St. Jude Cloud portal expands access to treasure trove of pediatric solid tumor data


An innovative, interactive cloud-based data portal debuted this week that lets academic researchers mine the world’s largest and most comprehensive collection of scientific resources for studying pediatric solid tumors and their related biology. The Childhood Solid Tumor Network (CSTN) data portal on St. Jude Cloud was created to improve access to the detailed data available through the network, stimulating the research and development of novel, lifesaving therapies.

The CSTN includes wide-ranging data on 170 patient-derived samples representing 21 different childhood , including neuroblastoma, rhabdomyosarcoma and rare tumors. The samples are orthotopic patient-derived xenografts, meaning the human tumor samples are implanted and grown in the corresponding location in mice.

Tumor samples and related data are shared with at no charge and with no obligation to collaborate. Michael Dyer, Ph.D., chair of the St. Jude Developmental Neurobiology department, and Alberto Pappo, M.D., of the St. Jude Oncology department, launched the network in 2013. The goal was to accelerate discoveries in the field. “There had been no significant improvement in outcomes for children with solid tumors in the past three decades,” said Dyer, who is a Howard Hughes Medical Institute investigator. Pediatric solid tumors are developmental tumors. To understand how the tumor begins, grows and spreads, they need to be studied in the environment in which they develop.

“As interest in the network grew, we realized scientists needed to dig deeper into the data,” Dyer said. “We created the interactive browser to make that possible.” The CSTN data portal was unveiled this week at the annual meeting of the American Association for Cancer Research, which was held virtually.

Web-based data

The portal makes it easier for researchers to download and analyze the data themselves.

Available data and analytic tools include:

  • Next-generation, whole genome sequencing of the patient tumors, germline and the orthotopic patient-derived xenografts. These are presented as an interactive application, allowing for customized heatmaps to represent mutations and individual gene searches. Raw genomic sequences are also uploaded and available.
  • Interactive browsers for epigenetic and, in some cases, proteomic data
  • Histology images with tissue-specific stains and electron microscopy images at three magnifications for each
  • Clonal analysis of the matched patient samples and orthotopic xenografts
  • Sample-level search and visualization of specific characterization data that let users filter by factors such as patient’s age at diagnosis or primary versus recurrent tumors

Preclinical pharmacokinetic reports, tumor propagation protocols and more

Single-cell RNA sequencing of patient and patient derived-orthotopic xenografts is underway. Additional tumor samples and data are added to the network as they become available.

Academic researchers can also request cryopreserved cells from orthotopic patient-derived xenografts as well as fresh frozen tissue or cells and formalin-fixed paraffin-embedded tissue blocks.

As of June 2020, more than 200 researchers from more than 100 institutions worldwide have requested and received more than 1,500 tumor samples from the network.

“We feel the network and data portal are the best way to make the most of the tissue samples that children and their parents have donated to provide resources to speed cures and understand the diseases,” said Asa Karlstrom, Ph.D., of Developmental Neurobiology. She was co-first author of a report on the data portal that was included in an AACR poster session.

Team creates resource for pediatric brain tumor research

St. Jude Cloud portal expands access to treasure trove of pediatric solid tumor data (2020, June 26)
retrieved 26 June 2020

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
part may be reproduced without the written permission. The content is provided for information purposes only.

(Visited 3 times, 1 visits today)

Related posts:

Dog in Georgia tests positive for virus that causes COVID-19
Pubs open, gyms shut: England's health dilemma
China plans reforms to organ donation rules
Covid 19: Making the poor poorer
Catalonia places 200,000 people under new lockdown following Covid-19 surge
US marks record 57,683 new COVID-19 cases in 24 hours: tracker
As much of US marks a muted Independence Day, Trump encourages big parties
WHO says first alerted to virus by its office, not China
Paris's Louvre reopens on Monday after lockdown losses of 'over €40 million'
How coronavirus self-isolation fatigue may lead to more beach drownings this summer
what's the new coronavirus saliva test, and how does it work?
The WHO's risky communication strategy created confusion around COVID-19
England's pubs, restaurants and hairdressers reopen as COVID-19 lockdown eases
French jihadist sentenced to 30 years for IS group executions in Syria
We looked at the health star rating of 20,000 foods and this is what we found
Trump rallies against anti-racism protesters seeking to 'defame' heroes
The US has bought most of the world's remdesivir. Here's what it means for the rest of us
Antibodies against phosphorylcholine give protection against rheumatic systemic disease
Researchers determine how much oxygen the brain needs
Britain eases virus quarantine as US under siege
Researchers find fans of apocalyptic movies may be coping with pandemic better
Some say allow family access to dying patients with COVID-19
11 of Our Best Weekend Reads
China aims to phase out sale of live poultry at food markets
U.S. Coronavirus Cases Are Rising Sharply, but Deaths Are Still Down
Spain counts 17 new virus deaths in 24 hours
At least thirty villagers massacred in central Mali terror attacks
Point-prevalence surveys in SNFs help cut COVID-19 transmission
Saudi Arabia passes 200,000 virus cases
French court opens inquiry into former PM Philippe in handling of Covid crisis
Protective antibodies identified for rare, polio-like disease in children
Air France to cut 7,580 jobs at French flagship carrier and regional unit Hop!
New French PM Castex says priority to meet Covid-19 pandemic, economic crisis as he takes helm
'Data not lying', WHO urges countries to 'wake up' and halt virus
Prosecutors seek life term for French jihadist accused of Syria executions
Mystery of hundreds of elephants found dead in Botswana
Injuries shoot up after fireworks laws loosened in West Virginia
‘We can’t afford an ounce of meat’: Economic crisis strangles Lebanon
Algeria welcomes remains of fighters against colonisation from France
Neurological symptoms described in children with COVID-19
United States: In Louisiana, Cajuns are keen to preserve their identity
HIV may not worsen COVID-19 outlook
250. Split-Lebertransplantation am UKR - Biermann Medizin
Live Coronavirus Updates: U.S. Leaders Change Course
EU authorises use of remdesivir to treat coronavirus
Turkey challenges allies and enemies alike in quest for ‘larger role on world stage’
Porres neuer Chefarzt in Leverkusen
Even gut immune response is site-specific
Systemische Therapie kann jetzt mit den Krankenkassen abgerechnet werden
Inflammatory Bowel Disease Tied to Increased Dementia Risk
Macron names Jean Castex as new French prime minister
Popular chemotherapy drug may be less effective in overweight and obese women
Studie: Junge Menschen rauchen und trinken weniger
Can an Algorithm Predict the Pandemic’s Next Moves?
Death toll climbs to more than 160 in Myanmar jade mine disaster
Israeli, UAE technology firms pen deal on virus research
Netanyahu's annexation plan, China's campaign against Uighurs and Hollywood before the censors
Uniklinik Köln: Augenheilkundliche Spezialbereiche jetzt in Deutschlands größtem Krebs-Ambulatorium
Dutch report new coronavirus infection on mink farm
Berufsverband will Weiterbildungsförderung auch für Urologen
French PM Édouard Philippe and his government resign as Macron prepares cabinet reshuffle
Florida under siege as pandemic accelerates
Japan asks US to extradite two men accused of helping ex-Nissan chief Ghosn escape
MB: EU-Ratspräsidentschaft als Chance für mehr Kooperation in Gesundheitsfragen nutzen
Monkeys infected with novel coronavirus developed short-term immunity
Das sichtbare Skelett 2.0 - Biermann Medizin
Peru surpasses 10,000 coronavirus deaths: health ministry
Herzreparatur mit der Gen-Schere - Biermann Medizin
UK to end quarantine for travelers from 'low-risk' countries
Turkish court opens trial of Saudi officials in killing of journalist Khashoggi
New study reveals how the brain organizes information about odors
French court to rule on reopening probe of former Rwandan president's assassination
Study could show why heart events increase seasonally
US Senate unanimously votes to approve draconian 'Hong Kong Autonomy Act'
US new single-day Covid-19 cases hit new worldwide record of over 55,000
Study says crowdsourced data could help map urban food deserts
Police in Europe arrest over 800 users of encrypted phone system used to plot crime
Artificial intelligence brings pancreatic cancer screening one step closer to reality
The Young Cut Loose in Myrtle Beach. The Virus Followed Them Home.
Study exposes disparities in health care access in rural Southern California
Florida State University Child Care Policy Draws Backlash
Surge in domestic child abuse during pandemic, reports specialist UK children's hospital
Live Coronavirus News: Updates and Video
Marijuana use while pregnant boosts risk of children's sleep problems
US sanctions against international court staff an act of ‘revenge’, says ICC’s Fatou Bensouda
New, more infectious strain of COVID-19 now dominates global cases of virus: study
‘We disinfect everything’: Amsterdam’s red-light district re-opens
France's Macron to embark on next phase of his presidency with ‘new team’
When Your Tween Is Bored
Why are more young people getting coronavirus?
Ideen-Wettbewerb: Woche des Sehens in Corona-Zeiten
French prosecutors seek trial for football star Karim Benzema over sextape scandal
Talking With Your Teen About Anti-Racism? Be Ready to Listen
COVID-19 death risk twice as high in New York City as some countries
Turkey demands apology from France over naval incident claim
CBM-Jahresbericht 2019: Mehr Geld für die Projektarbeit
Venezuela reverses decision to expel EU ambassador
How the body fights off urinary tract infections
Riechstörungen bei COVID-19: Was wissen Mediziner aktuell?
Did a Mutation Help the Coronavirus Spread? More Evidence, but Lingering Questions

Leave a Reply

Your email address will not be published. Required fields are marked *

Next Post

How the Coronavirus Short-Circuits the Immune System

Sat Jun 27 , 2020
At the beginning of the pandemic, the coronavirus looked to be another respiratory illness. But the virus has turned out to affect not just the lungs, but the kidneys, the heart and the circulatory system — even, somehow, our senses of smell and taste. Now researchers have discovered yet another […]