Home >> Tag Archives: Next-generation sequencing/Sanger sequencing

Tag Archives: Next-generation sequencing/Sanger sequencing

The outlook for in-house next-generation sequencing

May 2023—Bringing next-generation sequencing in-house was at the center of a March 27 roundtable led by CAP TODAY publisher Bob McGonnagle, with costs, reimbursement, equity, and the electronic health record part of the conversation. Jeremy Segal, MD, PhD, of the University of Chicago, explains why the Genomics Organization for Academic Laboratories was formed. “By lowering barriers and encouraging cooperation,” he said, “we’ve seen our labs increase the pace of development and the quality of the assays they’re bringing on.”

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No time to wait: How rapid NGS changed cancer care

November 2022—Rapid next-generation sequencing in a community hospital setting, performed by histotechnologists and interpreted by anatomic pathologists, is possible and paying off, and it “makes the pathologist a much more meaningful part of the precision oncology team,” says Brandon Sheffield, MD, of the Department of Laboratory Medicine, William Osler Health System, Brampton/Etobicoke, Ontario. “It has changed practice at our hospitals,” he says.

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Purchased for the pandemic? Rethinking instrumentation

October 2022—Who’s doing what with instruments purchased at the peak of the pandemic? That and next-generation sequencing are what CAP TODAY publisher Bob McGonnagle asked Compass Group members about when they met virtually on Sept. 6. The Compass Group is an organization of not-for-profit IDN system laboratory leaders who collaborate to identify and share best practices and strategies.

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In next-gen sequencing, aiming for wider access

May 2022—Next-generation sequencing—the worries, the wins, and what’s new. That’s what came up when CAP TODAY publisher Bob McGonnagle led an NGS-focused roundtable on March 14. With him were Jeremy Segal, MD, PhD, of the University of Chicago; Pierre Del Moral, PhD, MBA, and Fiona Nohilly of Illumina; Sohaib Qureshi, PhD, of Thermo Fisher Scientific; and Andy Johnson, DPhil, of Janssen. Here’s what they had to say.

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Compass group roundtable: ‘Gaps loom large’: labor shortage hitting hard

June 2021—A brief update on SARS-CoV-2 variant testing and then a look at the latest on the laboratory labor struggle. That’s what Compass Group members provided when they spoke May 4 in another of their monthly calls led by CAP TODAY publisher Bob McGonnagle. “We’ve accepted that if we’re going to solve the [labor] issue,” said Sam Terese of Alverno Laboratories, “we’ll have to create the workforce. They’re not coming to us in any other way.” With McGonnagle and Terese were Bob Stallone and James Crawford, MD, PhD, Northwell; Sterling Bennett, MD, MS, Intermountain; John Waugh, MS, MT(ASCP), Henry Ford; Peter Dysert, MD, Baylor Scott & White; Steven Carroll, MD, PhD, Medical University of South Carolina; Stan Schofield, MaineHealth; Gregory Sossaman, MD, Ochsner; Clark Day, Indiana University; Diana Kremitske, MS, MHA, MT(ASCP), Geisinger; Julie Hess, AdventHealth; Terrence Dolan, MD, Regional Medical Laboratory; and Dan Ingemansen, Sanford. The Compass Group is an organization of not-for-profit IDN system lab leaders who collaborate to identify and share best practices and strategies. Here is what they said.

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NGS in more labs? IFCC group aims to ease the way

May 2021—When it comes to next-generation sequencing, don’t count out community hospital labs, especially as black-box solutions come on the market. That’s the hope of members of an International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) working group that aims to help clinical labs develop in-house NGS programs. Large-scale genomic testing won’t be necessary or practical at the community hospital level. But hospital-based genomic testing programs should set out to meet the NCCN guideline targets and provide testing for which a wide range of sample input and quality can be accepted, says Robyn Sussman, PhD, a member of the IFCC working group and molecular development assistant director, Penn Precision and Computational Diagnostics, University of Pennsylvania Perelman School of Medicine.

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Eyes on faster, cheaper, simpler next-gen sequencing

May 2021—Next-generation sequencing analysis and interpretation, as well as reimbursement, were some of what CAP TODAY publisher Bob McGonnagle asked Illumina and Thermo Fisher executives and Jeremy Segal, MD, PhD, about when they gathered on a March 24 call. McGonnagle asked, too, about variants of unknown significance and for views on what lies ahead for NGS. “Circulating tumor DNA analysis is starting to move wholesale into the academic setting,” along with other applications, says Dr. Segal, of the University of Chicago.

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Looming unknowns with SARS-CoV-2 variants

March 2021—Listening to experts and others make predictions about the pandemic, it’s easy to think they’re obsessed with surfing: How will we deal with the next wave? The dangers are real. With SARS-CoV-2, the next wave might be swept in by emerging variants, with their uncertain but worrisome impact on transmission, severity of illness, treatments, and vaccine effectiveness.

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Markers, methods remake the NSCLC map

February 2021—Absorbing new biomarkers into lung cancer workups makes for a complicated diplomacy. How best to balance so many rivals? Does it make the most sense for laboratories to try to do everything at once, a full-court press involving next-generation sequencing panels? Or is it more practical to add a new marker only as a new targeted therapy receives approval? Where do RNA-based assays fit in? What about IHC? When do you make the switch? Or do you? And how best to handle cell-free DNA tests (which seem to be the rogue states in all this)? How do you weight external factors, such as reimbursement, existing equipment and capital expenditures, and physician expertise? Driving this all are medical breakthroughs. As with all forms of statecraft, the latest incident can change everything. For lung cancer, the most recent advance comes from the ADAURA trial, which showed a significant benefit of using osimertinib to treat stage IB to IIIA EGFR-mutation positive non-small-cell lung cancer.

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AMP case report: NGS as the tiebreaker in tumors with similar morphology and equivocal immunophenotype

May 2020—Traditionally, histopathologic diagnosis has been regarded as the gold standard for most disease processes including cancer. However, in certain circumstances, a final histopathologic diagnosis cannot be rendered despite extensive conventional ancillary testing such as immunohistochemistry. In recent years, molecular testing has revealed specific variant signatures for many tumors, which can be used to determine a final diagnosis.

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Mate pair sequencing yields rich new data

November 2019—The LUVOIR telescope proposed this year by NASA, when it is launched into orbit, will outperform the Hubble Telescope 40-fold in ability to detect and visualize deep space objects in detail. But while dazzling in concept, the LUVOIR is still in development. Interestingly, at the genomic level, a similarly impressive advance in detection called mate pair sequencing has already progressed from research to clinical use in diagnosing cancer. With mate pair sequencing, a novel next-generation sequencing technique, Mayo Clinic is advancing the laboratory’s current capabilities for visualizing genetic rearrangements, thus increasing the diagnostic yield of testing for a variety of neoplasms.

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AMP case report: NGS of a rare metastatic bladder adenocarcinoma

September 2019—Primary bladder adenocarcinoma is a rare vesicle malignancy accounting for up to two percent of malignant neoplasms of the bladder.1 They occur in males more than females and are classically seen in the fifth or sixth decade of life.2 Histologically they are of enteric, mucinous, or mixed types. Morphologically, the enteric type appears identical to a colonic adenocarcinoma and the mucinous type appears as neoplastic cells floating in pools of extravasated mucin. The mixed type is a mixture of the morphologies of the enteric and mucinous types. Immunohistochemically, adenocarcinomas of the urinary bladder classically express CK20 and CDX2.

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AMP case report: Detection of concurrent hematologic malignancies in solid tumor NGS testing may cause false-positive results

November 2018—CAP TODAY and the Association for Molecular Pathology have teamed up to bring molecular case reports to CAP TODAY readers. AMP members write the reports using clinical cases from their own practices that show molecular testing’s important role in diagnosis, prognosis, and treatment. The following report comes from Weill Cornell Medicine.

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In cancer sequencing, a new lingua franca

February 2017—NGS has taken its NBS, or next big step: a newly published joint consensus guideline on how to interpret and report sequence variants in cancer. With these 20 pages of best practices for making next-generation sequencing a regular part of cancer diagnostics, the field is moving, essentially, from frontier town to gated community.

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Method or test? Providing clarity to clinicians on NGS

September 2016—Whether it was “This is your brain on drugs,” “Take a bite out of crime,” or “Friends don’t let friends drive drunk” popping up onscreen, few of us watching TV in the 1970s and ’80s enjoyed having our programs interrupted by those public service announcements. Yet those important messages stuck in viewers’ brains—and stuck hard, if homages such as the Washington Post’s “10 Best PSAs of All Time” are anything to go by.

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Shorts on Standards: Update on the frontier of NGS, 7/16

July 2016—Next-generation sequencing has continued to deliver on its promises and potential in the diagnostic arena. However, as with any emerging and evolving technology, the medical and scientific community faces the challenge of assessing the implications and demonstrating definitive clinical uses of its expanding capabilities, especially in the context of medical efficacy, clinical utility, and cost efficiency.

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Next-gen sequencing workflow in full spate

April 2016—With next-generation sequencing’s clear benefits—for diagnosis, prognosis, treatment, and trials—come its new challenges, and clinical laboratories are doing what it takes and sharing how. Two plenary speakers at last year’s meeting of the Association for Molecular Pathology spoke of variant calling in the bioinformatic pipeline and validation, and of clinical reporting. Colin Pritchard, MD, PhD, of the University of Washington and one of the speakers, sees reporting a genomic sequencing assay as more like making a histologic diagnosis, which he calls craftwork, than reporting a sodium value. “That’s an idea that hasn’t really permeated yet,” he said.

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In next-gen sequencing, panel versus exome

January 2016—As next-generation sequencing takes its place in clinical laboratory medicine, a difference is developing between its use when there is a defined phenotype, as with hereditary oncology syndromes or hereditary cardiovascular disorders, and its use in diagnosing hereditary developmental disorders. In oncology, targeted panels remain the optimal mode of application.

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3 new NGS Surveys on CAP 2016 PT launchpad

November 2015—More than two years ago, when the CAP decided to move forward with proficiency testing for next-generation sequencing, the decision point was modest. “We estimated that about 35 labs would subscribe, based on survey information, and that was sufficient for us to move forward,” says Karl V. Voelkerding, MD, chair of the CAP Next-Generation Sequencing project team.

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What’s new in next-gen sequencing checklist requirements

August 2015—The first CAP accreditation checklist requirements specific to next-generation sequencing were published only three years ago. “In 2012, those 18 accreditation requirements were basically all new language that the College’s Next-Generation Sequencing Project Team developed and submitted for review,” says project team chair Karl Voelkerding, MD, of the University of Utah Department of Pathology and ARUP Laboratories.

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Paths to validating next-gen sequencing assays

July 2015—As more clinical laboratories tread the unfamiliar ground of next-generation sequencing, they are faced with the age-old challenges of establishing validation and quality control processes. Two experts tackled the topic of molecular QC during a recent CAP TODAY webinar presented in cooperation with Horizon Diagnostics and available for viewing on demand ...

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For viral diagnosis, metagenomic NGS

June 2015—A 20-year-old woman who had returned to the U.S. after two months of hiking in Western Australia presented with three days of acute febrile illness—fever, rash, headache, nausea, and muscle and joint pain. Testing for common infectious causes of acute febrile illness, including Epstein-Barr virus, cytomegalovirus, and human immunodeficiency virus, all turned up negative. While the woman was in Australia, she had been warned about an ongoing outbreak of an exotic alphavirus, Ross River virus, in the region where she was hiking.

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Groups closing the gap in reference materials for sequencing assays

March 2015—It’s a truism in the clinical laboratory that your results are only as good as the reference standards available to QC your assay. For measuring small analytes like glucose that’s not a problem. However, in clinical laboratories the analyte in question increasingly is DNA. In the past five years, next-generation sequencing has been adopted to detect variants in small targeted regions of specific genes, which is useful in oncology and medical genetics. More ambitious applications of NGS—whole genome and whole exome sequencing—have recently begun to enter the clinical realm as well.

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NGS informatics catching up to clinical demands

November 2014—When Birgit H. Funke, PhD, gave a talk earlier this year on incorporating bioinformatic tools and pipelines into medical NGS, at Molecular Medicine Tri-Con 2014, one of her slides showed the main bioinformatics activities needed to support sequencing. Among them were designing and building pipelines to manage genetic data, writing scripts for data analysis pipelines, and building custom applications.

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Virus or bacterium? Gene expression may tell

September 2014—At the 30th Annual Clinical Virology Symposium this spring, Gregory Storch, MD, related a typical case of a febrile child seen in the emergency department. Dr. Storch, a professor of pediatrics at Washington University School of Medicine, described a 20-month-old boy with a fever of 40°C, rash, cough, and nasal congestion but no gastrointestinal symptoms. White blood cell count was 7,800/µL. Blood culture was negative and a chest x-ray showed mild peribranchial thickening. Diagnosis, Dr. Storch says, was “viral syndrome.” The patient got a dose of ceftriaxone, which was “reasonable,” in Dr. Storch’s view, in light of the patient’s fever and the presence of bands on the peripheral blood smear.

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NGS to detect oncogenes—sizing panels, reporting results

June 2014—Scientific wonders always abound at the Advances in Genome Biology and Technology conference, and this year’s meeting in February was no exception. Attendees had their first opportunity at a scientific meeting to learn about the newly announced Illumina HiSeq X Ten, a combination of 10 HiSeq X systems, which, Illumina says, can sequence 16 whole human genomes per three-day run at a read depth of 30× and a cost of $1,000 per genome. At the other end of the scale, attendees saw the unveiling of Oxford Nanopore’s MinION, a sequencer the size of a pack of chewing gum.

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In encephalitis case, next-gen sequencing is the star

April 2014—In what may be a first for the burgeoning field of next-generation sequencing, this powerful new technology was used to identify the cause of encephalitis in a teenage boy who had been critically ill in the intensive care unit for several weeks. Diagnosis suggested a specific treatment. Within two weeks of initiating therapy, the boy had recovered and was discharged. It is becoming common practice to use NGS to detect mutations that can help select drug therapy in cancer cases and to find genetic variations responsible for inherited diseases. However, NGS has not previously been considered a useful tool in critical care situations, where a short turnaround time is crucial.

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