Genomics|Features|Cancer Genomics

Genomics|Features|Cancer Genomics

Cancer Genomics and Precision Medicine

Cancer Precision Medicine: Improving Evidence in Practice - September 2, 2015

Precision medicine at Memorial Sloan Kettering Cancer Center: clinical next-generation sequencing enabling next-generation targeted therapy trials.
Hyman DM et al. Drug Discov. Today 2015 Aug 27.

NCI-MATCH Trial Opens, AACR blog post, August 2015

NCI-MATCH launch highlights new trial design in precision-medicine era
McNeal C , JNCI, August 2015

The Cancer Genomics Resource List, 2014
Zutter MM et al. CAP Lab Improvement Program, Archives of Pathology, August 2015

Personalized medicine and economic evaluation in oncology: all theory and no practice?
Garattini L et al. Expert Rev Pharmacoecon Outcomes Res 2015 Aug 9. 1-6

Precision medicine trials bring targeted treatments to more patients, C. Helwick, ASCO Post, Jul 25

Next-generation sequencing to guide cancer therapy 
Gagan J et al, Genome Medicine, July 29, 2015

Feasibility of large-scale genomic testing to facilitate enrollment onto genomically matched clinical trials.
Meric-Bernstam F et al. J. Clin. Oncol. 2015 May 26.

Brave-ish new world-what's needed to make precision oncology a practical reality.
MacConaill LE et al. JAMA Oncol 2015 Jul 16.

Genomic profiling: Building a continuum from knowledge to care
Helen C et al. JAMA Oncology, July 2015

Are we there yet?
When it comes to curing cancer, targeted therapies and genomic sequencing are helping, but we still have far to go. Genome Magazine, June 29, 2015

Artificial intelligence, big data, and cancer
Kantarjian H et al, JAMA Oncology, June 2015

Multigene panel testing in oncology practice - how should we respond?
Kurian AW et al. JAMA Oncology, June 2015

Use of whole genome sequencing for diagnosis and discovery in the cancer genetics clinic.
Foley SB et al. EBioMedicine 2015 Jan 2(1) 74-81

The future of molecular medicine: biomarkers, BATTLEs, and big data 
ES Kim, ASCO University, June 2015

NCI-MATCH trial will link targeted cancer drugs to gene abnormalities

Targeted agent and profiling utilization registry study, from the American Society for Clinical Oncology

ASCO study aims to learn from patient access to targeted cancer drugs used off-label, American Society for Clinical Oncology

Improving evidence developed from population-level experience with targeted agents  [PDF 462.93 KB]
McLellan M et al Issue Brief. Conference on Clinical Cancer Research November 2014

Implementing personalized cancer care.
Schilsky RL et al. Nat Rev Clin Oncol 2014 Jul (7) 432-8

Accelerating the delivery of patient-centered, high-quality cancer care.
Abrahams E et al. Clin. Cancer Res. 2015 May 15. (10) 2263-7

Next-generation clinical trials: Novel strategies to address the challenge of tumor molecular heterogeneity.
Catenacci DV et al. Mol Oncol 2015 May (5) 967-996

Cancer Precision Medicine: Improving Evidence in Practice - May 29, 2015

Diagnosis and treatment of cancer using genomics
Vockley JG et al. BMJ, May 28, 2015

Targeted agent and profiling utilization registry study, from the American Society for Clinical Oncology

ASCO study aims to learn from patient access to targeted cancer drugs used off-label, American Society for Clinical Oncology

Improving evidence developed from population-level experience with targeted agents  [PDF 462.93 KB]
McLellan M et al Issue Brief. Conference on Clinical Cancer Research November 2014

Implementing personalized cancer care.
Schilsky RL et al. Nat Rev Clin Oncol 2014 Jul (7) 432-8

Accelerating the delivery of patient-centered, high-quality cancer care.
Abrahams E et al. Clin. Cancer Res. 2015 May 15. (10) 2263-7

Next-generation clinical trials: Novel strategies to address the challenge of tumor molecular heterogeneity.
Catenacci DV et al. Mol Oncol 2015 May (5) 967-996

Precision Medicine: Cancer and Genomics - May 12, 2015

Promise, peril seen in personalized cancer therapy, by Marie McCullough, Philadelphia Inquirer, May 10

A decision support framework for genomically informed investigational cancer therapy.
Meric-Bernstam F et al. J. Natl. Cancer Inst. 2015 Jul (7)

Divide and conquer: The molecular diagnosis of cancer, by Louis M. Staudt, National Cancer Insitute, Apr 13

Health: Make precision medicine work for cancer care
To get targeted treatments to more cancer patients pair genomic data with clinical data, and make the information widely accessible, Mark A. Rubin. Nature News, Apr 15

Using somatic mutations to guide treatment decisions
Horlings H et al. JAMA Oncology, March 12, 2015

The landscape of precision cancer medicine clinical trials in the United States
Roper N et al. Cancer Treatment Reviews 2015

What is “precision medicine? Information from the National Cancer Institute

Impact of cancer genomics on precision medicine for the treatment of cancer, from the Cancer Genome Atlas, NCI

US precision-medicine proposal sparks questions, by Sara Reardon, Nature News, Jan 22

Obama's 'precision medicine' means gene mapping, NBC News, Jan 21

What is President Obama's 'precision medicine' plan, and how might it help you? By Lenny Bernstein, Jan 21

Recent reviews

Companion diagnostics: the key to personalized medicine.
Jørgensen JT. Expert Rev Mol Diagn. 2015 Feb;15(2):153-6

Promoting precision cancer medicine through a community-driven knowledgebase.
Geifman N, et al. J Pers Med. 2014 Dec 15;4(4):475-88.

Toward a prostate cancer precision medicine.
Rubin MA. Urol Oncol. 2014 Nov 20.

Prioritizing targets for precision cancer medicine.
Andre F, et al. Ann Oncol. 2014 Dec;25(12):2295-303

Toward precision medicine with next-generation EGFR inhibitors in non-small-cell lung cancer.
Yap TA, Popat S. Pharmgenomics Pers Med. 2014 Sep 19;7:285-95.

Genomically driven precision medicine to improve outcomes in anaplastic thyroid cancer.
Pinto N, et al.  J Oncol. 2014;936285

Translating genomics for precision cancer medicine.
Roychowdhury S, Chinnaiyan AM. Annu Rev Genomics Hum Genet. 2014;15:395-415

The Cancer Genome Atlas: Accomplishments and Future - April 3, 2015

The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge
Tomczak K, et al. Contemp Oncol (Pozn). 2015; 19(1A): A68-A77.

The Cancer Genome Atlas' 4th Annual Scientific Symposium
May 11-12 ~ Bethesda, MD

The Cancer Genome Atlas (TCGA) Data Portal 
Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA

Cancer Genomics Hub: A resource of the National Cancer Institute, from the USC Genome Browser

Molecular classification of gastric adenocarcinoma: translating new insights from The Cancer Genome Atlas Research Network.
Sunakawa Y et al. Curr Treat Options Oncol 2015 Apr (4) 331

TCGA data and patient-derived orthotopic xenografts highlight pancreatic cancer-associated angiogenesis.
Gore J et al. Oncotarget 2015 Feb 25.

Radiogenomics of clear cell renal cell carcinoma: preliminary findings of The Cancer Genome Atlas-Renal Cell Carcinoma (TCGA-RCC) Imaging Research Group.
Shinagare AB et al. Abdom Imaging 2015 Mar 10.

Proteomics of colorectal cancer in a genomic context: First large-scale mass spectrometry-based analysis from the Cancer Genome Atlas.
Jimenez CR et al. Clin. Chem. 2015 Feb 26.

End of cancer-genome project prompts rethink
Geneticists debate whether focus should shift from sequencing genomes to analysing function. Heidi Ledford, Nature News and Comments, January 2015

Cancer Genomics: Insights into Driver Mutations - March 10, 2015

Seek and destroy: Relating cancer drivers to therapies
E. Martinez-Ledesma et al. Cell, March 9, 2015

In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities
C Rubio-Perez et al. Cancer Cell, March 9, 2015

MADGiC: a model-based approach for identifying driver genes in cancer.  [PDF 373.56 KB] 
Keegan D. Korthauer et al. Bioinformatics, January 2015 

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine. 
Benjamin J Raphael et al. Genome Medicine 2014

Novel recurrently mutated genes in African American colon cancers.
Guda K et al. Proc Natl Acad Sci U S A. 2015 Jan 12

Sparse expression bases in cancer reveal tumor drivers.
Logsdon BA, et al. Nucleic Acids Res. 2015 Jan 12

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.
Bertrand D, et al. Nucleic Acids Res. 2015 Jan 8

Identification of constrained cancer driver genes based on mutation timing.
Sakoparnig T, et al. PLoS Comput Biol. 2015 Jan 8;11(1):e1004027

CaMoDi: a new method for cancer module discovery.
Manolakos A, et al. BMC Genomics. 2014 Dec 12;15 Suppl 10:S8.

VHL, the story of a tumour suppressor gene.
Gossage L, et al. Nat Rev Cancer. 2014 Dec 23;15(1):55-64

Targeting the MET pathway for potential treatment of NSCLC.
Li A, et al. Expert Opin Ther Targets. 2014 Dec 23:1-12

Deciphering oncogenic drivers: from single genes to integrated pathways.
Chen J, et al. Brief Bioinform. 2014 Nov 5.

Driver and passenger mutations in cancer.
Pon JR, et al. Annu Rev Pathol. 2014 Oct 17

Hereditary Cancer Genetic Testing: Where are We? - December 18, 2014

NCI paper: Prevalence and correlates of receiving and sharing high-penetrance cancer genetic test results: Findings from the Health Information National Trends Survey 
Taber J.M. et al Public Health Genomics, January 2015

Clinical decisions: Screening an asymptomatic person for genetic risk--polling results 
Schulte J, et al. N Engl J Med 2014 Nov;371(20):e30

Testing for hereditary breast cancer: Panel or targeted testing? Experience from a clinical cancer genetics practice.
Doherty J, J Genet Couns. 2014 Dec 5

Hereditary colorectal cancer syndromes: American Society of Clinical Oncology clinical practice guideline endorsement of the familial risk-colorectal cancer: European Society for Medical Oncology clinical practice guidelines.
Stoffel EM, et al. J Clin Oncol. 2014 Dec 1

Population testing for cancer predisposing BRCA1/BRCA2 mutations in the Ashkenazi-Jewish community: A randomized controlled trial.
Manchanda R, et al. J Natl Cancer Inst. 2014 Nov 30;107(1)

Cost-effectiveness of population screening for BRCA mutations in Ashkenazi Jewish women compared with family history-based testing. 
Manchanda R et al. J Natl Cancer Inst. 2014 Nov 30;107(1). pii: dju380. doi: 10.1093/jnci/dju380. Print 2015 Jan.

Check out our Cancer Genetic Testing  Update Page for additional information and links

Cancer Genomic Tests (October 30, 2014)

Cancer Genomic Tests: Accelerating Translation - October 30, 2014

CDC-NCI paper: An overview of recommendations and translational milestones for genomic tests in cancer 
Christine Q. Chang et al. Genetics in Medicine, October 22, 2014

Check out the CDC evidence-based classification of cancer genomic tests

Check out the NCI Cancer Genomics and Epidemiology Navigator for latest information on cancer genomic tests  

EGAPP: A model process for evaluating genomic applications in practice and prevention. Check out cancer genomic tests, methods, evidence reviews and recommendation statements.

NCI Fact Sheet: Genetic testing for hereditary cancer syndromes

Cancer Genomics: Impact of Recent Insights - October 30, 2014

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. 
Katherine A. Hoadley et al. Cell, August 2014

Genome study overhauls cancer categories, shifts from tissues to molecular subtypes, by Kevin Mayer, Genetics Bioengineering News, Aug 8

It's time for us to think about cancer differently, by Paula Mejia, Newsweek, Aug 8

NIH- The Cancer Genome Atlas (TCGA) Initiative

NIH information: What is cancer genomics and the genetic basis of cancer?

Cancer Precision Medicine: Where Are We? - September 18, 2014

NIH announces the launch of 3 integrated precision medicine trials; ALCHEMIST is for patients with certain types of early-stage lung cancer, August 2014 

National Cancer Institute's Precision Medicine Initiatives for the New National Clinical Trials Network.Jeffrey Abrams et al. ASCO Annual Meeting 2014 

Personalized medicine: Special treatment. 
Michael Eisenstein. Nature, September 11, 2014

Why the controversy? Start sequencing tumor genes at diagnosis. Tumor sequencing at the time of diagnosis can give significant insight for successful cancer treatment, by Shelly Gunn, Genetic Engineering & Biotechnology News, Sep 10  

National Cancer Institute information: Precision medicine and targeted therapy

Genomics and precision oncology: What's a targeted therapy for cancer? An updated list of approved drugs from the National Cancer Institute (2014)

Therapy: This time it's personal
Gravitz L Nature 509, S52-S54 2014 May 29

Multi-marker solid tumor panels using next-generation sequencing to direct molecularly targeted therapies 
Michael Marrone, et al. PLoS Currents Evidence on Genomic Tests 2014 May 27

Impact of cancer genomics on precision medicine for the treatment of cancer, from the National Cancer Institute

Cancer genomics and precision medicine in the 21st century  [PDF 2.20 MB], power point presentation from the National Human Genome Research Institute