Applications

Deborah Josko

doi:10.29074/ascls.27.3.179

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Deborah Josko, Ph.D. MLT(ASCP)M, SM⇑
1. Associate Professor and Program Director, Department of Clinical Laboratory Sciences, Medical Laboratory Science Program, Rutgers, The State University of New Jersey – School of Health Related Professions, Scotch Plains, NJ

Address for correspondence: Deborah Josko, Ph.D. MLT(ASCP)M, SM, Associate Professor, Department of Clinical Laboratory Sciences, Medical Laboratory Science Program, Rutgers, The State University of New Jersey – School of Health Related Professions 1776 Raritan Road, Scotch Plains, NJ 07076. (908) 889-2422. daj100{at}shrp.rutgers.edu.

Discuss the various applications available on select next generation sequencing platforms.
Describe targeted, exome, transcriptome, microbial, de novo sequencing, etc.
List the assays that are FDA cleared for diagnostic use.
Examine the ACMG clinical laboratory standards for next generation sequencing.

Extract

Introduction The evolution of deoxyribonucleic acid (DNA) sequencing techniques along with the advent of various sequencing platforms has revolutionized the field of genomics, research and medicine. Each manufacturer markets its own platform utilizing unique methodologies from the Ion Torrent PGM™ which sequences DNA using a semi-conductor chip¹ to single molecule real time (SMRT) technology by Pacific Biosciences for carrying out sequencing using zero mode waveguides (ZMW).² Both principles were discussed in detail in the article entitled “Next Generation Sequencing - Platforms.”

Most sequencers have the ability to sequence the entire genome or small/targeted regions for research and clinical purposes. All sequencers perform an array of assays depending on the platform and applications available for that system. This article provides a brief overview of some of the applications available for research and clinical use and discusses the newly published clinical laboratory standards for next generation sequencing.

Next Generation Sequencing Applications: Ion Torrent PGM™ The Ion Torrent PGM™ by Life Technologies is able to perform targeted sequencing, exome sequencing, transcriptome sequencing and genome sequencing.³ For targeted sequencing, a variety of panels are available that are “ready to use.” However, one can also custom design their own panel based on the genomic sequences of interest.

According to the manufacturer's website, there are four “ready to use” panels available that include the “Ion AmpliSeq™ Cancer Hotspot Panel v2 which targets “hot spot” regions of 50 oncogenes and tumor suppressor genes; the Ion AmpliSeq™ Comprehensive Cancer Panel which targets greater than 400 oncogenes and tumor…

ABBREVIATIONS: ACMG - American College of Medical Genetics and Genomics; ATP - adenosine triphosphate; CLIA - Clinical Laboratory Improvement Amendments; CTFR - cystic fibrosis transmembrane conductance regulator; DNA - deoxyribonucleic acid; FDA - Food and Drug Administration; HLA - human leukocyte antigen; HUGO - human genome organization; ID - identification; NGS - next generation sequencing; PGM - Personal Genome Machine; PT - proficiency testing; RNA - ribonucleic acid; rRNA - ribosomal ribonucleic acid; SMRT - single molecule real time; SNP - single nucleotide polymorphism; ZMW - zero mode waveguides.

Discuss the various applications available on select next generation sequencing platforms.
Describe targeted, exome, transcriptome, microbial, de novo sequencing, etc.
List the assays that are FDA cleared for diagnostic use.
Examine the ACMG clinical laboratory standards for next generation sequencing.