A new genomic test for prostate cancer can help predict whether men are more likely to harbour an aggressive form of the disease, according to a new UC San Francisco study.
The test, which improves risk assessment when patients are first diagnosed, can also aid in determining which men are suitable for active surveillance – a way of managing the disease without direct treatment.
Prostate cancer often grows slowly, and many of the quarter-million patients diagnosed annually in the United States never need treatment, which typically involves surgery, radiation or both. Still, most patients with low-risk prostate cancer in this country immediately undergo treatment.
The researchers found the new test provides ‘statistically significant and clinically meaningful’ prognostic information, and can help identify many more low-risk men who could safely choose surveillance, sparing them from unnecessary treatment and avoidable adverse side effects. At the same time, the test can pinpoint men at apparent low-risk who in fact may have potentially aggressive tumours, the authors said.
The independent UCSF clinical study of 395 men validated the Oncotype DX Genomic Prostate Score (GPS), a biopsy-based pre-treatment tool of Genomic Health, Inc. as a predictor of high grade or extracapsular prostate cancer.
‘With the new test, we can more confidently recommend active surveillance when it is appropriate,’’ said the study’s lead author Matthew R. Cooperberg, MD, MPH, a UCSF assistant professor of urology and epidemiology & biostatistics. ‘And patients through active surveillance can avoid or delay surgery or radiation for their condition.
‘Active surveillance is increasingly acknowledged as a preferred strategy for most men with low-risk disease, but in practice it is used relatively infrequently,’ he noted. ‘There are many reasons why – financial, legal and cultural among others. Many men don’t want to live with anxiety over the chances of their disease progressing. So we need to predict with better accuracy which tumors harbor metastatic potential. If we are able to risk-stratify men more consistently and identify a greater proportion for active surveillance, we should be able to ameliorate over-treatment rates, and by extension help resolve the ongoing debate about PSA screening.’
The second most common cancer in men, prostate cancer affects about one man in six, according to the American Cancer Society. Typically the disease occurs in older men – the average age at diagnosis is about 67 – and an aggressive form kills as many as 30,000 men annually in the U.S. Most men, however, do not die from the disease because they have relatively indolent, low-risk tumours that do not progress even without treatment.
Active surveillance involves closely monitoring a patient’s condition through serial PSA screening and prostate biopsies, but otherwise the disease is not treated unless tests show the condition is getting worse. Active surveillance is not entirely benign – biopsies are uncomfortable and carry a risk of bleeding and infection. Moreover, some patients experience a higher level of anxiety over the potential of their cancers to advance.
While active surveillance can help patients avoid or delay surgery or radiation, scientists have faced a major challenge: how to identify – consistently and reliably – which patients can safely embark on it and which patients face clinically meaningful risk of disease progression.
In the new UCSF study, investigators evaluated the ability of the 17-gene assay through prostate needle biopsy specimens to predict pathologic stage and grade at prostatectomy. The researchers focused on whether the test’s biomarkers added independent predictive information beyond what could already be determined about a patient through standard PSA, Gleason grade and biopsy detail variables.
The men in the study, identified from the UCSF Helen Diller Family Comprehensive Cancer Center Urologic Oncology Database, ranged from 38 to 77 years old at the time they were diagnosed – the median age was 58. The patients represented a range of low- and intermediate-risk tumours in terms of clinical risk characteristics.
The researchers found that the test ‘contributed statistically significant, and clinically meaningful, additional prognostic information above and beyond existing, previously well-validated clinical risk stratification instruments.’
The authors noted a number of study limitations including an explicit intention to include men whose tumours were expected to show a wider range of risk. Further, they said with additional study, the test might be used to identify men with particularly low risk tumours who might be candidates for less-intense surveillance requiring – for example – fewer biopsies. University of California San Francisco

A new test may help to streamline genetic testing for Huntington Disease (HD) by generating accurate results, avoiding unnecessary additional testing, and improving turnaround time. The test, which uses chimeric or triplet repeat primed PCR (TP PCR) methodology, yielded results that were 100% concordant with standard genotyping methods in an analysis of 246 samples. The high sensitivity and specificity of the test could reduce the number of false negative results and facilitate both diagnosis and prognosis by correctly sizing the genetic abnormality characteristic of HD.
Huntington disease (also known as Huntington’s disease or Huntington’s chorea) is an inherited and progressive neuro-degenerative disorder that typically becomes apparent during a person’s thirties or forties. With time, HD patients develop diminished muscle co-ordination that is evident in walking, speaking, and swallowing and undergo changes in personality and thinking ability. A mutation in the Huntingtin gene leads to an abnormal number of repeats of a sequence of three nucleotides known as CAG. Based on the number of CAG repeats, a person may be deemed to be normal (10-35 repeats), at low risk (36-39 repeats), or at high risk (greater than 40 repeats) of having or developing HD symptoms. That is why accurately determining the number of CAG repeats is so important.
In this study, 246 samples that had been previously analysed by other methods were tested with the new method (TP PCR). The samples included 14 DNA reference samples from the Coriell Cell Repositories, three samples from the College of American Pathologists 2002 Survey, and 229 samples from individuals tested at ARUP Laboratories for clinical purposes by standard technologies, explained lead investigator Elaine Lyon, PhD, Medical Director of Molecular Genetics, ARUP Laboratories and its Institute for Clinical and Experimental Pathology, and Department of Pathology, University of Utah, Salt Lake City, UT. Normal samples were included as well as those with a wide range of CAG repeats. The samples were blinded and analysed.
The results showed that TP PCR correctly sized 240 of the 246 samples. All of the 100 samples in the normal and low risk groups were correctly sized. In the 146 samples of those known to be affected by HD (those with > 39 CAG repeats), the results for 140 correctly matched that found with other methods whereas the number of CAG repeats differed by ±1 in 6 samples, a difference said by the authors to be within the precision of the method at higher repeat numbers. Up to 101 CAG repeats could be accurately sized with this test. Even samples that were found to be challenging to analyse with other methods could be assessed solely and accurately by TP PCR.
Another advantage of this new method is its ability to identify true homozygous normal samples, thus avoiding further testing. With other methodologies, if a sample appears homozygous for the normal allele, additional testing, often with Southern blot analysis, is still recommended because of the risk of false negatives. ‘Southern blotting is expensive, labour intensive, requires high concentrations of DNA, and can delay turnaround time,’ says Dr. Lyon. However, when HD is suspected in children, Dr. Lyon and colleagues recommend that even with TP PCR, apparently homozygous samples should undergo further testing.
TP PCR uses a forward and reverse chimeric primer to amplify from multiple priming sites within the trinucleotide repeat. TP PCR produces a characteristic ladder on a fluorescence electropherogram that allows the rapid and inexpensive identification and quantification of expanded repeats. Major peaks and minor peaks (stutters) representing CAG repeats can be analysed and sized automatically using commercially available software. EurekAlert

Some diseases are caused by single gene mutations. Current techniques for identifying the disease-causing gene in a patient produce hundreds of potential gene candidates, making it difficult for scientists to pinpoint the single causative gene. Now, a team of researchers led by Rockefeller University scientists have created a map of gene ‘shortcuts’ to simplify the hunt for disease-causing genes.

The investigation, spearheaded by Yuval Itan, a postdoctoral fellow in the St. Giles Laboratory of Human Genetics of Infectious Diseases, has led to the creation of what he calls the human gene connectome, the full set of distances, routes (the genes on the way) and degrees of separation between any two human genes. Itan, a computational biologist, says the computer program he developed to generate the connectome uses the same principles that GPS navigation devices use to plan a trip between two locations. The research is reported in the online early edition of the journal Proceedings of the National Academy of Sciences.
‘High throughput genome sequencing technologies generate a plethora of data, which can take months to search through,’ says Itan. ‘We believe the human gene connectome will provide a shortcut in the search for disease-causing mutations in monogenic diseases.’

Itan and his colleagues, including researchers from the Necker Hospital for Sick Children and the Pasteur Institute in Paris and Ben-Gurion University in Israel, designed applications for the use of the human gene connectome. They began with a gene called TLR3, which is important for resistance to herpes simplex encephalitis, a life-threatening infection from the herpes virus that can cause significant brain damage in genetically susceptible children. Researchers in the St. Giles lab, headed by Jean-Laurent Casanova, previously showed that children with HSE have mutations in TLR3 or in genes that are closely functionally related to TLR3. In other words, these genes are located at a short biological distance from TLR3. As a result, novel herpes simplex encephalitis-causing genes are also expected to have a short biological distance from TLR3.

To test how well the human gene connectome could predict a disease-causing gene, the researchers sequenced exomes – all DNA of the genome that is coding for proteins – of two patients recently shown to carry mutations of a separate gene, TBK1.

‘Each patient’s exome contained hundreds of genes with potentially morbid mutations,’ says Itan. ‘The challenge was to detect the single disease-causing gene.’ After sorting the genes by their predicted biological proximity to TLR3, Itan and his colleagues found TBK1 at the top of the list of genes in both patients. The researchers also used the TLR3 connectome – the set of all human genes sorted by their predicted distance from TLR3 – to successfully predict two other genes, EFGR and SRC, as part of the TLR3 pathway before they were experimentally validated, and applied other gene connectomes to detect Ehlers-Danlos syndrome and sensorineural hearing loss disease causing genes.

‘The human gene connectome is, to the best of our knowledge, the only currently available prediction of the specific route and distance between any two human genes of interest, making it ideal to solve the needle in the haystack problem of detecting the single disease causing gene in a large set of potentially fatal genes,’ says Itan. ‘This can now be performed by prioritising any number of genes by their biological distance from genes that are already known to cause the disease. Rockefeller University

A new diagnostic test for a worm infection that can lead to severe enlargement and deformities of the legs and genitals is far more sensitive than the currently used test, according to results of a field study in Liberia, in West Africa, where the infection is endemic.
The new test found evidence of the infection – lymphatic filariasis – in many more people that the standard test had missed.
The study, the first to independently evaluate the new test, was led by researchers at Washington University School of Medicine in St. Louis and funded by the Bill & Melinda Gates Foundation.
The infection affects 120 million people living in 73 countries, leaving some 40 million profoundly disfigured and incapacitated. Both tests detect the presence of worms that cause lymphatic filariasis, a devastating mosquito-borne illness also known as elephantiasis.
But the new test has significant advantages over the test that has been used for more than a decade not only to diagnose the disease, but to map, monitor and evaluate the success of a massive global public health program aimed at completely eliminating the disease by 2020.
‘The older test has had a major impact, but the new one is even better,’ says lead author Gary J. Weil, MD, an infectious diseases specialist at Washington University School of Medine. ‘Annually, medication to treat and prevent the infection is distributed to more than 500 million people worldwide. The improved sensitivity of the new test will help determine whether the mass treatment program has been effective and also identify regions that need additional attention.’
An accompanying editorial by Maria Rebollo, MD, and Moses Bockarie, PhD, at the Centre for Neglected Tropical Diseases in the United Kingdom says the new diagnostic test ‘represents a major breakthrough for rapid diagnosis of lymphatic filariasis in the blood.’
The new test also has a longer shelf life, estimated at two years without refrigeration, compared with three months for the older version, and is expected to cost less.
Weil’s research team worked with colleagues at the Liberian Institute for Medical Research to conduct a side-by-side comparison of the new test strip and the currently used test. They evaluated the tests in 503 people ranging in age from 6 to 89.
Both versions of the test are manufactured by Alere Scarborough Inc. of Maine and detect the presence in the blood of a protein produced by the worm parasite Wuchereria bancrofti that causes lymphatic filariasis. The new test is performed by pricking the finger and placing a person’s blood onto the test strip, which looks similar to an over-the-counter pregnancy test. Like many pregnancy tests, the lymphatic filariasis test is positive if two lines appear in the test window and negative if only one line shows.
The study’s results show that the new test is highly sensitive, detecting nearly 26 percent more infections of lymphatic filariasis than the standard test (124/503 infections vs. 98/503 infections). The new test also was easier to perform and results were easier to read.
‘This gives us some indication of the numbers of infections we were missing with the older test,’ Weil says. ‘On a global scale, it’s a huge number of cases. We need to have an accurate test to be sure we are reaching all the people who have the disease or are at risk of developing it.’
Worldwide, some 1.4 billion people are at risk of lymphatic filariasis, which is endemic in many countries in Africa, Southeast Asia and other tropical regions. Worm larvae deposited by the bite of an infected mosquito enter the body and migrate to the lymphatic system, where they mature into adult worms.
The thread-like parasitic worms can live and reproduce in the body for years. Ultimately, this damages the lymphatic vessels that drain fluid from the tissues and causes the enormous swelling and disabling deformity of the legs and in males, the scrotum.
Weil has been active for years in efforts to eliminate lymphatic filariasis via mass drug administration, an approach that involves giving antifilarial drugs to everyone in areas with high infection rates. Organizers of the Global Programme to Eliminate Lymphatic Filariasis, launched in 2000, co-ordinate periodic, repeated mass drug administration of antifilarial medications to more than 500 million people annually, making it the world’s largest public health intervention program based on mass drug administration. Washington University School of Medicine

Unusually high calcium levels in the blood can almost always be traced to primary hyperparathyroidism, an under-treated, underreported condition that affects mainly women and the elderly, according to a new study by UCLA researchers.

The condition, which results from overactive parathyroid glands and includes symptoms of bone loss, depression and fatigue that may go undetected for years, is most often seen in African American women over the age of 50, the researchers discovered.
The study is one of the first to examine a large, racially and ethnically diverse population — in this case, one that was 65 percent non-white. Previous studies had focused on smaller, primarily Caucasian populations.
The four parathyroid glands, which are located in the neck, next to the thyroid, regulate the body’s calcium levels. When one is dysfunctional, it can cause major imbalances — for example, by releasing calcium from the bones and into the bloodstream. Over time, calcium loss from bones often leads to osteoporosis and fractures, and excessive calcium levels in the blood can cause kidney stones and worsening kidney function.
The UCLA researchers determined that hyperparathyroidism is the leading cause of high blood-calcium levels and is responsible for nearly 90 percent of all cases.
‘The findings suggest that hyperparathyroidism is the predominant cause of high calcium levels, so if patients find they have high calcium, they should also have their parathyroid hormone level checked,’ said the study’s lead author, Dr. Michael W. Yeh, an associate professor of surgery and endocrinology at the David Geffen School of Medicine at UCLA.

Hyperparathyroidism, which affects approximately 1 percent of the population, can be detected by measuring parathyroid hormone levels to determine if they are elevated or abnormal. UCLA