As things are ever-changing here at CHOP and in the CCCR, so too in the Diskin Lab. Dr. Diskin is overseeing the newly formed Center for Childhood Cancer Research Bioinformatics Core, a resource to be used by Cancer Center researchers to help analyze data sets. This is a collaborative effort between CCCR and the Department for Biomedical and Health Informatics (DBHI), and is aimed at supporting the bioinformatics research needs of CCCR investigators.
We are pleased to announce that Rebecca Kaufman, MS will be the first member of this newly formed team as a Bioinformatics Scientist. Welcome, Rebecca! We hope to expand the team soon.
This month Dr. Diskin was featured alongside some other stand-out researchers and colleagues leading valuable work here at CHOP for a series celebrating women in STEM.
Intelligence Meets Inspiration: Celebrating Women in STEM at CHOP
Persevere, persist, and prioritize. These are some of the powerful words of wisdom that women in science at Children’s Hospital of Philadelphia would like to share with the next generation of female scientists. To celebrate Women’s History Month this year, we are continuing our tradition of highlighting the talented researchers at CHOP who work in the science, engineering, math, and technology (STEM) fields, which have historically been underrepresented by women.
We are excited to announce Laura’s first research manuscript is online today in the American Journal of Human Genetics (AJHG)! In this genome-wide study of rare germline copy number variations (CNVs), we found that chromosome 16p11.2 microdeletion predisposes to neuroblastoma, with a much larger effect size than seen for common variants identified by GWAS. This represents the culmination of nearly a decade of work to establish the numbers needed to definitively reach this conclusion in a relatively rare childhood cancer. The 16p11.2 deletion corresponds to a rare genetic syndrome associated with autism and other neurodevelopmental disorders. When parental DNA was available, the 550-kb deletion arose de novo in children diagnosed with neuroblastoma. It will be of interest to consider implications for genetic counseling for those diagnosed with 16p11.2 deletion syndrome, particularly given the diversity of phenotypes associated with the chromosomal deletion. To view the full report, please visit https://doi.org/10.1016/j.ajhg.2019.07.020 .
Full pdf is available at the following Share Link: https://authors.elsevier.com/a/1ZgzkgeWuDj-
Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma
Neuroblastoma is a cancer of the developing sympathetic nervous system. It is diagnosed in 600–700 children per year in the United States and accounts for 12% of pediatric cancer deaths. Despite recent advances in our understanding of this malignancy’s complex genetic architecture, the contribution of rare germline variants remains undefined. Here, we conducted a genome-wide analysis of large (>500 kb), rare (<1%) germline copy number variants (CNVs) in two independent, multi-ethnic cohorts totaling 5,585 children with neuroblastoma and 23,505 cancer-free control children. We identified a 550-kb deletion on chromosome 16p11.2 significantly enriched in neuroblastoma cases (0.39% of cases and 0.03% of controls; p = 3.34 × 10−9). Notably, this CNV corresponds to a known microdeletion syndrome that affects approximately one in 3,000 children and confers risk for diverse developmental phenotypes including autism spectrum disorder and other neurodevelopmental disorders. The CNV had a substantial impact on neuroblastoma risk, with an odds ratio of 13.9 (95% confidence interval = 5.8–33.4). The association remained significant when we restricted our analysis to individuals of European ancestry in order to mitigate potential confounding by population stratification (0.42% of cases and 0.03% of controls; p = 4.10 × 10−8). We used whole-genome sequencing (WGS) to validate the deletion in paired germline and tumor DNA from 12 cases. Finally, WGS of four parent-child trios revealed that the deletion primarily arose de novo without maternal or paternal bias. This finding expands the clinical phenotypes associated with 16p11.2 microdeletion syndrome to include cancer, and it suggests that disruption of the 16p11.2 region may dysregulate neurodevelopmental pathways that influence both neurological phenotypes and neuroblastoma.
Diskin Lab welcomes incoming Informatics Student Intern Rebecca Kaufman to the team!
Rebecca is currently pursuing her masters’ degree in Bioinformatics at Temple University, planning to complete her program and graduate in December. In the meantime, Rebecca is blending well into the team and lending us a hand wherever a computational need arises. We’re happy to have you join us, Rebecca!
Amber was selected to present her work entitled, “Integrative mass spectrometry, RNA-sequencing and ChIP-sequencing identifies DLK1 as an epigenetically regulated target in neuroblastoma,” as a talk at the 67th ASMS Conference on Mass Spectrometry and Allied Topics. The conference is an annual gathering for the American Society for Mass Spectrometry (ASMS) and was held this year in Atlanta, Georgia.
“Alex” Lobin Lee successfully passed his qualifying exams unconditionally and is therefore free to focus on his thesis work. This comes after months of preparation and is a critical step in the career of a graduate student. Congratulations, Alex!
It is with heavy hearts that we say goodbye to Dr. Gonzalo Lopez Garcia. Gonzalo worked with Diskin lab for three years as a Bioinformatics Scientist, and has accepted a position at Icahn School of Medicine at Mount Sinai in NY. There, Gonzalo will be an Assistant Professor of Genetics and Genomic Sciences. Though we will certainly miss his charm, his expertise, his enthusiasm, and his beautiful figures for every type of data, we are certain he won’t miss the commute from Manhattan every day! We wish you all the best, Gonzalo, and we look forward to many collaborations in the future!
Dr. Diskin has been quite busy this Spring! In addition to her teaching GCB/CAMB 752 Seminar in Genomics, and leading her lab, she has been traveling all over speaking. Between the first week of March and early May, Sharon traveled to Washington DC, Frederick MD, San Francisco CA, Cambridge UK, and ending with Boston MA! Here is a glimpse:
March 7: She presented “An integrative proteogenomic approach identifies DLK1 as an oncoprotein and target for immunotherapy in high-risk neuroblastoma” at the US HUPO (United States Human Proteomics) Meeting.
March 28: Sharon gave a seminar entitled “Genetic Predisposition to Neuroblastoma: From Discovery to Translational Opportunities” at the National Cancer Institute’s Pediatric Oncology Branch.
April 5: In San Francisco at the UCSF Helen Diller Family Comprehensive Cancer Center Seminar, Sharon gave a lecture “Unraveling the Genetic Basis of Neuroblastoma: From Discovery to Clinical Implications”.
April 12th: Dr. Diskin was the invited speaker at the 5th Neuroblastoma United Kingdom (NBUK) Research Symposium at Cambridge. Her talk there was titled “Multi-omic surfaceome study identifies DLK1 as a candidate oncoprotein and immunotherapeutic target in neuroblastoma.”
May 7th: Her final trip of the Spring was to the Dana Farber Cancer Research Institute as part of their Seminars in Oncology series, her lecture was titled “Insights into neuroblastoma genetics and immunotherapy target identification revealed through integrative multi-omic approaches.”
A whirlwind of a Spring, for certain!
Center for Childhood Cancer Research
Children’s Hospital of Philadelphia
3401 Civic Center Boulevard
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