Genomics Researchers Highlight Droplet Digital PCR at ASHG 2018 Annual Meeting
Dr. Rebecca Margraf, PhD, Principal Investigator, Research and Development at ARUP Laboratories in Salt Lake City, will present research conducted using Droplet Digital PCR at the ASHG Annual Meeting.
Bio-Rad to Preview New Single-Cell ATAC-Seq Solution and New Single-Cell Droplet Digital PCR Application
San Diego, CA — Dozens of presentations will feature novel uses of Bio-Rad’s Droplet Digital PCR (ddPCR) technology at the American Society of Human Genetics (ASHG) 2018 Annual Meeting in San Diego, October 16–20.
During the meeting researchers will present studies that use Bio-Rad’s ddPCR technology throughout different areas of genomics. One theme found consistently among the research is ddPCR’s ability to detect mutations when compared with other methods, whether it’s due to ddPCR’s enhanced sensitivity or its ability to target specific areas of the genome, as described below in the summary of one of the posters that will be given during the meeting.
Multiplex ddPCR Detects a Biomarker of Nonsyndromic Hearing Loss
Geneticists who study the causes of hearing loss are very familiar with the STRC gene, in which a deletion mutation is present in 11% of individuals with nonsyndromic hearing loss. If someone has a mutation in this gene, they are almost certain to experience hearing loss. But STRC has a near identical but nonfunctioning copy called pSTRC, a pseudogene, that makes detecting this mutation difficult with standard techniques, including next-generation sequencing (NGS) and microarray.
“These genes are 98.9% identical — exons 1 through 15 are 100% identical — which complicates copy number analysis,” said Dr. Rebecca Margraf, PhD, Principal Investigator, Research and Development at ARUP Laboratories in Salt Lake City.
Because the QX200 Droplet Digital PCR System can detect copy numbers of deletion mutations in absolute quantities, Dr. Margraf and her team used it to improve the detection of STRC deletions. They developed four target assays to three specific locations within STRC that diverge in sequence from the homologous region in pSTRC and one area within the nearby CATSPER2 gene. Using the QX200 System, she multiplexed the assays, running two target assays along with a reference in one reaction.
When Dr. Margraf ran the samples with known and suspected homozygous STRC deletions, the platform amplified the reference assay but did not amplify the target assays, indicating the ddPCR assays can distinguish between STRC and pSTRC. The ddPCR assays generated the expected copy number for the known genotyped samples.
“The QX200 from Bio-Rad was easy to use and yielded accurate copy number results,” said Dr. Margraf. “Its multiplexing capability was a nice convenience when running these assays.”
Dr. Margraf anticipates that the STRC ddPCR assay will increase the clinical sensitivity of the NGS panel for all types of genetic hearing loss.
This poster (abstract PgmNr 2962) will be presented on Thursday, October 18, 3–4 PM, during the Molecular and Cytogenetic Diagnostics session.
Dr. Margraf will also be presenting her work at the Bio-Rad Workshop, held on Wednesday, October 17, 12:30–1:45 PM. Presenting in the workshop as well is Dr. Dianna Maar, PhD, Marketing Scientist for Bio-Rad’s Digital Biology Group. Maar’s talk will cover examples of how single-cell ddPCR can be used in targeted interrogation and quantification of single cells with the QX200 ddPCR System, allowing for identification and verification of gene edits, DNA transformations, and somatic changes of cell populations.
To learn more about Droplet Digital PCR and Bio-Rad’s new scATAC-Seq Solution for the ddSEQ Single-Cell Isolator, visit booth #805. There will be a raffle for copies of the new Digital PCR book by Springer Protocols.
Bio-Rad, Droplet Digital PCR, and ddPCR are trademarks of Bio-Rad Laboratories, Inc. in certain jurisdictions.
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