MPIP: Melanoma Patients Information Page

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DNA sequencer raises doctors' hopes for personalized medicine

The device could accelerate the use of genetic information in everyday medical care, physicians hope, improving diagnoses and treatments.

By Melissa Healy

January 3, 2014, 11:02 p.m.

Among the many stents, surgical clamps, pumps and other medical devices that have recently come before the Food and Drug Administration for clearance, none has excited the widespread hopes of physicians and researchers like a machine called the Illumina MiSeqDx.

This compact DNA sequencer has the potential to change the way doctors care for patients by making personalized medicine a reality, experts say.

"It's about time," said Michael Snyder, director of the Stanford Center for Genomics and Personalized Medicine.

Physicians who rely on genetic tests to guide their patients' treatment have had to order scans that reveal only small parts of a patient's genome, as if peeking through a keyhole, Snyder said: "Why would you study just a few genes when you can see the whole thing?"

Back in 2000, when the Human Genome Project completed its first draft of the 3 billion base pairs that make up a person's DNA, the effort took a full decade and cost close to $100 million. The Illumina MiSeqDx can pull off the same feat in about a day for less than $5,000 — and the results will be more accurate, two of the nation's top physicians gushed in the New England Journal of Medicine.

That confluence of "faster, cheaper and better" is likely to accelerate the use of genetic information in everyday medical care, Dr. Francis Collins, director of the National Institutes of Health, and Dr. Margaret Hamburg, commissioner of the FDA, wrote last month. DNA sequencing should guide physicians in choosing the best drug to treat a specific patient for a specific disease while risking the fewest side effects.

The Illumina MiSeqDx platform works by breaking down, rebuilding and recording the entire sequence of a person's DNA in a massively parallel fashion, completing the job in a matter of hours. The company intends to market the machine to diagnostic labs, medical centers and private practices, at a price slightly more than $125,000.

Now that MiSeqDx has been approved, several other whole-genome sequencers are likely to seek the FDA's blessing in the coming months, agency officials say.

Right away, the technology is poised to improve the diagnosis and treatment of cystic fibrosis. Two new assays for the chronic lung condition — both developed by Illumina for use on the MiSeqDx — were approved in November by the FDA. Instead of checking for the six mutations most commonly linked to the disease, the new tests are able to discern a total of 139 genetic variations that give rise to cystic fibrosis. They will also tell doctors whether a patient is among the 4% who has a mutation that's targeted by a specific, costly drug.

Whole-genome sequencing has begun to reshape the way physicians diagnose and treat cancer as well. For a growing number of patients, treatment is guided by a DNA scan that reveals which mutation gave rise to the malignancy, not the organ in which the cancer manifests itself.

Having a fuller, clearer picture of patients' complete genomes will also allow biomedical researchers to expand their understanding of how DNA variants work together to influence disease risk, said Dr. Robert Green, a medical geneticist at Harvard Medical School and Brigham and Women's Hospital in Boston.

In current practice, physicians use genetic tests to look for known mutations that show up in the "exome" — the 1.5% of the genome that dictates the composition and timing of how proteins are produced. When inherited in identifiable patterns, these mutations give rise to conditions like Huntington's disease and certain kinds of hearing loss.

But with machines such as MiSeqDx, researchers will be able to look for subtle variations and disease-causing patterns anywhere in DNA, including the long stretches that until recently were regarded as "junk." What they learn will enable doctors to warn their patients of their genetic vulnerabilities, allowing patients, in turn, to take steps to reduce their risk.

It may take a while for physicians to become proficient in conveying such information, and for patients to grasp its meaning, Green said.

"We know that people get state-of-the-art genetic counseling and still walk out of that office confused," he said.

Scientists promised that the age of personalized medicine had arrived when the Human Genome Project published our DNA blueprint. In the years since, that promise has proved elusive.

It was all very well to imagine that a single genetic scan would alert a patient to disease risks and — should he or she become ill — identify which treatments would work best.

In reality, the painstaking process of sequencing every patient's entire genome was a distant dream. Each expensive scan would take months to complete, making it a poor guide to treatment. Results were unreliable. And large stretches of the genome came out fuzzy, yielding a picture of a person's genetic makeup too uncertain to base medical decisions on.

And then there was the question of what it all meant. Where in the genome's 3 billion base pairs should doctors look for clues to a patient's future illness? Which genetic variations should prompt immediate action and which could be safely ignored? How should all of these genetic risks and their inherent uncertainties be explained to a patient?

Lawmakers and bioethicists began to lay the groundwork for this new world, wrestling with issues such as whether companies could refuse to hire someone or health insurers could deny them coverage on the basis of their DNA. The Genetic Information Nondiscrimination Act made these actions illegal in 2008.

Last month, the Presidential Committee for the Study of Bioethical Issues urged doctors to come up with guidelines for dealing with the incidental findings that are bound to come up when a patient's genome receives such thorough scrutiny. Physicians ordering such tests — and the patients receiving their results — should decide in advance how much of that incidental information they want to know, the panel recommended.

In approving the MiSeqDx, the FDA declared that it would regulate the complex and fast-evolving industry of genomic sequencing services. The agency has already flexed its muscles by ordering 23andMe — a high-profile Silicon Valley company that encourages consumers to examine their own DNA by sending in vials of saliva — to stop marketing its $99 tests to the public until it had demonstrated to the FDA that its findings were accurate and reliable.

Elizabeth Mansfield, who directs the personalized-medicine office in the FDA's Center for Devices and Radiological Health, acknowledged the skepticism about the agency's ability to regulate this emerging industry. But standards have been developed and conveyed to companies, she said.

"We certainly hope to see more" devices like MiSeqDx in the coming year, Mansfield said. "Bring it on.",0,436970.story#ixzz2pZsOAMZF


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High-Dose Interferon With Maintenance Treatment in High-Risk Melanoma


J. Clin. Oncol 2013 Dec 16;[EPub Ahead of Print], MJ Payne, K Argyropoulou, P Lorigan, JJ McAleer, D Farrugia, N Davidson, C Kelly, D Chao, E Marshall, C Han, S Wellman, MR Middleton

Research · January 02, 2014


  • In this phase II study, 194 patients with stage IIB, IIC, IIIB, or IIIC melanoma were randomly assigned to receive adjuvant high-dose intravenous interferon alfa-2b for 4 weeks +/− maintenance low-dose subcutaneous interferon alpha-2b for 48 weeks. Improved outcomes seen with maintenance therapy in terms of relapse-free survival were not significant (2-year RFS, 54% vs 50%; P = .569). Improvement of overall survival was of borderline significance (median OS, not reached vs 41 months; P = .05).
  • Results did not support the initiation of a phase III trial. More data are needed to determine the optimal duration of adjuvant interferon alpha-2b therapy.

- Richard Bambury, MD





High-dose interferon alfa-2b (HDI) has emerged as a potentially effective adjuvant therapy in patients with resected melanoma at high risk of recurrence. Evidence suggests it may be the early, very-high-dose part of the regimen that is critical. This pilot study sought to provide an early indication of whether the same effects can be achieved with the intravenous component of HDI alone and inform the feasibility and design of a phase III trial.


Patients with stage 2B, 2C, 3B, and 3C melanoma were randomly assigned to receive interferon alfa-2b (IFN-α-2b) 20 MIU/m(2) intravenously (IV) daily 5 days per week for 4 weeks (arm A) versus the same regimen followed by IFN-α-2b 10 MIU/m(2) administered subcutaneously three times per week for 48 weeks (arm B) and observed for relapse-free survival (RFS) and overall survival.



Between 2003 and 2009, 194 patients were enrolled (arm A, 96; arm B, 98). After median follow-up of 39.5 months, RFS was 22.7 months (95% CI, 14.1 to 38.1 months) in arm A versus 33.3 months (95% CI, 18.2 to not reached) in arm B (P = .28). The proportions of patients free of relapse at 2 years were 50% and 54.1% (P = .569; hazard ratio, 0.89), respectively. Overall survival favored arm B (median, 41.5 months v not reached; P = .05).



Clinical outcomes were better in patients who had the longer regimen. Our results do not support either the use of a month of IV HDI alone in place of the year-long regimen or the initiation of a larger trial on this question.

Journal of Clinical Oncology
Phase II Pilot Study of Intravenous High-Dose Interferon With or Without Maintenance Treatment in Melanoma at High Risk of Recurrence
J. Clin. Oncol 2013 Dec 16;[EPub Ahead of Print], MJ Payne, K Argyropoulou, P Lorigan, JJ McAleer, D Farrugia, N Davidson, C Kelly, D Chao, E Marshall, C Han, S Wellman, MR Middleton


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Single vs Multiple Fractions of Repeat Radiation for Painful Bone Metastases


Lancet Oncol 2013 Dec 23;[EPub Ahead of Print], E Chow, YM van der Linden, D Roos, WF Hartsell, P Hoskin, JSY Wu, MD Brundage, A Nabid, CJA Tissing-Tan, B Oei, S Babington, WF Demas, CF Wilson, RM Meyer, BE Chen, RKS Wong

Research · January 02, 2014


  • In an attempt to determine the benefit of repeat palliative radiotherapy to previously radiated painful bone metastasis, investigators randomized patients to 8 Gy in a single fraction or 20 Gy in multiple fractions and evaluated pain response at 2 months. Although the results are confounded by a high rate of not assessable patients in both arms, single-fraction radiation therapy appeared to be non-inferior and less toxic to multiple fractions.
  • While this trial appears to support a less intensive palliative radiation treatment, improved trial adherence in future explorations will help in firmly defining future treatment protocols.

- Chris Tully, MD


Commentary by
Lee S. Schwartzberg MD, FACP

Painful bone metastases remain one of the most feared and difficult consequences of advanced cancer. Radiation therapy provides relief of pain, and evidence has accumulated that a single fraction of 8 Gy can yield similar results to multiple smaller fractions over 1 to 2 weeks designed to deliver 20 Gy. Less is known about the benefit of single fraction vs multiple fractions when re-radiating lesions that either failed to respond to the first radiation or became painful again. Chow and colleagues performed a multicenter trial over several years designed to answer that question. They found that, in general, a single 8 Gy fraction yielded a noninferior result in terms of the primary endpoint of pain reduction compared with multiple fractions. However, the study was hampered by a high dropout rate and large number of patients who did not complete the pain assessment at the appropriate time. These complications were not unexpected as the trial dealt with a very advanced population. It was, therefore, gratifying to see that quality of life improved for the majority of patients in both arms after re-irradiation.

These results support the use of a convenient, single day/dose of 8 Gy when a bony lesion requires re-irradiation for pain control. Such an approach could be useful for palliation even in patients not receiving active cancer therapy and those on hospice care, given the significant improvement in pain, symptoms, and quality of life seen in many patients.



Although repeat radiation treatment has been shown to palliate pain in patients with bone metastases from multiple primary origin sites, data for the best possible dose fractionation schedules are lacking. We aimed to assess two dose fractionation schedules in patients with painful bone metastases needing repeat radiation therapy.


We did a multicentre, non-blinded, randomised, controlled trial in nine countries worldwide. We enrolled patients 18 years or older who had radiologically confirmed, painful (ie, pain measured as ≥2 points using the Brief Pain Inventory) bone metastases, had received previous radiation therapy, and were taking a stable dose and schedule of pain-relieving drugs (if prescribed). Patients were randomly assigned (1:1) to receive either 8 Gy in a single fraction or 20 Gy in multiple fractions by a central computer-generated allocation sequence using dynamic minimisation to conceal assignment, stratified by previous radiation fraction schedule, response to initial radiation, and treatment centre. Patients, caregivers, and investigators were not masked to treatment allocation. The primary endpoint was overall pain response at 2 months, which was defined as the sum of complete and partial pain responses to treatment, assessed using both Brief Pain Inventory scores and changes in analgesic consumption. Analysis was done by intention to treat.


Between Jan 7, 2004, and May 24, 2012, we randomly assigned 425 patients to each treatment group. 19 (4%) patients in the 8 Gy group and 12 (3%) in the 20 Gy group were found to be ineligible after randomisation, and 140 (33%) and 132 (31%) patients, respectively, were not assessable at 2 months and were counted as missing data in the intention-to-treat analysis. In the intention-to-treat population, 118 (28%) patients allocated to 8 Gy treatment and 135 (32%) allocated to 20 Gy treatment had an overall pain response to treatment (p=0·21; response difference of 4·00% [upper limit of the 95% CI 9·2, less than the prespecified non-inferiority margin of 10%]). In the per-protocol population, 116 (45%) of 258 patients and 134 (51%) of 263 patients, respectively, had an overall pain response to treatment (p=0·17; response difference 6·00% [upper limit of the 95% CI 13·2, greater than the prespecified non-inferiority margin of 10%]). The most frequently reported acute radiation-related toxicities at 14 days were lack of appetite (201 [56%] of 358 assessable patients who received 8 Gy vs 229 [66%] of 349 assessable patients who received 20 Gy; p=0·011) and diarrhoea (81 [23%] of 357 vs 108 [31%] of 349; p=0·018). Pathological fractures occurred in 30 (7%) of 425 patients assigned to 8 Gy and 20 (5%) of 425 assigned to 20 Gy (odds ratio [OR] 1·54, 95% CI 0·85–2·75; p=0·15), and spinal cord or cauda equina compressions were reported in seven (2%) of 425 versus two (<1%) of 425, respectively (OR 3·54, 95% CI 0·73–17·15; p=0·094).


In patients with painful bone metastases requiring repeat radiation therapy, treatment with 8 Gy in a single fraction seems to be non-inferior and less toxic than 20 Gy in multiple fractions; however, as findings were not robust in a per-protocol analysis, trade-offs between efficacy and toxicity might exist.

The Lancet Oncology
Single Versus Multiple Fractions of Repeat Radiation for Painful Bone Metastases: A Randomised, Controlled, Non-Inferiority Trial
Lancet Oncol 2013 Dec 23;[EPub Ahead of Print], E Chow, YM van der Linden, D Roos, WF Hartsell, P Hoskin, JSY Wu, MD Brundage, A Nabid, CJA Tissing-Tan, B Oei, S Babington, WF Demas, CF Wilson, RM Meyer, BE Chen, RKS Wong


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Anonymous's picture
Replies 2
Last reply 1/6/2014 - 3:37pm
Replies by: Janner, Anonymous

I have seen survival statistics based upon stage at initial diagnosis or based upon moving to a new stage, but have not seen survival statistics based upon going NED for a period of time.  In other words, if a stage 3c individual goes 1 year NED are her survival statistics improved vs what the statistics indicate at initial diagnosis?   I would assume the longer a person stays NED the better the chances of long term survival, but I have not seen those statistics.  I know everyone is different and one should not obsess over statistics, but I would like to see what they are if they exist.  I would appreciate it of someone could direct me to the right place.  Thank you.

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UrsulaZ's picture
Replies 6
Last reply 1/6/2014 - 5:24pm

Hello --

I have stage IV melanoma with several abdominal mets, and am travelling to Memorial-Sloan-Kettering in NY to be part of this trial:

CA209-004, A Phase Ib, Open-Label, Multicenter Dose-Escalation Study of MDX-1106 (Nivolumab; BMS-936558) in Combination with Ipilimumab (BMS-734016) in Subjects with Unresectable Stage III or Stage IV Malignant Melanoma

I've received my first four doses (the ipi & nivo in combination), and am now going to get the nivolumab alone every two weeks. 

I recently had my first scans, and there were no new mets, and an overall reduction in the existing lesions of 62%. (the largest was about 7 x 5 cm, and that's shrunk by half). 

They will scan again in mid-December.

I'm on Prednisone now for some Ipi-induced colitis, but that's OK. 

Cautiously relieved and hopeful that others can also benefit from the new research in the area. 


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BrianP's picture
Replies 9
Last reply 1/6/2014 - 9:39pm

I traveled down to Moffitt this past week to enter a MAGE vaccine trial for Stage IV NED patients.  Unfortunately due to some delays with pathology request the scans I had several weeks ago which indicated no disease are now not recent enough for the trial so I had to get rescanned.  The new scans showed evidence of disease so I had to come up with a new game plan.  I'm now looking to travel back down to Moffitt this upcoming week to enter the BMS Nivo/IPI combo trial.  There's been a lot of press on this new combo but surprisingly I haven't heard of many people on this forum enrolled in the trial.  Would love to hear from someone on the trial if they could share their experinences so far.  Thanks!


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Anonymous's picture
Replies 2
Last reply 1/6/2014 - 10:33pm
Replies by: POW, BrianP

My 34 year son was diagnosed two years ago

large mole on torso surgically removed with lymph nodes under arm, one of 12 nodes infected

radiation for 6 weeks then 12 months of interferon

july 2013 MRI showed small brain lesion and 3 new tumors on torso and back

radiation of total brain for 4 weeks plus 1 mega boost to exact spot

12 weeks of yervoy

good news brain MRI showed lesion gone

bad news tumors on torso 2mm larger and also on liver and spleen and new tumor on thigh and side torso

next step clinical trial - dr Laos at u of m has already closed his trial so have been recommended us to karmonas cancer at Wayne state

waiting now for appt date


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Pink's picture
Replies 3
Last reply 1/6/2014 - 10:40pm
Replies by: Bubbles, Pink

tomorriow going for another brain scan then Wed. meet with radiologist and neurp at Moffit. Initial MRI showed 3 small mets to brain. i am also going to start Ipi as soon as insurance approves it. if SRS does not work can they do it again  and does IPI cross the blood brain barrier.

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mwcollins's picture
Replies 18
Last reply 1/7/2014 - 7:26am

Hi all-

After reading many posts and with encouragement from my husband, I have finally decided to register on this website, and participate.  My husband is very active on this site, so here is my story.  My husband was origionally diagnosed in February of 2011.  At the time we were living a normal life. I was (and still am) a stay home mommy to 3 boys and 2 dogs.  The initial diagnosis scared the crap out of both of us, but surgery seemed to take care of it. We moved to North Carolina from upstate NY to try to fix the financial pitfall we were in, but a month and a half after moving, melanoma reared its ugly head again.  This time it had moved to a secondary lymph node.  Primary lymph nodes were clear and the PET scan was also clear other than the one tumor.  Here we are another 15 months later, and routine CT scans showed a thickness in the small bowel.  I brought up the idea of my husbands diverticulitis as being a possible cause.  I try to consider myself a silver lining type person, but I have to admit I am scared.  I have 3 wonderful boys all at ages that desparately needing their daddy.  Our oldest is 12 and quickly becoming a young man who needs his dad to help mold him. Our middle son is 11 and wants nothing more than to learn how to be a better athlete from his dad (my husband was a tri-sport athelete), and our little guy is 4 who wants nothing more than to use his daddy as his jungle gym. I try so hard to be the voice of optimism.  My husbands family has a long line of cancer (breast, colon, tongue and neck), but all survivors. I want to belive that my husband is going to be another one of the line to be a survivor, but there is a small part of me that is just so scared that our luck is running out.  We have talked about the "worst case", and I would probably move back to NY to be with family especially since I have the ability to obtain a job if I return (I haven't worked aside from being mommy since my oldest was born).  I DO NOT want to have to return to NY, but feel comforted to have the safety net.  More importantly, I just can't imagine living life without my husband.  We met in 1994, and married in 1998.  We have had a very typical marriage with it's ups and downs, but despite being together for almost 20 years, it just doesn't seem long enough!  I guess, I just wanted to introduce myself to the forum, and get some support.  I have read such amazing stories on this site, and am hoping to lean on many of you as I go through the roller coaster ride that is melanoma.  Not many people out there understand this life that we all live and I just want to say how glad I am to have the support.  I look forward to posting more and supporting y'all.




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mikvahnrose's picture
Replies 1
Last reply 1/7/2014 - 9:39am
Replies by: Janner

I got a shave biopsy of a suspicious mole about a month ago. December 2nd

The results came back that it was a Benign Compound Melanocytic Nevus. Read by a dermatopathologist so it makes me feel more confortable that it is not cancerous.

Well i now know that the mole wasnt cancerous, but within a month it has reappeared!!! Not the same size as it was before, it's smaller, but it came back. Is that normal?? Is that a concern that i should get it checked out again?

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Hi all, posting on behalf of my wife.

My wife was diagnosed barely in stage 3.  1.01mm on her leg, 6 cells found during biopsy.  She was not a good canidate for Interferon so we investigated and eventually ended up with the Dabrafenib and Trametinib on prescription.

She has been taking them for about 11 days.  She's had a few side effects, a rash, sickness but nothing extreme.

I am wondering if this is the worst it gets or is there a peak period for side effects or perhaps they just show up at any time.  Keep in mind this is all for a seemingly healthy person.


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Anonymous's picture
Replies 14
Last reply 1/7/2014 - 9:01pm
Replies by: Anonymous, Vermont_Donna, jmmm, POW

Ok, need help.  This is really confusing.  My husband is planning on starting short term disability from work on Monday.  His job is NOT protected by the FMLA.  We have to get the paperwork filled out by the doctor and are not quite sure of the best answers.  We were thinking that it would be best to say unknown about returning back to work, so that he could get his 12 weeks pay and maybe they will pay the health insurance premium instead of making us pay COBRA right away.  He would also like to keep his job if possible, just in case of a miracle.

But, then on the otherhand I heard that you should apply for SSDI right away, even if you are on short term disability.  How can you say that you might return to your job on one form and then a week later fill out another that says you are permanantly disabled? 

Also, it's quite possible that they will just lay him off during the 12 week short term period right?  Has that happened to anyone?  Then what happens?  Can they take away your long term disability plan that you paid for when you were employed now that you are no longer an employee?

Do you ever just get to skip short term disability and go straight to long term disability? I'm not talking SSDI, but Unum Long Term Disability? There seems to be some protection there.  It would help him with keeping his life insurance too, then he could get a premium of waiver and it wouldn't matter about not having the job to keep the benefits.  He paid for the life insurance, but it's through the company with Unum. If you could just skip the short term disability that would seem safest.  Everything is though Unum and work.  We don't really trust anyone and no attorneys around here know the answers. 

The best idea seems to be get approved for short term disability, apply for SSDI, then get approved by Unum for LTD and get a premium of waiver. Plus do all this before you may get laid off/fired or whatever.  Am I on the right track?

Sorry, this is a head full.  What can I say my head is full!  Not even sure if I made much sense.

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Hi all, posting on behalf of my wife.

My wife was diagnosed barely in stage 3.  1.01mm on her leg, 6 cells found during biopsy.  She was not a good canidate for Interferon so we investigated and eventually ended up with the Dabrafenib and Trametinib on prescription.

She has been taking them for about 11 days.  She's had a few side effects, a rash, sickness but nothing extreme.

I am wondering if this is the worst it gets or is there a peak period for side effects or perhaps they just show up at any time.  Keep in mind this is all for a seemingly healthy person.


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Anonymous's picture
Replies 10
Last reply 1/9/2014 - 12:31am

hi ... i'm a Danish guy looking to enter a Bristol Myers Sqiubb phase 3 trial of ipilumimab and/or nivolumab and I was wondering if anyone else in this forum is participating in this trial already and what your observations have been so far - both in terms of tumor effects as well as side effects ... looking forward to your comments !

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Replies by: Mat, aldakota22

I am so proud to be in this trial, for three years now. We must remember those first brave ones, who died from BRAF alone, and the courageous Dr. Flaherty and his crew, and the FDA itself, which allowed MEK inhibitors to be given at the same time. They saved my life and so many others, and those to come. I am just overwhelmed with gratitude.

The history of the world is the battle between superstition and intelligence.

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