Category Archives: Genome

Story highlights Kakaes: Many people and institutions are intoxicated by the potential of big data He warns data can mislead us and not every valid judgment can be summed up in a number

"Big data" and "evidence-based policy" are the dominant ideas of our moment. A May 2014 White House report put it this way: "Big data will become an historic driver of progress, helping our nation perpetuate the civic and economic dynamism that has long been its hallmark."

The White House report presents big data as an analytically powerful set of techniques. It says the social and economic value created by big data should be balanced against "privacy and other core values of fairness, equity and autonomy."

Konstantin Kakaes

But the White House effort to balance the costs and benefits of big data misses the bigger picture. There are limits to the analytic power of big data and quantification that circumscribe big data's capacity to drive progress.

Data-driven techniques are only one part of how government, industry and civil society should make important decisions. Bad use of data can be worse than no data at all. As a December 2014 New York Times Magazine story about Marissa Mayer, Yahoo's chief executive, pointed out:

"Mayer also favored a system of quarterly performance reviews, or Q.P.R.s, that required every Yahoo employee, on every team, be ranked from 1 to 5. The system was meant to encourage hard work and weed out underperformers, but it soon produced the exact opposite. Because only so many 4s and 5s could be allotted, talented people no longer wanted to work together; strategic goals were sacrificed, as employees did not want to change projects and leave themselves open to a lower score."

As the Yahoo example shows, the presumption that quantitative techniques objectively assess "what works" is deeply flawed. Many attempts to collect and interpret data not only miss key factors, but transform for the worse the systems they claim only to be measuring.

Sheri Lederman, a fourth grade teacher on Long Island, sued the New York State Education Department in October 2014 in what is perhaps the clearest legal test case of the dangers of big data. Lederman is highly regarded by her peers and superiors, an "exceptional educator" in the words of her school district's superintendent.

Yet a statistical technique called "value-added modeling" that purports to evaluate teachers based on students' standardized test scores said Lederman was ineffective. The American Statistical Association has criticized value-added modeling as an ineffective measure. "Ranking teachers by their VAM scores can have unintended consequences that reduce quality," the statisticians said.

Read the original:
Why you shouldn't fall in love with data

BIO 101 Week 2 Learning Team Human Genome Project /UOP Tutor
BIO 101 Week 2 Learning Team Human Genome Project To Buy This material Click below link http://www.uoptutors.com/BIO-101/BIO-101-Week-2-Learning-Team-Human-Genome-Project For more ...

By: Ketan Toshniwal

Read the original post:
BIO 101 Week 2 Learning Team Human Genome Project /UOP Tutor - Video

Invitae, which offers consumers a suite of genetic tests as a single service, announced terms for its IPO on Monday. The San Francisco, CA-based company plans to raise $75 million by offering 5.4 million shares at a price range of $13 to $15. At the midpoint of the proposed range, Invitae would command a fully diluted market value of $436 million.

Invitae, which was founded in 2010 and booked $1 million in sales for the 12 months ended September 30, 2014, plans to list on the NYSE under the symbol NVTA. J.P. Morgan is the sole bookrunner on the deal. It is expected to price during the week of February 9, 2015.

Investment Disclosure: The information and opinions expressed herein were prepared by Renaissance Capital's research analysts and do not constitute an offer to buy or sell any security. Renaissance Capital, the Renaissance IPO ETF (symbol: IPO) or the Global IPO Fund (symbol: IPOSX) , may have investments in securities of companies mentioned.

The views and opinions expressed herein are the views and opinions of the author and do not necessarily reflect those of The NASDAQ OMX Group, Inc.

Visit link:
Know your genome: Invitae sets terms for $75 million IPO

By Nicky PhillipsFeb. 2, 2015, 9 p.m.

A team of Australian scientists have invented a method to decipher a layer of information that garnishes genes, called methyl groups, which may explain the unknown cause of many cancers.

Scientific breakthrough: Susan Clark from the Garvan Institute of Medical Research and her team have for first the first time translated the methylome of breast cancer, finding distinct patterns associated with different types of breast cancer. Photo: Garvan Institute

Decoding the letters of the human genome revolutionised scientists' understanding of the role of genetic mutations in many diseases, including about one in every five cancers.

Now a team of Australian scientists have gone a step further, inventing a way to decipher another layer of information that garnishes genes, called methyl groups, which may explain the cause of many more cancers.

Methyl groups hang off sections of DNA like Christmas lights and act like a switch, affecting how genes are expressed in different cell types. Collectively called the methylome, they can also switch off tumour suppressor genes and switch on cancer promoting genes.

Susan Clark from the Garvan Institute of Medical Research and her team have for first the first time translated the methylome of breast cancer, finding distinct patterns associated with different types of breast cancer.

They have also found a way to classify women with the worst type of breast cancer, triple-negative, into two groups; those with a highly aggressive form and those with a lower-risk variety with a longer survival time. At present there is no reliable way to divide triple-negative cancers, which do not respond to targeted treatment, into these sub-groups.

With further testing, methylation signatures may be used as predictive biomarkers that doctors use to prescribe more appropriate treatments for women diagnosed with breast cancer in the future.

Professor Clark's team are the first in the world to sequence large chunks of the methylome from samples of cancer tissue that had been archived for up to two decades.

Visit link:
Forget the genome, Australian scientists crack the 'methylome' for an aggressive type of breast cancer

Contact Information

Available for logged-in reporters only

Newswise CHAPEL HILL -- A study co-led by a UNC Lineberger Comprehensive Cancer Center researcher has identified genomic changes in head and neck cancers linked to the sexually transmitted disease HPV -- the latest finding of a collaborative scientific effort designed to map out the genomic changes driving cancer.

The study by The Cancer Genome Atlas (TCGA) researchers analyzed the genomes of 279 head and neck cancer tumors. They identified subtypes of head and neck cancer based on their genomic characteristics, changes in smoking-related tumors, as well as genomic differences in head and neck cancer tumors linked to HPV, the most common sexually transmitted disease in the United States.

The findings were published online Jan. 28 in the journal Nature. Researchers hope the findings will help lead to potential new therapies and the identification of markers that can help identify patients likely to respond to a particular therapy, as well as help direct the best course of treatment for patients.

The rapid increase in HPV-related head and neck cancers, noticeably in oropharyngeal tumors, has created an even greater sense of urgency in the field, said D. Neil Hayes, MD, MPH, senior author of the study report, an associate professor of medicine at the University of North Carolina School of Medicine and a member of UNC Lineberger. Oropharyngeal cancer starts in the oropharynx, which is the part of the throat behind the mouth. Were uncovering differences between tumors with and without HPV infection, and these new data are allowing us to rethink how we approach head and neck cancers.

Smoking and alcohol use are main risk factors for head and neck cancer, according to the National Cancer Institute (NCI). But studies have shown that HPV-linked oropharyngeal cancer cases are on the rise. About 9,000 new oropharyngeal cancer cases are estimated to have been caused by HPV in the United States each year, according to the Centers for Disease Control and Prevention.

Comparatively, there were an estimated 55,000 new cases last year of all types of head and neck cancer, which include tumors of the mouth, throat, voice box, nasal cavity and salivary gland.1 In North Carolina, there were 1,850 new cases of head and neck cancer in 2012, which was up about 3 percent from 2011.2

In the HPV positive tumors in their sample, they found tumors with deletions and mutations of a gene called TRAF3, which is involved in anti-viral response. The researchers also found alterations of the FGFR3 gene and mutations in the PIK3CA gene in HPV positive tumors, which are also found in a much broader set of mutations in smoking-related tumors. PIK3CA has already been shown to be associated with HPV, Hayes said, but he said they showed the link clearly in their study.

And the study found that while the EGFR (epidermal growth factor receptor) gene is frequently altered in HPV-negative tumors in smokers, it is rarely abnormal in HPV-positive tumors.

More:
UNC Researcher Co-Leads Effort to Map Genomic Changes in Head and Neck Cancer

120Genome Hazard _PV

By: avjet

Link:
120Genome Hazard _PV - Video

National Human Genome Research Institute Study on Type II Diabetes
Brooke Wolford is a medical research scientist in the National Human Genome Research Institute at the National Institutes of Health.

By: LabTV

More here:
National Human Genome Research Institute Study on Type II Diabetes - Video

A push to use the human genome to make medicine more precise
President Obama introduced a new plan to create a database of genetic information of a million Americans in order to better tailor medical treatments for gro...

By: PBS NewsHour

The rest is here:
A push to use the human genome to make medicine more precise - Video

PAML: Francisco Velzquez, M.D. Discusses Genome Testing on "Balancing Act"
Lifetime Channel features PAML who is providing tools for early testing that are saving more lives. Dr. Francisco R. Velzquez, President and CEO, PAML a h...

By: PAML

Read more:
PAML: Francisco Velzquez, M.D. Discusses Genome Testing on "Balancing Act" - Video

Modules 5 and 6 Genome Annotation
Genome Annotation.

By: Karobi Moitra

Read more here:
Modules 5 and 6 Genome Annotation - Video