The UC Santa Cruz Treehouse Childhood Cancer Initative enables sharing of pediatric cancer genomic data. But more than that, it makes it possible to analyze a child's cancer data against both childhood and adult patient cohorts across all types of cancer.
NEW YORK – An interim analysis of the National Cancer Institute-Children’s Oncology Group (NCI-COG) Pediatric Molecular Analysis for Therapy Choice (MATCH) study — a precision medicine clinical trial for pediatric cancer — has found that 24 percent of participants are eligible to receive treatment with a targeted therapy, a match rate significantly higher than the 10 percent the researchers expected at the outset of the trial.
The study is the pediatric counterpart to the ongoing NCI-MATCH trial, which began in June 2015 and only accepts cancer patients who are aged 18 years and older. The Pediatric MATCH researchers are aiming to identify the specific genetic alterations occurring in each patient’s cancer, match patients to drugs targeted to those mutations, and then evaluate the effects of treatments ostensibly meant for adult patients on pediatric patients.
The interim results were released in the run-up to the American Society of Clinical Oncology’s annual meeting in Chicago next month. At a press conference to announce the results on Wednesday, COG Study Chair and Baylor College of Medicine Pediatrics-Oncology Professor Will Parsons said that 422 children, adolescents, and young adults between the ages of one and 21 years old were enrolled in the study between July 24, 2017, and Dec. 31, 2018.
“This is the first nationwide precision oncology trial for children,” Parsons said. “We initially projected a match rate of approximately 10 percent, and that was based on our understanding of the genetics of pediatric cancers — largely newly diagnosed cancers — but also the experience with adult-equivalent or similar adult studies.”
The pediatric patients were diagnosed with more than 60 different cancers, including 101 patients with various brain tumors, 300 patients with other solid tumors, and 21 patients with lymphomas or rare histiocytic disorders of the immune system. Of the patients with brain tumors, 47 percent were diagnosed with astrocytomas, and osteosarcomas made up the largest group of solid tumor diagnoses with 29 percent of the patients presenting with such a diagnosis.
Of the 422 patients who were enrolled, tumor samples were submitted for 390 of them, and testing was successfully completed on 357 of those. The researchers performed both DNA and RNA sequencing on more than 160 genes in the tumors to identify oncogenic alterations and to see if they could match the patients to one or more of the 10 targeted therapies being studied: larotrectinib (Vitrakvi), targeting NTRK; erdafitinib (Balversa), targeting FGFR; tazemetostat, an experimental drug targeting EZH2 and other genes in the SWI/SNF gene complex; LY3023414, a drug being developed to target the PI3K/MTOR pathway; selumetinib and ulixertinib, investigational therapies targeting the MAPK pathway; ensartinib, targeting ALK or ROS1; vemurafenib (Zelboraf), targeting BRAF; olaparib (Lynparza), targeting defects in DNA damage repair genes; and palbociclib (Ibrance), targeting cell cycle genes.
Parsons noted that the median turnaround time from receipt of the tumor to assignment of treatment was about 15 days.
Of the 390 patients whose tumors were submitted to the researchers, 112 (29 percent) were found to have a targetable genetic alteration such as a mutation, a fusion, or gene copy number, and 95 of the patients (24 percent) were found eligible for assignment to one of the treatment arms. As of the end of 2018, 39 of the patients had actually enrolled in a Pediatric MATCH treatment trial.
Importantly, Parsons noted in his presentation, the researchers detected targetable mutations in 26 percent of the patients with non-central nervous system solid tumors and in more than 40 percent of the patients with brain tumors. In the case of astrocytoma, the study found targetable mutations in 74 percent of patients with that diagnosis and was able to match those patients to nine of the 10 treatment arms.
The data demonstrated that this type of tumor sequencing has utility for both rare and common pediatric cancers, he said. There was also no significant difference in the detection rate between younger and older patients.
The broader implications
The results have implications beyond the immediate treatment of pediatric oncology patients. They also point to a viable strategy for nationwide molecular screening of children with cancer and could lead to a change in how pharmaceutical companies develop and test targeted cancer therapies.
Vivek Subbiah, an associate professor in the department of investigational cancer therapeutics at the University of Texas MD Anderson Cancer Center, told GenomeWeb that he was surprised and encouraged by how much higher the study’s actual match rate was compared to its anticipated match rate.
“We have reached a therapeutic plateau with conventional chemotherapy. Further refinements in chemotherapy have not rendered dramatic additional benefits in pediatric cancers and, unfortunately, a subset of pediatric patients with relapsed or refractory disease continue to have poor outcomes,” he said. “Pediatric cancer has been, I would say, the stepchild in drug therapies because industry-funded studies of new molecules rarely include pediatric patients. And the pediatric oncology research community has been dogged by lack of funding, lower patient numbers for clinical trial participation, and limited awareness of the benefits of clinical trials.”
But, despite these challenges, Subbiah added, he believes the Pediatric MATCH trial will “refresh” the field, providing renewed momentum and energy for COG and other pediatric research groups to work together on new studies and clinical trials, and accelerating close collaboration among academia, industry, regulators, and third party payors “to step up for that stepchild in drug development.”
He also noted that the interim results further emphasize the need to sequence every child with cancer. “If you want to win the battle against cancer in children, I think we need to have all the intelligence about that. Even if we don’t have drugs today, then we may be developing drugs tomorrow,” Subbiah said. “I think [the Pediatric MATCH study] shows that we are able to find actionable aberrations … even in relapsed or refractory patients.”
Indeed, the interim results seem to justify the growing popularity of combined DNA and RNA sequencing in pediatric cancer research. In February 2018 at the Molecular Medicine Tri-Conference in San Francisco, University of California, Santa Cruz Biomolecular Engineering Professor David Haussler gave an update on the California Kids Cancer Comparison (CKCC) project, saying researchers had been able to match 100 percent of their samples to possible treatments for the patients using molecular and gene expression data.
Researchers from the University of California, Santa Cruz — which is part of the Treehouse Childhood Cancer Initiative — have developed what they’re calling gene expression outlier analysis to see if they can identify overexpressed genes in pediatric cancers that can then be targeted with available cancer treatments.
And at the annual meeting of the American Association for Cancer Research in Atlanta in April, Co-Executive Director of the Institute for Genomic Medicine at Nationwide Children’s Hospital Elaine Mardis detailed her center’s efforts to combine DNA and RNA sequencing in the clinical cancer care setting in order to help patients.
Cool, cloudy weather can’t stop warm reunions and festival vibes at annual Alumni Weekend bash
UCSC | Dan White | April 30, 2019
It’s a well-known fact that cool weather and fog bring out the banana slugs in droves. That was certainly the case during UC Santa Cruz’s highly spirited—and often cloudy—Alumni Weekend, marked by myriad gatherings and offerings including reunions, lectures, gossip, chit-chat, jewelry-making, dancing, art tours, and “Slug Taxis’’ spiriting revelers from one event to the other.
It was impossible to do every activity, considering there were a whopping 75 events, representing all 10 colleges, and activities that appealed to all tastes, whether you were interested in the potential of life on other planets, or just wanted to hang out at the Porter College Makers Fair, with jewelry-making benches and a tie-dying tank for souvenir T-shirts.
More than a thousand people, including 560 alumni, converged on the hilly forested campus, flagging volunteer-driven “Slug Taxis” or boarding shuttles, which made it possible to zip from one remote corner of the campus to another with minimal hassles.
It was a weekend of almost constant anniversaries and reunions. Seymour Marine Discovery Center marked its 40th birthday, the Smith Renaissance Society had its 20-year celebration, and on Friday night at the Hay Barn near the base of campus, UC Santa Cruz’s original graduating class marked its 50th anniversary with an emotional evening of taking stock and reminiscing.
“It is a blessing to be here,” said Winnie Hoskyns-Abraham (Stevenson ’69, anthropology), who was known as Winnie Scherrer in her college years. “We have a lot of classmates who aren’t.”.
Also at the pioneer gathering, Laura Caldwell (Cowell ’69 college, literature), a retired school principal in Monterey, reflected on her decision to go to the fledgling UC campus in Santa Cruz.
“I was really drawn to the chance to be in the very first class,” she said. “There were no traditions. We were going to make the traditions. We were thrown together and living in these primitive trailers so we got acquainted right away.”
Around the same time as the pioneer reception, a group of proud Slugs, some of them decked out in their blue-and-gold regalia, packed Woodstock’s Pizza in downtown Santa Cruz for the Alumni Weekend kick-off. Beer and stories flowed throughout the night.
Mist on the meadow
Saturday’s celebration began in grainy fog that burned off in late morning. It was enough to make some revelers feel as if they were traveling through the mists of time.
“We’d like to transport ourselves back to school—a time without responsibilities except for grades,” said Kate Grant Bateman (Cowell ’98, American studies), who had just finished the 5K Fun Run across campus. She enjoyed the run, though she and several others got lost at one point. “At Kresge College, you’re supposed to make a right but we went straight. We went the long way—all uphills!”
That morning in Quarry Plaza, Gwynn Benner, assistant vice provost for UC Santa Cruz’s Division of Student Success, and Christina Yu (College Ten ’20, cognitive science), were at a table in the courtyard, getting the word out about the campus’s First-Generation Initiative, focused on responding to and supporting the fast-growing first-generation college student population on the UC Santa Cruz campus.
Yu, the Chancellor’s Undergraduate Internship Program intern for the First-Gen Initiative, is a first-generation student who is eager to help others. Born in China, she immigrated with her family to the United States when she was 5, and lived in San Francisco’s Chinatown. Mindful of her parents’ sacrifices, she put intense pressure on herself to succeed.
After teaming up with the First-Gen Initiative, Yu was heartened to find out that many other students had similar experiences. Even one of her academic advisors spoke to her about similar struggles. Now Yu has decided to follow her dream. She is now pursuing a career in education, and is planning to spend her summer teaching English to elementary school students in Taiwan.
Improvising and laughing your way through life
In terms of crowd participation and attendance, a special Cowell Colloquium with a mouthful of a title—“Where the Deer and the Antelope and the Banana Slug Roam: Hair Raising Tales from the Rough Terrain of the Western American Public Intellectual,’’ was one of the surprise hits of Alumni Weekend.
A throng of 200 people greeted the distinguished historian Patricia Nelson Limerick (Cowell ’72, American studies), founding director of the Center of the American West at the University of Colorado, where she is also a professor of environmental studies and history. She is the author of Desert Passages, The Legacy of Conquest, Something in the Soil, and A Ditch in Time. Limericktalked about the ways that improv theater training helped sustain her wild career.
During her frequently hilarious discussion with Cowell Provost Alan Christy, an associate history professor at UC Santa Cruz, she talked about her participation in the Original Banana Slug Improvisational Theater, and how this extracurricular activity ended up coming in handy every time she’s had to deal with stage fright, difficult personalities, conflicting ideologies, and charged situations.
“Every day of a public intellectual’s life is thin ice,” she said. “You are always stepping carefully. Even then, that won’t always save you.” Limerick said improv should be a UC Santa Cruz requirement, preparing students to deal with an ever-changing world.
High-impact science in the spotlight
Returning Slugs also got an accessible and enjoyable crash course in “High-Impact Science from PBSci” from four distinguished faculty members who all happen to be Slugs themselves. These lightning talks—each presentation lasted only six minutes or so—were a public forum to highlight the power of research.
“UC Santa Cruz is a place where we try to make sure that science doesn’t just stay in the academy,” said Physical & Biological Sciences Dean Paul Koch, distinguished professor of Earth and planetary sciences. “We want our work to have impact in the real world.”
The topics and speakers were:
Life and the Environment—Kristy Kroeker (Crown ‘01, marine biology)
Earth and the Cosmos—Natalie Batalha ( Ph.D. ’97, astrophysics)
Teaching Techniques for Today—Aura Alegra Eroy‑Reveles Ph.D. ’08, chemistry)
Another highlight was an eye-opening talk about “Radical Learning—The Heart of the UC Santa Cruz Experience.” Jody Greene, professor of literature, feminist studies, and history of consciousness, and director of the Center for Innovations in Teaching and Learning (CITL), led a team of faculty, graduate students, and undergraduates about ways to improve conditions in which students can learn.
Greene introduced an array of speakers—including faculty as well as a group of eloquent and enthusiastic student interns with CITL—who addressed the importance of understanding student strengths for learning and how faculty and staff can better support students including first-gen learners.
“We think what is going on at UC Santa Cruz is a renaissance,” said UC Santa Cruz Foundation Distinguished Professor of Psychology Barbara Rogoff, who is a CITL senior faculty fellow. “We are a model for making higher education much more accessible for learners.”
A weekend with engineering Slugs
Baskin School of Engineering had a full schedule of events throughout Alumni Weekend. Festivities began on Friday afternoon in Silicon Valley with a night of gaming and glimpses at the increasingly blurred edge between games and reality.
Saturday’s events included a selection of teach-ins in intimate classroom settings. Slugs nestled in to learn about “Responsible Data Science” from this year’s faculty lecturer Lise Getoor, professor of computer science and engineering. Abhradeep Guha Thakurta, assistant professor of computer science and engineering, gave a provocative lecture titled “Decoding Genetic Privacy.” Meanwhile, Slugs curious about energy and biofuel were treated to “Fuel, Food, and Pharma: Can Synthetic Biology Empower Social Change?” by David Bernick, assistant adjunct professor of biomolecular engineering.
Slugs also got behind-the-scenes laboratory tours with pennant-waving Baskin Engineering student ambassadors. The Institute for the Biology of Stem Cells, featuring Camilla Forsberg, professor of biomolecular engineering; the Hybrid Systems Lab, featuring Ricardo Sanfelice, professor of electrical and computer engineering, and The CAVE, featuring Sri Kurniawan, professor of computational media, and Mircea Teodorescu, associate professor of electrical and computer engineering, all opened their doors and explained their research.
The three-year, $450,000 grant will support Vaske’s research on the use of genomic markers to guide treatment decisions for children with cancer. Vaske, who holds the Colligan Presidential Chair in Pediatric Genomics, said the project aims to increase the number of pediatric cancer patients who could benefit from targeted therapies.
Vaske’s team has developed a novel RNA sequencing analysis that can reveal abnormally active genes in a patient’s cancer cells. The researchers plan to identify highly expressed genes that could be targeted with drugs and study the biological effects of those genes. They will also evaluate whether the increased expression of these genes is predictive of how the cells respond to cancer-fighting drugs.
Another part of the project will use nanopore sequencing technology developed by UCSC biomolecular engineers David Deamer and Mark Akeson. Working with Akeson’s lab, Vaske’s team will use the technology to profile cancer cell lines and identify the genetic changes responsible for abnormal gene expression patterns.
Combining DNA and RNA sequencing data has proven to be beneficial for researchers seeking to understand more about the biology of adult cancers. Just as the advent of genomics testing helped to make cancer care more personalized for adults, the addition of transcriptomics testing and deep bioinformatics analysis to genomics may generate even more detailed information that clinicians may use to potentially determine diagnosis, prognosis, or make treatment decisions.
Similarly, this paradigm may be coming into play in pediatric cancer care. Pediatric cancers are often problematic for researchers looking for targetable somatic mutations as they’re lacking in druggable DNA targets. In this context, transcriptomics analysis can help to fill in the gaps.
Researchers with the Treehouse Childhood Cancer Initiative are particularly focused on using RNA sequencing data to analyze entire genetic pathways, with the hypothesis that because cancer drugs are aimed at these specific pathways, they could be effective in treating pediatric cancers, even if they don’t have somatic mutations.
Even more specifically, researchers from the University of California, Santa Cruz — which is part of the Treehouse Initiative — have developed what they’re calling gene expression outlier analysis to see if they can identify overexpressed genes that can then be targeted with available cancer treatments. They’re also aiming to determine if this kind of RNA-based analysis can bolster efforts to match patients to drugs as opposed to using tumor mutation analysis only.
Science Magazine | March 15, 2019 | Olena Morozova Vaske and David Haussler
Last month, in a conference call held by the U.S. Department of Health and Human Services and National Institutes of Health (NIH), it was revealed that a large focus of President Trump’s pledge to fund childhood cancer research will be genomic data sharing. Although the United States has only 5% of the world’s pediatric cancer cases, it has disproportionately more resources and access to genomic information compared to low-income countries. We hope that the spotlight on genomic data sharing in the United States will galvanize the world’s pediatric cancer community to elevate genomic data sharing to a level where its full potential can finally be realized.
Pediatric cancers are rare, affecting 50 to 200 children per million a year worldwide. Thus, with 16 different major types and many subtypes, no cancer center encounters large cohorts of patients with the same diagnosis. To advance their understanding of particular cancer subtypes, pediatric oncologists must have access to data from similar cases at other centers. Because subtypes of pediatric cancer are rare, assembling large cohorts is a limiting factor in clinical trials as well. Here, too, data sharing is the first critical step.
Typically, pediatric cancers don’t have the number of mutations that make immunotherapies effective, and only a few subtypes have recurrent mutations that can be used to develop gene-targeted therapies. However, the abnormal expression level of genes gives a vivid picture of genetic misregulation, and just sharing this information would be a huge step forward. Using gene expression and mutation data, analysis of genetic misregulation in different pediatric cancer subtypes could point the way to new treatments. [Read more …]
President Donald Trump’s proposal in his State of the Union address earlier this month to spend $500 million over 10 years on pediatric cancer research will begin in 2020 with a focus on sharing patients’ data, federal officials say. That plan is getting a mixed response from researchers and patient advocates, who also worry that the initiative will come at expense of other parts of the National Cancer Institute’s (NCI’s) budget.
During his speech, Trump described a “very brave” guest sitting with first lady Melania Trump—10-year-old brain cancer survivor Grace Eline, who raised funds for pediatric cancer research before developing the disease herself. “Many childhood cancers have not seen new therapies in decades. My budget will ask the Congress for $500 million over the next 10 years to fund this critical life-saving research,” Trump said. A $50-million-a-year boost would mean an 11% increase over the $462 million that NCI and other National Institutes of Health (NIH) institutes expect to spend this year on pediatric cancer. (In contrast, Trump administration officials have warned that they expect to issue a budget request to Congress next month that calls for an overall 5% cut to nondefense spending in the 2020 fiscal year that begins 1 October.)
The Trump announcement came as a surprise to staff at NCI and cancer patient groups. NCI officials say details are still being worked out. But during a conference call with researchers and advocates on 14 February, NCI Director Ned Sharpless in Bethesda, Maryland, who has made “big data” part of his agenda, said data sharing will be a major initial thrust of the initiative. An NCI spokesperson explains to ScienceInsider that $50 million in 2020 “would afford a unique opportunity to leverage the power of existing data and develop new knowledge that will drive discovery and development of new approaches to treat childhood cancers.”
That’s welcome news to University of California, Santa Cruz, genomics researcher Olena Morozova Vaske, who with David Haussler runs a pediatric cancer genome project. She and Haussler say that because pediatric cancers are very rare, it’s crucial to combine patient data from academic and industry clinical trials as well as international patients. That will take implementing new standards and building new digital infrastructure. Existing databases “need to all be talking to each other so we can consolidate data,” Vaske says. “You really have to make sure you’re capturing information from every single patient.”
NEW YORK (GenomeWeb) – Next-generation sequencing technology as applied to various cancers has led to the discovery of several DNA mutations thought to be responsible in some way for the development or proliferation of those cancers. This, in turn, has led to the development of several treatments targeted at those specific mutations. But what can be done to treat cancers in the same manner if they don’t have actionable mutations that can be targeted?
Some groups are increasingly turning to transcriptomics to help fill in the gaps, and they’re finding that the combination of DNA and RNA analysis is allowing for more precision in matching cancer patients to available treatments. For example, last June, researchers from the WIN Consortium found that adding RNA-based testing to DNA analysis in 303 cancer patients increased the treatment match rate to 35 percent from 23 percent with DNA-based analysis alone.
The issue of targetable somatic mutations is especially problematic in pediatric cancers, as these cancers are known to be lacking in druggable DNA targets. In order to solve that problem, researchers with the Treehouse Childhood Cancer Initiative are instead focusing on using RNA sequencing data to analyze entire genetic pathways. Their hypothesis is that because cancer drugs are aimed at these specific pathways, they could be effective in treating pediatric cancers, even if they don’t have somatic mutations.
Even more specifically, researchers from the University of California, Santa Cruz — which is part of the Treehouse Initiative — have developed what they’re calling gene expression outlier analysis to see if they can identify overexpressed genes that can then be targeted with available cancer treatments. Much like the WIN Consortium, they’re also aiming to determine if this kind of RNA-based analysis can bolster efforts to match patients to drugs as opposed to using tumor mutation analysis only.
“What we really want is to identify genes that are significantly overexpressed and significantly underexpressed in the given patient. There are no good methods for that,” UCSC Assistant Professor of Molecular, Cell, and Developmental Biology Olena Vaske said. “The standard differential expression analysis is comparing two groups of samples to each other and finding differences and similarities between groups. But, in a clinical setting we really have the one patient in question. And so those group-type of approaches don’t work. Because of that, we developed an approach that uses outlier analysis, which is more suitable for a single patient.”
Vaske and her group are currently conducting a study of 11,340 pediatric cancer patients, who have submitted clinical and omics data, including transcriptomic data, to the Treehouse Initiative.
“The hypothesis is that overexpressed oncogenes are cancer drivers in addition to mutations. So, our goal is to find overexpressed oncogenes in individual patients,” Vaske said. “There are some drugs that target specific mutation and those would not work for our purposes. But there are also drugs that just target the pathway and they can target a wild-type protein, and so those are the drugs that we can hypothesize would be effective in these cases.”
Once the researchers have identified a potentially actionable overexpressed gene, they try to match it to an available drug. They then communicate their findings to the patient’s clinician, who ultimately makes the treatment decisions.
“What we do is present the analysis,” Isabel Bjork, director of operations and pediatric programs at the UC Santa Cruz Genomics Institute, added. “Olena goes through it and reports on what the team has found with the clinical team, but the clinical team is responsible for making any treatment decisions.”
Investiture is a formal ceremony designed to publicly recognize both faculty members who are appointed to named professorships and the generous donors who made these appointments possible. Recently, we had the opportunity to celebrate our co-founder for her inaugural appointment to a named chair supporting pediatric cancer genomics, endowed by Santa Cruz residents Bud and Rebecca Colligan.
Olena Morozova Vaske, assistant professor of molecular, cell, and developmental biology at UC Santa Cruz, was honored as the first holder of the Colligan Presidential Chair in Pediatric Genomics in an investiture ceremony on Tuesday, February 19, at the University Center.
Chancellor George Blumenthal said at the ceremony that when he began at UC Santa Cruz, there were just four professorships. With the Colligan Chair, UC Santa Cruz can now count 40 chairs, a sign of the growth and maturity of the campus community.
The Colligan Chair will provide important support for Vaske’s ongoing work with the Treehouse Childhood Cancer Initiative. The gift has supported a new lab in the MCD Biology Department at UC Santa Cruz, where Vaske will be studying the genes identified in the Treehouse analyses to better understand their roles in pediatric cancer. This “wet lab” research will complement the data analysis currently performed by the Treehouse team and may yield valuable new biological insights into pediatric cancer.
Endowments are a precious resource, particularly for a young institution such as UC Santa Cruz. They can increase a campus’s ability to attract and retain distinguished academics and they also provide an opportunity for donors to significantly impact scientific research. We are thrilled to be able to celebrate this named chair and look forward to the research that will result from the Colligan’s generous gift.
Read more about the ceremony, the Colligans and Dr. Vaske’s research here.
Check out images from the event below!
The celebration of the cross-disciplinary endowed chair included (on left) Paul Koch, dean of Physical and Biological Sciences, and Alexander Wolf, dean of the Baskin School of Engineering. Also pictured are Rebecca Colligan, Olena Vaske, Bud Colligan, and Chancellor Blumenthal.
Paul Koch, dean of physical and biological sciences, Olena Morozova Vaske and Alexander Wolf, dean of the Baskin School of Engineering
Bud, Rebecca Colligan and Chancellor Blumenthal.
Lu & David Haussler
Olena Morozova Vaske receiving her medal from Chancellor Blumenthal
The Colligan’s medal
Treehouse team members enjoy the reception
Adjunct faculty member and former Treehouse team member Ted Goldstein
Investiture ceremony honors Vaske as the inaugural holder of the Colligan Presidential Chair in Pediatric Genomics
Feb. 21, 2019 | Tim Stephans
Olena Morozova Vaske, assistant professor of molecular, cell, and developmental biology at UC Santa Cruz, was honored as the inaugural holder of the Colligan Presidential Chair in Pediatric Genomics in an investiture ceremony on Tuesday, February 19, at the University Center.
The chair was established in 2016 with a gift from John “Bud” and Rebecca Colligan and matching funds from the UC Regents. The initial focus of the chair is to advance efforts to use genomic data to defeat childhood cancer.
Vaske cofounded the Treehouse Childhood Cancer Initiative when she was a postdoctoral researcher working with David Haussler, professor of biomolecular engineering and director of the UC Santa Cruz Genomics Institute. She maintained her involvement in Treehouse during a postdoctoral fellowship in clinical molecular genetics at UCSF, then returned to UC Santa Cruz in the fall of 2018 to join the faculty of the Department of Molecular, Cell and Developmental (MCD) Biology.
The Treehouse Childhood Cancer Initiative is working to change the story for childhood cancer patients by leveraging genomic data and computational approaches to identify less toxic and more effective treatments. We do this by analyzing a child’s cancer data against both childhood and adult patient cohorts across all types of cancer, comparing individual pediatric tumors against a vast database of 11,000+ tumors. This “pan-cancer” analysis of adult and pediatric tumors may predict situations in which an adult drug might work on a subset of pediatric patients. We support the sharing and distribution of genomic information to researchers everywhere because large genomic datasets can be used as comparison data, offering clinical teams the genomic information needed to better understand what is happening with kids who are suffering from relapsed, refractory and rare cancers.
Synovial sarcoma is a rare and aggressive cancer which occurs most commonly in the arms and legs, near joints and tendons. With support from The Live for Others Foundation, founded by teenager Tim Vorenkamp who tragically passed away from synovial sarcoma in 2016, Treehouse is now able to focus research efforts on accessing synovial sarcoma tumor data from different institutions, including hospitals and research centers, to improve comparative computational analysis we can provide for children currently in treatment with a synovial sarcoma diagnosis. Over the last year, we have more than doubled the number of synovial sarcoma tumor data in our database. We are currently working to assess additional synovial sarcoma data, which will further enhance the value of our research.
Ultimately, the goal of Treehouse is to offer synovial sarcoma cancer patients hope by connecting the dots: when we can point to molecular-level similarities linking a patient’s cancer with cancer tumors that were treated successfully, new treatment possibilities open.