Concordance Of Genomic Alterations Research Articles

Concordance and Clinical Significance of Genomic Alterations in Progressive Tumor Tissue and Matched Circulating Tumor DNA in Aggressive-Variant Prostate Cancer.

Sequencing of ctDNA is a minimally invasive approach to reveal the genomic alterations of cancer, however, its comparison with sequencing of tumor tissue has not been well documented in real-world patients with aggressive-variant prostate cancer (AVPC). Concordance of genomic alterations was assessed between progressive tumor tissue and matched ctDNA by next-generation sequencing for 63 AVPC patients. Associations of genomic alterations with progression-free survival (PFS) and overall survival (OS) were investigated using Kaplan-Meier and Cox regression analyses. A total of 161 somatic mutations (SMs) and 84 copy number variants (CNVs) were detected in tumors, of which 97 were also found in ctDNA, giving concordance of 39.6% (97/245) across all SMs and CNVs, 49.7% for SMs only and 20.2% for CNVs only. Across all AVPC patients, chemotherapy was associated with significantly longer median PFS (6 vs. 0.75 mo., P=0.001) and OS (11 vs. 8 mo., P < 0.001) than next-generation hormonal therapy (NHT). Among types of chemotherapy, additional platinum-based chemotherapy was associated with significantly longer median PFS and OS than docetaxel only in patients with TP53, RB1 or PTEN alterations, and in those with ctDNA% ≥ 13.5%. The concordance analysis first provides evidence for combining the sequencing of ctDNA and tumor tissue in real-world AVPC patients. Chemotherapy is associated with significantly better survival than NHT, and the benefit of additional platinum-based chemotherapy may depend on the presence of alterations in TP53, RB1 or PTEN and on a sufficiently high proportion of ctDNA in AVPC patients.

Concordance of genomic alterations in anal cancer by next-generation sequencing in tissue and circulating tumor DNA.

2 Background: The feasibility of identifying genomic alterations via next-generation sequencing (NGS) of peripheral blood (PB) to spare patients an invasive biopsy is an active area of investigation. High concordance of mutations between tissue and PB has been observed in several cancer types. However, the concordance between tissue and PB in patients with SCCA is unknown. Methods: We identified 11 patients with SCCA who had NGS (TEMPUS) performed on tissue and PB between 2017 - 2022. The IRB at Vanderbilt-Ingram Cancer Center approved this study. Results: See Table. Conclusions: In 6 of the 11 patients, concordant genomic alterations found in tissue were also identified in PB. More patients with anal cancer should be studied to better understand this phenomenon and the impact of therapy on ctDNA kinetics.[Table: see text]

Concordance between the tumor mutational status and circulating tumor DNA in patients with colorectal cancer

Background. Circulating tumor DnA (ctDnA) may act as a potential biomarker for predicting disease progression in patients with colorectal cancer (CRC), which are radically cured or receiving chemotherapy.Objective: to evaluate the sensitivity of the investigated ctDnA detection assay and quantify the concordance of genomic alterations between ctDnA and matched primary tumor tissue of patients with CRC.Materials and methods. we included patients with histologically confirmed stage I–Iv CRC treated in n.n. Blokhin Cancer Research Center from 2016 to 2021. DnA was purified from tissue samples using QIAamp DnA formalin-fixed paraffin-embedded (ffPE) Tissue Kit (QIAgEn, germany). next-generation sequencing (ngS) technique was used to detect genetic mutations in primary tumor. ctDnA mutations were detected by droplet digital PCR.Results. The sensitivity of platform (assay) for detecting genetic alterations in tissue samples was 97.82 %; in ctDnA – 51.20 % for all stages and 64.5 % for stage Iv CRC. Across eight genes (KRAS, TP53, APC, PIK3CA, BRAF, FBXW7, MB21D2, and SMAD4) concordance between primary tumor and ctDnA was 69.4 % (95 % CI 62.2–76.0). Sensitivity for all stages is 51.2 % (95 % CI 45.8–56.6), for metastatic CRC 64.5 % (95 % CI 53.3–74.5). The concordance across all genes was 65.4 % (95 % CI 57.1–73.1) and 83.8 % (95 % CI 69.6–92.9) for stage I–III and stage Iv CRC, respectively. The concordance rate between ctDnA and primary tumor tissue for KRAS alterations across all stages and stage Iv CRC was 78.3 % (95 % CI 66.7–87.3) and 90.9 % (95 % CI 64.7–99.0), respectively. with increasing tumor stage (T), the number of matches raised across all genes with the highest number observed in nx category.Conclusion. The study indicates high concordance between tumor tissue and ctDnA, especially for KRAS and BRAF genes in patients with metastatic CRC, suggesting the clinical utility of ctDnA testing as a minimally invasive method and alternative to tissue biopsy.

Concordance of Genomic Alterations between Circulating Tumor DNA and Matched Tumor Tissue in Chinese Patients with Breast Cancer.

Purpose Circulating tumor DNA (ctDNA) served as a noninvasive method with less side effects using peripheral blood. Given the studies on concordance rate between liquid and solid biopsies in Chinese breast cancer (BC) patients were limited, we sought to examine the concordance rate of different kinds of genomic alterations between paired tissue biopsies and ctDNA samples in Chinese BC cohorts. Materials and Methods In this study, we analyzed the genomic alteration profiles of 81 solid BC samples and 41 liquid BC samples. The concordance across 136 genes was evaluated. Results The median mutation counts per sample in 41 ctDNA samples was higher than the median in 81 tissue samples (p=0.0254; Wilcoxon rank sum test). For mutation at the protein-coding level, 39.0% (16/41) samples had at least one concordant mutation in two biopsies. 20.0% tissue-derived mutations could be detected via ctDNA-based sequencing, whereas 11.7% ctDNA-derived mutations could be found in paired tissues. At gene amplification level, the overall concordant rate was 68.3% (28/41). The concordant rate at gene level for each patient ranged from 83.8% (114/136) to 99.3% (135/136). And, the mean level of variant allele frequency (VAF) for concordant mutations in ctDNA was statistically higher than that for the discordant ones (p < 0.001; Wilcoxon rank sum test). Across five representative genes, the overall sensitivity and specificity were 49.0% and 85.9%, respectively. Conclusion Our results indicated that ctDNA could provide complementary information on genetic characterizations in detecting single nucleotide variants (SNVs) and insertions and deletions (InDels).

Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Cell-Free DNA in Stage I–IV Non–Small Cell Lung Cancer

Molecular biomarkers hold promise for personalization of cancer treatment. However, a typical tumor biopsy may be difficult to acquire and may not capture genetic variations within or across tumors. Given these limitations, tumor genotyping using next-generation sequencing of plasma-derived circulating tumor (ct)-DNA has the potential to transform non-small cell lung cancer (NSCLC) management. Importantly, mutations detected in biopsied tissue must also be detected in plasma-derived ctDNA at different disease stages. Using the AVENIO ctDNA Surveillance kit (research use only), mutations in ctDNA from NSCLC subjects were compared with those identified in matched tumor tissue samples, retrospectively. Plasma and tissue samples were collected from 141 treatment-naïve NSCLC subjects (stage I, n=48; stage II, n=37; stage III, n=33; stage IV, n=23). In plasma samples, the median numbers of variants per subject were 4, 6, 8, and 9 in those with stage I, II, III, and IV disease, respectively. The corresponding values in tissue samples were 5, 5, 6, and 4. The overall tissue-plasma concordance of stage II through IV was 62.2% by AVENIO software call. On multivariate analysis, concordance was positively and significantly associated with tumor size and cancer stage. Next-generation sequencing-based analyses with the AVENIO ctDNA Surveillance kit could be an alternative approach to detecting genetic variations in plasma-derived ctDNA isolated from NSCLC subjects.

Abstract P5-11-05: Concordance of genomic alterations with targeted sequencing of circulating tumor DNA (ctDNA) and circulating tumor cells (CTC) in endocrine-resistant metastatic breast cancer

Abstract Background: Liquid biopsy has emerged as a valuable strategy for analyzing resistance biomarkers in advanced breast cancer. Differences in genomic alterations between CTC and cfDNA has been reported before and may reflect differences in the cell compartments of origin. Our aim was to determine the mutational concordance between CTC and cfDNA in luminal metastatic breast cancer (MBC) with different levels of endocrine resistance. Methods: We evaluated the mutational spectrum in matched cfDNA and CTC samples of 38 patients with luminal (hormone receptors [HR] positive, HER2 negative) MBC. Using QIAmp Circulating Nucleic Acid Kit, cfDNA was isolated from plasma samples (5 mL), and from CTC samples obtained from plasma (7.5 mL). CTC were isolated by Epcam-based immune-magnetic enrichment and confirmed with AdnaTest Breast Cancer Detect (Epcam, Muc1, HER2). Sequencing of both cfDNA and CTC was performed using the Oncoming Breast cfDNA Assay (150 hotspots, 10 genes). Limit of detection range was 0.01-0.15%, with 92.1% cases equal or less than 0.1%. Concordance between mutational profile of CTC and cfDNA was analyzed and correlated with endocrine resistance and patient characteristics. Results: Forty-seven patients with HR+ HER2- MBC were included, yielding enough cfDNA for analysis in 38 cases (80%), with isolation of CTC in 8 cases (16.7%). Rate of mutation detection in CTC was 87.5% (7/8), with TP53 mutations in all cases and no cases of ESR1 mutations; two cases of ERBB3 and PIK3CA mutations were found only in CTC, without a correlate in cfDNA. In cfDNA, genetic alterations were observed in 63.4% of cases, with 70.8% of TP53 mutations, 37.5% of PI3KCA mutations and 25% ESR1 mutations (2 D538G, 3 Y537S, 2 V392I). Average number of mutations was 2.28 in CTC and 1.96 in cfDNA, with a range of 1-4 in both cases. Concordance between cfDNA and CTC was low, with only 20% of CTC mutations simultaneously detected in cfDNA. CTC were only detected in cases with primary or secondary endocrine resistance. The percentage of patients with genetic alterations in cfDNA varied according to the degree of endocrine resistance (no resistance, 42.8%; secondary resistance, 65.2%; primary resistance, 75%), although the difference was not statistically significant. An association was found between the rate of detection of mutations in cfDNA and the response status (progression disease: 90.9%; stable disease: 57.1%; objective response: 33.3%) (p=0.04). Conclusions: The low rate of CTC detection in HR positive MBC may limit its utility for guiding therapeutic decisions. However, the information provided by CTC sequencing does not completely overlap with the data provided by cfDNA, and may be complementary to cfDNA in endocrine-resistant MBC. Citation Format: Ayala de la Peña F, Navarro Manzano E, Fernández Pérez MP, García Martínez E, de la Morena Barrio P, Ivars Rubio A, González Billalabeitia E, Fernández Sánchez A, Teruel Montoya R, Marín Zafra G. Concordance of genomic alterations with targeted sequencing of circulating tumor DNA (ctDNA) and circulating tumor cells (CTC) in endocrine-resistant metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-11-05.

Analysis of genomic alterations in matched circulating tumor cell DNA (CTC DNA) and plasma tumor DNA (ctDNA) in men with metastatic castration resistant prostate cancer (mCRPC).

5065Background: CTC and ctDNA-based, actionable genomic alterations are being increasingly utilized for precision oncology therapies. However, the concordance of genomic alterations in CTC DNA vs. ...

Concordance of genomic alterations (GA) in synchronous tumor biopsies (tBx) and circulating tumor (ct) DNA from metastatic breast cancer (MBC) patients (pts).

1073Background: Next generation sequencing (NGS) of tBx is the basis for precision medicine. Most tBx used for NGS are archival primary tumors, often acquired several years before starting matched ...

Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Circulating Tumor DNA in Breast Cancer.

While identifying genomic alterations in tumor tissue is the current gold-standard technique for molecular profiling, circulating tumor DNA (ctDNA) represents a noninvasive method of assessing genomic alterations using peripheral blood. The concordance of genomic alterations between two commercially available ctDNA and tissue biopsies was compared in 45 patients with breast cancer using paired next-generation sequencing tissue and ctDNA biopsies. Across all genes, concordance between the two platforms was 91.0% to 94.2%. When only considering genomic alterations in either assay (e.g., excluding wild type/wild type genes), concordance was 10.8% to 15.1% with full plus partial concordance of 13.8% to 19.3%. Concordant mutations were associated with significantly higher variant allele frequency. Over half of mutations detected in either technique were not detected using the other biopsy technique. Including variants of unknown significance, the average number of alterations per patient was significantly higher for tissue (4.56) compared with ctDNA (2.16). When eliminating alterations not detectable in the ctDNA assay, mean number of alterations for tissue and ctDNA was similar (2.67 for tissue, 2.16 for ctDNA). Across five representative genes (TP53, PIK3CA, ERBB2, BRCA1, and BRCA2), sensitivity and specificity were 35.7% and 95.0%, respectively. Concordance when genomic alterations was detected in either tissue or ctDNA was low with each technique detecting a significant amount of nonoverlapping mutations. Potential explanations for the lack of concordance include tumor heterogeneity, different sequencing techniques, spatial and temporal factors, and potential germline DNA contamination. The study indicates that both tissue and blood-based NGS may be necessary to describe the complex biology of breast cancer. Mol Cancer Ther; 16(7); 1412-20. ©2017 AACR.

Concordance between comprehensive cancer genome profiling in plasma and matched tumor specimens.

e23146 Background: The importance and clinical use of liquid biopsies to identify somatic, targetable alterations in the plasma of cancer patients is steadily increasing. However, their concordance with alterations identified in cancer specimens tested in routine diagnostics is not being monitored. In a cohort of non-squamous cell lung cancer patients, our aim was to systematically compare alterations found by a massively parallel sequencing liquid biopsy assay covering 39 cancer related genes (NEOliquid) with alterations identified by routine diagnostics in a certified central pathology laboratory. Methods: Routine Diagnostics: DNA mutational analysis was performed using cobas or Sanger-Sequencing. Rearrangements were identified using immunohistochemistry or FISH. NEOliquid assay: Cell-free DNA from plasma was subjected to hybrid-capture based next-generation sequencing to detect point mutations, small insertions and deletions, copy number alterations and genomic translocations in 39 clinically relevant genes in a single assay. To evaluate and compare the performance of liquid biopsies, we applied the NEOliquid tests on blood samples of 82 non-squamous NSCLC patients and correlated them with results of routine diagnostics of matched tissue samples. Results: Routine diagnostics for lung cancer related oncogenes (EGFR, ALK, ROS1, KRAS, BRAF) identified a total of 50 somatic alterations of which 37 were point mutations, 11 InDels and 2 gene fusions. NEOliquid analysis of the corresponding plasma sample revealed a total of 34 alterations, including 21 targetable driver alterations. Overall, the concordance of mutation calls between routine diagnostic testing and NEOliquid was 97.6%, with a sensitivity of &gt; 70% and a specificity of 100%. Importantly, NEOliquid identified additional clinically relevant genomic alterations, not covered by routine testing. Conclusions: We have shown high concordance of genomic alterations identified from liquid biopsies and tumor tissue specimens. The excellent specificity of actionable alterations identified by NEOliquid offers analytical performance for routine diagnostic use.

Abstract 3601A: Concordance of genomic alterations between primary and metastatic matched breast tumors

Abstract Cancer therapy exerts a strong selection pressure that shapes tumor evolution. Recent studies have demonstrated high rates of concordance (greater than 80%) between primary tumor and recurrences. The main objective of our study was to demonstrate the molecular evolution of breast cancer using next-generation sequencing (NGS) at initial diagnosis and after metastatic progression beyond at least 1 line of treatment. Methods: We conducted a retrospective analysis of tumors in patients with metastatic breast cancer (MBC). Breast cancer specimens from metastatic sites following at least 1 line of treatment were obtained and analyzed using NGS from an existing prospective molecular profiling study (NCT02416518). Eligible participants from this study had their archival primary tumor specimens obtained and analyzing using the same NGS techniques. Samples were analyzed using Foundation One NGS, evaluating 343 genomic alterations. Concordance of genomic alterations from initial diagnosis to disease progression after metastatic recurrence was the primary endpoint. This study population was from an integrated, community-based healthcare system, serving rural populations primarily in the Dakotas and Minnesota. Results: A total of 10 patients had evaluable primary tumors and matched metastatic specimens. For the 20 tumors evaluable for matched analysis, we found 126 unique gene alterations from the 343 genes assayed, of which 31 (24.6%) were actionable (defined as alterations with established or investigational therapeutics based on literature review). Each tumor had an average of 30.4 alterations (range 15-43) and 7 actionable alterations, (range 0-12). There was only 1 patient that had no actionable alteration in the primary or metastatic tumor. Taking the 10 individual patients into consideration, we found a concordance rate of 64% for all gene alterations and a 61.2% concordance rate for the actionable gene alterations between the two time points. The most common actionable alteration was the activating PIK3CA gene alteration, which had 100% concordance in the 6 patients that had the alteration. The other key actionable alterations with 100% concordance involved the AR, BRCA2, CCND1, CDKN2B, ERBB2, PTEN, and ROS1. Conclusion: Contrasting with prior studies, in our small sample there was moderate concordance of gene alterations between primary and metastatic tumor samples. Despite this, high concordance of key actionable alterations (PIK3CA, PTEN, CCND1, ERBB2) was maintained throughout the disease course. This suggests therapeutic potential early on in the disease course, as key actionable driver mutations are present at diagnosis and persist beyond metastatic disease progression. Citation Format: Anu G. Gaba, Steven F. Powell, Paul A. Thompson, Megan L. Landsverk, Chun-Hung Chan, Jennifer L. Weiss, Lora J. Black, James M. Ford. Concordance of genomic alterations between primary and metastatic matched breast tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3601A.

Abstract 5233: Concordance of genomic alterations by next generation sequencing (NGS) in tumor tissue vs. cell-free DNA

Abstract Introduction: Genomic analysis of circulating tumor cell-free DNA (cfDNA) represents a non-invasive method of assessing genomic alterations using peripheral blood. We compared the concordance between cfDNA and tissue biopsies across genomic alterations in 65 genes in this pilot retrospective study. Methods: 54 consecutive patients with cfDNA NGS testing (Guardant360) were identified. Of these, 28 had tissue DNA NGS testing (Foundation One). 65 genes were common to both assays. Concordance was defined as the absence or presence of the identical genomic sequencing alteration(s) in a single gene. The analysis included non-synonymous DNA mutations, rearrangements, and copy number variants regardless of clone percentage. Results: There were 14 lung cancers and 14 other advanced solid tumors. Including all alterations and variants of unknown significance (VUS), the average number of alterations per patient for tissue and cfDNA was 4.82 (SD 3.02) and 2.96 (SD 3.01), respectively. Concordance between the two assays was 91.9%. Among only genes with reported genomic alterations in either assay (n = 170), concordance was 12.4%. Concordance was similar when stratifying based on timeframe between biopsies (median time interval between assays; 89 days). 21.5% of alterations found in tissue were detected in cfDNA. 34.9% of alterations found in cfDNA were detected in tissue. Across the 5 most common genes, sensitivity and specificity were 40.0% and 94.2%, respectively (Table 1). Discussion: Concordance between tumor tissue and cfDNA NGS was 91.9%. The cfDNA assay had high specificity, but low sensitivity. In addition, more mutations were detected in tissue. Reasons for these findings may include different sequencing techniques, spatial and temporal factors, tumor heterogeneity, and inclusion of subclones. [AD and YC contributed equally.] Table 1: Diagnostic Accuracy across 5 Most Common Genes Tissue MutationsSensitivity (%)Specificity (%)PPV (%)NPV (%)Diagnostic Accuracy (%)cfDNA mutations(+)(-)TP53(+)82(-)8850.080.080.050.057.1EGFR(+)12(-)22333.392.033.392.085.7KRAS(+)41(-)22166.795.580.091.389.3APC(+)01(-)4230.095.80.085.282.1CDKN2A(+)10(-)52216.7100.0100.081.582.1Total positive146Total negative2197Total (positive + negative)3510340.094.270.082.280.4 PPV: positive predictive value NPV: negative predictive value Citation Format: Young Kwang Chae, Andrew A. Davis, Benedito A. Carneiro, Sunandana Chandra, Nisha Mohindra, Aparna Kalyan, Jason Kaplan, Maria Matsangou, Leonidas C. Platanias, Massimo Cristofanilli, Francis J. Giles. Concordance of genomic alterations by next generation sequencing (NGS) in tumor tissue vs. cell-free DNA. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5233.

Concordance of genomic alterations by next generation sequencing (NGS) in tumor tissue vs. cell-free DNA in advanced breast cancer.

11528Background: Cell-free DNA (cfDNA) is a non-invasive method of assessing mutations in the blood. This study compared the concordance between cfDNA and tissue biopsies across DNA genomic alterations in patients with advanced breast cancer (ABC). Methods: Forty-five patients with ABC who had both NGS testing with cfDNA (Guardant) and tissue DNA (Foundation One) for clinical management were included. 45-67 genes were common to both assays depending on when the assays were performed. Concordance was defined as the presence or absence of the identical genomic sequencing alteration(s) in a single gene. Results: Median time between assays was 3.3 months [range, 0-67 months]. Including all alterations and variants of unknown significance, the average number per patient for tissue and cfDNA was 4.50 (SD 2.96) and 1.98 (SD 2.13), respectively. Concordance between the two assays was 91.2%. Among only genes with reported genomic alterations in either assay (N=232), concordance was 10.3%. 15.0% of alterations foun...

Abstract PD3-6: ConvertHER: Evolution of genomic alterations from primary to metastatic breast cancer

Abstract Background: Changes in breast cancer receptor status over disease progression and treatment have been described to a point that could alter response to therapy. There is growing interest in delivering biomarker/genomically-based targeted therapies. We aimed to determine the concordance of genomic alterations between primary (P) and metastatic (M) breast cancer in a prospective collection study. Methods: Targeted capture and next-generation sequencing was performed on formalin-fixed paraffin-embedded (FFPE) samples, profiling 202 cancer relevant genes in 61 pairs (primary and corresponding recurrence/metastasis). Tumors were classified at baseline as [hormone receptor (HR)+/HER2-, HR+/HER2+, HER-/HER2+, and triple negative breast cancer (TNBC)]. We aligned data to human reference assembly hg19 using Burrows-Wheeler Aligner's (BWA) and removed duplicated reads. We identified somatic mutations variants and called copy number alterations (CNA) using an algorithm which reports gain or loss status of each exon. Alterations potentially targetable with established or investigational therapeutics were considered "actionable." Results: Of the 61 cases, 15% changed breast cancer subtype. Of 747 mutations detected in 156 genes, 309 (41%) were discordant. Median number of mutations were 10 (range 6-11) in P and 8 (range 6-10) in M. Most common mutations occurred at NOTCH2, PCLO, MAP3K1, MLL3, NOTCH4, CRIPAK, TP53, PIK3CACSMD1, and FLG. Mutations were less common in HR-/HER2+ tumors in both P and M. Mutation discordance was not different in cases of changed breast cancer subtype (P=.31). Of 986 CNA detected in 173 genes, 758 (77%) were discordant. There was an increased frequency of EGFR1, ERBB2, FGFR3, CRIPAK, MEN1 and WT1 amplifications in M. CNA were less common in HR-/HER2+ tumors in both P and M. CNA discordances were more common in cases of changed breast cancer subtype (P&amp;lt;.0001) and driven by HER2- tumors. Fifty-eight (95%) patients had actionable alterations that could inform targeted treatment options. Conclusion: Deep targeted exome sequencing of cancer-related genes revealed potentially targeted alterations. We found 41% and 77% mutation and CNA discordance between P and M. CNA were more common when breast cancer subtype changed. Citation Format: Ana Maria Gonzalez-Angulo, Ana Lluch, Agda K Eterovic, Angel Guerrero, Xiaofeng Zheng, Ramon Perez, Shuying Liu, José I Chacón, Ken Chen, Silvia Antolin, Gordon B Mills, Jaime Ferrer, Octavio Burgues, Begona Bermejo, Elia Munoz, Rosalia Caballero, Eva Carrasco, Eduardo Martinez, Funda Meric-Bernstam. ConvertHER: Evolution of genomic alterations from primary to metastatic breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD3-6.

Clinical next generation sequencing (NGS) of fine needle aspiration (FNA) biopsies in non-small cell lung (NSCLC) and pancreatic cancers.

11100 Background: FNA is a common diagnostic procedure for the evaluation of pulmonary and pancreatic masses. We sought to determine whether NGS could be performed on these small specimens and to characterize heterogeneity across classes of genomic alterations (GA) in a subset of paired FNA and matched resected primary tumors. Methods: DNA was isolated from formalin fixed paraffin embedded (FFPE) sections of FNA cell blocks using 40µm total sections for NSCLC and 20µm total sections for pancreatic cancers in a CLIA-certified lab (Foundation Medicine). DNA sequencing was performed for 3,320 exons of 182 cancer-related genes and 37 introns of 14 genes frequently rearranged in cancer on indexed, adaptor ligated, hybridization-captured libraries to a median depth of 931x for the NSCLC and 416x for the pancreatic FNAs. Results: Genomic profiles were successfully generated from 19/19 of the NSCLC and 22/23 of the pancreatic FNA cases. We found 97 GA in the 19 NSCLC FNAs (range 2-9, average 5.1 GA per patient). 68% of the patients had GA in TP53 and 21% in KRAS. Only 16% (3/19) patients did not exhibit an actionable alteration. We found 99 GA in the 23 pancreatic cancer FNAs (range 0-12, average 4.3 per patient). 74% of the patients had GA in KRAS. There was 94% concordance of GA found in 4 matched FNA and primary tumor pairs for the pancreatic cases. For the single discordance, manual inspection of the reads of the discordant allele indicated evidence of loss of heterozygosity. Conclusions: NGS can be reliably performed on small FNA samples processed into cell blocks, and the GA discovered significantly correlates with the GA found in matched primary tumors. This study demonstrates the feasibility of NGS in analyzing FNA samples and further broadens the spectrum of commonly encountered specimen types to which this approach can be successfully applied.