SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing.

Copy number variants (CNVs) represent major etiologic factors in rare genetic diseases. Current clinical CNV interpretation workflows require extensive back-and-forth with multiple tools and databases. This increases complexity and time burden, potentially resulting in missed genetic diagnoses. We present the Suite for CNV Interpretation and Prioritization (SCIP), a software package for the clinical interpretation of CNVs detected by whole-genome sequencing (WGS). The SCIP Visualization Module near-instantaneously displays all information necessary for CNV interpretation (variant quality, population frequency, inheritance pattern, and clinical relevance) on a single page-supported by modules providing variant filtration and prioritization. SCIP was comprehensively evaluated using WGS data from 1027 families with congenital cardiac disease and/or autism spectrum disorder, containing 187 pathogenic or likely pathogenic (P/LP) CNVs identified in previous curations. SCIP was efficient in filtration and prioritization: a median of just two CNVs per case were selected for review, yet it captured all P/LP findings (92.5% of which ranked 1st). SCIP was also able to identify one pathogenic CNV previously missed. SCIP was benchmarked against AnnotSV and a spreadsheet-based manual workflow and performed superiorly than both. In conclusion, SCIP is a novel software package for efficient clinical CNV interpretation, substantially faster and more accurate than previous tools (available at https://github.com/qd29/SCIP , a video tutorial series is available at https://bit.ly/SCIPVideos ).

Variations in sexual fitness among natural strains of the opportunistic human fungal pathogen Aspergillus fumigatus.

Aspergillus fumigatus is a ubiquitous ascomycete fungus, naturally inhabiting the soil and compost piles. Its conidia readily disperse into the atmosphere and cause opportunistic infections known as aspergillosis. With the emerging resistance to many antifungal drugs, our understanding of A. fumigatus epidemiology has become increasingly important for developing effective control and treatment strategies. As a pathogen capable of both sexual and asexual reproduction, mutations causing drug resistance and increased virulence could be spread rapidly in A. fumigatus populations. However, relatively little is known about the distributions of sexual reproductive fitness among natural strains of A. fumigatus. Here we investigated the formation of sexual reproductive structure (i.e. cleistothecia) and sexual spore viability among 60 natural strains of A. fumigatus. These strains were from six geographically distant countries (India, China, Canada, Cameroon, Saudi Arabia, and New Zealand), with 10 strains (including five MAT1-1 strains and five MAT1-2 strains) from each country. These strains were crossed in all combinations with strains of the opposite mating type. In addition, all 60 strains were crossed with either AFB62-1 (MAT1-1) or AFIR928 (MAT1-2), two reference supermater strains. Of the 900 crosses among the 60 natural strains, 136 crosses (15.1%) produced cleistothecia. Our analyses revealed that strains from China had the highest average ability to form cleistothecia, followed by those from New Zealand, Saudi Arabia, India, Canada, and Cameroon. Among the crosses that produced cleistothecia, about 40% produced viable ascospores, with the rate of ascospore germination varied significantly among crosses. Interestingly, neither the ability to form cleistothecia nor ascospore germination rate showed any distinct relationships with either geographic or genetic distance between parental strains. Our results suggest that genetic exchange among geographically and genetically divergent strains of A. fumigatus are possible. However, the rates of genetic exchange likely vary among strains and populations in nature.

Donor mucosal immunocytes perpetuate refractory GVHD after intestinal transplantation without engrafting in recipient bone marrow: Case report and review of the literature.

GVHD as a complication of SOT presents both a diagnostic and therapeutic challenge. Typically affecting the skin, gastrointestinal tract, and liver, GVHD occurs when donor lymphocytes engrafted in recipient tissues are activated by host antigen-presenting cells resulting in cytokine release and donor cell-mediated cytotoxicity to host tissue. Here, we describe a 5-year-old girl who developed fatal, refractory GVHD after isolated intestinal transplantation when recipient immune cells failed to repopulate the allograft in the setting of CMV viremia. Persistence of the donor immune cells in the allograft mucosa, rather than engraftment in the recipient bone marrow, likely perpetuated this refractory GVHD. Early diagnosis and intervention are critical to reduce morbidity and mortality. Thus, periodic monitoring of peripheral blood and allograft mucosal chimerism with sensitive detection methods may allow early detection and potentially curative enterectomy in similar cases of refractory GVHD.

Succinate Dehydrogenase-Deficient Gastrointestinal Stromal Tumor With SDHC Germline Mutation and Bilateral Renal and Neck Cysts.

Gastrointestinal stromal tumors (GISTs) are rare in children. Succinate dehydrogenase (SDH)-deficient GISTs are wild type and lack KIT proto-oncogene receptor tyrosine kinase and platelet-derived growth factor receptor A ( KIT or PDGFRA) mutations. These tumors result from germline SDH mutations, somatic SDH mutations, or SDH epimutants. Germline mutations in SDH genes ( SDHA, SDHB, SDHC, or SDHD) suggest Carney-Stratakis syndrome, a paraganglioma syndrome with predisposition for GIST. Negative immunohistochemistry for SDHB indicates dysfunction of the mitochondrial complex regardless of the subunit affected. We present an adolescent male with an SDH-deficient GIST and SDHC germline mutation who developed bilateral renal cysts and neck cysts, not previously described in children with this mutation. Germline testing is critical when SDH mutations are discovered due to treatment and surveillance implications. Further investigations are necessary to fully define the phenotypic expression of this mutation.

Improvements in intestine transplantation.

Transplantation of the intestine in children has presented significant challenges even as it has become a standard to treat nutritional failure due to short gut syndrome. These challenges have been addressed in part by significant improvements in short and long-term care. Noteworthy enhancements include reduced need for intestine transplantation, drug-sparing immunosuppressive regimens, immune monitoring, and improved surveillance and management of PTLD and non-adherence.

Post-transplant lymphoproliferative disorder in pediatric intestinal transplant recipients: A literature review.

Intestinal transplantation is a successful treatment for children with intestinal failure, but has many potential complications. PTLD, a clinically and histologically diverse malignancy, occurs frequently after intestinal transplantation and can be fatal. The management of this disease is particularly challenging. The rejection-prone intestinal allograft requires high levels of immunosuppression, a precondition for PTLD. While EBV infection clearly plays a role in disease pathogenesis, the relatively naïve immune system of children is another likely contributor. As a result, pediatric intestine recipients have a higher risk of developing PTLD than other solid organ recipients. Other risk factors for disease development such as molecular and genomic changes that precipitate malignant transformation are not fully understood, especially among children. Studies on adults have started to describe the molecular pathogenesis of PTLD, but the genomic landscape of the malignancy remains largely undefined in pediatric intestinal transplant patients. In this review, we describe what is known about PTLD in pediatric patients after intestinal transplant and highlight current knowledge gaps to better direct future investigations in the pediatric population.

Hormone Therapy and Venous Thromboembolism in a Transgender Adolescent.

Venous thromboembolism can be precipitated by both genetic and acquired factors, but the role of testosterone therapy is less clear. Here, we present a 17-year-old transgender adolescent, transitioning from female to male, receiving both estrogen and testosterone therapy, who developed a pulmonary embolism without an underlying genetic thrombophilic condition. As transgender medical care evolves, the use of testosterone as cross-sex hormone therapy in adolescents is likely to increase. Our review suggests that care must be taken when initiating treatment with testosterone, and modification of other thrombophilic risks should be explored before starting therapy in this population.