzyme in solution by stopped-flow pH and temperature jump experiments. These studies identify two distinct processes. Er + H+ in equilibrium Ey (I), is the extremely rapid, Kfast about 10(5) sec-1, pH dependent dissociation of the metal complex. Ey in equilibrium Ey' (II), is much slower, Kslow about 5 sec-1, pH independent interconversion of two distinct populations of protein molecules, Ey and Ey', in which the yellow azo-Tyr-248 is different conformations. These two conformations can be differentiated readily by stopped-flow pH-jump experiments, since I is three to four orders of magnitude faster than II. Mathematical expressions derived from this mechanism accurately predict all observations over the pH range from 6.0 to 8.5. In a previous stopped-flow pH-jump experiment, Lipcomb and coworkers [Quiocho, F. A., McMurray, C. H. & Lipcomb, W. H. (1972), Proc. Nat. Acad. Sci. USA 69, 2850-2854] recognized only a single process with a rate constant of about 6 sec-1, but not the major, very rapid rate observed here. The failure to detect this fast process led to the postulation of a number of explanations intended to account for the detection of only a single, slow rate. The present observations show that the premise for those conjectures is not valid. The azoprobe reveals the existence of rapidly interconvertible substructures of carboxypeptidase A, and the results support the view that in solution, enzymes can adopt multiple, readily interconvertible and related conformations which could then either facilitate or impede catalysis. In crystals, rearrangement of molecular structure could be severely impaired or restricted, and crystallization might single out either active or inactive conformations. In the latter case, such crystals would have greatly reduced activities and markedly altered catalytic behavior, as is observed for carboxypeptidase A. In combination with detailed kinetic analysis of crystals, conformational analysis in solution should be a valuable guide to discern enzyme mechanisms and select crystals for x-ray structure analysis.

Intramolecular arsanilazotyrosine-248-Zn complex of carboxypeptidase A: a monitor of catalytic events

The intensely chromophoric intramolecular coordination complex formed between arsanilazotyrosine-248 and the active site zinc atom of azocarboxypeptidase A (Johansen, J. T. & Vallee, B. L. (1971) Proc. Nat. Acad. Sci. USA 68, 2532-2535) is a spectrokinetic probe of catalytic events. The interconversion of the azoTyr-248-Zn complex and its constituents is measured by stopped-flow pH and temperature-jump methods. The rate of interconversion, 64,000 sec-1, is orders of magnitude faster than that of the catalytic step itself (about 0.01-100 sec-1). Rapidly turned over peptide and ester substrates disrupt the azoTyr-248-Zn complex before hydrolysis occurs. As a consequence, formation of azoTyr-248, substrate binding, and catalysis can all be monitored while catalysis is actually in progress. The results of these dynamic studies specify a course of catalytic events, different from those postulated based on x-ray structure analysis. If azoTyr-248 is displaced, the direction is opposite to the inward movement postulated on the basis of x-ray studies and is not unique to induction by substrates, since rapid changes in pH also result in analogous spectral changes. AzoTyr-248 carboxypeptidase has all the features which are essential for mechanistic studies: (1) It is enzymatically active; (2) the spectra of the metal complex differ characteristically from those of its constituents; (3) it responds dynamically to environmental factors; and (4) the response time of the probe itself is much more rapid than is required for the measurement of the catalytic step. These combined kinetic and spectral properties of the metal complex render it a powerful spectrokinetic probe to visualize and discern microscopic details of the catalytic process.

Nuclear magnetic resonance study of ligand binding to Mn-aspartate transcarbamylase

Aspartate transcarbamylase from Escherichia coli has been prepared with up to four of zinc ions replaced by manganese, and the effect of this substitution on the proton nuclear magnetic resonance properties of succinate bound to the catalytic site and of cytidine 5'-triphosphate bound to the regulatory site has been determined, The specific activity and allosteric properties of the Mn-substituted enzyme are essentially identical with those of the native enzyme. The longitudinal relaxation time, T1, of the succinate protons is shortened by the native enzyme and is shortened further by the Mn-substituted enzyme at both 100 and 220 MHz in D2O solutions of 0.02 M immidazole chloride (pH 7.0), 10 minus 3 M beta-mercaptoethanol, 0;2 mM ethylenediamenetetraacetic acid, and 2.5 mM carbamyl phosphate over a temperature range of 5 to 35 degrees. Under the same conditions, the transverse relaxation time, T2, of the succinate protons at 90 MHz is shortened to the same extent by native and Mn-substituted enzyme. The temperature dependence of the relaxation times indicates that the shortening of the transverse relaxation time is determened by the lifetime of bound succinate, whereas the further shortening of the longitudinal relaxation time by the Mn-substituted enzyme is due to dipolar relaxation, i.e. to the interaction between Mn and the succinate protons. The distance between the Mn and the protons of succinate bound to the enzyme can be calculated from the relaxation time measurements and is 15,3 A. The dipolar interaction correlation time which is needed for the calculation of this distance, was found to be 3.5 X 10 minus 9 sec from the frequency dependence of T1. The transverse relaxation time of the C-6 proton of CTP is shortened to the same extent by both the native and Mn-substituted enzyme in D2O solutions of 0.02 M imidazole chloride (pH 7.0), 10 MINUS 3 M beta-mercaptoethanol, 0.2 mM ethylenediaminetetraacetic acid, and 2.5 mM carbamyl phosphate over the temperature 5-30 degrees. Since the temperature depencece of the relaxation time indicates the relaxation is not exchange limited, the manganese must be too distant from the bound CTP for an appreciable interaction to occur. This requires that the manganese be greater than 20A from the CTP. These results are used together with other available structural data to construct a schematic model for aspartate transcarbamylase.