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Archive for the ‘Genomic Testing: Methodology for Diagnosis’ Category

Immuno-Therapy Strategies on BioMarker’s cutoff value for defining PD-L1 positive/negative patients: First-line and Second-line setting – FDA stand on BMS’s “Test-free Prescribing” in Opdivo (nivolumab) vs Merck’s “Companion Diagnostic” in Keytruda (pembrolizumab) vs Genetech’s “Complementary Diagnostics” and”Companion Diagnostic”?? in Tecentriq (atezolizumab)

Posted in Biomarkers & Medical Diagnostics, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Screening, FDA Regulatory Affairs, Genetics & Innovations in Treatment, Genome Biology, Genomic Testing: Methodology for Diagnosis, Immunotherapy, tagged "Test-free Prescribing", First-line and Second-line setting, Keytruda (pembrolizumab), Opdivo (nivolumab), PD-L1 positive/negative patients, Tecentriq (atezolizumab) on September 13, 2016| Leave a Comment »

Immuno-Therapy Strategies on BioMarker’s cutoff value for defining PD-L1 positive/negative patients: First-line and Second-line setting – FDA stand on BMS’s “Test-free Prescribing” in Opdivo (nivolumab) vs Merck’s “Companion Diagnostic” in Keytruda (pembrolizumab) vs Genetech’s “Complementary Diagnostics” and “Companion Diagnostic”?? in Tecentriq (atezolizumab)

Reporter: Aviva Lev-Ari, PhD, RN

 

UPDATED on 3/11/2019

Roche’s I-O drug Tecentriq picks up key first-in-class breast cancer nod

In a first for the immuno-oncology field, Roche’s Tecentriq has a big new approval in breast cancer. And once again, the Swiss drugmaker has nabbed a piece of the immuno-oncology market all for itself.

On Monday, the FDA greenlighted the immuno-oncology drug, in combination with Celgene chemo drug Abraxane, as a treatment for patients with triple-negative breast cancer (TNBC) whose tumors express the protein PD-L1. The go-ahead makes it the first immunotherapy regimen cleared in TNBC—and in breast cancer in general.

Regulators based their positive decision on data presented last fall that showed that adding Tecentriq to Abraxane in newly diagnosed patients could pare down the risk of disease worsening or death by 20%. The duo staved off progression by a median 7.2 months, compared with 5.5 months for Abraxane on its own.

Now, Roche will lead the way in TNBC without market competition from its PD-1/PD-L1 nemeses—at least for now. Tecentriq’s other two therapy areas, bladder cancer and lung cancer, are ultracrowded, thanks to drugs such as Merck’s Keytruda and Bristol-Myers Squibb’s Opdivo, both of which hit the scene before Tecentriq did.

“The response from the physician community has been phenomenal,” Amreen Husain, M.D., global development team leader for Roche immuno-oncology, said in an October interview.

RELATED: ESMO: Roche’s Tecentriq posts ‘unprecedented’ benefit in triple-negative breast cancer

But when it comes to breast cancer, Roche is used to leading the way, and the company will no doubt lean on its marketing expertise—gleaned through years selling drugs like Herceptin and, more recently, Perjeta and Kadcyla—to get Tecentriq off the ground.

RELATED: Can Kadcyla give Roche a softer landing when Herceptin biosims hit? New data could help

Meanwhile, the approval is an exciting one for doctors and patients who’ve battled the notoriously tough-to-treat disease for years with few good options.

SOURCE

https://www.fiercepharma.com/marketing/roche-s-tecentriq-picks-up-key-first-class-breast-cancer-nod-tnbc-ok?mkt_tok=eyJpIjoiWXpFNU5qaGxNV1V3TkRBMSIsInQiOiJVMDdzbWpGQkJuRmpiT2FzaHR3dlwvM2hFQWd5RGkyXC9XMUJ5NHA5YjU5T21jT050Rk9IamtpalNWV3R3YjgzT2lMMEE3OUdpQnhDS3Y2aUNJVW1lMGtpUUY2Z0VGVFJVSkVHUTUrTWVYVjA3VXptMm9WWnlsdVc1VTRRSHg3SXFHIn0%3D

 

UPDATED on 2/14/2019

Dive Insight:

Checkpoint inhibitors like Merck’s Keytruda (pembrolizumab) have changed cancer care across a number of tumor types, but none are currently approved for prostate cancer. Neither are any of three PARP inhibitors currently on the U.S. market for ovarian and breast cancers.

Merck hopes to change that through these late-stage studies, pairing Keytruda with the PARP inhibitor Lynparza (olaparib), chemotherapy and approved prostate cancer agent Xtandi (enzalutamide).

Patients with mCRPC pose a particular challenge to treat. Metastatic cancer has spread to other parts of the body, while castration-resistant tumors have continued to grow despite surgery or treatment to lower the amount of male sex hormones, or androgens, that typically drive prostate cancer.

Current treatment options for this type of prostate cancer are led by Zytiga (abiraterone acetate), a Johnson & Johnson drug now facing generic competition, and Pfizer and Astellas’ Xtandi.

Merck’s Phase 1b/2 study tested four Keytruda combinations, pairing the immunotherapy with both of those current treatment options as well as with chemotherapy and with Lynparza, which is jointly owned by AstraZeneca and Merck.

Results presented Thursday came from a small number of patients, but showed some positive responses in previously treated patients.

SOURCE

https://www.biopharmadive.com/news/merck-plans-trio-of-phase-3-keytruda-studies-in-prostate-cancer/548466/

 

UPDATED on 5/1/2018

Dive Insight:

While both Keytruda and Opdivo won initial U.S. approval just months apart in 2014, Bristol-Myers’ drug saw much faster sales growth to start. Securing OKs in first-line lung cancer has been Merck’s ticket to catching Bristol-Myers, and Keytruda sales in the first quarter were roughly even with Opdivo’s.

Merck expects the success of its KEYNOTE-189 study will further drive uptake of Keytruda as a first-line treatment for advanced NSCLC. Results, presented last month at the annual meeting of the American Association of Cancer Research, showed a combination of Keytruda and chemotherapy cut the risk of death in half compared to chemotherapy alone.

Importantly, data supported the combination’s benefit across varying levels of PD-L1 expression , a biomarker used to identify patients most likely to respond to immunotherapy. Merck previously won a conditional approval for the combo from a smaller study, but physicians have been hesitant to broadly prescribe without further data.

Now, impressive results in hand, Merck hopes more doctors will prescribe Keytruda plus chemotherapy to NSCLC patients with PD-L1 expression levels below 50% or even below 1% — patient populations currently not served by Keytruda monotherapy.

SOURCE

https://www.biopharmadive.com/news/merck-keytruda-immunotherapy-lead-q1-earnings-pipeline/522513/

UPDATED on 3/26/2018

Gaining steam in PD-1/L1 race, Roche reports positive PhIII OS data on Tecentriq combo in NSCLC

by brittany meiling — on March 26, 2018 06:29 AM EDT

https://endpts.com/gaining-steam-in-pd-1-l1-race-roche-reports-positive-phiii-os-data-on-tecentriq-combo-in-nsclc/?utm_medium=email&utm_campaign=Monday%20March%2026%202018&utm_content=Monday%20March%2026%202018+CID_12d9cbde6620f32af9d31d31236c94c4&utm_source=ENDPOINTS%20emails&utm_term=Gaining%20steam%20in%20PD-1L1%20race%20Roche%20reports%20positive%20PhIII%20OS%20data%20on%20Tecentriq%20combo%20in%20NSCLC

 

UPDATED on 3/20/2018

In a phase 3 study, Roche’s Tecentriq combined with chemo beat out solo chemo at cutting the risk of disease worsening or death in previously untreated patients with the squamous form of the disease. As of now, researchers haven’t seen evidence of a benefit to overall survival, but the trial, dubbed IMpower131, is continuing to collect that data.

The results hand Roche the chance to nab a first-to-market lead in the front-line squamous setting. Squamous NSCLC affects just 25% to 30% of all NSCLC patients, but it’s more complicated, and patients have fewer treatment options than those with non-squamous NSCLC, Jefferies analyst Ian Hilliker wrote in a note to clients. Hilliker predicts $1.1 billion in peak sales for Tecentriq in that set of patients.

SOURCE

https://www.fiercepharma.com/pharma/roche-s-tecentriq-triumphs-squamous-lung-cancer-can-it-make-its-mark-against-merck?mkt_tok=eyJpIjoiTlRrM09UQTFNVFEzTjJRNCIsInQiOiJNUnhJMThFZGw5ZERKS1N3Q3dQbGg2dmE1NHhTSFhYZjcycVdMcTAwaTZ1cWxZV3ZJQStqZXJZb0lJUkowNmdXZVk1dnFCc1hVVUlSZitWZ2pPMlJYc25VUXVXY0JxeDdYbUw2XC9uOHgzYWNFb3lObGhrTXd6T25IRWFoTTZTZXcifQ%3D%3D&mrkid=993697

 

UPDATED on 11/21/2017

Roche Cancer Drug Rises To Challenge Merck, Bristol-Myers

Matthew Herper , FORBES STAFF

Roche’s study had three arms. All patients received carboplatin and paclitaxel, the cancer drug once sold as Taxol. The control group also received Avastin, one of Roche’s best-selling cancer drugs. Then two groups got Tecentriq, one with Avastin and one without. What Roche has announced today is that the Avastin-Tecentriq-chemotherapy combination did better than Avastin and chemotherapy alone, and that the survival results so far are “encouraging.” That leaves a big question: how are the patients who got Tecentriq, but not Avastin, doing?

SOURCE

https://www.forbes.com/sites/matthewherper/2017/11/20/roche-cancer-drug-rises-to-challenge-merck-bristol-myers/#1a08271b52a8

 

UPDATED on 7/25/2017

Close to a year after Merck $MRK won an accelerated FDA OK to use its PD-1 checkpoint star Keytruda for treating second-line cases head and neck squamous cell carcinoma in combination with platinum-containing chemo, the pharma giant announced that its big Phase III study for that indication failed.

The pivotal KEYNOTE-040 trial failed to meet the primary endpoint on overall survival in comparing the blockbuster checkpoint against standard therapies, the pharma giant reported. But the current approval stands nevertheless, Merck said in a statement.

“The company noted that the FDA remains comfortable with the drug’s current accelerated approval in this indication despite the trial results,” observed Leerink’s Seamus Fernandez. “Importantly, Keytruda appears to have another shot on goal for full approval in H&N cancer, as the Keynote-048 study in first-line patients could, if positive, serve as the confirmatory trial.”

SOURCE

https://endpts.com/merck-hit-with-another-late-stage-setback-on-checkpoint-star-keytruda/?utm_medium=email&utm_campaign=Tuesday%20%20July%2025%202017&utm_content=Tuesday%20%20July%2025%202017+CID_15fd9125b2763ceaf79f421345542d44&utm_source=ENDPOINTS%20emails&utm_term=Merck%20hit%20with%20another%20late-stage%20setback%20on%20checkpoint%20star%20Keytruda

UPDATED on 5/11/2017

Merck increases grip on its lead in lung cancer, winning approval for Keytruda/chemo combo as first-line therapy

by john carroll — on May 10, 2017 05:35 PM EDT Updated: 06:00 PM

https://endpts.com/merck-increases-grip-on-its-lead-in-lung-cancer-winning-approval-for-keytrudachemo-combo-as-first-line-therapy/?utm_medium=email&utm_campaign=Thursday%20%20May%2011%202017&utm_content=Thursday%20%20May%2011%202017+CID_33f2ef8a9bb6f964b9d7568cf79c80be&utm_source=ENDPOINTS%20emails&utm_term=Merck%20increases%20grip%20on%20its%20lead%20in%20lung%20cancer%20winning%20approval%20for%20Keytrudachemo%20combo%20as%20first-line%20therapy

UPDATED on 5/10/2017

Roche’s shocking Tecentriq fail raises red flag for bladder cancer rivals

Roche’s Tecentriq wasn’t supposed to fail its phase 3 trial in second-line bladder cancer. But that’s what it just did—and the data shortfall not only endangers the drug’s conditional FDA approval, but could augur trouble ahead for other checkpoint inhibitors that followed Tecentriq into the field.

Tecentriq, approved last year on the basis of phase 2 data showing a durable response to the drug, failed to prove it could actually prolong patients’ lives, the company said Wednesday. The bladder cancer indication, Tecentriq’s first, accounts for about 70% of the med’s current sales, analysts say, and the FDA could well decide to strike that approval off the drug’s label.

“[W]e assume that this will put this indication at risk of being removed from the label,” Leerink analyst Seamus Fernandez wrote Wednesday morning, noting that the results were unexpected. “This comes as a surprise to us, considering Merck’s Keytruda showed an overall survival benefit.”

SOURCE

http://www.fiercepharma.com/pharma/roche-s-shocking-tecentriq-fail-raises-red-flag-for-bladder-cancer-rivals?utm_medium=nl&utm_source=internal&mrkid=993697&mkt_tok=eyJpIjoiTVRCbFltUXpZMk0wTURRMCIsInQiOiIydnRsZ0xzT3prd3EzYVNoV0xyT1ZCWnFCaDFScVdwd1dyMmpMZjQycU9zOEVJSTVZalY5dHNyQ1E0XC96eXhadkpRSE5JRGoydHNzNFA2WUVaRzRVbUxmNmhicVZ4YkE3c1NmNkhoSUxBK0VmU2dUM3FBWEhrOFp2UHoySXhrUUEifQ%3D%3D

UPDATED on 4/13/2017

World’s Top Ten Cancer Drugs by 2020  (million USD)

https://pharmaceuticalintelligence.com/2017/04/13/worlds-top-ten-cancer-drugs-by-2020-million-usd/

Opdivo Setback May Yield Lessons for Pharma Advancing Immunotherapies With PD-L1 Testing

https://www.genomeweb.com/molecular-diagnostics/opdivo-setback-may-yield-lessons-pharma-advancing-immunotherapies-pd-l1

UPDATED on 10/9/2016

Opdivo (nivolumab) Shows Durable Response in Longest Follow-up for a PD-1 Inhibitor in Previously Treated Advanced Non-Small Cell Lung Cancer

BMY | 6 hours ago

Opdivo (nivolumab) Shows Durable Response in Longest Follow-up for a PD-1 Inhibitor in Previously Treated Advanced Non-Small Cell Lung Cancer

Updated data from CheckMate -057 and -017 show Opdivo-treated patients had tripled the duration of response compared to those treated with docetaxel, with a minimum follow-up of two years

In CheckMate -057, durable responses and complete responses were observed with Opdivo in both PD-L1 expressors and non-expressors

Patient-reported outcomes from CheckMate -057 show favorable overall health status with Opdivo versus docetaxel in previously treated advanced non-small cell lung cancer patients

Bristol-Myers Squibb Company (NYSE: BMY) announced today updated results from two pivotal Phase 3 studies, CheckMate -057 and CheckMate -017, which showed more than one-third of previously treated metastatic non-small cell lung cancer (NSCLC) patients in both trials experienced ongoing responses with Opdivo, compared to no ongoing responses in the docetaxel arm. The median duration of response (DOR) with Opdivo versus docetaxel in CheckMate -057 was 17.2 months (95% CI: 8.4, NE) and 5.6 months (95% CI: 4.4, 6.9), respectively, and in CheckMate -017 it was 25.2 months (95% CI: 9.8, 30.4) and 8.4 months (95% CI: 8.4, NE), respectively. In CheckMate -057, patients with PD-L1 ≥1% had a median DOR of 17.2 months (95% CI: 8.4, NE) and in patients with PD-L1 <1%, it was 18.3 months (95% CI: 5.5, NE). In both studies, durability of response was observed in both PD-L1 expressors and non-expressors, and in CheckMate -057, one out of the four complete responses occurred in a patient with <1% PD-L1 expression.

There were no new safety signals identified for Opdivo in the pooled safety analysis from both studies. No new treatment-related deaths occurred between one and two years’ minimum follow-up despite the longer treatment exposure, and new events were observed in 11/418 patients with an additional one year of follow up.

These findings were presented today, October 9, during a poster discussion session at the 2016 European Society for Medical Oncology Congress from 3:46-4:06 p.m. CEST (Abstract #1215PD).

“Further evaluation of Opdivo in previously treated non-small cell lung cancer showed continued superior survival and the potential for durable responses compared to docetaxel across histologies in this patient population,” said Martin Reck, M.D., Ph.D., head of thoracic oncology at the Hospital Grosshansdorf. “Notably, the median duration of response with Opdivo was more than three times that observed with docetaxel.”

Read more at

http://www.stockhouse.com/news/press-releases/2016/10/09/opdivo-nivolumab-shows-durable-response-in-longest-follow-up-for-a-pd-1#QVs566rlK9JKSMC8.99

UPDATED on 9/25/2016

Genentech dives into mRNA, betting $310M on BioNTech’s personalized cancer vaccine tech

by john carroll
September 21, 2016 02:00 AM EDT
Updated: 10:20 AM

http://endpts.com/genentech-budgets-310m-in-cash-to-seal-personalized-cancer-vaccine-pact-with-biontech/?utm_campaign=Wednesday%20%20September%2021%202016&utm_term=Genentech%20bets%20on%20BioNTech%20personalized%20mRNA%20cancer%20therapies&utm_content=39262747&utm_medium=social&utm_source=linkedin

For a review of all the complexities involved in the emerging market for BioMarkers in Immuno-Therapy, see

Opdivo Setback May Yield Lessons for Pharma Advancing Immunotherapies With PD-L1 Testing

https://www.genomeweb.com/molecular-diagnostics/opdivo-setback-may-yield-lessons-pharma-advancing-immunotherapies-pd-l1

PD-L1 testing as part of the tumor profiling workup for patients. Diaceutics’ surveys show a sharp uptick in the number of labs offering PD-L1 testing over the past year-and-a-half and 52 labs in the US offer at least one PD-L1 test. The company also reviewed biomarkers being studied in 95 Phase II/III NSCLC, and found that approximately half are incorporating patients’ PD-L1 status either alone or in combination with other markers, such as EGFR and ALK mutations.

At Cancer Genetics over the past year, there has also been a notable ramp up in orders for PD-L1 testing for lung cancer patients, but also for melanoma and head and neck cancer patients.

Labs are also challenged by having to decide whether to invest in validating and offering all four FDA-approved PD-L1 tests. “If you look from a laboratory perspective, in the ideal world, you need one test, and clear instructions about the algorithm and cutoff values to assign patients to treatment,” Braendle said. “Four different tests creates quite a confusing situation for the labs and the physicians.”

SOURCES

Diaceutics Group Report Reveals Significant Real-Time PD-L1 Testing Gaps in the US

http://www.diaceutics.com/diaceutics-group-report-reveals-significant-real-time-pd-l1-testing-gaps-in-the-us-3/

 

Opdivo Setback May Yield Lessons for Pharma Advancing Immunotherapies With PD-L1 Testing

https://www.genomeweb.com/molecular-diagnostics/opdivo-setback-may-yield-lessons-pharma-advancing-immunotherapies-pd-l1

 

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On its way for an IPO: mRNA platform Immune-Oncology, Moderna, is recruiting 100 new Life Scientists in Cambridge, MA

Posted in BioTechnology - Venture Creation, BioTechnology - Venture Creation, Venture Capital, Computational Biology/Systems and Bioinformatics, Diagnostic Immunology, Drug Delivery Platform Technology, Drug Development Process, Drug Discovery Chemistry, Genetics & Innovations in Treatment, Genome Biology, Genomic Testing: Methodology for Diagnosis, Human Immune System in Health and in Disease, Immuno-Oncology & Genomics, Immunodiagnostics, Immunotherapy, Infectious Disease Immunodiagnostics, mRNA platform in Drug DIscovery, RNA Biology, RNA Biology, Cancer and Therapeutics, tagged mRNA-based therapy, vascular endothelial growth factor-A (VEGF-A) on September 7, 2016| Leave a Comment »

On its way for an IPO: mRNA platform, Moderna, Immune Oncology is recruiting 100 new Life Scientists in Cambridge, MA

Curator: Aviva Lev-Ari, PhD, RN

 

Deals:

Moderna has now raised $1.9 billion from investors like AstraZeneca – 9% stack [AstraZeneca’s Pascal Soriot helped get that all started with a whopping $240 million upfront in its 2013 deal, which was tied to $180 million in milestones.], with another $230 million on the table from grants. In addition to the financing announcement this morning, Moderna is also unveiling a pact to develop a new Zika vaccine, with BARDA putting up $8 million to get the program started while offering an option on $117 million more to get through a successful development program.

Novel Strategy in Biotech:

in biotech. Instead of grabbing one or two new drugs and setting out to gather proof-of-concept data to help establish its scientific credibility, the company has harvested a huge windfall of cash and built a large organization before even entering the clinic. And it did that without turning to an IPO.

Pipeline include:

• The deal with AstraZeneca covers new drugs for cardiovascular, metabolic and renal diseases as well as cancer.
• partners filed a European application to start a Phase I study of AZD8601, an investigational mRNA-based therapy that encodes for vascular endothelial growth factor-A (VEGF-A)
• Moderna CEO spelled out plans to get the first 6 new drugs in the clinic by the end of 2016.
• The first human study was arranged for the infectious disease drug mRNA 1440, which began an early stage study in 2015.
• Moderna built up a range of big preclinical partnerships.
• CEO Bancel says the number of drugs in development has swelled to 11, with the first set of data slated to be released in 2017.
• Moderna also plans to add about 10 drugs to the clinic by next summer,

 

SOURCES

UPDATED: Booming Moderna is raising $600M while ramping up manufacturing and clinical studies

by john carroll – August 29, 2016

http://endpts.com/booming-moderna-is-adding-600m-while-ramping-up-manufacturing-and-clinical-studies/ 

$1.9B in: Moderna blueprints $100M facility, plans to double the pipeline after a $474M megaround

by john carroll – September 7, 2016

http://endpts.com/moderna-blueprints-100m-facility-plans-to-double-the-pipeline-after-a-474m-megaround/?utm_source=Sailthru&utm_medium=email&utm_campaign=Issue:%202016-09-07%20BioPharma%20Dive%20%5Bissue:7155%5D&utm_term=BioPharma%20Dive

 

Moderna Therapeutics Deal with Merck: Are Personalized Vaccines here?

Curator & Reporter: Stephen J. Williams, PhD – August 11, 2016

https://pharmaceuticalintelligence.com/2016/08/11/moderna-therapeutics-deal-with-merck-are-personalized-vaccines-here/

 

at #JPM16 – Moderna Therapeutics turns away an extra $200 million: with AstraZeneca (collaboration) & with Merck ($100 million investment)

Reporter: Aviva Lev-Ari, PhD, RN – January 13, 2016

https://pharmaceuticalintelligence.com/2016/01/13/at-jpm16-moderna-therapeutics-turns-away-an-extra-200-million-with-astrazeneca-collaboration-with-merck-100-million-investment/

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Crowdsourcing Genetic Data Yields Discovery of DNA loci associated with Major Depressive Disorder (MDD) in European Descendants

Posted in Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Computational Biology/Systems and Bioinformatics, Exosomes, Gene Regulation, Gene Regulation and Evolution, Genetics & Innovations in Treatment, Genome Biology, Genomic Endocrinology, Genomic Testing: Methodology for Diagnosis, Innovations in Neurophysiology & Neuropsychology, Neurological Diseases, Next Generation Sequencing (NGS), Personalized and Precision Medicine & Genomic Research, tagged behavioral phenotypes, biological mechanisms of depression, diagnoses of depression, European ancestry, genome-wide association studies (GWAS), histone methylation, loci associated with the risk of developing major depressive disorder (MDD), neurobiology of depression, neurodevelopment, neurogenesis and synaptic modification, Tissue and gene enrichment assays, weighted genetic risk score (GRS) on August 9, 2016| Leave a Comment »

Crowdsourcing Genetic Data Yields Discovery of DNA loci associated with Major Depressive Disorder (MDD) in European Descendants

 

Reporter: Kelly Perlman, Life Sciences Student and Research Assistant, McGill University

 

UPDATED on 11/24/2019

Can AI help diagnose depression? It’s a long shot

At the moment, machine intelligence is just as subjective as human intelligence

Alejandra Canales

https://www.salon.com/2019/11/23/can-ai-help-diagnose-depression-its-a-long-shot_partner/amp?__twitter_impression=true

Researchers from Pfizer Global Research and Development, 23andMe, and the Massachusetts General Hospital have published a study in Nature Genetics, pinpointing 15 genetic loci associated with the risk of developing major depressive disorder (MDD) in individuals of European ancestry. Evidence from previous research suggests that MDD is heritable, but the details of the specific gene correlates are unclear. The identification of loci where single nucleotide polymorphisms (SNPs) related to MDD exist could provide better insight into the neurobiology of depression, and therefore better treatment options.

23andMe, a private biotechnology company situated in California, offers a DNA sequencing service in which consumers send in a saliva swab for testing, and later receive a report listing the findings of the analysis related to ancestry, physical and behavioral traits, along with risk of inheriting certain diseases. The participants of this study had agreed to provide the results of their genetic testing for scientific research.

The results of 75,607 participants with self-reported diagnoses of depression were compared to the results of 231,747 participants reporting having never experienced depression. This data was combined with the results of previously published MDD genome-wide association studies (GWAS). To test the whether these results could be replicated, another set of results from 23andMe was analyzed, in which there were 45,773 MDD subjects, and 106,354 controls.

After the joint analysis, 17 SNPs were identified at 15 different loci. Tissue and gene enrichment assays showed that the genes that were over-expressed in the CNS were related to functions including neurodevelopment, histone methylation, neurogenesis and synaptic modification.

The team then created a weighted genetic risk score (GRS) in which they compared the 17 SNPs with factors including medication use, comorbid diseases and behavioral phenotypes, all of which were correlated with the GRS. Of note, the GRS was very highly correlated with age of onset of MDD.

The crowdsourcing of genetic data proves to be an efficient and powerful tool for large-scale MDD studies. Pooling large subject databases together is essential in order to account for the heterogeneous nature of the disease. Despite not being able to precisely assess each subject’s disease phenotype, scientists can make more rapid headway by collaborating with biotechnology companies in the quest to better understand the biological mechanisms of depression. Ron Perlis, M.D., M.Sc., of the Massachusetts General Hospital and co-author of this paper explained that “finding genes associated with depression should help make clear that this is a brain disease, which we hope will decrease the stigma still associated with these kinds of illnesses”.

 

Details on specific significant genes:

http://www.genecards.org/cgi-bin/carddisp.pl?gene=OLFM4

http://www.genecards.org/cgi-bin/carddisp.pl?gene=TMEM161B

http://www.genecards.org/cgi-bin/carddisp.pl?gene=MEF2C

http://www.genecards.org/cgi-bin/carddisp.pl?gene=MEIS2

http://www.genecards.org/cgi-bin/carddisp.pl?gene=TMCO5A

http://www.genecards.org/cgi-bin/carddisp.pl?gene=NEGR1

 

SOURCES

Hyde, C. L., Nagle, M. W., Tian, C., Chen, X., Paciga, S. A., Wendland, J. R., . . . Winslow, A. R. (2016). Identification of 15 genetic loci associated with risk of major depression in individuals of European descent. Nature Genetics Nat Genet. doi:10.1038/ng.3623

Major Depressive Disorder Loci Discovered in Large GWAS Enabled by 23andMe Participants’ Data. (2016, August 01). Retrieved August 09, 2016, from https://www.genomeweb.com/microarrays-multiplexing/major-depressive-disorder-loci-discovered-large-gwas-enabled-23andme

 

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Through Data Science and Cloud Technology: Stanford Medicine and Google will transform Patient Care and Medical Research

Posted in Accountable Care Organizations, Computational Biology/Systems and Bioinformatics, Genome Biology, Genomic Testing: Methodology for Diagnosis, HealthCare IT, Healthcare Reform, Personalized and Precision Medicine & Genomic Research on August 9, 2016| Leave a Comment »

 Through Data Science: Stanford Medicine and Google will transform Patient Care and Medical Research

Reporter: Aviva Lev-Ari, PhD, RN

 

Stanford Medicine integrates research, medical education and health care at its three institutions –Stanford University School of Medicine, Stanford Health Care (formerly Stanford Hospital & Clinics), and Lucile Packard Children’s Hospital Stanford. For more information, please visit the Office of Communication & Public Affairs site at http://mednews.stanford.edu.

 

Stanford’s forthcoming Clinical Genomics Service, which puts genomic sequencing into the hands of clinicians to help diagnose disease, will be built using Google Genomics, a service that applies the same technologies that power Google Search and Maps to securely store, process, explore and share genomic data sets.

The Clinical Genomics Service will enable physicians at Stanford Health Care and Stanford Children’s Health to order genome sequencing for patients who have distinctive or unusual symptoms that might be caused by a wayward gene. The genomic data would then go to the Google Cloud Platform to join masses of aggregated and anonymous data from other Stanford patients. “As the new service launches,” said Euan Ashley, MRCP, DPhil, a Stanford associate professor of medicine and of genetics, “we’ll be doing hundreds and then thousands of genome sequences.”

The Clinical Genomics Service aims to make genetic testing a normal part of health care for patients. “Genetic testing is built into the whole system,” said Ashley. A physician who thinks a genome-sequencing test could help a patient can simply request sequencing along with other blood tests, he said. “The DNA gets sequenced and a large amount of data comes back,” he said. At that point, Stanford can use Google Cloud to analyze the data to decide which gene variants might be responsible for the patient’s health condition. Then a data curation team will work with the physician to narrow the possibilities, he said.

“This collaboration will enable Stanford to discover new ways to advance medicine to the benefit of Stanford patients and families,” said Ed Kopetsky, chief information officer at Lucile Packard Children’s Hospital Stanford and Stanford Children’s Health. “Together, Stanford Medicine and Google are making a major contribution and commitment in curing diseases that afflict children not just in our community, but throughout the world. It’s an extraordinary investment, and we’re proud to play such a large role in transforming patient care and research.”

Read more at the SOURCE

 

Stanford Medicine, Google team up to harness power of data science for health care

By JENNIE DUSHECK

Jennie Dusheck is a science writer for the medical school’s Office of Communication & Public Affairs. Email her at dusheck@stanford.edu.

SOURCE

http://med.stanford.edu/news/all-news/2016/08/stanford-medicine-google-team-up-to-harness-power-of-data-science.html

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Using Online Mendelian Inheritance in Man (OMIM) database and the Human Genome Mutation Database (HGMD) Pro 2015.2 for Quantification of the growth in gene-disease and variant-disease associations

Posted in Computational Biology/Systems and Bioinformatics, Exosomes, Genetics & Innovations in Treatment, Genome Biology, Genomic Testing: Methodology for Diagnosis, Mutagenesis, Next Generation Sequencing (NGS) on July 22, 2016| Leave a Comment »

Using Online Mendelian Inheritance in Man (OMIM) database and the Human Genome Mutation Database (HGMD) Pro 2015.2 for Quantification of the growth in gene-disease and variant-disease associations

Reporter: Aviva Lev-Ari, PhD, RN

 

Reanalysis of Clinical Exome Data Over Time Could Yield New Diagnoses

Jul 22, 2016

|

Christie Rizk

NEW YORK (GenomeWeb) – Clinical exomes that are re-evaluated in a systematic way could yield new diagnoses and prove useful to clinicians, according to a study published yesterday in Genetics in Medicine.

A team of researchers from Stanford University set out to examine whether nondiagnostic clinical exomes could provide new information for patients if they were re-examined with current bioinformatics software and knowledge of disease-related variants as presented in the literature.

Clinical exome sequencing yields no diagnosis for about 75 percent of patients evaluated for possible Mendelian disorders, wrote senior author Gill Bejerano and his colleagues. But a reanalysis of exome and phenotypic data from 40 such individuals using current methods identified a definitive diagnosis for four of them — 10 percent — the team said.

In these cases, the causative variant was de novo and found in a relevant autosomal-dominant disease gene. At the time these exomes were first sequenced, the researchers wrote, the existing literature on these causative genes was either “weak, nonexistent, or not readily located.” When the exomes were re-examined by his team, Bejerano noted, the supporting literature was more robust.

SOURCE

https://www.genomeweb.com/sequencing/reanalysis-clinical-exome-data-over-time-could-yield-new-diagnoses?utm_source=SilverpopMailing&utm_medium=email&utm_campaign=Daily%20News:%20Reanalysis%20of%20Clinical%20Exome%20Data%20Over%20Time%20Could%20Yield%20New%20Diagnoses%20-%2007/22/2016%2011:20:00%20AM

At ACMG, Researchers Report Data Re-Analysis, Matchmaking Boosts Solved Exome Cases

Mar 10, 2016

|

Julia Karow

img_0094.jpg

In addition to re-analyzing exome data, the researchers have been working on establishing causality for novel candidate disease genes through patient matches. For this, the team has been using the GeneMatcher website, which allows them to find other clinicians and researchers around the world who have patients, or animal models, with mutations in the same genes as their own patients. Through an API developed by the Matchmaker Exchange project, GeneMatcher submitters can also query the PhenomeCentral and Decipher databases. As of March, more than 4,000 genes had been submitted to GeneMatcher from more than 1,300 submitters in 48 countries, and 1,900 matches had been made, Sobreira reported.

Her team has so far submitted data from 104 families, involving 280 genes, and has had 314 matches so far, involving 113 genes. Several cases have been successes, meaning the researchers could establish that a candidate gene is indeed disease causing, and several others are pending, both from Hopkins and from other groups. The total number of solved cases tracing their success to GeneMatcher is currently unknown, Sobreira said, but the organizers are planning to survey submitters about their success rate in the near future.

SOURCE

https://www.genomeweb.com/molecular-diagnostics/acmg-researchers-report-data-re-analysis-matchmaking-boosts-solved-exome-cases

 

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