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Major challenges related to tumor biological characteristics in accurate mutation detection of colorectal cancer by next-generation sequencing

Next-generation sequencing (NGS) has been used in mutation detection of colorectal cancer (CRC). We here interrogated 747 CRC samples to detect mutations in 22 cancer-related genes by using NGS, and to explore some key challenges related to tumor biology. RAS mutations (KRAS or NRAS mutations), RAS/... Full description

Journal Title: Cancer letters 2017-12-01, Vol.410, p.92-99
Main Author: Li, Weihua
Other Authors: Qiu, Tian , Guo, Lei , Ying, Jianming
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: Ireland: Elsevier B.V
ID: ISSN: 0304-3835
Link: https://www.ncbi.nlm.nih.gov/pubmed/28942013
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title: Major challenges related to tumor biological characteristics in accurate mutation detection of colorectal cancer by next-generation sequencing
format: Article
creator:
  • Li, Weihua
  • Qiu, Tian
  • Guo, Lei
  • Ying, Jianming
subjects:
  • Adjuvant treatment
  • Antineoplastic Agents - therapeutic use
  • Biomarkers, Tumor - genetics
  • Biopsy
  • Cancer
  • Chemotherapy
  • Class I Phosphatidylinositol 3-Kinases - genetics
  • Colorectal cancer
  • Colorectal Neoplasms - drug therapy
  • Colorectal Neoplasms - genetics
  • Colorectal Neoplasms - pathology
  • Diagnosis
  • DNA Mutational Analysis - methods
  • Gene mutations
  • Genetic aspects
  • Genetic Predisposition to Disease
  • GTP Phosphohydrolases - genetics
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Membrane Proteins - genetics
  • Metastasis
  • Mutation
  • Mutation Rate
  • Neoplasm Metastasis
  • Next-generation sequencing
  • Phenotype
  • Predictive Value of Tests
  • Proto-Oncogene Proteins B-raf - genetics
  • Proto-Oncogene Proteins p21(ras) - genetics
  • Reproducibility of Results
  • Retrospective Studies
  • Treatment Outcome
  • Tumor cellularity
  • Tumor heterogeneity
ispartof: Cancer letters, 2017-12-01, Vol.410, p.92-99
description: Next-generation sequencing (NGS) has been used in mutation detection of colorectal cancer (CRC). We here interrogated 747 CRC samples to detect mutations in 22 cancer-related genes by using NGS, and to explore some key challenges related to tumor biology. RAS mutations (KRAS or NRAS mutations), RAS/BRAF/PIK3CA mutations (mutations in KRAS, NRAS, BRAF or PIK3CA) and mutation burden (mutations in any of the 22 detected genes) were observed in 53.0% (396/747), 57.1% (431/747) and 84.2% (629/747) of specimens, respectively. Higher mutation frequencies were observed in biopsy specimens with ≥20% tumor cellularity than those with
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 0304-3835
fulltext: fulltext
issn:
  • 0304-3835
  • 1872-7980
url: Link


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titleMajor challenges related to tumor biological characteristics in accurate mutation detection of colorectal cancer by next-generation sequencing
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descriptionNext-generation sequencing (NGS) has been used in mutation detection of colorectal cancer (CRC). We here interrogated 747 CRC samples to detect mutations in 22 cancer-related genes by using NGS, and to explore some key challenges related to tumor biology. RAS mutations (KRAS or NRAS mutations), RAS/BRAF/PIK3CA mutations (mutations in KRAS, NRAS, BRAF or PIK3CA) and mutation burden (mutations in any of the 22 detected genes) were observed in 53.0% (396/747), 57.1% (431/747) and 84.2% (629/747) of specimens, respectively. Higher mutation frequencies were observed in biopsy specimens with ≥20% tumor cellularity than those with <20% tumor cellularity, but these differences were not observed in resection samples. Intratumor mutational heterogeneity was estimated by mutant allele frequency and tumor cellularity, and more likely to occur in PIK3CA mutant tumors. No significant differences of mutation frequencies were detected between primary and metastatic tumors. Additionally, specimens after chemotherapy showed lower mutation frequencies compared with specimens without chemotherapy. Together, our findings demonstrate that poor tumor cellularity, tumor heterogeneity and adjuvant therapy may confound the molecular diagnosis of CRC, and should be highlighted with prospective quality assessment during tissue process. •Biopsy samples with ≥20% tumor content show higher mutation frequencies than those with <20%.•Intratumor mutational heterogeneity is more likely to occur in PIK3CA mutant tumors.•Mutational heterogeneity between primary and metastatic tumors is uncommon.•Post-chemotherapy samples show lower mutation frequencies than pre-chemotherapy samples.
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languageeng
publisherIreland: Elsevier B.V
subjectAdjuvant treatment ; Antineoplastic Agents - therapeutic use ; Biomarkers, Tumor - genetics ; Biopsy ; Cancer ; Chemotherapy ; Class I Phosphatidylinositol 3-Kinases - genetics ; Colorectal cancer ; Colorectal Neoplasms - drug therapy ; Colorectal Neoplasms - genetics ; Colorectal Neoplasms - pathology ; Diagnosis ; DNA Mutational Analysis - methods ; Gene mutations ; Genetic aspects ; Genetic Predisposition to Disease ; GTP Phosphohydrolases - genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Membrane Proteins - genetics ; Metastasis ; Mutation ; Mutation Rate ; Neoplasm Metastasis ; Next-generation sequencing ; Phenotype ; Predictive Value of Tests ; Proto-Oncogene Proteins B-raf - genetics ; Proto-Oncogene Proteins p21(ras) - genetics ; Reproducibility of Results ; Retrospective Studies ; Treatment Outcome ; Tumor cellularity ; Tumor heterogeneity
ispartofCancer letters, 2017-12-01, Vol.410, p.92-99
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descriptionNext-generation sequencing (NGS) has been used in mutation detection of colorectal cancer (CRC). We here interrogated 747 CRC samples to detect mutations in 22 cancer-related genes by using NGS, and to explore some key challenges related to tumor biology. RAS mutations (KRAS or NRAS mutations), RAS/BRAF/PIK3CA mutations (mutations in KRAS, NRAS, BRAF or PIK3CA) and mutation burden (mutations in any of the 22 detected genes) were observed in 53.0% (396/747), 57.1% (431/747) and 84.2% (629/747) of specimens, respectively. Higher mutation frequencies were observed in biopsy specimens with ≥20% tumor cellularity than those with <20% tumor cellularity, but these differences were not observed in resection samples. Intratumor mutational heterogeneity was estimated by mutant allele frequency and tumor cellularity, and more likely to occur in PIK3CA mutant tumors. No significant differences of mutation frequencies were detected between primary and metastatic tumors. Additionally, specimens after chemotherapy showed lower mutation frequencies compared with specimens without chemotherapy. Together, our findings demonstrate that poor tumor cellularity, tumor heterogeneity and adjuvant therapy may confound the molecular diagnosis of CRC, and should be highlighted with prospective quality assessment during tissue process. •Biopsy samples with ≥20% tumor content show higher mutation frequencies than those with <20%.•Intratumor mutational heterogeneity is more likely to occur in PIK3CA mutant tumors.•Mutational heterogeneity between primary and metastatic tumors is uncommon.•Post-chemotherapy samples show lower mutation frequencies than pre-chemotherapy samples.
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0Adjuvant treatment
1Antineoplastic Agents - therapeutic use
2Biomarkers, Tumor - genetics
3Biopsy
4Cancer
5Chemotherapy
6Class I Phosphatidylinositol 3-Kinases - genetics
7Colorectal cancer
8Colorectal Neoplasms - drug therapy
9Colorectal Neoplasms - genetics
10Colorectal Neoplasms - pathology
11Diagnosis
12DNA Mutational Analysis - methods
13Gene mutations
14Genetic aspects
15Genetic Predisposition to Disease
16GTP Phosphohydrolases - genetics
17High-Throughput Nucleotide Sequencing
18Humans
19Membrane Proteins - genetics
20Metastasis
21Mutation
22Mutation Rate
23Neoplasm Metastasis
24Next-generation sequencing
25Phenotype
26Predictive Value of Tests
27Proto-Oncogene Proteins B-raf - genetics
28Proto-Oncogene Proteins p21(ras) - genetics
29Reproducibility of Results
30Retrospective Studies
31Treatment Outcome
32Tumor cellularity
33Tumor heterogeneity
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6Class I Phosphatidylinositol 3-Kinases - genetics
7Colorectal cancer
8Colorectal Neoplasms - drug therapy
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11Diagnosis
12DNA Mutational Analysis - methods
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27Proto-Oncogene Proteins B-raf - genetics
28Proto-Oncogene Proteins p21(ras) - genetics
29Reproducibility of Results
30Retrospective Studies
31Treatment Outcome
32Tumor cellularity
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abstractNext-generation sequencing (NGS) has been used in mutation detection of colorectal cancer (CRC). We here interrogated 747 CRC samples to detect mutations in 22 cancer-related genes by using NGS, and to explore some key challenges related to tumor biology. RAS mutations (KRAS or NRAS mutations), RAS/BRAF/PIK3CA mutations (mutations in KRAS, NRAS, BRAF or PIK3CA) and mutation burden (mutations in any of the 22 detected genes) were observed in 53.0% (396/747), 57.1% (431/747) and 84.2% (629/747) of specimens, respectively. Higher mutation frequencies were observed in biopsy specimens with ≥20% tumor cellularity than those with <20% tumor cellularity, but these differences were not observed in resection samples. Intratumor mutational heterogeneity was estimated by mutant allele frequency and tumor cellularity, and more likely to occur in PIK3CA mutant tumors. No significant differences of mutation frequencies were detected between primary and metastatic tumors. Additionally, specimens after chemotherapy showed lower mutation frequencies compared with specimens without chemotherapy. Together, our findings demonstrate that poor tumor cellularity, tumor heterogeneity and adjuvant therapy may confound the molecular diagnosis of CRC, and should be highlighted with prospective quality assessment during tissue process. •Biopsy samples with ≥20% tumor content show higher mutation frequencies than those with <20%.•Intratumor mutational heterogeneity is more likely to occur in PIK3CA mutant tumors.•Mutational heterogeneity between primary and metastatic tumors is uncommon.•Post-chemotherapy samples show lower mutation frequencies than pre-chemotherapy samples.
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