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

Issue link:

Contents of this Issue


Page 9 of 47

8 Clinical OMICs March/April 2017 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)

Articles in this issue

Links on this page

Archives of this issue

view archives of Clinical OMICS - MAR-APR 2017