Clinical OMICS

MAR-APR 2017

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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8 Clinical OMICs March/April 2017 www.clinicalomics.com News Single-Cell Method IDs Imprinted Genes Only about 1 in 200 genes is imprinted, or expressed, in a parent-of-origin manner—whereby the paternal allele is expressed and the maternal allele is silenced, or vice versa . Although they are relatively rare, imprinted genes are sites of heightened risk . An imprinted gene's "expressed" allele may not, in fact, be expressed, should it happen to be defective . Alterna- tively, an imprinted gene's silenced allele may lose its epigenetic imprint- ing and become activated . Either way, the imprinted gene may lose its deli- cately biased expression and instigate disease—a rare disease such as Prad- er-Willi syndrome or Angelman syn- drome, or a common disease such as diabetes or cancer . To date, the detection of imprinted genes has meant using RNA sequenc- ing (RNA-Seq) on whole-tissue sam- ples . This technique, however, tends to miss genes that are expressed at low levels. Also, it lacks sufficient resolu- tion to determine whether imprinted genes may be restricted to specific cell types . These limitations can be overcome with a new technique called human single-cell allele-specific gene expres- sion . Unlike bulk RNA-Seq, the new technique combines single-cell RNA- Seq and whole genome sequencing into a bioinformatics framework to analyze genomic imprinting in specific cell types and in different individuals. The technique was detailed February 9 in the American Journal of Human Genetics, in an article entitled, "Detec- tion of Imprinted Genes by Single-Cell Allele-Specific Gene Expression." The article described how researchers at the University of Geneva (UNIGE) devised a way to sequence a patient's genome, along with the genomes of the patient's parents, to identify the paren- tal origin of the alleles transcribed in the patient's cells . "[In this study], 1,084 individ- ual primary fibroblasts were RNA sequenced, and more than 700,000 informative heterozygous single-nu- cleotide variations (SNVs) were gen- otyped," the article's authors wrote. "The allele-specific coverage per gene of each SNV in each single cell was used to fit a beta-binomial distribu- tion to model the likelihood of a gene being expressed from one and the same allele." This approach allowed the research- ers to validate the imprinting status of all the known imprinted genes expressed in fibroblasts. The research- ers also discovered nine novel imprinted genes and demonstrated that some were restricted to certain tissues or cell types . "We establish the profile of the allelic expression for thousands of genes in each single cell," said Federico San- toni, a UNIGE researcher and the first author of the study . "We then process this data to identify the specific signa- ture of each imprinted gene." ©UNIGE Imprinted gene and non-imprinted gene. to help guide treatment without interrupting the physician's clinical work- flow. The new system integrates the latest cancer research available, treat- ment regimens, and complementary therapies into the Allscripts Sunrise EHR, giving oncologists the ability to create a curated list of care protocols at the point of care. "Clinical Pathways presents all appropriate treatment options. It also helps eliminate potential guesswork by clinicians routinely inun- dated with new data and oncology research," said George Daneker Jr., M.D., CMO at CTCA at Southeastern Regional Medical Center. "We cre- ated an ecosystem of treatment options, customized to the CTCA standard of care, for patients to review and choose from that's safe and efficient." n jeangill / Getty Images (continued from previous page)

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