Test Feasibility of Next-Generation Sequencing Assays in Clinical Mutation Detection of Small Biopsy and Fine Needle Aspiration Specimens

Next-Generation Sequencing Analysis on Image-Guided Biopsy Samples in Early-Stage Lung Cancer: Feasibility Study and Comparison With Surgical Samples

Introduction

Limited information exists on next-generation sequencing (NGS) success for lung tumors of 30 mm or less. We aimed to compare NGS success rates across biopsy techniques for these tumors, assess DNA sequencing quality, and verify reliability against surgical resection results.

Methods

We used data from the Initiative for Early Lung Cancer Research on Treatment study, including patients with lung tumors measuring 30 mm or less who had surgery and NGS on biopsies since 2016. We collected data on biopsy type, nodule characteristics, complications, sequencing feasibility, clinical actionable variants, surgery type, and TNM classification. We compared NGS feasibility and quality between biopsy methods and, for those with NGS on surgical samples, compared feasibility, quality, and detection of actionable variants.

Results

Among the 654 participants with lung tumors of 30 mm or less who underwent surgery, 70 had NGS on prior biopsies. The median age was 68.5; 51.4% were male individuals, and 75.7% were smokers. The mean diameter of biopsied nodules was 17.7 mm, with 67.1% fine-needle aspiration, 17.1% computed tomography-guided transthoracic core needle biopsies, and 17.1% endobronchial ultrasound-guided transbronchial needle aspiration. DNA sequencing was feasible in 97.1% of biopsy samples; 2.9% had low tumor cellularity. Coverage depth was achieved in 89.7% of biopsies. RNA sequencing was successful in 66.2% of biopsies, especially in core needle biopsies. Actionable alterations were found in 41.4% of patients. Among the participants, 30% had NGS on surgical samples. RNA sequencing was more feasible on surgical samples (95.2% versus 42.9% for biopsies). NGS on surgical samples matched biopsy results in 90% of patients, with 10% showing additional alterations.

Conclusion

DNA sequencing succeeded in 97.1% of biopsies of nodules 30 mm or less, whereas RNA sequencing feasibility was lower. NGS on biopsy samples is generally reliable but requires careful review.

Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison

Background

Successful practice of precision medicine in advanced lung cancers relies on therapeutic regimens tailored to individual molecular characteristics. The aim of this study was to investigate the accuracy of small specimens for molecular profiling using next-generation sequencing (NGS).

Methods

Genetic alternations, tumor mutational burden (TMB), status of microsatellite instability (MSI), and expression of programmed death ligand 1 (PD-L1) were compared side-by-side between the concurrently obtained core needle biopsy (CNB) and resection specimens in 17 patients with resectable non-small cell lung cancers.

Results

DNA yield and library complexity were significantly lower in CNB specimens (both p < 0.01), whereas the insert size, sequencing depth, and Q30 ratio were similar between the matched specimens (all p > 0.05). The total numbers of genetic alternations detected in resection and CNB specimens were 186 and 211, respectively, with 156 alternations in common, yielding a specific concordance rate of 83.9%. The prevalence of mutations in 8 major driver genes was 100% identical between surgical and CNB specimens, though the allele frequency was lower in CNB specimens, with a median underestimation of 57%. Results of TMB were similar (p = 0.547) and MSI status was 100% matched in all paired specimens.

Conclusions

Pulmonary CNB specimens were suitable for NGS given the satisfactory accuracy when compared to corresponding surgical specimens. NGS results yielding from CNB specimens should be deemed reliable to provide instructive information for the treatment of advanced lung cancers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13000-022-01255-y.

Percutaneous Image-Guided Biopsy for a Comprehensive Hybridization Capture-Based Next-Generation Sequencing in Primary Lung Cancer: Safety, Efficacy, and Predictors of Outcome

Introduction

To evaluate factors associated with successful comprehensive genomic sequencing of image-guided percutaneous needle biopsies in patients with lung cancer using a broad hybrid capture-based next-generation sequencing assay (CHCA).

Methods

We conducted a single-institution retrospective review of image-guided percutaneous transthoracic needle biopsies from January 2018 to December 2019. Samples with confirmed diagnosis of primary lung cancer and for which CHCA had been attempted were identified. Pathologic, clinical data and results of the CHCA were reviewed. Covariates associated with CHCA success were tested for using Fisher's exact test or Wilcoxon ranked sum test. Logistic regression was used to identify factors independently associated with likelihood of CHCA success.

Results

CHCA was requested for 479 samples and was successful for 433 (91%), with a median coverage depth of 659X. Factors independently associated with lower likelihood of CHCA success included small tumor size (OR = 0.26 [95% confidence interval (CI): 0.11-0.62, p = 0.002]), intraoperative inadequacy on cytologic assessment (OR = 0.18 [95% CI: 0.06-0.63, p = 0.005]), small caliber needles (≥20-gauge) (OR = 0.22 [95% CI: 0.10-0.45, p < 0.001]), and presence of lung parenchymal abnormalities (OR = 0.12 [95% CI: 0.05-0.25, p < 0.001]). Pneumothorax requiring chest tube insertion occurred in 6% of the procedures. No grade IV complications or procedure-related deaths were reported.

Conclusions

Percutaneous image-guided transthoracic needle biopsy is safe and has 91% success rate for CHCA in primary lung cancer. Intraoperative inadequacy, small caliber needle, presence of parenchymal abnormalities, and small tumor size (≤1 cm) are independently associated with likelihood of failure.

Role of Image-Guided Percutaneous Needle Biopsy in the Age of Precision Medicine

PURPOSE OF REVIEW

With the remarkable progress in cancer precision medicine, the demand for biopsy has been increasing, and the role of biopsy has been changing. In this review, we discuss the current state and recent advances in the role of image-guided percutaneous needle biopsy (PNB) in facilitating precision medicine.

RECENT FINDINGS

Biopsies are useful not only in the diagnosis of cancer and histological sub-type but also in the analysis of its molecular characteristics for targeted treatments. PNB specimens have been shown to provide high DNA yields for genomic analysis. Liquid biopsy is an emerging technology but is under development; therefore, PNB is the current standard of practice and is performed complimentarily with liquid biopsy. In the age of precision medicine, interventional oncologists play a key role in optimal tissue collection for adequate genomic analysis. Effective PNB may improve its diagnostic utility and help optimize precision medicine.

Double PIK3CA Alterations and Parallel Evolution in Colorectal Cancers

OBJECTIVES

To demonstrate clinicopathologic features and evaluate the clonality of double PIK3CA alterations in colorectal cancers (CRCs).

METHODS

Clonality was examined in 13 CRCs with double PIK3CA alterations (1.7% of CRCs or 9.6% of PIK3CA-mutated CRCs). Multiregional analyses were performed to confirm subclonal PIK3CA alterations.

RESULTS

PIK3CA alterations were detected within exon 9 (51%), exon 20 (23%), exon 1 (15%), and exon 7 (6.0%). CRCs with exon 7 alterations showed a significantly higher incidence of double PIK3CA alterations. Most double PIK3CA alterations consisted of a hotpsot alteration and an uncommon alteration; they were often clonal and present within a single tumor population. Multiregional analyses of CRCs with predicted subclonal double-alterations revealed multiclonal CRCs with divergent PIK3CA variant status originating from a common APC- and KRAS-mutated founder lineage of adenoma.

CONCLUSIONS

The findings supported multiclonal CRCs resulting from parallel evolution during the progression from adenoma to adenocarcinoma within the mitogen-activated protein kinase pathway, as previously demonstrated, or the mammalian target of rapamycin pathway. Further studies are warranted to elucidate clinical significance and potential targeted therapy for CRC patients with double PIK3CA alterations and impacts on clinical decision-making in patients with multiclonal CRCs harboring divergent PIK3CA mutational status.

Targeted Next-Generation Sequencing Validates the Use of Diagnostic Biopsies as a Suitable Alternative to Resection Material for Mutation Screening in Colorectal Cancer

BACKGROUND

Mutation testing in the context of neoadjuvant therapy must be performed on biopsy samples. Given the issue of tumour heterogeneity, this raises the question of whether the biopsies are representative of the whole tumour. Here we have compared the mutation profiles of colorectal biopsies with their matched resection specimens.

METHODS

We performed next-generation sequencing (NGS) analysis on 25 paired formalin-fixed, paraffin-embedded colorectal cancer biopsy and primary resection samples. DNA was extracted and analysed using the TruSight tumour kit, allowing the interrogation of 26 cancer driver genes. Samples were run on an Illumina MiSeq. Mutations were validated using quick-multiplex-consensus (QMC)-polymerase chain reaction (PCR) in conjunction with high resolution melting (HRM). The paired biopsy and resection tumour samples were assessed for presence or absence of mutations, mutant allele frequency ratios, and allelic imbalance status.

RESULTS

A total of 81 mutations were detected, in ten of the 26 genes in the TruSight kit. Two of the 25 paired cases were wild-type across all genes. The mutational profiles, allelic imbalance status, and mutant allele frequency ratios of the paired biopsy and resection samples were highly concordant (88.75-98.85%), with all but three (3.7%) of the mutations identified in the resection specimens also being present in the biopsy specimens. All 81 mutations were confirmed by QMC-PCR and HRM analysis, although four low-level mutations required a co-amplification at lower denaturation temperature (COLD)-PCR protocol to enrich for the mutant alleles.

CONCLUSIONS

Diagnostic biopsies are adequate and reliable materials for molecular testing by NGS. The use of biopsies for molecular screening will enhance targeted neoadjuvant therapy.

Co-occurring genetic alterations and primary EGFR T790M mutations detected by NGS in pre-TKI-treated NSCLCs

INTRODUCTION

Next-generation sequencing (NGS)-based assays to understand various mutations and co-occurrence of genomic alterations in non-small cell lung cancer (NSCLC) have enabled understanding of treatment impact on clinical outcomes.

METHODS

This retrospective study was conducted in 1353 formalin-fixed paraffin-embedded (FFPE) tissues from surgically resected, pre-TKI-treated NSCLC patients with identified gene alterations. Genomic DNA and RNA extraction was followed by NGS library preparation and sequencing using the Ion Ampliseq Colon and Lung Cancer Gene Panel V2 and the AmpliSeq RNA Lung Cancer Research Fusion Panel.

RESULTS

A total of 2328 alterations in 25 genes were detected from the 1293 patients. DNA mutations and RNA fusions co-occurred in 27 patients with TP53 being the most common co-occurring DNA mutation (43.8%) with concurrent ALK fusions. Analysis of the 975 patients with EGFR mutations revealed that the incidence of dual EGFR L858R/T790M mutations was higher compared to EGFR 19del/T790M, and the mean allele fraction (MAF) of T790M was lower compared to 19del in dual EGFR 19del/T790M patients.

CONCLUSION

NSCLC patients represented genetically heterogeneous subgroup with a high frequency of co-occurring mutations in cancer-associated pathways. This diverse mutational profile may have key clinical and research implications for understanding the variability of treatment outcome in pre-TKI-treated NSCLC population. The differences in the MAF of EGFR T790M may determine different responses to TKI therapy in patients harboring dual mutations.

Establishment and characterization of a new patient-derived anaplastic thyroid cancer cell line (C3948), obtained through fine-needle aspiration cytology

PURPOSE

Anaplastic thyroid cancer (ATC) is among the most aggressive and unresectable tumors, presenting a bad prognosis. A better comprehension of the functional and molecular mechanisms behind the aggressiveness of this cancer, as well as new biomarkers for aggressiveness, prognosis, and response to therapy are required. However, owing to their irresectability, ATC tissue is not always accessible. Here we describe the establishment and characterization of a new patient-derived cell line, obtained from an unresectable ATC through fine-needle aspiration cytology (FNAC).

METHODS

The morphology, expression of epithelial and thyroid markers, cytogenetic, mutational and gene expression profiles, doubling time, and drug-resistance profile of the new cell line, designated C3948, were investigated using several methodologies: immunostaining, karyotype analysis, comparative genomic hybridization (CGH), fluorescent in situ hybridization (FISH), next-generation sequencing (NGS), Sanger sequencing, gene expression microarrays, cell counting, and IC₅₀ determination.

RESULTS

Results indicate that C3948 cell line has a histological phenotype representative of original ATC cells and a completely aberrant karyotype with many chromosomal losses and gains; harbors mutated TP53, STK11, and DIS3L2 genes; presents a gene expression profile similar to C643 ATC commercial cell line, but with some unique alterations; has a doubling time similar to C643; and the IC₅₀ profile for paclitaxel, doxorubicin, and cisplatin is similar to C643, although higher for cisplatin.

CONCLUSIONS

These observations are consistent with a typical ATC cell profile, supporting C3948 cell line as a novel preclinical model, and FNAC as a useful approach to better study anaplastic thyroid cancer, including testing of new anticancer therapies.

Clinical mutational profiling and categorization of BRAF mutations in melanomas using next generation sequencing

Background

Analysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the MAPK pathway.

Methods

In this analysis BRAF, KIT, NRAS, and PIK3CA mutations were examined by next generation sequencing (NGS) in 446 melanomas in a clinical diagnostic setting. KRAS and HRAS were also analyzed to elucidate coexisting BRAF and RAS mutations. BRAF mutations were categorized into class-1 (kinase-activated, codon 600), class-2 (kinase-activated, non-codon 600) and class-3 (kinase-impaired), based on the newly proposed classification scheme.

Results

NGS demonstrated high analytic sensitivity. Among 355 mutations detected, variant allele frequencies were 2–5% in 21 (5.9%) mutations and 2–10% in 47 (13%) mutations. Mutations were detected in BRAF (42%), NRAS (25%), KIT (4.9%) and PIK3CA (2.7%). The incidence of class-1, class-2 and class-3 mutations were 33% (26% p.V600E and 6.1% p.V600K), 3.1 and 4.9% respectively. With a broader reportable range of NGS, class-1, class-2 and class-3 mutations accounted for 77, 7.4 and 12% of all BRAF mutations. Class-3 mutations, commonly affecting codons 594, 466 and 467, showed a higher incidence of coexisting RAS mutations, consistent with their RAS-dependent signaling. Significant association with old age and primary tumors of head/neck/upper back suggest chronic solar damage as a contributing factor for melanomas harboring BRAF p.V600K or class-3 mutations.

Conclusion

This study categorizes the range, frequency, coexisting driver mutations and clinical characteristics of the three classes of BRAF mutations in a large cohort of melanomas in a clinical diagnostic setting. Further prospective studies are warranted to elucidate the clinical outcomes and benefits of newly developed targeted therapy in melanoma patients carrying each class of BRAF mutation.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5864-1) contains supplementary material, which is available to authorized users.

Interference of tumour mutational burden with outcome of patients with head and neck cancer treated with definitive chemoradiation: a multicentre retrospective study of the German Cancer Consortium Radiation Oncology Group

BACKGROUND

Tumour mutational burden (TMB) estimated from whole exome sequencing or comprehensive gene panels has previously been established as predictive factor of response to immune checkpoint inhibitors (ICIs). Its predictive value for the efficacy of concurrent chemoradiation (cCRTX), a potential combination partner of ICI, remains unknown.

METHODS

The accuracy of TMB estimation by an in-house 327-gene panel was established in the Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) data set. Interference of TMB with outcome after cCRTX was determined in a multicentre cohort of patients with locally advanced HNSCC uniformly treated with cCRTX. Targeted next-generation sequencing was successfully applied in 101 formalin-fixed, paraffin-embedded pretreatment tumour samples. In a subset of cases (n = 40), tumour RNA was used for immune-related gene expression profiling by the nanoString platform. TMB was correlated with TP53 genotype, human papilloma virus (HPV) status, immune expression signatures and survival parameters. Results were validated in the TCGA HNSCC cohort.

RESULTS

A high accuracy of TMB estimation by the 327-gene panel was established. High TMB was significantly associated with an increased prevalence of TP53 mutations and immune gene expression patterns unrelated to T cell-inflamed gene expression profiles. Kaplan-Meier analysis revealed significantly reduced overall survival in the patient group with high TMB (hazard ratio for death: 1.79, 95% confidence interval: 1.02-3.14; P = 0.042) which remained significant after correcting for confounding factors in the multivariate model. The prognostic value of TMB was confirmed in the TCGA HNSCC cohort.

CONCLUSION

High TMB identifies HNSCC patients with poor outcome after cCRTX who might preferentially benefit from CRTX-ICI combinations.

Feasibility of genomic profiling with next-generation sequencing using specimens obtained by image-guided percutaneous needle biopsy

Aims: The demand for specimen collection for genomic profiling is rapidly increasing in the era of personalized medicine. Percutaneous needle biopsy is recognized as minimally invasive, but the feasibility of comprehensive genomic analysis using next-generation sequencing (NGS) is not yet clear. The purpose of this study was to evaluate the feasibility of genomic analysis using NGS with specimens obtained by image-guided percutaneous needle biopsy with 18-G needles. Patients and methods: Forty-eight patients who participated in a clinical study of genomic profiling with NGS with the specimen obtained by image-guided needle biopsy were included. All biopsies were performed under local anesthesia, with imaging guidance, using an 18-G cutting needle. A retrospective chart review was performed to determine the rate of successful genomic analysis, technical success rate of biopsy procedure, adverse events, rate of success in pathological diagnosis, and cause of failed genomic analysis. Results: The success rate of genomic analysis was 79.2% (38/48). The causes of failure were unprocessed for DNA extraction due to insufficient specimen volume (6/10), insufficient DNA volume (2/10), and deteriorated DNA quality (2/10). The rate of successful genomic analysis excluding NGS analysis that failed for reasons unrelated to the biopsy procedures was 95.2% (40/42). Technical success of biopsy was achieved in all patients without severe adverse events. The rate of success in the pathological diagnosis was 97.9% (47/48). Conclusions: Image-guided needle biopsy specimens using an 18-G cutting needle yielded a successful NGS genomic analysis rate with no severe adverse events and could be an adoptable method for tissue sampling for NGS.

Three-year review of gene sequencing analyses of pulmonary non-small cell lung cancers obtained by fine-needle aspiration or surgical biopsy: mutation and failure rates

INTRODUCTION

Mutational analysis is becoming the standard of diagnostic workup. Sufficient amounts of and quality tumor tissue can be challenging when faced with a small biopsy or biopsy by fine-needle aspiration (FNA).

MATERIALS AND METHODS

We reviewed the failures of FNA and surgical biopsy to yield sequencing data and causes thereof over a 3-year period. We executed a search of the laboratory information system for requests to perform our targeted 50-gene assay by massively parallel sequencing on surgical biopsies and FNAs and compared the results.

RESULTS

Three failure causes were assigned: insufficient tissue as defined by the pathologist, failure to meet quality control indicating library preparation or sequencing failure, and failure of pre-qualifying step for DNA integrity. A total of 327 of 354 cases were successfully sequenced (92%), including 151 FNA cases and 203 biopsies, with 16 (10.6%) and 11 (5.4%) failures, respectively. The Fisher's exact test two-tailed P-value equals 0.050381, making the difference between FNA and biopsy not statistically significant. Insufficient tissue, quality control failure, and DNA integrity were identified as the cause of the failure in 10 (62%), 3 (19%), and 3 (19%) FNA biopsies, and in 5 (45.5%), 1 (9%), and 5 (45.5%) surgical biopsies. The most common cause of failure of FNA was insufficient tissue. For surgical biopsies, DNA integrity and insufficient tissue were equally as likely to be implicated. Both FNA and surgical biopsy have a low failure rate overall without statistical significance between them.

CONCLUSIONS

Although surgical biopsy is considered the gold standard, these findings support FNA as an equal modality.

Minimally Invasive Real-Time Detection of Actionable Mutations in Patients With Metastatic Solid Tumors Using Fine-Needle and Liquid Biopsies

Purpose

Fine-needle biopsy (FNB) and liquid biopsy are minimally invasive methods of tumor sampling that provide feasible means to assess tumor genotypes in real time. However, more data are needed to establish the strength of these methods by benchmarking against the current gold standard methods, core-needle biopsy (CNB) or surgical excision of the tumor.

Patients and Methods

Eligible patients with advanced solid tumors were prospectively recruited. We performed mutation profiling using matched tumor DNA obtained by CNB, FNB and liquid biopsy, and matrix-assisted laser desorption/ionization time-of-flight custom mass-spectrometry or targeted next-generation DNA sequencing. The actionability of detected mutations was determined using the OncoKB Web tool. Agreement between mutations detected in CNBs, FNBs, and circulating tumor DNA (ctDNA) was examined.

Results

Forty-one patients underwent tumor biopsy. Thirty CNBs (73%) and 34 FNBs (83%) had sufficient tumor and DNA for mutation profiling. Median DNA yield from CNB and FNB were 775 ng (interquartile range, 240 to 347 4ng) and 649 ng (interquartile range, 180 to1350 ng), respectively. Of 29 CNB/FNB pairs available for comparison, actionable mutation results were concordant in 28 (96%). Six of nine actionable mutations (67%) that were found by CNB, FNB, or both were detectable in ctDNA. Two additional actionable mutations were found exclusively in ctDNA.

Conclusion

Optimally processed FNB and liquid biopsy can be used routinely for tumor mutation profiling to identify actionable mutations.

Clinical Validation of Coexisting Activating Mutations Within EGFR, Mitogen-Activated Protein Kinase, and Phosphatidylinositol 3-Kinase Pathways in Lung Cancers

CONTEXT.—

Mutations within the same signature transduction pathway are redundant and, therefore, most are mutually exclusive. Laboratory errors, however, may introduce unexpected coexisting mutations.

OBJECTIVE.—

To validate coexisting mutations within epidermal growth factor receptor (EGFR), mitogen-activated protein kinase, and phosphatidylinositol 3-kinase pathways.

DESIGN.—

In this retrospective study for quality assessment of next-generation sequencing in a clinical diagnostics setting, coexisting mutations within EGFR, KRAS, NRAS, BRAF, AKT1, and PIK3CA genes were examined in 1208 non-small cell lung cancers.

RESULTS.—

EGFR mutations did not coexist with BRAF mutations, neither kinase-activated nor kinase-impaired mutations. There was a low but similar incidence (3.3%-5.1%) of PIK3CA mutations in BRAF-, EGFR-, and KRAS-mutated lung cancers and a rare incidence of coexisting KRAS and EGFR mutations detected in 1 of 1208 lung cancers (0.08%) or 1 of 226 EGFR-mutated lung cancers (0.4%). Coexisting BRAF p.V600E mutation was observed in 3 of 4 AKT1 p.E17K-mutated lung cancers. Mutational profiling of DNA reisolated from subareas with the same or different histomorphology, using an alternative assay, confirmed that coexisting mutations might present within the same (whole or subclonal) population or different populations and clarified that the so-called coexisting activating KRAS and BRAF mutations originally reported in a specimen were indeed present in separate lung nodules submitted in the same block.

CONCLUSIONS.—

The results supported that EGFR and BRAF mutations are early driver mutations in lung cancers. Guidelines from official organizations to establish standard operating procedures are warranted to validate unexpected coexisting mutations and, if clinically indicated, to determine their presence in the same or different tumor populations.

Genetic polymorphism in psoriasis and its meaning for the treatment efficacy in the future

The concept of personalized medicine is a new individualized approach which helps application of the targeted therapy. In fact, tailored medicine is mostly present in the field of life-threatening diseases such as oncology. However, skin diseases as such might be regarded as a potential area of implementation of this approach in the future. Stratified medicine in polygenetic and heterogeneous diseases, such as psoriasis, is more complex. Rapid development of science and novel molecular techniques led to better understanding of molecular pathogenetic pathways of many diseases including psoriasis. Identification of the particular immunopathogenetic pathways led to further development of targeted therapies such as biologic drugs. Actually the goal of individualized therapy is to determine the identical homogenous subgroups of patients, according to a biomarker, in which the response to that therapy will be the best and will carry the lowest risk of side effects. This review attempts to analyze the associations between polymorphisms of certain genes and the increased risk of developing psoriasis or psoriatic arthritis. The review of literature has also included the studies investigating the associations between gene polymorphisms and response to biologic therapy in psoriasis and psoriatic arthritis patients.

Molecular Screening of Small Biopsy Samples Using Next-Generation Sequencing in Korean Patients with Advanced Non-small Cell Lung Cancer: Korean Lung Cancer Consortium (KLCC-13-01)

Background

Non-small cell lung cancer (NSCLC) is a common type of cancer with poor prognosis. As individual cancers exhibit unique mutation patterns, identifying and characterizing gene mutations in NSCLC might help predict patient outcomes and guide treatment. The aim of this study was to evaluate the clinical adequacy of molecular testing using next-generation sequencing (NGS) for small biopsy samples and characterize the mutational landscape of Korean patients with advanced NSCLC.

Methods

DNA was extracted from small biopsy samples of 162 patients with advanced NSCLC. Targeted NGS of genomic alterations was conducted using Ion AmpliSeq Cancer Hotspot Panel v2.

Results

The median age of patients was 64 years (range, 32 to 83 years) and the majority had stage IV NSCLC at the time of cancer diagnosis (90%). Among the 162 patients, 161 patients (99.4%) had novel or hotspot mutations (range, 1 to 21 mutated genes). Mutations were found in 41 genes. Three of the most frequently mutated genes were TP53 (151, 93.2%), KDR (104, 64.2%), and epidermal growth factor receptor (EGFR; 69, 42.6%). We also observed coexistence of EGFR and other oncogene (such as KRAS, PIC3CA, PTEN, and STK11) mutations. Given that 69.6% (48/69) of EGFR mutant patients were treated with EGFR tyrosine kinase inhibitors, EGFR mutant status had higher prognostic ability in this study.

Conclusions

These results suggest that targeted NGS using small biopsy samples is feasible and allows for the detection of both common and rare mutations in NSCLC.

Clinical mutational profiling of 1006 lung cancers by next generation sequencing

Analysis of lung adenocarcinomas for actionable mutations has become standard of care. Here, we report our experience using next generation sequencing (NGS) to examine AKT1, BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA genes in 1006 non-small cell lung cancers in a clinical diagnostic setting. NGS demonstrated high sensitivity. Among 760 mutations detected, the variant allele frequency (VAF) was 2-5% in 33 (4.3%) mutations and 2-10% in 101 (13%) mutations. A single bioinformatics pipeline using Torrent Variant Caller, however, missed a variety of EGFR mutations. Mutations were detected in KRAS (36% of tumors), EGFR (19%) including 8 (0.8%) within the extracellular domain (4 at codons 108 and 4 at codon 289), BRAF (6.3%), and PIK3CA (3.7%). With a broader reportable range, exon 19 deletion and p.L858R accounted for only 36% and 26% of EGFR mutations and p.V600E accounted for only 24% of BRAF mutations. NGS provided accurate sequencing of complex mutations seen in 19% of EGFR exon 19 deletion mutations. Doublet (compound) EGFR mutations were observed in 29 (16%) of 187 EGFR-mutated tumors, including 69% with two non-p.L858R missense mutations and 24% with p.L858 and non-p.L858R missense mutations. Concordant VAFs suggests doublet EGFR mutations were present in a dominant clone and cooperated in oncogenesis. Mutants with predicted impaired kinase, observed in 25% of BRAF-mutated tumors, were associated with a higher incidence of concomitant activating KRAS mutations. NGS demonstrates high analytic sensitivity, broad reportable range, quantitative VAF measurement, single molecule sequencing to resolve complex deletion mutations, and simultaneous detection of concomitant mutations.

Molecular Diagnostics for Precision Medicine in Colorectal Cancer: Current Status and Future Perspective

Precision medicine, a concept that has recently emerged and has been widely discussed, emphasizes tailoring medical care to individuals largely based on information acquired from molecular diagnostic testing. As a vital aspect of precision cancer medicine, targeted therapy has been proven to be efficacious and less toxic for cancer treatment. Colorectal cancer (CRC) is one of the most common cancers and among the leading causes for cancer related deaths in the United States and worldwide. By far, CRC has been one of the most successful examples in the field of precision cancer medicine, applying molecular tests to guide targeted therapy. In this review, we summarize the current guidelines for anti-EGFR therapy, revisit the roles of pathologists in an era of precision cancer medicine, demonstrate the transition from traditional “one test-one drug” assays to multiplex assays, especially by using next-generation sequencing platforms in the clinical diagnostic laboratories, and discuss the future perspectives of tumor heterogeneity associated with anti-EGFR resistance and immune checkpoint blockage therapy in CRC.