Digital DNA lifecycle security and privacy: an overview.

DNA sequencing technologies have advanced significantly in the last few years leading to advancements in biomedical research which has improved personalised medicine and the discovery of new treatments for diseases. Sequencing technology advancement has also reduced the cost of DNA sequencing, which has led to the rise of direct-to-consumer (DTC) sequencing, e.g. 23andme.com, ancestry.co.uk, etc. In the meantime, concerns have emerged over privacy and security in collecting, handling, analysing and sharing DNA and genomic data. DNA data are unique and can be used to identify individuals. Moreover, those data provide information on people's current disease status and disposition, e.g. mental health or susceptibility for developing cancer. DNA privacy violation does not only affect the owner but also affects their close consanguinity due to its hereditary nature. This article introduces and defines the term 'digital DNA life cycle' and presents an overview of privacy and security threats and their mitigation techniques for predigital DNA and throughout the digital DNA life cycle. It covers DNA sequencing hardware, software and DNA sequence pipeline in addition to common privacy attacks and their countermeasures when DNA digital data are stored, queried or shared. Likewise, the article examines DTC genomic sequencing privacy and security.

Temporal trends in childhood cancer survival in Egypt, 2007 to 2017: A large retrospective study of 14 808 children with cancer from the Children's Cancer Hospital Egypt.

Childhood cancer is a priority in Egypt due to large numbers of children with cancer, suboptimal care and insufficient resources. It is difficult to evaluate progress in survival because of paucity of data in National Cancer Registry. In this study, we studied survival rates and trends in survival of the largest available cohort of children with cancer (n = 15 779, aged 0-18 years) from Egypt between 2007 and 2017, treated at Children's Cancer Hospital Egypt-(CCHE), representing 40% to 50% of all childhood cancers across Egypt. We estimated 5-year overall survival (OS) for 14 808 eligible patients using Kaplan-Meier method, and determined survival trends using Cox regression by single year of diagnosis and by diagnosis periods. We compared age-standardized rates to international benchmarks in England and the United States, identified cancers with inferior survival and provided recommendations for improvement. Five-year OS was 72.1% (95% CI 71.3-72.9) for all cancers combined, and survival trends increased significantly by single year of diagnosis (P < .001) and by calendar periods from 69.6% to 74.2% (P < .0001) between 2007-2012 and 2013-2017. Survival trends improved significantly for leukemias, lymphomas, CNS tumors, neuroblastoma, hepatoblastoma and Ewing Sarcoma. Survival was significantly lower by 9% and 11.2% (P < .001) than England and the United States, respectively. Significantly inferior survival was observed for the majority of cancers. Although survival trends are improving for childhood cancers in Egypt/CCHE, survival is still inferior in high-income countries. We provide evidence-based recommendations to improve survival in Egypt by reflecting on current obstacles in care, with further implications on practice and policy.

Prognostic Factors and Treatment Outcome of Pediatric Anaplastic Large Cell Lymphoma Treated at the Children Cancer Hospital Egypt.

INTRODUCTION: The aim of the current study is to report the epidemiologic data, response rate, treatment outcome, and overall survival of anaplastic large cell lymphoma (ALCL) patients during the 8-year period. PATIENTS AND METHODS: A retrospective study included all patients with newly diagnosed ALCL from July 2007 till December 2015. RESULTS: A total of 48 patients were enrolled. The majority (66.7%) were male individuals. Twenty-one patients (43.7%) were low stage I or II, whereas 27 (56.2%) had advanced stage III or IV. Two patients (4.2%) died during induction chemotherapy. Disease status at last follow-up showed 35 patients (72.9%) in complete remission, 5 (10.5%) relapse, and 5 disease progression. The median time to relapse was 17.2 months. Four patients (8.4%) were salvaged by high-dose chemotherapy ifosphamide, carboplatine, etoposide followed by autologous hematopoietic stem cell transplantation, whereas 5 (10.5%) died out of disease progression. The 5-year overall survival and event-free survival were 81.2% and 68.6%, respectively. Median FU period was 58.7 month. Multivariate analysis included age, sex, stage, and response to chemotherapy and showed no statistical significance. CONCLUSION: Treatment of ALCL according to the Children's Oncology Group ANHL 0131 protocol is well tolerated. The relapsing patient could be salvaged by high-dose chemotherapy and autologous hematopoietic stem cell transplantation.

Outcome of High-risk Langerhans Cell Histiocytosis (LCH) in Egyptian Children, Does Intermediate-dose Methotrexate Improve the Outcome?

High-risk multisystem organ (RO+) Langerhans cell histiocytosis (LCH) has the least survival. We present the outcome of RO+ LCH in a pediatric single center. Fifty RO+ LCH patients, treated between 07/2007 and 07/2015, were retrospectively analyzed. Induction vinblastine (VBL) and prednisone (PRED) with intermediate-dose methotrexate (idMTX) was adopted until 2012 (n=20) wherein idMTX was omitted (n=30). The 3-year overall survival (OS) of MTX and non-MTX groups was 75% and 63%, respectively, P=0.537, while the event-free survival (EFS) was 36.9% and 13.2%, respectively, P=0.005. At week 12 of induction, "better status" was obtained in 80% of those receiving MTX, and 55% of those who were not. The statistically significant factors associated with both poor OS and EFS were trihemopoietic cytopenias, hepatic dysfunction, tri RO+ combination, and single induction. The factors associated with disease progression (DP) on induction were trihemopoietic cytopenias, hepatic dysfunction, and lack of idMTX, while those for disease reactivations (REA), the season of autumn/winter, lung disease, male sex, and idMTX were the associated factors. The 1-year OS was remarkably affected with the occurrence of DP versus REA versus none, wherein it was 47%, 93%, and 95%, respectively, P=0.001. In conclusion, idMTX is associated with better EFS. DP on induction remains of dismal prognosis in relation to disease REA afterwards. Risk stratification should highlight the role of trihemopoietic cytopenias, hepatic dysfunction, tri RO+, central nervous system risk site, and lung association.

OpenSHS: Open Smart Home Simulator.

This paper develops a new hybrid, open-source, cross-platform 3D smart home simulator, OpenSHS, for dataset generation. OpenSHS offers an opportunity for researchers in the field of the Internet of Things (IoT) and machine learning to test and evaluate their models. Following a hybrid approach, OpenSHS combines advantages from both interactive and model-based approaches. This approach reduces the time and efforts required to generate simulated smart home datasets. We have designed a replication algorithm for extending and expanding a dataset. A small sample dataset produced, by OpenSHS, can be extended without affecting the logical order of the events. The replication provides a solution for generating large representative smart home datasets. We have built an extensible library of smart devices that facilitates the simulation of current and future smart home environments. Our tool divides the dataset generation process into three distinct phases: first design: the researcher designs the initial virtual environment by building the home, importing smart devices and creating contexts; second, simulation: the participant simulates his/her context-specific events; and third, aggregation: the researcher applies the replication algorithm to generate the final dataset. We conducted a study to assess the ease of use of our tool on the System Usability Scale (SUS).

Low-grade Nonrhabdomyosarcoma Soft Tissue Sarcoma: What is Peculiar for Childhood.

BACKGROUND: Nearly half of soft tissue sarcomas are nonrhabdomyosarcomas (NRSTSs). The low-grade (LG) form comprises a heterogenous group of diseases that rarely metastasize but are known for local recurrence. AIM OF THE STUDY: The aim of the study was to retrospectively evaluate pediatric LG-NRSTS with regard to demography, survival, and factors affecting outcome in Egyptian patients. PATIENTS AND METHODS: The study reviewed 66 NRSTS patients who presented to the Pediatric Oncology Department, National Cancer Institute, Cairo University, between January 2008 and December 2013. RESULTS: Out of the reviewed cases 32 patients had LG tumors and were eligible for analysis. The male to female ratio was 1:1 and the median age was 7.5 years (range, 1 mo to 18 y). Desmoid fibromatosis (N=18) showed frequent local recurrence and nearly half of this group was alive without disease. No recurrence of the disease occurred in the nonfibromatosis group (n=14) and all patients were alive and free of disease. The 5-year overall survival was 88% for the entire group of study patients versus 45% for event-free survival. Tumors >5 cm in diameter and fibromatosis histology subtype were associated with lower EFS. CONCLUSIONS: LG-NRSTS generally has good prognosis, with overall survival reaching 90%. However, aggressive fibromatosis usually runs a poorer course in the form of high incidence of local recurrence and lower survival rates. This needs to be further assessed in larger prospective studies including novel therapies in addition to the current conventional modalities.

High risk Langerhans cell histiocytosis in children: the role of salvage in improving the outcome. A single center experience.

BACKGROUND: In pediatric multi-system high risk organs (RO +) Langerhans cell histiocytosis (LCH), failing 1st line treatment has the highest mortality. We aim to present the outcome of failure of 1st line whether due to disease progression (DP) at end of induction or reactivation (REA) after initial better status response. PATIENTS AND METHODS: Sixty-seven RO + LCH patients with hemopoietic, hepatic or splenic involvement, treated between 2007 and 2019 were retrospectively analyzed. The median follow-up (IQR) is 6 years (4-8.8 y).They were subjected to 2 eras of treatment; one with salvage by 2-Cda based regimen (2-CdABR) and another without. RESULTS: Of 67 patients, M/F 40/27, median age 1.74 y (0.2-10 y), 42 failed 1st line (62.7%). Of them DP n = 22 (52%) and REA n = 20 (48%). Of those with DP, 9/22 patients received 2-CdABR, where 5 survived in better status. While the remaining 13 did not receive 2-CdABR and all of them died. Otherwise, of those with REA, 12/20 reactivated on RO + mode. Of them, 8/12 received 2-CdABR, where only one survived in better status and the remaining 4 received vinblastine-based regimen,where 2 died and 2 were rescued. RO + 5-year overall survival (OS) was 65% (CI 95% 54 -78) while the event free survival (EFS) 36% (26.3-50.1). The OS of DP 27% (14-54) versus REA 67% (49-93) p 0.004. OS of DP with 2-CdABR 56% (31-97.7) versus 8% without (2-51), p < 0.001. While OS of REA with 2-CdABR 38% (13-100) versus 74% without (53-100) p 0.7. CONCLUSION: Survival of RO + remains limited. Failure of 1st line in RO + due to DP carries worse prognosis in relation to REA. In DP those who were not salvaged by 2-CdABR, showed dismal outcome. This could not be shown when applied in REA.

Pediatric pulmonary multisystem langerhans cell histiocytosis: does lung lesion severity affect the outcome?

BACKGROUND: The pediatric pulmonary multisystem Langerhans cell histiocytosis (PPM LCH) is associated with either low risk or high risk organ(s). The nodulo-cystic lung lesions although pathognomonic, yet are very variable in severity and remain a source of controversy in certifying pulmonary LCH diagnosis. The study aimed to examine the prognostic value of clinical respiratory manifestations and radiological lung lesions severity. This is through associating a CT chest triad of bilateral, extensive and diffuse lesions. It is a retrospective study of 350 LCH patients who received systemic treatment at Children's Cancer Hospital Egypt during the period from 2007 to 2020. RESULTS: Sixty-seven patients (67/350-19.1%) had PPM LCH at presentation. Severe lung lesions were present in 24 of them. The median follow-up period was 61 months (IQR: 3.4-8.3). The 5-year overall survival (OS) and event free survival (EFS) was 89% and 56.6% respectively. The EFS, for severe radiological lesions triad was 38% ± 20.7 versus 66% ± 16.2 for non-severe lesions triad p 0.002, while for presence of chest X-ray changes 27% ± 22.344 versus absence of chest X ray changes 66% ± 14.7 p 0.001, for clinical respiratory manifestations 13% ± 13.9 versus none 62% ± 22.9 p < 0.001, for RO- with severe lung lesions 47% ± 30.4 versus RO- without severe lung lesions 69% ± 5.9 p 0.04. There was a tendency for the independent prognostic impact of severe lung involvement; aHR = 1.7 (95% CI 0.92-3.13, p = 0.09). CONCLUSION: Although the lung is a low -risk organ per se in LCH, our study demonstrates a non negligeable prognostic impact of severe lung involvement in the risk stratification of pediatric LCH. This warrants further study and external validation.

Cost-effectiveness of childhood cancer treatment in Egypt: Lessons to promote high-value care in a resource-limited setting based on real-world evidence.

Background: Childhood cancer in low-and middle-income countries is a global health priority, however, the perception that treatment is unaffordable has potentially led to scarce investment in resources, contributing to inferior survival. In this study, we analysed real-world data about the cost-effectiveness of treating 8886 children with cancer at a large resource-limited paediatric oncology setting in Egypt, between 2013 and 2017, stratified by cancer type, stage/risk, and disease status. Methods: Childhood cancer costs (USD 2019) were calculated from a health-system perspective, and 5-year overall survival was used to represent clinical effectiveness. We estimated cost-effectiveness as the cost per disability-adjusted life-year (cost/DALY) averted, adjusted for utility decrement for late-effect morbidity and mortality. Findings: For all cancers combined, cost/DALY averted was $1384 (0.5 × GDP/capita), which is very cost-effective according to WHO-CHOICE thresholds. Ratio of cost/DALY averted to GDP/capita varied by cancer type/sub-type and disease severity (range: 0.1-1.6), where it was lowest for Hodgkin lymphoma, and retinoblastoma, and highest for high-risk acute leukaemia, and high-risk neuroblastoma. Treatment was cost-effective (ratio <3 × GDP/capita) for all cancer types/subtypes and risk/stage groups, except for relapsed/refractory acute leukaemia, and relapsed/progressive patients with brain tumours, hepatoblastoma, Ewing sarcoma, and neuroblastoma. Treatment cost-effectiveness was affected by the high costs and inferior survival of advanced-stage/high-risk and relapsed/progressive cancers. Interpretation: Childhood cancer treatment is cost-effective in a resource-limited setting in Egypt, except for some relapsed/progressive cancer groups. We present evidence-based recommendations and lessons to promote high-value in care delivery, with implications on practice and policy. Funding: Egypt Cancer Network; NIHR School for Primary Care Research; ALSAC.

Patterns, risk factors and outcome predictors of posterior reversible encephalopathy syndrome in pediatric cancer patients.

The purpose of this study was to assess the clinical and radiological patterns and outcome predictors of posterior reversible encephalopathy syndrome (PRES) in pediatric cancer patients. A retrospective study included patients who developed PRES during their treatment at the Children's Cancer Hospital Egypt. A total of 50 patients developed PRES. Leukemia and lymphoma were the commonest diagnoses (64%). Regarding the MRI findings, occipital affection was the most common (92%), followed by frontal and temporal lobes involvement in 32% and 22% respectively and advanced PRES was described in 8 patients. Of the whole patients, 80% had complete clinical resolution and 60% showed complete radiological resolution at 2 weeks' evaluation and 2 patients died out of PRES. Unfavorable outcome was associated with those who had motor dysfunction, status epilepticus at presentation, frontal lobe and thalamic affection and atypical PRES. PRES might present in atypical sites with poor outcome including death.

Skeletal involvement in children with Langerhans cell histiocytosis: healing, complications, and functional outcome.

INTRODUCTION: Skeletal involvement in children with Langerhans cell histiocytosis (LCH) is a common feature of the disease. Several options for the treatment of these skeletal lesions have been reported. We describe our experience in the treatment of skeletal involvement of LCH in this retrospective case series study, entailing anatomic distribution, pattern of healing, skeletal deformities, and functional outcome of skeletal LCH. METHODS: A retrospective analysis was conducted for patients diagnosed with LCH and having skeletal lesions in the period between 2007 and 2015. Out of a total of 229 cases, 191 (83.4%) had skeletal involvement. Bone healing was divided into partial and complete based on the size of lesion and cortical changes in plain radiograph. Skeletal deformities were serially measured. Time to pain control, resumption of weight bearing, and the final functional status of the patient were reviewed. RESULTS: The mean age at presentation was 4.4 years (3 m-14.8 y) and the mean follow-up period was 53.3 months (0.2-120.7). After screening of skeletal and extra-skeletal lesions, 59 patients (31%) had M-S (Multisystem) LCH and 132 (69%) had S-S (Single system) LCH. Unifocal bone lesions were found in 81 (42.5%) patients, and multifocal bone lesions in 110 patients (57.5%). Single or multiple bone lesions were found in the craniofacial bones in 152 patients (79.5%), femur in 19 patients, (10%), ribs in 18 patients (9.4%), spine in 15 patients (8.1%), pelvis in 14 patients (7.3%), scapula in 8 patients (4.1%), humerus in 6 (3.1%), clavicle in 6 patients (3.1%), tibia in 3 patients (1.5%), radius in 3 patients (1.5%), and the ulna in 2 patients (1%) patients. No lesions were found in the fibula, hand, or foot. Out of all skeletal lesions, 179 (93.7%) patients were treated either medically or conservatively and 12 patients (6.2%) were treated surgically. The mean time to complete healing was 5.2 months (2-12). Skeletal complications included: pathologic fractures (9 vertebra plana, 5 long bone, 1 iliac bone), deformities (9 thoracolumbar kyphosis, 2 cervical spine subluxations, 2 coxa vara deformity of the proximal femur and one flattening of iliac bone). CONCLUSION: Non-operative treatment can lead to adequate bone healing in few months period. Partial or complete remodeling of bone deformities can be observed without surgical correction. However, surgical intervention might be indicated when cervical spine affection may lead to instability and subsequent neurological affection. Functional impairment is rarely caused by skeletal lesions in LCH.

Role of FDG-PET scan in the management of pediatric mature B cell non-Hodgkin's lymphoma. CCHE experience.

AIM OF WORK: To evaluate the sensitivity (Se), specificity (Sp), and predictive values (PV) of PET scan during management of pediatric mature B cell non-Hodgkin's lymphoma (NHL) in comparison with conventional computed tomography (CT) scan. PATIENTS AND METHODS: A retrospective study enrolled on pediatric NHL patients at Children Cancer Hospital Egypt (CCHE) during the period from July 2007 to the end of June 2013. RESULTS: For 115 pediatric patients diagnosed with mature B cell NHL, 152 PET and 152 CT scans were done simultaneously. Median age was 5.7years. They were 85 males (74%) and 30 females (26%). One hundred twenty six scans (82.9%) were done for 100 (87%) Burkitt lymphoma (BL) patients, while 26 scans (17.1%) were done for 15 (13.0%) patients with diffuse large B cell NHL (DLBC). Nineteen examination (12.5%) were done before starting chemotherapy (group 1), 107 (70.3%) at time of evaluation (group 2), and 26 (17.1%) during follow up (group C). Overall sensitivity was 91.6% for PET and 70.0% for conventional CT (p=0.02). Specificity was 84.1% for PET and 58.9% for CT (p<0.001). Positive predictive value (PPV) for PET was 50%, while was 22% for CT scan (p<0.001). Negative predictive value (NPV) for PET was 98%, and 92% for CT (p=0.01). CONCLUSION: PET scan is significantly more sensitive than conventional CT in the management of aggressive pediatric mature B cell NHL. PET negativity is an excellent indicator of tumor response.

Langerhans Cell Histiocytosis (LCH) in Egyptian Children: Does Reactivation Affect the Outcome?

OBJECTIVE: To report a single centre outcome of management of Langerhans cell histiocytosis (LCH), a clonal disease with involvement of various body systems. METHODS: Retrospective analysis of 80 pediatric LCH patients at Children Cancer Hospital-Egypt between July 2007 and December 2011 was performed. Patients were stratified and treated according to LCH III protocol. The median follow up period was 42 mo (range: 1.18 to 71 mo). RESULTS: At wk 6 and 12, 'better' response was obtained in 61 (76 %) and 74 (93 %) patients respectively. Afterwards, reactivation occurred in 25 patients (38 %), of them multiple episodes occurred in 5 patients (6.25 %), managed by repetition of 1st line treatment for once or more. The 5 y overall survival (OS) and event free survival (EFS) was 96.3 and 55 % respectively. At last follow up, better status was reached in 70 patients, 3 in each 'intermediate' and 'worse' status. Three high risk patients died and one patient was lost to follow up. CONCLUSIONS: In a single Egyptian pediatric LCH experience, the response to treatment is satisfactory and survival remains the rule except in high risk organs disease that still needs a new molecule for salvage. However in multiple reactivations, patients do well with repetition of the 1st line of treatment with or without methotrexate.

Results of treatment of lymphoblastic lymphoma at the children cancer hospital Egypt - A single center experience.

Introduction Lymphoblastic lymphoma (LBL) and acute lymphoblastic leukemia (ALL) are neoplasms of immature B or T-cell precursors. They are considered as a unique biological entity in the 2008 World Health Organization Classification of Hematologic Neoplasm. Both entities are arbitrarily separated by a cut-off point of 20-25% of blast cells in the bone marrow. Treatment of LBL has evolved over time from conventional high-grade NHL schedules to ALL-derived protocols. The aim of this work is to report the clinical characteristics, overall survival (OS), event free survival (EFS), and common chemotherapy toxicities of lymphoblastic lymphoma (LBL) patients during a 5.5year period. Patients and methods A Retrospective review of patient's charts diagnosed and treated as LBL during the period between July 2007 and end of December 2012 was done. Patients were treated according to St. Jude Children Research Hospital ALL Total Therapy XV protocol, standard risk arm. Results This study included 77 patients. T-cell LBL patients were 67, while 10 were of B-cell origin. The median age at diagnosis was 9years (95% CI: 7-10). The majority were males 54/77. Stage III patients were 51, stage IV 13, stage II 11 and stage I 2 patients. Two patients were excluded from analysis as they died before receiving chemotherapy. Complete remission post induction chemotherapy was seen in 22 patients considered early responders, and partial remission in 55 considered late responders. With a median follow up duration of 47months (95% CI: 38-56), the 4year overall survival and event free survival were 86.45% (95% CI: 73.78-94.09) and 82.18% (95% CI: 69.25-90.61) respectively. Twelve patients died during the study period; 2 early deaths before starting chemotherapy from disease progression, 2 in CR due to chemotherapy related toxicity and 8 from disease progression. All the relapsed patients were T-cell, had advanced disease at presentation (6 with stage III; 2 with stage IV). Two patients (2.6%) had isolated local, BM, and CNS relapse each, while 1 (1.3%) had both local and CNS relapse. Disease recurrence was local in 3 patients (3.9%), and systemic in 5 (6.4%), while it was early in 6 (7.8%), and late in 2 (2.6%) patients. Median time to disease progression was 20months (range 5-39months). All relapsed patients did not survive salvage chemotherapy. The most common chemotherapy toxicities were cerebral venous thrombosis (20%), followed by bone infarcts (10.6%), and avascular necrosis (AVN) of head of femur (9.3%). One patient developed secondary acute myeloid leukemia after 3years of FU with unfavorable cytogenetic abnormalities. Conclusion Results of treatment of LBL on the St Jude's total therapy XV study are comparable to most of the similar reported studies. Outcome of relapsing patients is extremely poor, hence there is a need to identify biologic or clinical prognostic factors including minimal residual tumor to better evaluate chemotherapy response. Steroid induced AVN, and cerebral vascular thrombosis were the main chemotherapeutic adverse events.

Outcome of pediatric parameningeal rhabdomyosarcoma. The Children Cancer Hospital, Egypt, experience.

BACKGROUND: PM RMS represents a diagnostic and therapeutic problem as it is less visible than other superficial head and neck sites, and has tendency to local and intracranial extension. OBJECTIVES: The aim of this work is to study the treatment outcome, overall survival (OS) and event free survival (EFS) of pediatric PM RMS patients diagnosed and treated at the Children Cancer Hospital-Egypt [CCHE-57357] during a 4 year period. METHODS: Retrospective review of charts of newly diagnosed pediatric PM RMS patients diagnosed and treated in CCHE during the period between July 2007 and the end of June 2011. RESULTS: Forty-two pediatric patients with PM RMS with age ranging from 3 months to 17.7 years (median 6.9 years) were studied. The follow up period ranged from 4 to 55 months with a median of 24.8 months. Twenty-one patients [50%] were stage III, while 11 patients [26.1%] were stage IV. The 3-year overall survival (OS) was 58.4 ± 8.9%. OS was 65.9 ± 10% for non metastatic tumors while it was 35.8 ± 16.2% for the metastatic ones (p=0.039). The 3-year event-free survival (EFS) was 48 ± 8.6% for the whole group. The non-metastatic and metastatic patients had 3-year EFS of 56.5 ± 9.7% and 24.9 ± 14.9% respectively. This difference was not statistically significant (p=0.127). CONCLUSION: PM RMS remains a diagnostic and therapeutic problem. Late presentation and advanced local disease compromise treatment options and decrease OS and EFS.