Cloud-based interactive analytics for terabytes of genomic variants data.

MOTIVATION: Large scale genomic sequencing is now widely used to decipher questions in diverse realms such as biological function, human diseases, evolution, ecosystems, and agriculture. With the quantity and diversity these data harbor, a robust and scalable data handling and analysis solution is desired. RESULTS: We present interactive analytics using a cloud-based columnar database built on Dremel to perform information compression, comprehensive quality controls, and biological information retrieval in large volumes of genomic data. We demonstrate such Big Data computing paradigms can provide orders of magnitude faster turnaround for common genomic analyses, transforming long-running batch jobs submitted via a Linux shell into questions that can be asked from a web browser in seconds. Using this method, we assessed a study population of 475 deeply sequenced human genomes for genomic call rate, genotype and allele frequency distribution, variant density across the genome, and pharmacogenomic information. AVAILABILITY AND IMPLEMENTATION: Our analysis framework is implemented in Google Cloud Platform and BigQuery. Codes are available at https://github.com/StanfordBioinformatics/mvp_aaa_codelabs. CONTACT: cuiping@stanford.edu or ptsao@stanford.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Verruca plana as a complication of CO2 laser treatment: a case report.

Carbon dioxide (CO2) laser treatment is a common therapeutic modality for many dermatologic conditions. It uses a high energy, infrared beam of light, which selectively targets water-containing tissue resulting in controlled ablative resurfacing. This modality, however, can manifest significant cosmetic side effects. Here we report a case of verruca plana manifesting as a response to CO2 laser treatment. A 74-year-old female with recent Mohs surgery for a basal cell carcinoma, presented for full-face-fractionated CO2 treatment to address her surgical scars in addition to treating her mild diffuse actinic damage. Six weeks post treatment, the patient developed erythematous thin plaques over the areas that had been treated. Histology was consistent with verruca plana. Lesions showed mild improvement with topical tretinoin. Verruca plana are benign and typically self-limited; however, they can present a significant cosmetic burden to patients and are an important complication to consider when performing elective cosmetic procedures.

Microcystic adnexal carcinoma in the axilla of an 18-year-old woman.

Microcystic adnexal carcinoma (MAC) is an uncommon adnexal neoplasm with a predilection for the head and neck. The tumor rarely metastasizes but is locally aggressive and commonly demonstrates perineural invasion. MAC occurs most often in older adults. This report describes a young woman with a MAC in her left axilla who required two stages of Mohs micrographic surgery followed by a wide local excision because of persistent perineural invasion in close proximity to the brachial plexus. Other cases presenting in the pediatric age group are discussed.

Simulation in dermatologic surgery: a new paradigm in training.

BACKGROUND: Simulation-based training has become popular in many surgical residencies for acquiring procedural skills, but simulator use is rare in dermatologic training. OBJECTIVE: To evaluate the perceived efficacy of obtaining dermatologic procedural skills using simulators. METHODS AND MATERIALS: Opinions of dermatology residents and staff regarding simulator use were assessed using questionnaires completed after a 2-day surgical symposium in which participants were instructed on and practiced with simulators and cadavers. RESULTS: Overall, 93.9% strongly agreed that simulators are helpful in acquiring procedural skills. More than three-quarters of participants agreed that simulators are useful in acquiring, refining, assessing, and learning these skills. Many participants further thought that simulator use would be beneficial in learning anatomy and trouble-shooting techniques. An overwhelming majority of those surveyed believed that training on simulators would be helpful in learning various dermatologic procedures; 90.9% of participants thought that training using simulators should be, at least in part, a mandatory component of residency. It was felt that this training should be conducted at the beginning of residency, with additional with sessions held throughout training. CONCLUSION: Simulation offers an excellent model for the acquisition and assessment of dermatologic procedural skills. Cost and availability of instructors remain obstacles. Further studies are required to evaluate the implementation and effectiveness of these models.

Impact of osteopathic manipulative techniques on the management of dizziness caused by neuro-otologic disorders: systematic review and meta-analysis.

CONTEXT: Osteopathic manipulative treatment (OMT) has been utilized by osteopathic clinicians as primary or adjunctive management for dizziness caused by neuro-otologic disorders. To our knowledge, no current systematic reviews provide pooled estimates that evaluate the impact of OMT on dizziness. OBJECTIVES: We aimed to systematically evaluate the effectiveness and safety of OMT and analogous techniques in the treatment of dizziness. METHODS: We performed a literature search in CINAHL, Embase, MEDLINE, Allied and Complementary Medicine Database (AMED), EMCare, Physiotherapy Evidence Database (PEDro), PubMed, PsycINFO, Osteopathic Medicine Digital Library (OSTMED.DR), and Cochrane Central Register of Controlled Trials (CENTRAL) from inception to March 2021 for randomized controlled trials (RCTs) and prospective or retrospective observational studies of adult patients experiencing dizziness from neuro-otological disorders. Eligible studies compared the effectiveness of OMT or OMT analogous techniques with a comparator intervention, such as a sham manipulation, a different manual technique, standard of care, or a nonpharmacological intervention like exercise or behavioral therapy. Assessed outcomes included disability associated with dizziness, dizziness severity, dizziness frequency, risk of fall, improvement in quality of life (QOL), and return to work (RTW). Assessed harm outcomes included all-cause dropout (ACD) rates, dropouts due to inefficacy, and adverse events. The meta-analysis was based on the similarities between the OMT or OMT analogous technique and the comparator interventions. The risk of bias (ROB) was assessed utilizing a modified version of the Cochrane Risk of Bias Tool for RCTs and the Cochrane Risk of Bias in Non-randomized Studies - of Interventions (ROBINS-I) for observational studies. The quality of evidence was determined utilizing the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) approach. RESULTS: There were 3,375 studies identified and screened, and the full text of 47 of them were reviewed. Among those, 12 (11 RCTs, 1 observational study, n=367 participants) met the inclusion criteria for data extraction. Moderate-quality evidence showed that articular OMT techniques were associated with decreases (all p<0.01) in disability associated with dizziness (n=141, mean difference [MD]=-11, 95% confidence interval [CI]=-16.2 to -5.9), dizziness severity (n=158, MD=-1.6, 95% CI=-2.4 to -0.7), and dizziness frequency (n=136, MD=-0.6, 95% CI=-1.1 to -0.2). Low-quality evidence showed that articular OMT was not associated with ACD rates (odds ratio [OR]=2.2, 95% CI=0.5 to 10.2, p=0.31). When data were pooled for any type of OMT technique, findings were similar; however, disability associated with dizziness and ACD rates had high heterogeneity (I2=59 and 46%). No studies met all of the criteria for ROB. CONCLUSIONS: The current review found moderate-quality evidence that treatment with articular OMT techniques was significantly associated with decreased disability associated with dizziness, dizziness severity, and dizziness frequency. However, our findings should be interpreted cautiously because of the high ROB and small sample sizes in the eligible studies.

Triage in Mohs micrographic surgery.

Mohs micrographic surgery can be unpredictable with respect to the level of difficulty of individual cases, especially when pre-operative information is limited. In a retrospective study, Sahai and Walling found complex tumors as defined by requiring four or more stages to clearance to be associated with: recurrent tumors, basal cell carcinoma (BCC) with aggressive histology, tumors with a pre-operative size greater than 1 cm and tumors on the nose.1 The authors created a simplified system for "triaging" Mohs surgery cases in order to predict case complexity and, thus, be better able to manage the scheduling of those cases. Data gathered from 12 months of utilizing this system was used to validate the system's ability to predict case complexity with respect to number of stages for tumor clearance and complexity of reconstruction.

Extent and diversity of human alternative splicing established by complementary database annotation and microarray analysis.

Alternative splicing generates functional diversity in higher organisms through alternative first and last exons, skipped and included exons, intron retentions and alternative donor, and acceptor sites. In large-scale microarray studies in humans and the mouse, emphasis so far has been placed on exon-skip events, leaving the prevalence and importance of other splice types largely unexplored. Using a new human splice variant database and a genome-wide microarray to probes thousands of splice events of each type, we measured differential expression of splice types across six pair of diverse cell lines and validated the database annotation process. Results suggest that splicing in humans is more complex than simple exon-skip events, which account for a minority of splicing differences. The relative frequency of differential expression of the splice types correlates with what is found by our annotation efforts. In conclusion, alternative splicing in human cells is considerably more complex than the canonical example of the exon skip. The complementary approaches of genome-wide annotation of alternative splicing in human and design of genome-wide splicing microarrays to measure differential splicing in biological samples provide a powerful high-throughput tool to study the role of alternative splicing in human biology.

The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.

The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Links to resources and documentation can be found at www.isb-cgc.org Cancer Res; 77(21); e7-10. ©2017 AACR.

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.

Genome-wide characteristics of de novo mutations in autism.

De novo mutations (DNMs) are important in Autism Spectrum Disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole genome sequencing (WGS) of 200 ASD parent-child trios and characterized germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (p=4.2×10-10). However, when clustered DNMs (those within 20kb) were found in ASD, not only did they mostly originate from the mother (p=7.7×10-13), but they could also be found adjacent to de novo copy number variations (CNVs) where the mutation rate was significantly elevated (p=2.4×10-24). By comparing DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (p=8.0×10-9; OR=1.84), of which 15.6% (p=4.3×10-3) and 22.5% (p=7.0×10-5) were in the non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, boundaries involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD risk- and epigenetic- genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the etiology of ASD.

Histopathologic features in a case of hyperimmunoglobulinemia D syndrome.

We describe a case of Mevalonate Kinase Deficiency (MKD) also known as Hyperimmunoglobulinemia D Syndrome (HIDS) presenting as a Sweet-like syndrome in a 5-week-old with multiple erythematous plaques, fever, aseptic meningitis, and bronchiolitis. The locations of the predominant plaques were periumbilical and periocular, which originally prompted concern for omphalitis and preseptal cellulitis. Histopathology demonstrated a neutrophilic and histiocytic dermatitis with prominent squamous syringometaplasia and leukocytoclasis in the absence of a vasculitis. This case is reported here due to the unique findings of a prominent histiocytic component in addition to the typically described neutrophilic infiltrate.

PET/CT imaging of squamoid eccrine ductal carcinoma.

Squamoid eccrine ductal carcinoma is an extremely uncommon type of eccrine carcinoma (EC). An important distinguishing feature of EC is potential for metastasis. Eccrine carcinoma has been reported to metastasize in up to 50% of cases. Despite tumor aggressivity, no recommendations for staging exist. We present the case of a 91-year-old woman with a lesion involving the left index finger confirmed to be squamoid eccrine ductal carcinoma by dermatopathologic evaluation. 18F-FDG PET/CT images revealed widespread multifocal FDG-avid metastatic disease. Although rare, staging of EC with 18F-FDG PET/CT imaging of the entire body is indicated.

Botulinum toxin: An effective treatment for prosthesis-related hyperhidrosis in patients with traumatic amputations.

Hyperhidrosis-related to prosthesis use in patients who have suffered a traumatic limb amputation presents itself as a barrier to comfort, prosthesis use and overall quality of life. This review intends to encourage dermatologists to consider the use of botulinum toxin A or B for the treatment of hyperhidrosis in the residual limb and may serve as a stimulus for a modern, in-depth, and more comprehensive study. A review of the literature was conducted using the PubMed database, focusing on hyperhidrosis treatment after traumatic limb amputation. Articles discussing hyperhidrosis treatment for amputations secondary to chronic medical conditions were excluded. Seven case studies published over the last 12 years have demonstrated positive outcomes of this treatment strategy. Overall, there is little data examining this topic and current publications focus primarily on small case series. A larger, double-blind, placebo-controlled study would likely benefit veterans, service members, and civilians.