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Researchers confirm whole-genome sequencing can identify cancer-related mutations and risk.

UT Southwestern Medical Center researchers have demonstrated that whole-genome sequencing can be used to identify patients’ risk for hereditary cancer, which can potentially lead to improvements in cancer prevention, diagnosis, and care.  This is the first study that has used whole-genome sequencing to evaluate a series of 258 cancer patients’ genomes to improve the ability to diagnose cancer-predisposing mutations. The opensource study is published in the journal EBioMedicine.

Whole-genome sequencing is a new genetic tool that can determine more of a person’s DNA sequence than ever before. The current study shows that nearly 90 percent of clinically identified mutations were confidently detected and additional cancer gene mutations were discovered, which together with the decreasing costs associated with whole-genome sequencing means that this method will improve patient care, as well as lead to discovery of new cancer genes.

Presently the researchers help patients assess their risk for many types of cancer, including kidney, skin, lung, breast, ovarian, colon, endocrine and prostate cancers. If a known genetic predisposition to cancer is found, the team counsel the patient about the best ways to detect early cancers or, better yet, prevent cancers from ever forming.

About 5 to 10 percent of all cancers are caused by known inherited gene mutations. These mutations are passed down from generation to generation. Mutations in the BRCA1 and BRCA2 genes are the most common cause of hereditary breast cancer. BRCA gene mutations are best known for their breast cancer risk, but they also cause increased risk for ovarian, prostate, pancreatic, and other cancers. In addition, there are many different genes, including ATM, CDH1, CHEK2, PALB2, PTEN, and TP53, that are associated with an increased risk for breast cancer, and researchers are continually discovering additional genes that may affect cancer predisposition.

In this study, researchers developed new methods to analyze the large amount of data generated by whole-genome sequencing. Specifically, the team devised a method to compare the group of patients with BRCA1 or BRCA2 mutations to a group of patients without BRCA mutations. All expected BRCA1 and BRCA2 mutations were detected in the BRCA group, with at least 88.6 percent of mutations confidently detected. In contrast, different cancer gene mutations were found in the cohort without BRCA mutations.

The team state that the results demonstrate that whole-genome sequencing can detect new cancer gene mutations in non-BRCA ‘mystery’ patients, demonstrating the added value whole-genome sequencing brings to the future cancer clinic, although further investigation is needed in order to be able to interpret the precise clinical implications of the mutations found.

Mystery patients are those who have a strong family history for cancer but after standard genetic testing, no genetic diagnoses are made. In the current study, sequencing allowed the researchers to discover novel candidate cancer gene mutations in these patients.

Source:  UT Southwestern Medical Center

Epigenetic methylation is a well-balanced process in healthy cells. But in some diseases, in particular cancers, aberrant CpG methylation changes may occur, and both genomewide hypomethylation and gene-specific hypermethylation in promoters of tumor suppressor genes can be observed. Many studies have shown that tumor emergence and growth are associated with changes in DNA methylation patterns, such as the case of prostate cancer development. Therefore, one of the most important application areas for epigenetic research is in the diagnosis and treatment of cancer — using DNA methylation patterns to detect cancer at very early stages, to classify tumors, and to predict and monitor response to drug treatments.  © QIAGEN 2013–14. All rights reserved.
Epigenetic methylation is a well-balanced process in healthy cells. But in some diseases, in particular cancers, aberrant CpG methylation changes may occur, and both genomewide hypomethylation and gene-specific hypermethylation in promoters of tumor suppressor genes can be observed.
Many studies have shown that tumor emergence and growth are associated with changes in DNA methylation patterns, such as the case of prostate cancer development. Therefore, one of the most important application areas for epigenetic research is in the diagnosis and treatment of cancer — using DNA methylation patterns to detect cancer at very early stages, to classify tumors, and to predict and monitor response to drug treatments. © QIAGEN 2013–14. All rights reserved.

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