Cell-free DNA (cfDNA) in the blood provides a noninvasive diagnostic avenue for patients with cancer1. However, characteristics of the origins and molecular features of cfDNA are poorly understood. We developed an approach to evaluate fragmentation patterns of cfDNA across the genome and found that cfDNA profiles of healthy individuals reflected nucleosomal patterns of white blood cells, while patients with cancer had altered fragmentation profiles. We applied this method to analyze fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric, or bile duct cancer and 245 healthy individuals. A machine learning model incorporating genome-wide fragmentation features had sensitivities of detection ranging from 57% to >99% among the seven cancer types at 98% specificity, with an overall AUC of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation based cfDNA analyses detected 91% of cancer patients. The results of these analyses highlight important properties of cfDNA and provide a proof of principle approach for screening, early detection, and monitoring of human cancer.

Genomic deletions and duplications play an important role in the etiology of human disease. Versatile tests are required to detect these rearrangements, both in research and diagnostic settings. Multiplex ligation-dependent probe amplification (MLPA) is such a technique, allowing the rapid and precise quantification of up to 40 sequences within a nucleic acid sample using a one-tube assay. Current MLPA probe design, however, involves time-consuming and costly steps for probe generation. To bypass these limitations we set out to use chemically synthesized oligonucleotide probes only. The inherent limitations of this approach are related to oligonucleotide length, and thus the number of probes that can be combined in one assay is also limited. This problem was tackled by designing a two-color assay, combining two sets of probes, each amplified by primers labeled with a different fluorophore. In this way we successfully combined 28 probes in a single reaction. The assay designed was used to screen for the presence of deletions and duplications in patients with hereditary multiple exostoses (HME). Screening 18 patients without detectable point mutations in the EXT1 and EXT2 genes revealed five cases with deletions of one or more exons: four in EXT1 and one in EXT2. Our results show that a two-color MLPA assay using only synthetic oligonucleotides provides an attractive alternative for probe design. The approach is especially suited for cases in which the number of patients to be tested is limited, making it financially unattractive to invest in cloning.

The impulse oscillometry system (IOS) was introduced as a new technique to assess airflow obstruction in patients who are not able to perform forced breathing maneuvers, e.g., subjects with cerebral palsy or severe mental retardation, and young children. This study evaluates the sensitivity and specificity of IOS parameters to quantify changes in airflow obstruction in comparison with forced expiratory volume in the first second (FEV(1)) and peak expiratory flow (PEF) measurements. Measurements of FEV(1), PEF, and resistance (R) and reactance (X) at frequencies of 5-35 Hz were performed in 19 children with asthma before, during, and after methacholine challenge and subsequent bronchodilatation. All parameters changed significantly during tests. Values of R5 and R10 correlated with FEV(1) (r = -0.71 and -0.73, respectively, P < 0.001), as did values of X5 and X10 (r = 0.52 and 0.57, respectively, P < 0.01). Changes in R preceded changes in PEF and FEV(1) during methacholine challenge. The area under the receiver operating characteristic (ROC) curve to predict a 15% fall in FEV(1) showed better sensitivity and specificity for R5 (area under the curve, 0.85) compared to PEF (0.79) or R10 (0.73). We conclude that IOS parameters can be easily used as an indirect measure of airflow obstruction. This might be helpful in patients who are not able to perform forced breathing maneuvers. In individual subjects, R values measured at 5 Hz showed to be superior to PEF measurements in the detection of a 15% fall in FEV(1).

A large number of sequence variants identified in BRCA1 and BRCA2 cannot be distinguished as either disease-causing mutations or neutral variants. These so-called unclassified variants (UVs) include variants that are located in the intronic sequences of BRCA1 and BRCA2. The purpose of this study was to assess the use of splice-site prediction programs (SSPPs) to select intronic variants in BRCA1 and BRCA2 that are likely to affect RNA splicing. We performed in vitro molecular characterization of RNA of six intronic variants in BRCA1 and BRCA2. In four cases (BRCA1, c.81-6T4A and c.498615G4T; BRCA2, c.76171 2T4G and c.875415G4A) a deleterious effect on RNA splicing was seen, whereas the c.135-15_-12del variant in BRCA1 showed no effect on RNA splicing. In the case of the BRCA2 c.68-7T4A variant, RNA analysis was not sufficient to establish the clinical significance. Six SSPPs were used to predict whether an effect on RNA splicing was expected for these six variants as well as for 23 intronic variants in BRCA1 for which the effect on RNA splicing has been published. Out of a total of 174 predictions, 161 (93%) were informative (i.e., the wild-type splice-site was recognized). No falsenegative predictions were observed; an effect on RNA splicing was always predicted by these programs. In four cases (2.5%) a false-positive prediction was observed. For DNA diagnostic laboratories, these programs are therefore very useful to select intronic variants that are likely to affect RNA splicing for further analysis.

IMPORTANCE As the resolution of the coronavirus disease 2019 (COVID-19) crisis is unforeseeable, and/or a second wave of infections may arrive in the fall of 2020, it is important to evaluate patients' perspectives to learn from this. OBJECTIVE To assess how Dutch patients with cancer perceive cancer treatment and follow-up care (including experiences with telephone and video consultations [TC/VC]) and patients' well-being in comparison with a norm population during the COVID-19 crisis. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional study of patients participating in the Dutch Patient Reported Outcomes Following Initial Treatment and Long-term Evaluation of Survivorship (PROFILES) registry and a norm population who completed a questionnaire from April to May 2020. MAIN OUTCOMES AND MEASURES Logistic regression analysis assessed factors associated with changes in cancer care (treatment or follow-up appointment postponed/canceled or changed to TC/VC). Differences in quality of life, anxiety/depression, and loneliness between patients and age-matched and sex-matched norm participants were evaluated with regression models. RESULTS The online questionnaire was completed by 4094 patients (48.6% response), of whom most were male (2493 [60.9%]) and had a mean (SD) age of 63.0 (11.1) years. Of these respondents, 886 (21.7%) patients received treatment; 2725 (55.6%) received follow-up care. Treatment or follow-up appointments were canceled for 390 (10.8%) patients, whereas 160 of 886 (18.1%) in treatment and 234 of 2725 (8.6%) in follow-up had it replaced by a TC/VC. Systemic therapy, active surveillance, or surgery were associated with cancellation of treatment or follow-up appointment. Younger age, female sex, comorbidities, metastasized cancer, being worried about getting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and receiving supportive care were associated with replacement of a consultation with a TC/VC. Patients and norm participants reported that the COVID-19 crisis made them contact their general practitioner (852 of 4068 [20.9%] and 218 of 979 [22.3%]) or medical specialist/nurse (585 of 4068 [14.4%] and 144 of 979 [14.7%]) less quickly when they had physical complaints or concerns. Most patients who had a TC/VC preferred a face-to-face consultation, but 151 of 394 (38.3%) were willing to use a TC/VC again. Patients with cancer were more worried about getting infected with SARS-CoV-2 compared with the 977 norm participants (917 of 4094 [22.4%] vs 175 of 977 [17.9%]). Quality of life, anxiety, and depression were comparable, but norm participants more often reported loneliness (114 of 977 [11.7%] vs 287 of 4094 [7.0%]) than patients with cancer (P = .009). CONCLUSIONS AND RELEVANCE Among patients with cancer in the Netherlands, 1 in 3 reported changes in cancer care in the first weeks of the COVID-19 crisis. Long-term outcomes need to be monitored. The crisis may affect the mental well-being of the general population relatively more than that of patients with cancer.

Background: Systematic evaluation and validation of new prognostic and predictive markers, technologies and interventions for colorectal cancer (CRC) is crucial for optimizing patients' outcomes. With only 5-15% of patients participating in clinical trials, generalizability of results is poor. Moreover, current trials often lack the capacity for post-hoc subgroup analyses. For this purpose, a large observational cohort study, serving as a multiple trial and biobanking facility, was set up by the Dutch Colorectal Cancer Group (DCCG). Methods/design: The Prospective Dutch ColoRectal Cancer cohort is a prospective multidisciplinary nationwide observational cohort study in the Netherlands (yearly CRC incidence of 15 500). All CRC patients (stage I-IV) are eligible for inclusion, and longitudinal clinical data are registered. Patients give separate consent for the collection of blood and tumor tissue, filling out questionnaires, and broad randomization for studies according to the innovative cohort multiple randomized controlled trial design (cmRCT), serving as an alternative study design for the classic RCT. Objectives of the study include: 1) systematically collected long-term clinical data, patient-reported outcomes and biomaterials from daily CRC practice; and 2) to facilitate future basic, translational and clinical research including interventional and cost-effectiveness studies for both national and international research groups with short inclusion periods, even for studies with stringent inclusion criteria. Results: Seven months after initiation 650 patients have been enrolled, eight centers participate, 15 centers await IRB approval and nine embedded cohort-or cmRCT-designed studies are currently recruiting patients. Conclusion: This cohort provides a unique multidisciplinary data, biobank, and patient-reported outcomes collection initiative, serving as an infrastructure for various kinds of research aiming to improve treatment outcomes in CRC patients. This comprehensive design may serve as an example for other tumor types.

BackgroundThe RECOURSE trial showed clinical efficacy for trifluridine/tipiracil for refractory metastatic colorectal cancer patients. We assessed the feasibility and effectiveness of trifluridine/tipiracil in daily clinical practice in The Netherlands.MethodsMedical records of patients from 17 centers treated in the trifluridine/tipiracil compassionate use program were reviewed and checked for RECOURSE eligibility criteria. Baseline characteristics, safety, and survival times were compared, and prespecified baseline characteristics were tested in multivariate analyses for prognostic significance on overall survival (OS).ResultsA total of 136 patients with a median age of 62 years were analyzed. Forty-three patients (32%) did not meet the RECOURSE eligibility criteria for not having received all prior standard treatments (n = 35, 26%) and/or ECOG performance status (PS) 2 (n = 12, 9%). The most common grade ≥3 toxicities were neutropenia (n = 44, 32%), leukopenia (n = 8, 6%), anemia (n = 7, 5%), and fatigue (n = 7, 5%). Median progression-free survival (PFS) and median OS were 2.1 (95% CI, 1.8–2.3) and 5.4 months (95% CI, 4.0–6.9), respectively. Patients with ECOG PS 2 had a worse median OS (3.2 months) compared to patients with ECOG PS 0–1 (5.9 months). ECOG PS, KRAS-mutation status, white blood cell count, serum lactate dehydrogenase, and alkaline phosphatase were prognostic factors for OS.ConclusionsOur data show that treatment with trifluridine/tipiracil in daily clinical practice is feasible and safe. Differences in patient characteristics between our population and the RECOURSE study population should be taken into account in the interpretation of survival data. Our results argue against the use of trifluridine/tipiracil in patients with ECOG PS 2.FundingJohannes J.M. Kwakman received an unrestricted research grant from Servier.

Multiple osteochondromas (MO) is an autosomal dominant condition, caused by mutations in either the EXT1 or the EXT2 gene. The DNA of a cohort of 35 patients, clinically suspected to be affected with MO, was screened for mutations by a combination of direct sequence analysis and multiplex ligation-dependent probe amplification (MLPA). In this cohort, 26 pathogenic gene alterations were found (74%). With sequence analysis mutations were detected in 22 patients (63%). In total, 10 mutations were detected in the EXT1 and 12 in the EXT2 gene. The number of the splice site mutations detected was larger than expected from the literature. In addition, with the MLPA four deletions of one or more exons were found in this cohort. Two patients, of whom one had a negative family history, showed deletions of exon 1 of the EXT1 gene, which is possibly a deletion hot spot. In patients suspected to be affected by MO, we recommend a quantitative analysis such as MLPA, followed by direct sequence analysis for the screening of the EXT1 and EXT2 genes.