Performing Whole-Exome Sequencing on FFPE Mutation Samples

Posted by Luke Doiron on Apr 28, 2016 7:00:00 AM

Whole-exome sequencing (WES) technology has rapidly been embraced as a valuable and cost-effective method for sequencing the expressed genes in a genome (i.e. the exome). WES benefits researchers and clinicians seeking to identify the mutations found in many types of tumors and other difficult-to-treat disorders such as Alzheimer’s disease. As investigators gain greater insight via WES and other massive parallel sequencing methods into the biology and genetics of disease, the goal is to find and exploit new clinically useful therapy targets.

However, one of the obstacles to the routine use of WES is obtaining enough samples to perform the large-scale studies necessary to advance and inform cancer research and clinical care. One solution might be the literally millions of formalin-fixed, paraffin-embedded (FFPE) specimens stored in tissue banks and biorepositories across the globe, many of which are well-annotated, with good histology, pathology, and clinical care data attached.

Yet, it’s a well-known fact that if FFPE specimens are not properly fixed using the right fixation agents, and/or improperly stored, the extracted DNA material may be too poor in quality to be used for exome sequencing studies. In addition, sometimes a difficult extraction process leads to low yields and/or very small sample sizes that are less useful for sequencing protocols. This has led to investigations aimed at determining whether FFPE archival specimens are reliable and valid sources of extracted DNA material.

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Best Practice PBMC Protocols

Posted by Luke Doiron on Apr 26, 2016 8:00:00 AM

Proper handling of fresh or cryopreserved peripheral blood mononuclear cells (PBMC) is critical to ensuring the good viability of isolated PBMCs and reliable results. Over the years, a variety of processes have been studied to determine the best practices for PBMC collection, isolation, and thawing (if using cryopreserved specimens). Here is a review of PBMC protocols that tend to produce optimum results.

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The Current State of Inflammatory Bowel Disease

Posted by Quinton Stevens on Apr 23, 2016 12:00:00 PM


Many people have heard of “mainstream diseases,” Media is often overflowing with reports, news, movies, commercials, and documentaries of a plethora of big name incurable ailments. Usually, though, the myriad of diseases thrown at us never includes anything on any diseases of the autoimmune type; 9 out of 10 people cannot even bring the name to mind of one autoimmune disease.


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Recent Research Studies on Triple-Negative Breast Cancer

Posted by Luke Doiron on Apr 21, 2016 8:00:00 AM

Patients diagnosed with triple-negative breast cancer (TNBC) have a poorer prognosis than those with most other breast cancer subtypes. This unfortunate fact is due to the lack of expression of three receptors - estrogen, progesterone, and HER2 - which characterize other breast cancer tumors and which have proven to be good therapeutic targets. TNBC, characterized by an aggressive biology, makes up about 15 percent of all breast cancers and typically affects premenopausal women, particularly younger African-Americans. Because of TNBC’s aggressiveness and lack of response to drugs used to treat other breast cancer subtypes, researchers are actively seeking safer, more effective and targeted therapies to improve survival and reduce cancer recurrence.

Here are a few interesting recent research studies on triple negative breast cancer:

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Somatic Gene Mutations Seen in FFPE Cancer Specimens

Posted by Luke Doiron on Apr 19, 2016 4:59:20 PM

Advancements in genetic mutation analysis of tumor specimens are helping scientists learn more about the molecular basis of many types of cancer. These mutations may be inherited (a germline mutation), or they occur afresh (a somatic mutation). The latter are not inherited and don't arise in reproductive cells and have long been recognized as key features in cancer cells. In a survey of 200 types of cancers, 1,000 somatic mutations were found in about 500 protein kinase genes. Somatic gene mutations provide important clues to the drivers of tumorigenesis and offer new and diverse targets for drug discovery. Mutation profiling for personalized patient treatment is an ongoing goal of cancer researchers around the globe.

The ability to access and utilize the millions of archival formalin-fixed paraffin-embedded (FFPE) specimens is critical to advance cancer research. This has historically been a challenge in some cases due to DNA damage that can be caused by improper fixation and/or storage conditions for these FFPE samples. To investigate the viability of utilizing FFPE cancer specimens for studying gene mutations, a number of recent studies have been conducted utilizing newer technologies that circumvent the nucleic acid degradation sometimes seen in FFPE specimens.

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What Makes Lupus So Severe

Posted by Quinton Stevens on Apr 16, 2016 12:00:00 PM

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An Analysis of Late Stage Prostate Cancer Genetic Research

Posted by Luke Doiron on Apr 14, 2016 8:00:00 AM

Many people mistakenly believe that all prostate cancer is a slow-growing disease, and therefore not as serious as other types of cancers. What is not commonly understood is the fact that prostate cancer is expected to be the cause of over 26,000 deaths in the U.S. in 2016, according to the National Cancer Institute. Furthermore, prostate cancer is the second leading cause of cancer death in males, with only lung cancer ahead of it.

One of the reasons prostate cancer deaths are still unacceptably high is due to a particularly lethal form of the cancer known as metastatic castration-resistant prostate cancer (MCRPC). This late-stage prostate cancer has not, until recently, been rigorously studied to understand more about the gene changes that drive this type of prostate cancer. Today, a number of research institutions are performing genetic analysis on tumor specimens taken from the sites of metastases in patients with MCRPC, including the liver, bones and lymph nodes. The goal is to identify causal mutations and look for targeted therapies that could be effective in treating late stage prostate cancer, including drugs already approved to treat other cancer types with similar genetic characteristics.

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The Impact of Medication for Early Stage Breast Cancer

Posted by Luke Doiron on Apr 12, 2016 8:00:00 AM

Earlier diagnosis and better treatment choices for cancer patients continue to drive reduced death rates for the most common forms of cancer, including breast cancer. According to a recent National Cancer Institute report, the 10-year (2003 - 2012) trend for breast cancer shows a 1.9% decrease in death rates. For patients diagnosed with breast cancer, improved treatment options can significantly increase survival, depending upon the cancer stage at diagnosis.

Breast cancer is typically categorized as stage I, II (A or B), III (A, B or C), or IV. These stages are defined based on tumor size and whether cancer has spread (metastasized). Stages I, IIA and IIB, as well as IIIA, are characterized as early stage breast cancer, because while there may be cancer spread to nearby lymph nodes, there is no metastasis to distant areas of the body.

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