IntroductionHIV-based lentiviral vectors are rapidly becoming the retrovirus vector system of choice for research and clinical gene transfer applications. The enhanced ability of lentiviral vectors to transduce both quiescent stem cells 1 and nondividing terminally differentiated cells 2 has led to the development of a wide range of therapeutic gene delivery vectors, 3 as well as promising research tools such as short hairpin RNA gene knockdown libraries 4 and vectors for induction of pluripotency in terminally differentiated cells. 5 Early gamma-retroviral clinical gene therapy vectors restored immune function in patients with X-linked severe combined immunodeficiency (SCID-X1), but they were subsequently found to cause proliferative disorders via transactivation of protooncogenes. 6,7 Newer lentiviral vector designs may significantly reduce that risk, and they await clinical testing for final validation of their predicted safety. Clinical-scale production of these vectors, however, is problematic, as the generation of stable producer cell lines is made significantly more difficult by their self-inactivating (SIN) long terminal repeats (LTRs). As a result, most clinical-grade production of lentiviral vectors is currently being performed using cumbersome transient transfection processes.Insertional mutagenesis by previous gamma-retroviral gene therapy vectors occurred when strong viral enhancers within the LTR activated genes (eg, LMO2) surrounding the integrated vector. 6,7 SIN vector designs completely eliminate the viral enhancers and promoters in the LTR, and when coupled with appropriate internal promoters having less or no enhancer activity, they have been shown to significantly reduce oncogene activation. [8][9][10] Chromatin insulator sequences have also been inserted into SIN LTRs and appear to protect neighboring genes from residual transactivation from the internal promoters. 11 When inserted into the LMO2 locus in Jurkat cells, lentiviral vector genomes containing an internal EF1␣ promoter flanked by SIN LTRs and chicken HS4 chromatin insulators caused only minimal transactivation of the LMO2 promoter. 12 Clinical-scale production of such safety-modified vectors would be greatly facilitated by stable producer cell lines, which allow convenient generation of standardized, large-volume supernatants for downstream process optimization and preclinical studies. Although there have been numerous reports of lentiviral packaging cell lines, 13-22 all high-titer (Ͼ 10 7 transducing units per milliliter [TU/mL]) stable producer lines described in these publications were created by the traditional method of viral transduction of packaging cell lines using non-SIN vector supernatants, which efficiently creates populations of cells with vector genomes integrated at sites favorable for active transcription, and in multiple copies per cell. SIN vector genomes, by virtue of the inactivating deletion in the LTR, are thus incompatible with this method. "Conditional SIN" vectors, 22 which contain regulatable enhancers ...

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. STATEMENT OF SIGNIFICANCEPediatric cancers are driven by diverse genomic lesions and sequencing has proven useful in evaluating high risk and relapsed/refractory cases. We show that combined whole genome, exome, and RNA-sequencing of tumor and paired normal tissues enables identification and characterization of genetic drivers across the full spectrum of pediatric cancers.Research.

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Background Patients with cancer are increasingly offered genomic sequencing, including germline testing for cancer predisposition or other disorders. Such testing is unfamiliar to patients and families, and clear communication is needed to introduce genomic concepts and convey risk and benefit information. Methods Parents of children with cancer were offered the opportunity to have their children’s tumor and germline examined with clinical genomic sequencing. Families were introduced to the study with a 2‐visit informed consent model. Baseline genetic knowledge and self‐reported literacy/numeracy were collected before a study introduction visit, during which basic concepts related to genomic sequencing were discussed. Information was reinforced during a second visit, during which informed consent was obtained and a posttest was administered. Results As reflected by the percentage of correct answers on the pretest and posttest assessments, this model increased genetic knowledge by 11.1% (from 77.8% to 88.9%; P < .0001) in 121 parents participating in both the study introduction and consent visits. The percentage of parents correctly identifying the meaning of somatic and germline mutations increased significantly (from 18% to 59% [somatic] and from 31% to 64% [germline]; P < .0001). Nevertheless, these concepts remained unfamiliar to one‐third of the parents. No relation was identified between the change in the overall percentage of correct answers and self‐reported literacy, numeracy, or demographics. Conclusions The use of a 2‐visit communication model improved knowledge of concepts relevant to genomic sequencing, particularly differences between somatic and germline testing; however, these areas remained confusing to many participants, and reinforcement may be necessary to achieve complete understanding.

Patients harboring germline pathogenic biallelic variants in genes involved in the recognition and repair of DNA damage are known to have a substantially increased cancer risk. Emerging evidence suggests that individuals harboring heterozygous variants in these same genes may also be at heightened, albeit lesser, risk for cancer. Herein, we sought to determine whether heterozygous variants in RECQL4, the gene encoding an essential DNA helicase that is defective in children with the autosomal recessive cancer-predisposing condition Rothmund–Thomson syndrome (RTS), are associated with increased risk for childhood cancer. To address this question, we interrogated germline sequence data from 4435 pediatric cancer patients at St. Jude Children's Research Hospital and 1127 from the National Cancer Institute Therapeutically Applicable Research to Generate Effective Treatment (TARGET) database and identified 24 (0.43%) who harbored loss-of-function (LOF) RECQL4 variants, including five of 249 (2.0%) with osteosarcoma (OS). These RECQL4 variants were significantly overrepresented in children with OS, the cancer most frequently observed in patients with RTS, as compared to 134,187 noncancer controls in the Genome Aggregation Database (gnomAD v2.1; P = 0.00087, odds ratio [OR] = 7.1, 95% CI, 2.9–17). Nine of the 24 (38%) individuals possessed the same c.1573delT (p.Cys525Alafs) variant located in the highly conserved DNA helicase domain, suggesting that disruption of this domain is central to oncogenesis. Altogether these data expand our understanding of the genetic factors predisposing to childhood cancer and reveal a novel association between heterozygous RECQL4 LOF variants and development of pediatric OS.