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1. Detection of Circulating Tumor DNA in Plasma: A Potential Biomarker for Esophageal Adenocarcinoma.

Author: Egyud M, Tejani M, Pennathur A, Luketich J, Sridhar P, Yamada E, Ståhlberg A, Filges S, Krzyzanowski P, Jackson J, Kalatskaya I, Jiao W, Nielsen G, Zhou Z, Litle V, Stein L, and Godfrey T
Subjects: Adenocarcinoma blood, Adenocarcinoma genetics, Biomarkers, Tumor blood, Biomarkers, Tumor genetics, Circulating Tumor DNA blood, Disease Progression, Esophageal Neoplasms blood, Esophageal Neoplasms genetics, Female, Humans, Liquid Biopsy, Male, Adenocarcinoma diagnosis, Circulating Tumor DNA genetics, DNA, Neoplasm genetics, Esophageal Neoplasms diagnosis, Mutation, Neoplasm Staging methods
Abstract: Background: Recent literature has demonstrated the potential of "liquid biopsy" and detection of circulating tumor (ct)DNA as a cancer biomarker. However, to date there is a lack of data specific to esophageal adenocarcinoma (EAC). This study was conducted to determine how detection and quantification of ctDNA changes with disease burden in patients with EAC and evaluate its potential as a biomarker in this population., Methods: Blood samples were obtained from patients with stage I to IV EAC. Longitudinal blood samples were collected from a subset of patients. Imaging studies and pathology reports were reviewed to determine disease course. Tumor samples were sequenced to identify mutations. Mutations in plasma DNA were detected using custom, barcoded, patient-specific sequencing libraries. Mutations in plasma were quantified, and associations with disease stage and response to therapy were explored., Results: Plasma samples from a final cohort of 38 patients were evaluated. Baseline plasma samples were ctDNA positive for 18 patients (47%) overall, with tumor allele frequencies ranging from 0.05% to 5.30%. Detection frequency of ctDNA and quantity of ctDNA increased with stage. Data from longitudinal samples indicate that ctDNA levels correlate with and precede evidence of response to therapy or recurrence., Conclusions: ctDNA can be detected in plasma of EAC patients and correlates with disease burden. Detection of ctDNA in early-stage EAC is challenging and may limit diagnostic applications. However, our data demonstrate the potential of ctDNA as a dynamic biomarker to monitor treatment response and disease recurrence in patients with EAC., (Copyright © 2019 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.)
Published: 2019
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2. Photodynamic therapy with curative intent for Barrett's esophagus with high grade dysplasia and superficial esophageal cancer.

Author: Keeley SB, Pennathur A, Gooding W, Landreneau RJ, Christie NA, and Luketich J
Subjects: Adenocarcinoma complications, Adenocarcinoma diagnostic imaging, Adenocarcinoma mortality, Adenocarcinoma pathology, Adult, Aged, Aged, 80 and over, Barrett Esophagus diagnostic imaging, Barrett Esophagus mortality, Barrett Esophagus pathology, Dihematoporphyrin Ether therapeutic use, Endoscopy, Digestive System, Endosonography, Esophageal Neoplasms complications, Esophageal Neoplasms diagnostic imaging, Esophageal Neoplasms mortality, Esophageal Neoplasms pathology, Female, Follow-Up Studies, Humans, Male, Middle Aged, Photochemotherapy adverse effects, Photochemotherapy mortality, Photosensitizing Agents therapeutic use, Survival Rate, Time Factors, Tomography, X-Ray Computed, Treatment Outcome, Adenocarcinoma drug therapy, Barrett Esophagus complications, Barrett Esophagus drug therapy, Esophageal Neoplasms drug therapy, Photochemotherapy methods
Abstract: Background: Photodynamic therapy (PDT) has been used to palliate advanced, obstructing, or bleeding esophageal cancers (ECs) and Barrett's high-grade dysplasia (HGD). Few investigators, though, have described using PDT to cure either disease., Methods: We performed a retrospective review from 1997-2005 of 50 patients with HGD or EC. All patients refused surgical resection or were physiologically unfit. They were instead treated using PDT with curative intent. Clinical follow-up, long-term survival, complications, and recurrence were evaluated., Results: Thirteen patients (26%) had Barrett's HGD, 6 (12%) had small, intramural carcinomas, 16 (32%) had T1 N0 tumors, 14 (28%) had T2 N0 tumors, and 1 (2%) had a small, polypoid T3 lesion. The mean length of follow-up was 28.1 months. Sixteen patients (32%) are alive without recurrence, 15 (30%) are living with residual or recurrent disease and have received additional PDT, and the remainder (38%) died of recurrent EC or other causes and had known recurrence. Sixteen (32%) patients received adjuvant chemotherapy, radiation, or both. Esophageal stricture occurred in 21 (42%) patients. There was no procedure-related mortality., Conclusions: PDT may represent a reasonable alternate to esophagectomy for high-risk patients with HGD or superficial esophageal cancer. Due to superior survival and local control, we still favor esophagectomy for patients without physiologic impairment. However, PDT appears to potentially cure approximately one-third of superficial esophageal cancers and provide local control of high-grade dysplasia in a similar subset of patients.
Published: 2007
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3. Endoscopic ultrasound compared with laparoscopy for staging esophageal cancer.

Author: Kaushik N, Khalid A, Brody D, Luketich J, and McGrath K
Subjects: Adenocarcinoma pathology, Aged, Esophageal Neoplasms pathology, Female, Humans, Lymphatic Metastasis, Male, Middle Aged, Neoplasm Staging, Retrospective Studies, Adenocarcinoma diagnostic imaging, Adenocarcinoma surgery, Endosonography, Esophageal Neoplasms diagnostic imaging, Esophageal Neoplasms surgery, Laparoscopy
Abstract: Background: Endoscopic ultrasonography (EUS) is an accurate modality for locoregional staging of esophageal cancer. Given an increasing prevalence of distal esophageal adenocarcinoma, some centers employ laparoscopic staging (LS) in addition to noninvasive staging methods. We sought to compare EUS and LS for nodal staging in patients with esophageal cancer., Methods: All newly diagnosed, EUS-staged esophageal cancer cases during an 18-month period were reviewed. Patients who underwent both EUS and LS comprised the study cohort; EUS records, operative notes, and pathology reports were reviewed. Inability to pass the radial echoendoscope through the malignant stricture despite dilation was considered an incomplete EUS examination., Results: Forty-seven patients were identified who underwent both modalities for staging; of these, 70% had complete EUS evaluation. For nodal staging, EUS-fine-needle aspiration was 90% accurate as compared with LS. Overall, staging accuracy of EUS compared with LS was 72%. Accuracy was 76% for patients with complete EUS staging compared with 64% for patients with incomplete EUS examinations. Staging differences were mostly reflected in distant metastases detected at LS (17%)., Conclusions: Endoscopic ultrasonography is nearly as accurate as LS in nodal staging for esophageal cancer. The value of LS is accurate abdominal nodal staging and detection of occult distant metastases. Laparoscopic staging should, therefore, be incorporated into staging algorithms for neoadjuvant protocols. In the absence of preoperative therapy, LS should be performed at the time of planned esophagectomy. In those without occult metastases, curative resection may be attempted.
Published: 2007
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4. Detection of unsuspected left hepatic lobe metastases during EUS staging of cancer of the esophagus and cardia.

Author: McGrath K, Brody D, Luketich J, and Khalid A
Subjects: Aged, Cardia diagnostic imaging, Esophageal Neoplasms diagnostic imaging, Female, Humans, Male, Stomach Neoplasms diagnostic imaging, Adenocarcinoma diagnostic imaging, Adenocarcinoma secondary, Carcinoma, Squamous Cell pathology, Carcinoma, Squamous Cell secondary, Cardia pathology, Endosonography, Esophageal Neoplasms pathology, Liver Neoplasms diagnostic imaging, Liver Neoplasms secondary, Neoplasm Staging methods, Stomach Neoplasms pathology
Abstract: Background: High resolution imaging of the left hepatic lobe can be obtained via endoscopic ultrasound (EUS), allowing for detection of unsuspected metastatic disease during cancer staging. The frequency at which occult liver metastases are detected during EUS staging of cancer of the esophagus and cardia is unknown., Methods: Over an 18-month period, 98 patients underwent EUS staging for a new diagnosis of cancer of the esophagus and cardia. Wire-guided dilation was performed if necessary. Standard radial examination was followed by curvilinear evaluation with attention to the left hepatic lobe. All suspicious liver lesions were aspirated under EUS guidance., Results: The radial and curvilinear echoendoscope were successfully passed to the antrum in 86% and 81% of cases, respectively, without complication. Thirty-two percent of patients required dilation. Lesions suspicious for left hepatic lobe metastases were found in 7% of cases that could be completely evaluated by EUS, all of which underwent EUS-guided fine needle aspiration. All lesions were proven metastases: four true-positive and one false-negative cytologic result., Conclusion: Curvilinear EUS examination of the left hepatic lobe in addition to standard radial EUS examination can be performed safely when staging cancer of the esophagus and cardia. Dedicated left hepatic lobe examination should be performed as it avoids unnecessary surgery in a subset of these patients by detection of occult liver metastases.
Published: 2006
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5. Correlation between dysplasia and mutations of six tumor suppressor genes in Barrett's esophagus.

Author: Raja S, Finkelstein SD, Baksh FK, Gooding WE, Swalsky PA, Godfrey TE, Buenaventura PO, and Luketich JD
Subjects: Adenocarcinoma pathology, Barrett Esophagus pathology, Cell Transformation, Neoplastic pathology, Esophageal Neoplasms pathology, Esophagus pathology, Genotype, Humans, Loss of Heterozygosity genetics, Polymerase Chain Reaction, Sequence Analysis, DNA, Adenocarcinoma genetics, Barrett Esophagus genetics, Cell Transformation, Neoplastic genetics, DNA Mutational Analysis, Esophageal Neoplasms genetics, Genes, Tumor Suppressor physiology
Abstract: Background: Barrett's esophagus (BE) may progress to adenocarcinoma through dysplastic progression. Classification of dysplasia in BE has significant interobserver variability. Our objective was to determine whether genetic alterations in BE correlate with degrees of histologic dysplasia., Methods: Fixed tissue from 37 patients with BE and adenocarcinoma was studied for six tumor suppressor genes. Tissues were microdissected and analyzed for loss of heterozygosity. Microdissection of individual crypts showing metaplasia and dysplasia were performed and analyzed for 23 of the 37 patients whose tumors were heterozygous for at least four of the six genes studied., Results: Frequency of alterations for MXI1, hOGG1, p53, MTS1, DCC, and APC were 7 of 32 (22%), 12 of 35 (34%), 12 of 26 (46%), 17 of 30 (57%), 17 of 27 (63%), and 23 of 36 (64%), respectively. Analysis of BE demonstrated that crypts with metaplasia, low-grade dysplasia, and high-grade dysplasia strongly correlated with alterations in tumor suppressor genes (p < 0.0001)., Conclusions: This pilot study demonstrates that genetic analysis can be performed on individual crypts in patients with BE, and that alterations may facilitate objective classification of the severity of dysplasia.
Published: 2001
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6. Topographic analysis of K- ras mutations in histologically normal lung tissues and tumours of lung cancer patients.

Author: Keohavong P, Mady HH, Gao WM, Siegfried JM, Luketich JD, and Melhem MF
Subjects: Adenocarcinoma pathology, Electrophoresis, Polyacrylamide Gel, Humans, Lung Neoplasms pathology, Polymerase Chain Reaction, Adenocarcinoma genetics, Genes, ras, Lung Neoplasms genetics, Mutation
Abstract: Mutations in the K- ras gene are very common in lung tumours and are implicated in the development of lung cancer, but the timing of their occurrence remains poorly understood. We investigated K- ras mutations in cell samples microdissected by laser capture microscopy at multiple sites from lung tissue sections representing tumour tissue and matched histologically normal tissue obtained from 48 lung cancer patients. K- ras mutations were detected in cell samples from 10 of 38 (26.3%) lung adenocarcinomas and in none of the histologically normal or tumour cell samples taken from 10 lung squamous cell carcinomas. Of the K- ras mutation-positive adenocarcinomas, in 4 cases a mutation was found in only the tumour tissue, in 1 case a mutation was found only in the histologically normal tissue, and in 5 cases mutations were found in both the tumour tissue and histologically normal tissue. Among these 5 cases, 2 had identical mutations in both the tumour tissue and histologically normal tissue, 2 had 1 mutation in the tumour tissue and 2 mutations in the histologically normal tissue, 1 of which was identical to the mutation found in the tumour, and 1 case had 2 codon 12 mutations in tumour tissue and 2 mutations, in codons 9 and 11, in histologically normal tissue. These results showed that K- ras mutations are frequent in histologically normal cells taken from outside lung adenocarcinomas and suggest that some of these mutations may represent early events which could pave the way of lung carcinogenesis.
Published: 2001
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7. CALGB 9380: a prospective trial of the feasibility of thoracoscopy/laparoscopy in staging esophageal cancer.

Author: Krasna MJ, Reed CE, Nedzwiecki D, Hollis DR, Luketich JD, DeCamp MM, Mayer RJ, and Sugarbaker DJ
Subjects: Adenocarcinoma surgery, Adult, Aged, Aged, 80 and over, Biopsy, Needle, Carcinoma, Squamous Cell diagnosis, Carcinoma, Squamous Cell surgery, Esophageal Neoplasms surgery, Esophagectomy, Esophagoscopy, Feasibility Studies, Female, Humans, Male, Middle Aged, North Carolina, Predictive Value of Tests, Prospective Studies, Sensitivity and Specificity, Adenocarcinoma pathology, Carcinoma, Squamous Cell pathology, Esophageal Neoplasms pathology, Laparoscopy methods, Neoplasm Staging methods, Thoracoscopy methods
Abstract: Background: The staging of esophageal cancer is imprecise. Thoracoscopic/laparoscopic (TS/LS) staging has been proposed as a more accurate lymph node (LN) staging method. We report the experience of an Intergroup NCI trial (CALGB 9380) evaluating the feasibility and accuracy of this staging modality., Patients and Methods: From February 1995 to September 1999, 134 patients were entered in the study. This study represents the analysis of final data on 113 patients. TS/LS was considered feasible if TS and 1 LN sampled at least 3 LN by LS; a confirmed positive node was found; or T4 or M1 disease was documented. If this was accomplished in more than 70% of patients, TS/LS was believed to be feasible., Results: The LN stations most frequently sampled in the thorax (134 patients) were levels 2 (33%), 3 (38%), 4 (40%), 7 (76%), 8 (69%), 9 (55%), and 10 (43%) and in the abdomen levels 17 (70%) and 20 (55%). The frequency of positive LN by level were as follows: 2 (10%), 3 (8%), 4 (10%), 7 (10%), 8 (25%), 9 (10%), 10 (10%), 17 (34%), and 20 (27%). Noninvasive tests (computed tomographic scan, magnetic resonance imaging, esophageal ultrasound scan) each incorrectly identified TN staging as noted by missed positive or false-negative LN or metastatic disease found at TS/LS staging in 50%, 40%, and 30% of patients, respectively. Median operating time was 210 minutes (range, 40 to 865 minutes). Median postoperative hospital stay was 3 days (range, 1 to 35 days). There were no deaths or major complications. Seventy-three percent of patients met the definition for feasibility. In 30 patients TS was not feasible. Positive LN disease was found in 43 patients; 32 were deemed N0. Ten patients had T4/M1 disease. Of the 32 potentially resectable N0 patients, 14 patients had preoperative induction therapy; 13 patients went directly to operation with N0 confirmed in 9 patients, NX in 1 and N1 in 3. Three patients were unresectable, 1 patient died, and 1 was lost to follow-up., Conclusions: In summary, the feasibility of TS/LS was confirmed. It doubled the number of positive LNs identified by conventional, noninvasive staging. The overall accuracy remains to be defined by analysis of the LN negative group in follow-up. Although the positive predictive value was high, further study is warranted to confirm the role of TS/LS in the staging algorithm of esophageal cancer.
Published: 2001
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8. Minimally invasive surgical staging for esophageal cancer.

Author: Luketich JD, Meehan M, Nguyen NT, Christie N, Weigel T, Yousem S, Keenan RJ, and Schauer PR
Subjects: Adult, Aged, Endosonography, Female, Humans, Male, Middle Aged, Minimally Invasive Surgical Procedures methods, Tomography, Emission-Computed methods, Tomography, X-Ray Computed, Video-Assisted Surgery methods, Adenocarcinoma pathology, Carcinoma, Squamous Cell pathology, Esophageal Neoplasms pathology, Neoplasm Staging methods
Abstract: Background: The incidence of esophageal adenocarcinoma is increasing in the United States, and the 5-year survival rate is dismal. Preliminary data suggest that conventional imaging is inaccurate in staging esophageal cancer and could limit accurate assessment of new treatments. The objective of this study was to compare minimally invasive surgical staging (MIS) with conventional imaging for staging esophageal cancer., Methods: Patients with potentially resectable esophageal cancer were eligible. Staging by conventional methods used computed tomography (CT) scan of the chest and abdomen, and endoscopic ultrasound (EUS), whereas MIS used laparoscopy and videothoracoscopy. Conventional staging results were compared to those from MIS., Results: In 53 patients, the following stages were assigned by CT scan and EUS: carcinoma in situ (CIS; n = 1), I (n = 1), II (n = 23), III (n = 20), IV (n = 8). In 17 patients (32.1%), MIS demonstrated inaccuracies in the conventional imaging, reassigning a lower stage in 10 patients and a more advanced stage in 7 patients., Conclusions: In 32.1% of patients with esophageal cancer, MIS changed the stage originally assigned by CT scan and EUS. Therefore, MIS should be applied to evaluate the accuracy of new noninvasive imaging methods and to assess new therapies for esophageal cancer.
Published: 2000
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9. Adenocarcinoma in a mid-esophageal diverticulum.

Author: Avisar E and Luketich JD
Subjects: Carcinoma, Squamous Cell diagnosis, Cell Transformation, Neoplastic pathology, Humans, Incidence, Male, Middle Aged, Neoplasm Staging, Adenocarcinoma pathology, Diverticulum, Esophageal pathology, Esophageal Neoplasms pathology
Abstract: The incidence of esophageal adenocarcinoma has been increasing compared with squamous cell carcinoma. The most common location of adenocarcinoma of the esophagus is the distal one third. Cancer developing in an esophageal diverticulum is uncommon, but tumors of squamous cell origin in esophageal diverticula have been reported previously. We describe an adenocarcinoma in a midesophageal diverticulum and review malignancies occurring in esophageal diverticula.
Published: 2000
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10. Evaluation of distant metastases in esophageal cancer: 100 consecutive positron emission tomography scans.

Author: Luketich JD, Friedman DM, Weigel TL, Meehan MA, Keenan RJ, Townsend DW, and Meltzer CC
Subjects: Adenocarcinoma diagnostic imaging, Adenocarcinoma pathology, Adenocarcinoma surgery, Adult, Aged, Aged, 80 and over, Esophageal Neoplasms pathology, Esophageal Neoplasms surgery, Female, Fluorodeoxyglucose F18, Humans, Male, Middle Aged, Minimally Invasive Surgical Procedures, Neoplasm Metastasis, Neoplasm Staging, Sensitivity and Specificity, Tomography, X-Ray Computed, Adenocarcinoma secondary, Esophageal Neoplasms diagnostic imaging, Tomography, Emission-Computed
Abstract: Background: Pilot studies suggest positron emission tomography (PET) scanning may be superior to conventional imaging in staging esophageal cancer, especially in the detection of radiographically occult distant metastases. This report summarizes our experience with PET in staging esophageal cancer., Methods: One hundred consecutive PET scans in 91 patients with esophageal cancer referred for surgery were prospectively collected (1995 to 1998) and compared with computerized tomography (CT) and bone scan. PET images were acquired after injection of 18F-fluorodeoxyglucose and evaluated for abnormal uptake. Minimally invasive surgical staging (MIS) and/or clinical correlation were used to confirm or refute imaging results., Results: MIS or clinical correlation confirmed 70 distant metastases in 39 cases. PET detected 51 metastases in 27 of 39 cases (69% sensitivity, 93.4% specificity, 84% accuracy) compared with CT, which detected 26 metastases in 18 of 39 cases (46.1% sensitivity, 73.8% specificity, 63% accuracy) (p < 0.01)., Conclusions: PET was more accurate than CT in detecting distant metastases, but was only 69% sensitive compared with minimally invasive staging.
Published: 1999
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11. Detection of occult lymph node metastases in esophageal cancer by minimally invasive staging combined with molecular diagnostic techniques.

Author: Kassis ES, Nguyen N, Shriver SP, Siegfried JM, Schauer PR, and Luketich JD
Subjects: Adenocarcinoma surgery, Base Sequence, Biopsy, Needle, Esophageal Neoplasms surgery, Female, Humans, Lymph Nodes pathology, Lymphatic Metastasis, Male, Minimally Invasive Surgical Procedures, Molecular Sequence Data, Neoplasm Staging, Polymerase Chain Reaction, Reference Values, Sensitivity and Specificity, Adenocarcinoma pathology, Adenocarcinoma secondary, Biomarkers, Tumor analysis, Carcinoembryonic Antigen analysis, Esophageal Neoplasms pathology, RNA, Messenger analysis, RNA, Neoplasm analysis
Abstract: Background and Objectives: Lymph node metastases are the most important prognostic factor in patients with esophageal cancer. Histologic examination misses micrometastases in up to 20% of lymph nodes evaluated. In addition, non-invasive imaging modalities are not sensitive enough to detect small lymph nodes metastases. The objective of this study was to investigate the use of reverse transcriptase-polymerase chain reaction (RT-PCR) of messenger RNA (mRNA) for carcinoembryonic antigen (CEA) to increase the detection of micrometastases in lymph nodes from patients with esophageal cancer., Methods: RT-PCR of CEA mRNA was performed in lymph nodes from patients with malignant and benign esophageal disease. Each specimen was examined histopathologically and by RT-PCR and the results were compared., Results: Metastases were present in 29 of 60 (48%) lymph nodes sample by minimally invasive staging from 13 patients with esophageal cancer when examined histopathologically. RT-PCR identified nodal metastases in 46 of these 60 (77%) samples. RT-PCR detected CEA mRNA in all 29 histologically positive samples and in 17 histologically negative lymph nodes. All lymph nodes from patients with benign disease (n = 15) were negative both histopathologically and by RT-PCR. The stage of two patients was reclassified based on the RT-PCR results, which identified lymph node spread undetected histopathologically. Both of these patients developed recurrent disease after resection of the primary tumor., Conclusions: RT-PCR is more sensitive than histologic examination in the detection of lymph node metastases in esophageal cancer and can lead to diagnosis of a more advanced stage in some patients. The combination of minimally invasive surgical techniques in combination with new molecular diagnostic techniques may improve our ability to stage cancer patients.
Published: 1998

12. Minimally invasive approach to esophagectomy.

Author: Luketich JD, Nguyen NT, Weigel T, Ferson P, Keenan R, and Schauer P
Subjects: Adenocarcinoma pathology, Aged, Aged, 80 and over, Barrett Esophagus pathology, Esophageal Neoplasms pathology, Esophagoscopy, Female, Humans, Male, Middle Aged, Minimally Invasive Surgical Procedures methods, Prognosis, Thoracoscopes, Thoracoscopy methods, Treatment Outcome, Video Recording, Adenocarcinoma surgery, Barrett Esophagus surgery, Esophageal Neoplasms surgery, Esophagectomy methods, Laparoscopy methods
Abstract: Background: Recent advances in laparoscopic and thoracoscopic surgery have made it possible to perform esophagectomy using minimally invasive techniques. The aim of this report was to present our preliminary experience with minimally invasive esophagectomy., Methods: We reviewed our experience on eight patients who underwent minimally invasive esophagectomy using either laparoscopic and/or thoracoscopic techniques from June 1996 to May 1997. Indications for esophagectomy included stage I carcinoma (5), palliative resection (1), Barrett's with high grade dysplasia (1) and end stage achalasia (1)., Results: The average age was 68 years (54-82). The surgical approach to esophagectomy included laparoscopic transhiatal esophagectomy with cervical anastomosis (n = 4), thoracoscopic and laparoscopic esophagectomy with cervical anastomosis (n = 1), and laparoscopic mobilization with right mini-thoracotomy and intra-thoracic anastomosis (n = 3). Conversion to mini-laparotomy was required in two patients (25%) to complete esophageal dissection and facilitate gastric pull-up. The mean operative time was 460 minutes. The mean intensive care stay was 1.9 days (range of 0-7 days) with a mean hospital stay of 13.8 days. Minor complications included atrial fibrillation (n = 1), pleural effusion (n = 2) and persistent air leak (n = 1). Major complications included cervical anastomotic leak (n = 1), and delayed gastric emptying requiring pyloroplasty (n = 1). There was no perioperative mortality., Conclusions: This preliminary experience suggests that minimally invasive esophagectomy is safe and feasible in centers with experience in advanced minimally invasive surgical procedures. Further studies are necessary to determine advantages over open esophagectomy.
Published: 1998

13. Minimally invasive surgical biopsy confirms PET findings in esophageal cancer.

Author: Luketich JD, Schauer P, Urso K, Townsend DW, Belani CP, Cidis Meltzer C, Ferson PF, and Keenan RJ
Subjects: Adenocarcinoma pathology, Adenocarcinoma secondary, Aged, Esophageal Neoplasms pathology, Fluorodeoxyglucose F18, Humans, Liver Neoplasms diagnostic imaging, Liver Neoplasms pathology, Liver Neoplasms secondary, Lumbar Vertebrae diagnostic imaging, Lumbar Vertebrae pathology, Lymphatic Metastasis diagnostic imaging, Lymphatic Metastasis pathology, Male, Middle Aged, Minimally Invasive Surgical Procedures, Neoplasm Staging, Radiopharmaceuticals, Sacroiliac Joint diagnostic imaging, Sacroiliac Joint pathology, Spinal Neoplasms diagnostic imaging, Spinal Neoplasms pathology, Spinal Neoplasms secondary, Adenocarcinoma diagnostic imaging, Biopsy methods, Esophageal Neoplasms diagnostic imaging, Laparoscopy, Tomography, Emission-Computed
Abstract: This report describes our initial experience using positron emission tomography (PET) scanning in esophageal cancer patients. In two patients PET identified distant metastatic disease missed by conventional staging. Laparoscopic biopsy provided histological confirmation of metastases. In the third patient, locoregional lymph nodes were identified by PET and confirmed by surgical staging. In this preliminary report, PET appears to be a promising new noninvasive modality for staging patients with esophageal cancer.
Published: 1997
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14. Minimally invasive surgical staging is superior to endoscopic ultrasound in detecting lymph node metastases in esophageal cancer.

Author: Luketich JD, Schauer P, Landreneau R, Nguyen N, Urso K, Ferson P, Keenan R, and Kim R
Subjects: Adenocarcinoma diagnostic imaging, Endosonography, Esophageal Neoplasms diagnostic imaging, Humans, Laparoscopy, Lymph Nodes pathology, Lymphatic Metastasis, Minimally Invasive Surgical Procedures, Neoplasm Staging, Prospective Studies, Sensitivity and Specificity, Thoracoscopy, Video Recording, Adenocarcinoma secondary, Esophageal Neoplasms pathology
Abstract: Objective: Endoscopic ultrasonography is frequently used to locally stage esophageal cancer, but few studies exist to validate its accuracy for lymph node metastases. Our objective was to compare endoscopic ultrasonography with video-assisted thoracoscopic and laparoscopic staging in evaluating lymph node metastases in esophageal cancer., Methods: Twenty-six patients with potentially resectable esophageal cancer were identified by conventional imaging. Endoscopic ultrasonography was performed followed by laparoscopic and thoracoscopic staging, and locoregional staging was compared., Results: In eight patients endoscopic ultrasonography indicated N0 disease, but laparoscopy and thoracoscopy documented N1 disease in six. In five of 26 (19%) obstruction prevented endoscopic ultrasonography; three had N1 by laparoscopy and thoracoscopy. Thirteen patients had N1 disease according to endoscopic ultrasonography, and 12 of 13 (92%) had N1 disease by laparoscopy and thoracoscopy. The sensitivity and specificity of endoscopic ultrasonography for nodal evaluation were 65% and 66%, respectively. Sensitivity decreased to 44% for lymph node metastases less than 1 cm. No instances of T4 disease were found by surgical staging when endoscopic ultrasonography indicated T3 disease. Endoscopic ultrasonography revealed no distant metastases in any patient, but in four of 26 (15%) laparoscopy identified liver metastases., Conclusions: The accuracy of endoscopic ultrasonography in the diagnosis of lymph node metastases in esophageal cancer was 65% and only 44% for lymph node metastases less than 1 cm diameter. Laparoscopy and thoracoscopy improved the accuracy of staging lymph node metastases in esophageal cancer and had the advantage of evaluating the thoracic and abdominal cavities for metastases.
Published: 1997
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15. Detection of low-fraction K-ras mutations in primary lung tumors using a sensitive method.

Author: Keohavong P, Zhu D, Melacrinos AC, DeMichele MA, Weyant RJ, Luketich JD, Testa JR, Fedder M, and Siegfried JM
Subjects: Aged, Electrophoresis, Female, Humans, Male, Middle Aged, Polymerase Chain Reaction, Sensitivity and Specificity, Adenocarcinoma genetics, Carcinoma, Adenosquamous genetics, Carcinoma, Squamous Cell genetics, Codon genetics, Genes, ras genetics, Lung Neoplasms genetics, Mutation genetics
Abstract: Mutations in the K-ras gene are often identified in lung tumors and are implicated in the development of lung cancer. We used a sensitive method to analyze low-fraction mutations occurring in codon 12 of the K-ras gene in 114 primary lung tumors, including 77 adenocarcinomas, 31 squamous cell carcinomas and 6 adenosquamous carcinomas, which had previously been shown to be negative for codon 12 K-ras mutation in a first screening using less sensitive methods. Sixteen of these tumors were found to contain a low-fraction mutation, including 9 mutations among the adenocarcinomas, six mutations among the squamous cell carcinomas and one mutation among the adenosquamous carcinomas. Our study also showed that the occurrence of low-fraction mutation was associated with a positive smoking history, as was previously found for the occurrence of high-fraction mutation. Patients with low-fraction mutations were younger (mean age 58.8 years) than those with either high-fraction mutations (63.2 years) or no mutation (66 years). Patients with low-fraction mutations were more often stage 1 (8 of 10) than patients with either high fraction mutations (22 of 44) or no mutation (33 of 71). Moreover, the overall survival was better for the group with a low-fraction mutation than both the high-fraction mutation group and the group with no K-ras mutation, but due to small sample size, the difference was not statistically significant. Our results suggest that using highly sensitive methods of K-ras mutant detection in tumor DNA could obscure differences between patients in whom the mutation is found throughout the tumor, those in whom the mutation is only present in a small subpopulation and those who have no mutation.
Published: 1997
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16. Worldwide Esophageal Cancer Collaboration: clinical staging data.

Author: Rice, T. W., Apperson-Hansen, C., DiPaola, L. M., Semple, M. E., Lerut, T. E. M. R., Orringer, M. B., Chen, L.-Q., Hofstetter, W. L., Smithers, B. M., Rusch, V. W., Wijnhoven, B. P. L., Chen, K. N., Davies, A. R., D'Journo, X. B., Kesler, K. A., Luketich, J. D., Ferguson, M. K., Räsänen, J. V., van Hillegersberg, R., and Fang, W.
Subjects: ESOPHAGEAL cancer, ESOPHAGECTOMY, DESCRIPTIVE statistics, CANCER patients, BODY mass index, ADENOCARCINOMA
Abstract: To address uncertainty of whether clinical stage groupings (cTNM) for esophageal cancer share prognostic implications with pathologic groupings after esophagectomy alone (pTNM), we report data-simple descriptions of patient characteristics, cancer categories, and non-risk-adjusted survival-for clinically staged patients from the Worldwide Esophageal Cancer Collaboration (WECC). Thirty-three institutions from six continents submitted data using variables with standard definitions: demographics, comorbidities, clinical cancer categories, and all-cause mortality from first management decision. Of 22,123 clinically staged patients, 8,156 had squamous cell carcinoma, 13,814 adenocarcinoma, 116 adenosquamous carcinoma, and 37 undifferentiated carcinoma. Patients were older (62 years) men (80%) with normal body mass index (18.5-25 mg/kg2, 47%), little weight loss (2.4 ± 7.8 kg), 0-1 ECOG performance status (67%), and history of smoking (67%). Cancers were cT1 (12%), cT2 (22%), cT3 (56%), cN0 (44%), cM0 (95%), and cG2-G3 (89%); most involved the distal esophagus (73%). Non-risk-adjusted survival for squamous cell carcinoma was not distinctive for early cT or cN; for adenocarcinoma, it was distinctive for early versus advanced cT and for cN0 versus cN+. Patients with early cancers had worse survival and those with advanced cancers better survival than expected from equivalent pathologic categories based on prior WECC pathologic data. Thus, clinical and pathologic categories do not share prognostic implications. This makes clinically based treatment decisions difficult and pre-treatment prognostication inaccurate. These data will be the basis for the 8th edition cancer staging manuals following risk adjustment for patient characteristics, cancer categories, and treatment characteristics and should direct 9th edition data collection. [ABSTRACT FROM AUTHOR]
Published: 2016
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17. Gastrointestinal Adenocarcinomas of the Esophagus, Stomach, and Colon Exhibit Distinct Patterns of Genome Instability and Oncogenesis

Author: Dulak, A. M., Schumacher, S. E., van Lieshout, J., Imamura, Y., Fox, Cameron, Shim, B., Ramos, A. H., Saksena, G., Baca, Sylvan, Baselga, J., Tabernero, J., Barretina, J., Enzinger, Peter, Corso, G., Roviello, F., Lin, Lin, Bandla, S., Luketich, J. D., Pennathur, A., Meyerson, Matthew, Ogino, Shuji, Shivdasani, Ramesh, Beer, Dennis, Godfrey, T. E., Beroukhim, Rameen, and Bass, Adam
Subjects: esophagus, stomach, colon, adenocarcinoma, copy-number
Abstract: A more detailed understanding of the somatic genetic events that drive gastrointestinal adenocarcinomas is necessary to improve diagnosis and therapy. Using data from high-density genomic profiling arrays, we conducted an analysis of somatic copy-number aberrations (SCNAs) in 486 gastrointestinal adenocarcinomas including 296 esophageal and gastric cancers. Focal amplifications were substantially more prevalent in gastric/esophageal adenocarcinomas than colorectal tumors. We identified 64 regions of significant recurrent amplification and deletion, some shared and others unique to the adenocarcinoma types examined. Amplified genes were noted in 37% of gastric/esophageal tumors, including in therapeutically targetable kinases such as ERBB2, FGFR1, FGFR2, EGFR, and MET, suggesting the potential utility of genomic amplifications as biomarkers to guide therapy of gastric and esophageal cancers where targeted therapeutics have been less developed compared to colorectal cancers. Amplified loci implicated genes with known involvement in carcinogenesis but also pointed to regions harboring potentially novel cancer genes, including a recurrent deletion found in 15% of esophageal tumors where the Runt transcription factor subunit RUNX1 was implicated, including by functional experiments in tissue culture. Together, our results defined genomic features that were common and distinct to various gut-derived adenocarcinomas, potentially informing novel opportunities for targeted therapeutic interventions., Accepted Manuscript
Published: 2012
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18. Comprehensive Characterization of Cancer Driver Genes and Mutations

Author: Matthew H. Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C. Wendl, Jaegil Kim, Brendan Reardon, Patrick Kwok-Shing Ng, Kang Jin Jeong, Song Cao, Zixing Wang, Jianjiong Gao, Qingsong Gao, Fang Wang, Eric Minwei Liu, Loris Mularoni, Carlota Rubio-Perez, Niranjan Nagarajan, Isidro Cortés-Ciriano, Daniel Cui Zhou, Wen-Wei Liang, Julian M. Hess, Venkata D. Yellapantula, David Tamborero, Abel Gonzalez-Perez, Chayaporn Suphavilai, Jia Yu Ko, Ekta Khurana, Peter J. Park, Eliezer M. Van Allen, Han Liang, Michael S. Lawrence, Adam Godzik, Nuria Lopez-Bigas, Josh Stuart, David Wheeler, Gad Getz, Ken Chen, Alexander J. Lazar, Gordon B. Mills, Rachel Karchin, Li Ding, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, David I. Heiman, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Shiyun Ling, Wenbin Liu, Yiling Lu, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. Aredes, Armaz Mariamidze, Bailey M.H., Tokheim C., Porta-Pardo E., Sengupta S., Bertrand D., Weerasinghe A., Colaprico A., Wendl M.C., Kim J., Reardon B., Ng P.K.-S., Jeong K.J., Cao S., Wang Z., Gao J., Gao Q., Wang F., Liu E.M., Mularoni L., Rubio-Perez C., Nagarajan N., Cortes-Ciriano I., Zhou D.C., Liang W.-W., Hess J.M., Yellapantula V.D., Tamborero D., Gonzalez-Perez A., Suphavilai C., Ko J.Y., Khurana E., Park P.J., Van Allen E.M., Liang H., Caesar-Johnson S.J., Demchok J.A., Felau I., Kasapi M., Ferguson M.L., Hutter C.M., Sofia H.J., Tarnuzzer R., Yang L., Zenklusen J.C., Zhang J.J., Chudamani S., Liu J., Lolla L., Naresh R., Pihl T., Sun Q., Wan Y., Wu Y., Cho J., DeFreitas T., Frazer S., Gehlenborg N., Getz G., Heiman D.I., Lawrence M.S., Lin P., Meier S., Noble M.S., Saksena G., Voet D., Zhang H., Bernard B., Chambwe N., Dhankani V., Knijnenburg T., Kramer R., Leinonen K., Liu Y., Miller M., Reynolds S., Shmulevich I., Thorsson V., Zhang W., Akbani R., Broom B.M., Hegde 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Thompson E., Yena P., Bowen J., Gastier-Foster J.M., Gerken M., Leraas K.M., Lichtenberg T.M., Ramirez N.C., Wise L., Zmuda E., Corcoran N., Costello T., Hovens C., Carvalho A.L., de Carvalho A.C., Fregnani J.H., Longatto-Filho A., Reis R.M., Scapulatempo-Neto C., Silveira H.C.S., Vidal D.O., Burnette A., Eschbacher J., Hermes B., Noss A., Singh R., Anderson M.L., Castro P.D., Ittmann M., Huntsman D., Kohl B., Le X., Thorp R., Andry C., Duffy E.R., Lyadov V., Paklina O., Setdikova G., Shabunin A., Tavobilov M., McPherson C., Warnick R., Berkowitz R., Cramer D., Feltmate C., Horowitz N., Kibel A., Muto M., Raut C.P., Malykh A., Barnholtz-Sloan J.S., Barrett W., Devine K., Fulop J., Ostrom Q.T., Shimmel K., Wolinsky Y., Sloan A.E., De Rose A., Giuliante F., Goodman M., Karlan B.Y., Hagedorn C.H., Eckman J., Harr J., Myers J., Tucker K., Zach L.A., Deyarmin B., Hu H., Kvecher L., Larson C., Mural R.J., Somiari S., Vicha A., Zelinka T., Bennett J., Iacocca M., Rabeno B., Swanson P., Latour 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Scarpace L., Girard N., Aymerich M., Campo E., Gine E., Guillermo A.L., Van Bang N., Hanh P.T., Phu B.D., Tang Y., Colman H., Evason K., Dottino P.R., Martignetti J.A., Gabra H., Juhl H., Akeredolu T., Stepa S., Hoon D., Ahn K., Kang K.J., Beuschlein F., Breggia A., Birrer M., Bell D., Borad M., Bryce A.H., Castle E., Chandan V., Cheville J., Copland J.A., Farnell M., Flotte T., Giama N., Ho T., Kendrick M., Kocher J.-P., Kopp K., Moser C., Nagorney D., O'Brien D., O'Neill B.P., Patel T., Petersen G., Que F., Rivera M., Roberts L., Smallridge R., Smyrk T., Stanton M., Thompson R.H., Torbenson M., Yang J.D., Zhang L., Brimo F., Ajani J.A., Gonzalez A.M.A., Behrens C., Bondaruk J., Broaddus R., Czerniak B., Esmaeli B., Fujimoto J., Gershenwald J., Guo C., Lazar A.J., Logothetis C., Meric-Bernstam F., Moran C., Ramondetta L., Rice D., Sood A., Tamboli P., Thompson T., Troncoso P., Tsao A., Wistuba I., Carter C., Haydu L., Hersey P., Jakrot V., Kakavand H., Kefford R., Lee K., Long G., 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K., Fehrenbach A., Kendler A., Sifri S., Steele R., Jimeno A., Carey F., Forgie I., Mannelli M., Carney M., Hernandez B., Campos B., Herold-Mende C., Jungk C., Unterberg A., von Deimling A., Bossler A., Galbraith J., Jacobus L., Knudson M., Knutson T., Ma D., Milhem M., Sigmund R., Godwin A.K., Madan R., Rosenthal H.G., Adebamowo C., Adebamowo S.N., Boussioutas A., Beer D., Giordano T., Mes-Masson A.-M., Saad F., Bocklage T., Landrum L., Mannel R., Moore K., Moxley K., Postier R., Walker J., Zuna R., Feldman M., Valdivieso F., Dhir R., Luketich J., Pinero E.M.M., Quintero-Aguilo M., Carlotti C.G., Dos Santos J.S., Kemp R., Sankarankuty A., Tirapelli D., Catto J., Agnew K., Swisher E., Creaney J., Robinson B., Shelley C.S., Godwin E.M., Kendall S., Shipman C., Bradford C., Carey T., Haddad A., Moyer J., Peterson L., Prince M., Rozek L., Wolf G., Bowman R., Fong K.M., Yang I., Korst R., Rathmell W.K., Fantacone-Campbell J.L., Hooke J.A., Kovatich A.J., Shriver C.D., DiPersio J., Drake B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., Godzik A., Lopez-Bigas N., Stuart J., Wheeler D., Chen K., and Karchin R.
Subjects: 0301 basic medicine, Oncology, Entropy, Programmed Cell Death 1 Receptor, biochemistry, genetics, molecular Biology (all), Biochemistry, B7-H1 Antigen, structure analysi, Principal Component Analysi, Neoplasms, Databases, Genetic, LS2_1, LS4_6, Missense mutation, Statistical analysis, 610 Medicine & health, Exome sequencing, Confusion, Principal Component Analysis, Melanoma, Sciences bio-médicales et agricoles, structure analysis, Algorithm, oncology, Cancer gene, Adenocarcinoma, Microsatellite Instability, ALGORITMOS, medicine.symptom, Algorithms, Human, medicine.medical_specialty, driver gene discovery, Computational biology, Biology, Characterization (mathematics), General Biochemistry, Genetics and Molecular Biology, Article, NO, 03 medical and health sciences, Internal medicine, medicine, Humans, mutations of clinical relevance, Gene, Biochemistry, Genetics and Molecular Biology(all), Microsatellite instability, Computational Biology, Cancer, medicine.disease, Cancérologie, 030104 developmental biology, Precision oncology, Mutation, Neoplasm, Human genome, Colon adenocarcinoma, human activities, Genetics and Molecular Biology(all)
Abstract: Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%–85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors. A comprehensive analysis of oncogenic driver genes and mutations in >9,000 tumors across 33 cancer types highlights the prevalence of clinically actionable cancer driver events in TCGA tumor samples., 0, info:eu-repo/semantics/published
Published: 2018
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19. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

Author: Yang Liu, Nilay S. Sethi, Toshinori Hinoue, Barbara G. Schneider, Andrew D. Cherniack, Francisco Sanchez-Vega, Jose A. Seoane, Farshad Farshidfar, Reanne Bowlby, Mirazul Islam, Jaegil Kim, Walid Chatila, Rehan Akbani, Rupa S. Kanchi, Charles S. Rabkin, Joseph E. Willis, Kenneth K. Wang, Shannon J. McCall, Lopa Mishra, Akinyemi I. Ojesina, Susan Bullman, Chandra Sekhar Pedamallu, Alexander J. Lazar, Ryo Sakai, Vésteinn Thorsson, Adam J. Bass, Peter W. Laird, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Inode Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. 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C., Jungk C., Unterberg A., von Deimling A., Bossler A., Galbraith J., Jacobus L., Knudson M., Knutson T., Ma D., Milhem M., Sigmund R., Godwin A.K., Madan R., Rosenthal H.G., Adebamowo C., Adebamowo S.N., Boussioutas A., Beer D., Giordano T., Mes-Masson A.-M., Saad F., Bocklage T., Landrum L., Mannel R., Moore K., Moxley K., Postier R., Walker J., Zuna R., Feldman M., Valdivieso F., Dhir R., Luketich J., Pinero E.M.M., Quintero-Aguilo M., Carlotti C.G., Dos Santos J.S., Kemp R., Sankarankuty A., Tirapelli D., Catto J., Agnew K., Swisher E., Creaney J., Robinson B., Shelley C.S., Godwin E.M., Kendall S., Shipman C., Bradford C., Carey T., Haddad A., Moyer J., Peterson L., Prince M., Rozek L., Wolf G., Bowman R., Fong K.M., Yang I., Korst R., Rathmell W.K., Fantacone-Campbell J.L., Hooke J.A., Kovatich A.J., Shriver C.D., DiPersio J., Drake B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., and Bass A.J.
Subjects: 0301 basic medicine, Male, Cancer Research, Colorectal cancer, MICROSATELLITE INSTABILITY, Cancer Genome Atlas Research Network, medicine.disease_cause, Heterogeneous-Nuclear Ribonucleoproteins, COLORECTAL-CANCER, Epigenesis, Genetic, genomic, Chromosome instability, LS2_1, LS4_6, rectum, Gene Regulatory Networks, 610 Medicine & health, Poly-ADP-Ribose Binding Proteins, Poly-ADP-Ribose Binding Protein, Gastrointestinal Neoplasms, colorectal, Gene Regulatory Network, NEOPLASIAS GASTROINTESTINAIS, RNA-Binding Proteins, SOX9 Transcription Factor, DNA-Binding Proteins, GENOME, Oncology, Gastrointestinal Neoplasm, DNA methylation, Adenocarcinoma, Female, KRAS, NK CELLS, MutL Protein Homolog 1, Life Sciences & Biomedicine, STEM-CELLS, epigenetic, stomach, Human, tumor, esophagu, cancer, colon, esophagus, methylation, Biology, MLH1, Polymorphism, Single Nucleotide, Article, NO, Proto-Oncogene Proteins p21(ras), 03 medical and health sciences, Chromosomal Instability, medicine, Humans, 1112 Oncology and Carcinogenesis, Oncology & Carcinogenesis, Science & Technology, CpG Island Methylator Phenotype, MUTATIONS, HUMAN-CELLS, Microsatellite instability, DNA, DNA Polymerase II, Cell Biology, DNA Methylation, medicine.disease, Aneuploidy, digestive system diseases, 030104 developmental biology, Mutation, Cancer research, Heterogeneous-Nuclear Ribonucleoprotein, GENERATION SEQUENCING DATA, 1109 Neurosciences, GASTRIC-CANCER
Abstract: We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and comprised those enriched for insertions/deletions, representing microsatellite instability cases with epigenetic silencing of MLH1 in the context of CpG island methylator phenotype, plus tumors with elevated single-nucleotide variants associated with mutations in POLE. Tumors with chromosomal instability were diverse, with gastroesophageal adenocarcinomas harboring fragmented genomes associated with genomic doubling and distinct mutational signatures. We identified a group of tumors in the colon and rectum lacking hypermutation and aneuploidy termed genome stable and enriched in DNA hypermethylation and mutations in KRAS, SOX9, and PCBP1. Liu et al. analyze 921 gastrointestinal (GI) tract adenocarcinomas and find that hypermutated tumors are enriched for insertions/deletions, upper GI tumors with chromosomal instability harbor fragmented genomes, and a group of genome-stable colorectal tumors are enriched in mutations in SOX9 and PCBP1.
Published: 2018
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