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Cancer genomic heterogeneity presents significant challenges for understanding oncogenic processes and for cancer's clinical management. Variation in driver mutation frequency between patients with the same tumor type as well as within an individual patients' cancer can shape the use of mutations as diagnostic, prognostic, and predictive biomarkers. We have characterized genomic heterogeneity between and within canine splenic hemangiosarcoma (HSA), a common naturally occurring cancer in pet dogs that is similar to human angiosarcoma (AS). HSA is a clinically, physiologically, and genomically complex canine cancer that may serve as a valuable model for understanding the origin and clinical impact of cancer heterogeneity. We conducted a prospective collection of 52 splenic masses from 43 dogs (27 HSA, 15 benign masses, and 1 stromal sarcoma) presenting for emergency care with hemoperitoneum secondary to a ruptured splenic mass. Multi-platform genomic analysis included matched tumor/normal targeted sequencing panel and exome sequencing. We found candidate somatic cancer driver mutations in 14/27 (52%) HSAs. Among recurrent candidate driver mutations, TP53 was most commonly mutated (30%) followed by PIK3CA (15%), AKT1 (11%), and CDKN2AIP (11%). We also identified significant intratumoral genomic heterogeneity, consistent with a branched evolution model, through multi-region exome sequencing of three distinct tumor regions from selected primary splenic tumors. These data provide new perspectives on the genomic landscape of this veterinary cancer and suggest a cross-species value for using HSA in pet dogs as a naturally occurring model of intratumoral heterogeneity. [ABSTRACT FROM AUTHOR]

Abstract Background The burden of cerebrovascular disease in developing countries is rising sharply. The prevalence of established risk factors of stroke is exceptionally high in Pakistan. However, there is limited data on the burden of stroke and transient ischemic attack (TIA) in South Asia. We report the first such study conducted in an urban slum of Karachi, Pakistan. Methods Individuals 35 years of age or older were invited for participation in this investigation through simple random sampling. A structured face-to-face interview was conducted using a pre-tested stroke symptom questionnaire in each participant to screen for past stroke or TIA followed by neurological examination of suspected cases. Anthropometric measurements and random blood glucose levels were recorded. Multivariable logistic regression was used to determine the association of vascular risk factors with prevalence of stroke. Results Five hundred and forty five individuals (49.4% females) participated in the study with a response rate of 90.8%. One hundred and four individuals (19.1%) were observed to have a prior stroke while TIA was found in 53 individuals (9.7%). Overall, 119 individuals (21.8% with 66.4% females) had stroke and/or TIA. Female gender, old age, raised random blood glucose level and use of chewable tobacco were significantly associated with the prevalence of cerebrovascular disease. Conclusion This is the first study demonstrating an alarmingly high life-time prevalence of cerebrovascular disease in Pakistan. Individual and public health interventions in Pakistan to increase awareness about stroke, its prevention and therapy are warranted.

Abstract Background Intracranial stenosis is the most common cause of stroke among Asians. It has a poor prognosis with a high rate of recurrence. No effective medical or surgical treatment modality has been developed for the treatment of stroke due to intracranial stenosis. We aim to identify risk factors and biomarkers for intracranial stenosis and to develop techniques such as use of transcranial doppler to help diagnose intracranial stenosis in a cost-effective manner. Methods/Design The Karachi Intracranial Stenosis Study (KISS) is a prospective, observational, case-control study to describe the clinical features and determine the risk factors of patients with stroke due to intracranial stenosis and compare them to those with stroke due to other etiologies as well as to unaffected individuals. We plan to recruit 200 patients with stroke due to intracranial stenosis and two control groups each of 150 matched individuals. The first set of controls will include patients with ischemic stroke that is due to other atherosclerotic mechanisms specifically lacunar and cardioembolic strokes. The second group will consist of stroke free individuals. Standardized interviews will be conducted to determine demographic, medical, social, and behavioral variables along with baseline medications. Mandatory procedures for inclusion in the study are clinical confirmation of stroke by a healthcare professional within 72 hours of onset, 12 lead electrocardiogram, and neuroimaging. In addition, lipid profile, serum glucose, creatinine and HbA1C will be measured in all participants. Ancillary tests will include carotid ultrasound, transcranial doppler and magnetic resonance or computed tomography angiogram to rule out concurrent carotid disease. Echocardiogram and other additional investigations will be performed at these centers at the discretion of the regional physicians. Discussion The results of this study will help inform locally relevant clinical guidelines and effective public health and individual interventions.

A 40-year- old patient was admitted through the acute medical take with pleuritic chest pain and rigours. He had a medical history of opiate dependence and was receiving 60 mg of methadone once daily. He was diagnosed with a community-acquired pneumonia and treated with amoxicillin and clarithromycin. After administration of only two concomitant doses of methadone and oral clarithromycin, he developed an opioid toxidrome with type-2 respiratory failure, a decreased level of consciousness and pinpoint pupils. The patient was treated with naloxone and his symptoms improved. Retrospectively, it was suspected that an interaction between clarithromycin and methadone might have contributed to the toxidrome. Respiratory failure has not been previously prescribed for this combination of medication and is of high importance for physicians and pharmacists around the world. [ABSTRACT FROM AUTHOR]

Detecting cancer by urine cell-free DNA: Detection of cell-free DNA (cfDNA) in urine could be a noninvasive approach to diagnose cancer. However, urine cfDNA is very fragmented, making it difficult to use. Markus et al. analyzed fragmentation patterns in urine and plasma cfDNA using whole-genome sequencing in healthy individuals and those with cancer. Compared to cfDNA from healthy individuals, tumor-derived fragmentation patterns ending within recurrently protected regions occurred more frequently in urine. By comparing genome-wide differences in urine cfDNA fragmentation patterns, the authors could distinguish cancer samples from controls, suggesting that this approach might complement plasma cfDNA as a cancer diagnostic. Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented. Whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we characterized fragmentation patterns in urine cfDNA using whole-genome sequencing. Size distribution of urine cfDNA fragments showed multiple strong peaks between 40 and 120 base pairs (bp) with a modal size of 81- and sharp 10-bp periodicity, suggesting transient protection from complete degradation. These properties were robust to preanalytical perturbations, such as at-home collection and delay in processing. Genome-wide sequencing coverage of urine cfDNA fragments revealed recurrently protected regions (RPRs) conserved across individuals, with partial overlap with nucleosome positioning maps inferred from plasma cfDNA. The ends of cfDNA fragments clustered upstream and downstream of RPRs, and nucleotide frequencies of fragment ends indicated enzymatic digestion of urine cfDNA. Compared to plasma, fragmentation patterns in urine cfDNA showed greater correlation with gene expression and chromatin accessibility in epithelial cells of the urinary tract. We determined that tumor-derived urine cfDNA exhibits a higher frequency of aberrant fragments that end within RPRs. By comparing the fraction of aberrant fragments and nucleotide frequencies of fragment ends, we identified urine samples from cancer patients with an area under the curve of 0.89. Our results revealed nonrandom genomic positioning of urine cfDNA fragments and suggested that analysis of fragmentation patterns across recurrently protected genomic loci may serve as a cancer diagnostic. [ABSTRACT FROM AUTHOR]

Early detection, no time travel needed: Analysis of tumor DNA shed into a patient's circulation can provide a noninvasive means of detecting the presence of a tumor and analyzing its DNA for targetable mutations. Unfortunately, it can be difficult to detect small amounts of tumor DNA in the blood, especially in patients who have already undergone initial chemotherapy treatment. To address this problem, McDonald et al. developed a method of targeted digital sequencing (TARDIS), which is customized for each patient but can then be used to monitor the patient over time for and allow early detection of tumor recurrence. Longitudinal analysis of circulating tumor DNA (ctDNA) has shown promise for monitoring treatment response. However, most current methods lack adequate sensitivity for residual disease detection during or after completion of treatment in patients with nonmetastatic cancer. To address this gap and to improve sensitivity for minute quantities of residual tumor DNA in plasma, we have developed targeted digital sequencing (TARDIS) for multiplexed analysis of patient-specific cancer mutations. In reference samples, by simultaneously analyzing 8 to 16 known mutations, TARDIS achieved 91 and 53% sensitivity at mutant allele fractions (AFs) of 3 in 104 and 3 in 105, respectively, with 96% specificity, using input DNA equivalent to a single tube of blood. We successfully analyzed up to 115 mutations per patient in 80 plasma samples from 33 women with stage I to III breast cancer. Before treatment, TARDIS detected ctDNA in all patients with 0.11% median AF. After completion of neoadjuvant therapy, ctDNA concentrations were lower in patients who achieved pathological complete response (pathCR) compared to patients with residual disease (median AFs, 0.003 and 0.017%, respectively, P = 0.0057, AUC = 0.83). In addition, patients with pathCR showed a larger decrease in ctDNA concentrations during neoadjuvant therapy. These results demonstrate high accuracy for assessment of molecular response and residual disease during neoadjuvant therapy using ctDNA analysis. TARDIS has achieved up to 100-fold improvement beyond the current limit of ctDNA detection using clinically relevant blood volumes, demonstrating that personalized ctDNA tracking could enable individualized clinical management of patients with cancer treated with curative intent. [ABSTRACT FROM AUTHOR]

Background: External ventricular drains (EVD) are commonly utilized for temporary diversion of cerebrospinal fluid (CSF). Many neurosurgeons prefer long-tunneled EVDs in their routine practice. However, it is still unclear whether this extended tunneling helps in reducing CSF infection. Keeping this in mind, we decided to compare infection rates in long-tunneled versus short-tunneled EVDs in the setting of a developing country. Materials and Methods: A prospective study of 60 patients was conducted. Consenting patients who underwent short-tunneled (Group A) or long-tunneled (Group B) EVDs between January 2008 and June 2009 were followed during the course of their inpatient care. All operational protocol was standardized during the trial. Serial samples of CSF were analyzed to detect infection. Results: Mean age of patients was 33.6 years with 32 males (53.3%). Mean duration of long-tunneled EVD was 13.4 ± 7.2 days, whereas that of short-tunneled EVD was 5.3 ± 2.7 days (P < 0.001). Three patients with long-tunneled EVD (10.0%), whereas one patient with short-tunneled EVD (3.3%) developed drain-related infections; however, this was non-significant (P = 0.301). However, patients with short-tunneled EVD got infected earlier on day 3when compared with the long-tunneled EVDs, which got infected after a mean duration of 7.3 days. The overall risk of infection for long-tunneled EVDs was 7.46 per 1,000 ventricular drainage days which was comparable to the risk of 6.33 per 1,000 ventricular drainage days seen for short-tunneled EVDs. Conclusion: Long-tunneled EVDs appear to only delay potential infections without having any effect on the actual risk of infection. Long-tunneled EVD in a resource-limited setting is technically challenging and may not yield additional benefits to the patient. However, larger and prospective studies are needed to establish the rate of infections and other complications. [ABSTRACT FROM AUTHOR]

Epithelial ovarian cancer is a highly heterogeneous disease and remains the most lethal gynaecological malignancy in the Western world. Therapeutic approaches need to account for inter-patient and intra-tumoural heterogeneity and detailed characterization of in vitro models representing the different histological and molecular ovarian cancer subtypes is critical to enable reliable preclinical testing. There are approximately 100 publicly available ovarian cancer cell lines but their cellular and molecular characteristics are largely undescribed. We have characterized 39 ovarian cancer cell lines under uniform conditions for growth characteristics, mRNA/microRNA expression, exon sequencing, drug response for clinically-relevant therapeutics and collated all available information on the original clinical features and site of origin. We tested for statistical associations between the cellular and molecular features of the lines and clinical features. Of the 39 ovarian cancer cell lines, 14 were assigned as high-grade serous, four serous-type, one low-grade serous and 20 non-serous type. Three morphological subtypes: Epithelial (n = 21), Round (n = 7) and Spindle (n = 12) were identified that showed distinct biological and molecular characteristics, including overexpression of cell movement and migration-associated genes in the Spindle subtype. Comparison with the original clinical data showed association of the spindle-like tumours with metastasis, advanced stage, suboptimal debulking and poor prognosis. In addition, the expression profiles of Spindle, Round and Epithelial morphologies clustered with the previously described C1-stromal, C5-mesenchymal and C4 ovarian subtype expression profiles respectively. Comprehensive profiling of 39 ovarian cancer cell lines under controlled, uniform conditions demonstrates clinically relevant cellular and genomic characteristics. This data provides a rational basis for selecting models to develop specific treatment approaches for histological and molecular subtypes of ovarian cancer. [ABSTRACT FROM AUTHOR]

Cancer genome sequencing studies have identified numerous driver genes, but the relative timing of mutations in carcinogenesis remains unclear. The gradual progression from premalignant Barrett's esophagus to esophageal adenocarcinoma (EAC) provides an ideal model to study the ordering of somatic mutations. We identified recurrently mutated genes and assessed clonal structure using whole-genome sequencing and amplicon resequencing of 112 EACs. We next screened a cohort of 109 biopsies from 2 key transition points in the development of malignancy: benign metaplastic never-dysplastic Barrett's esophagus (NDBE; n = 66) and high-grade dysplasia (HGD; n = 43). Unexpectedly, the majority of recurrently mutated genes in EAC were also mutated in NDBE. Only TP53 and SMAD4 mutations occurred in a stage-specific manner, confined to HGD and EAC, respectively. Finally, we applied this knowledge to identify high-risk Barrett's esophagus in a new non-endoscopic test. In conclusion, mutations in EAC driver genes generally occur exceptionally early in disease development with profound implications for diagnostic and therapeutic strategies. [ABSTRACT FROM AUTHOR]

The article discusses research on the lower genetic determinants in the major blood lipids among Pakistanis in comparison with those of Europeans. Assessed were variants across 2000 genes in 3200 Pakistanis using the same gene array and lipid assays used with those of 2450 Germans. Findings showed that there were several lipid-related genetic variants present among Pakistanis and Europeans while there is a difference in allelic frequencies and effect of sizes of lipid-related variants between Europeans and Pakistanis.

Background: Morbidity associated with primary headache disorders is a major public health problem with an overall prevalence of 46%. Tension-type headache and migraine are the two most prevalent causes. However, headache has not been sufficiently studied as a cause of morbidity in the developing world. Literature on prevalence and classification of these disorders in South Asia is scarce. The aim of this study is to describe the classification and clinical features of headache patients who seek medical advice in Pakistan. Methods and Results: Medical records of 255 consecutive patients who presented to a headache clinic at a tertiary care hospital were reviewed. Demographic details, onset and lifetime duration of illness, pattern of headache, associated features and family history were recorded. International Classification of Headache Disorders version 2 was applied. 66% of all patients were women and 81% of them were between 16 and 49 years of age. Migraine was the most common disorder (206 patients) followed by tension-type headache (58 patients), medication-overuse headache (6 patients) and cluster headache (4 patients). Chronic daily headache was seen in 99 patients. Patients with tension-type headache suffered from more frequent episodes of headache than patients with migraine (p<0.001). Duration of each headache episode was higher in women with menstrually related migraine (p = 0.015). Median age at presentation and at onset was lower in patients with migraine who reported a first-degree family history of the disease (p = 0.003 and p<0.001 respectively). Conclusions/Significance: Patients who seek medical advice for headache in Pakistan are usually in their most productive ages. Migraine and tension-type headache are the most common clinical presentations of headache. Onset of migraine is earlier in patients with first-degree family history. Menstrually related migraine affects women with headache episodes of longer duration than other patients and it warrants special therapeutic consideration. Follow-up studies to describe epidemiology and burden of headache in Pakistan are needed. [ABSTRACT FROM AUTHOR]

This paper presents the results of an exploratory study carried out to learn about the use and impact of Information and Communication Technologies (ICT) on Small and Medium Sized Enterprises (SMEs) in Oman. The study investigates ICT infrastructure, software used, driver for ICT investment, perceptions about business benefits of ICT and outsourcing trends of SMEs. The study provides an insight on the barriers for the adoption of ICT. Data on these aspects of ICT was collected from 51 SMEs through a survey instrument. The results of the study show that only a small number of SMEs in Oman are aware of the benefits of ICT adoption. The main driving forces for ICT investment are to provide better and faster customer service and to stay ahead of the competition. A majority of surveyed SMEs have reported a positive performance and other benefits by utilizing ICT in their businesses. Majority of SMEs outsource most of their ICT activities. Lack of internal capabilities, high cost of ICT and lack of information about suitable ICT solutions and implementation were some of the major barriers in adopting ICT. These findings are consistent with other studies e.g. (Harindranath et al 2008). There is a need for more focus and concerted efforts on increasing awareness among SMEs on the benefits of ICT adoption. The results of the study recognize the need for more training facilities in ICT for SMEs, measures to provide ICT products and services at an affordable cost, and availability of free professional advice and consulting at reasonable cost to SMEs. Our findings therefore have important implication for policy aimed at ICT adoption and use by SMEs. The findings of this research will provide a foundation for future research and will help policy makers in understanding the current state of affairs of the usage and impact of ICT on SMEs in Oman. [ABSTRACT FROM AUTHOR]

Circulating tumor DNA holds substantial promise as an early detection biomarker, particularly for cancers that do not have currently accepted screening methodologies, such as ovarian, pancreatic, and gastric cancers. Many features intrinsic to ctDNA analysis may be leveraged to enhance its use as an early cancer detection biomarker: including ctDNA fragment lengths, DNA copy number variations, and associated patient phenotypic information. Furthermore, ctDNA testing may be synergistically used with other multi-omic biomarkers to enhance early detection. For instance, assays may incorporate early detection proteins (i.e., CA-125), epigenetic markers, circulating tumor RNA, nucleosomes, exosomes, and associated immune markers. Many companies are currently competing to develop a marketable early cancer detection test that leverages ctDNA. Although some hurdles (like early stage disease assay accuracy, high implementation costs, confounding from clonal hematopoiesis, and lack of clinical utility studies) need to be addressed before integration into healthcare, ctDNA assays hold substantial potential as an early cancer screening test. [ABSTRACT FROM AUTHOR]