TY - JOUR
T1 - Analysis of pre-analytic factors affecting the success of clinical next-generation sequencing of solid organ malignancies
AU - Chen, Hui
AU - Luthra, Rajyalakshmi
AU - Goswami, Rashmi S.
AU - Singh, Rajesh R.
AU - Roy-Chowdhuri, Sinchita
N1 - Publisher Copyright:
© 2015 by the authors; licensee MDPI, Basel, Switzerland.
PY - 2015/8/28
Y1 - 2015/8/28
N2 - Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
AB - Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
KW - Next-generation sequencing
KW - Pre-analytic factors
KW - Targeted hotspot mutation analysis
KW - Tissue qualification
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U2 - 10.3390/cancers7030859
DO - 10.3390/cancers7030859
M3 - Review article
C2 - 26343728
AN - SCOPUS:84940979557
SN - 2072-6694
VL - 7
SP - 1699
EP - 1715
JO - Cancers
JF - Cancers
IS - 3
ER -