His department runs the clinical genetics laboratory at Mount Sinai. Schadt, PhD, Crystal professor and chair of the Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, also spans the size range of gene panels. While larger panels are attractive, “they have to be prudently applied,” Dr. Most tumors now have more than three genes ordered, making broader panel testing practically necessary. Singh adds, saying there has been a shift in the mentality of the doctors ordering tests. “It is not easy to do all of these markers with single-gene assays, especially in solid tumors,” Dr. We asked, ‘Why not bring it to the clinic?’” “People were aware that the technology was powerful and was generating discovery markers like never before. Singh, PhD, assistant professor in the Department of Hematopathology, Division of Pathology and Laboratory Medicine. “When we started doing it, there was nothing,” says Rajesh R. ![]() They presented some of their data at last year’s meeting of the Association for Molecular Pathology. Ladanyi, who is also chief of the molecular diagnostics service at MSKCC.Ĭlinical investigators in the molecular diagnostics laboratory at MD Anderson Cancer Center have looked in the past few years at both smaller and larger panels. ![]() We are moving in the same direction,” says Dr. Our assay is similar to FoundationOne’s updated gene list. “It includes all coding exons of 341 cancer genes and picks up selected rearrangements and copy number changes in those genes. Ladanyi, the William Ruane chair in molecular oncology at Memorial Sloan Kettering Cancer Center, tells CAP TODAY.Ī year ago he and MSKCC colleagues developed their own in-house assay, called MSK-IMPACT, that’s similar to FoundationOne. “The data certainly support the notion that this kind of assay that is more comprehensive than what most centers have previously used is worth doing, at least in cases where a standardized assay doesn’t come up with anything,” Dr. Marc Ladanyi, MD, collaborated with Foundation Medicine in this work. Ross, Merrill professor and chair of pathology and laboratory medicine at Albany (NY) Medical College. “Of the first 1,000 lung cancer patients, more than 800 had alterations that we thought were actionable,” says Dr. They get a new targeted therapy or are referred to a clinical trial for which the variant qualifies them. Jeffrey Ross, MD, FMI’s medical director, says that more than 80 percent of NSCLC patients tested with FoundationOne have an alteration. Lipson, who is senior director of computational biology methods in the Foundation Medicine reference laboratory, told attendees. Finding these alterations “can result in immediate benefit for patients with metastatic disease,” Dr. (FMI), noted that its 236-gene FoundationOne test “uncovered a high frequency of alterations which can inform targeted treatment decisions” in non-small cell lung cancer. Speaking for a big panel, Doron Lipson, PhD, of Foundation Medicine Inc. These are typically single nucleotide variants or small deletions. Some sequence every exon of a cancer gene or whole genes others sequence only so-called hotspots, regions where pathogenic variants cluster and where well-known, frequently theranostic mutations are located. NGS for determining the vaginal microbiome in clinical samplesįirst, what size oncogene panel is optimal? Laboratories are evaluating various homebrew and commercial panels consisting of 23 to 409 genes. Two fundamental questions are still being hashed out, however. ![]() (See page 38 for microbiological applications.) Interviews with these presenters, and others who have experience in this area, provide a convincing case for the value of NGS in this setting. But what if you don’t need to sequence 18,000 whole human genomes this year, or don’t have $10 million to acquire the HiSeq X Ten? And perhaps you want to do clinical next-generation sequencing now, which the MinION is not quite ready for.Ī scan of the scientific program turned up several talks on using NGS platforms for their most prominent clinical application to date-analyzing genes of cancer patients for variants that are relevant to causation of cancer and, in some cases, can point to targeted therapies.
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