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Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer

Tumor mutational burden (TMB) has emerged as a predictive biomarker of response to immune checkpoint inhibitors. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Here we evaluate bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples. In CheckMate 026, TMB was retrospectively assessed in 312 patients with non-small cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne CDx™ assay. TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. Parameter variation can therefore impact TMB calculations, highlighting the need for standardization. Encouragingly, WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90) and differences could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms and centers is achievable.

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Please follow the directions posted in DATA SHARING RESEARCH REQUEST (p39 - https://fasttrack.bms.com/resource/HelpFile ) to request access for CA209-026 clinical trial data. We are committed to providing you with answers to your questions and concerns. Please contact us using the information below, and we will respond to your inquiry as quickly as possible. Technical Support Main Number: +1 844-439-5499 (US only) For Outside US, please see the “International BMS Help Desk Phone Number Guide” Main Email: hd-sci-apps@bms.com Purpose Use this job aid to submit a request for Data Sharing Research. This guide will take you through all of the tabs required to submit a request successfully. This submission guide is to request data collected by BMS from a previously completed BMS Sponsored Study. If this does not apply to your study, STOP HERE. Please navigate to the appropriate request submission guide for more information. 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The above image is just for informational purposes only All Data Access Requests for BMS Clinical Study data must come through this FastTrack Collaborative Data Sharing Process; including: * Requests for data as a part of an existing collaboration * Requests for access to data previously deposited in a third-party, controlled access database (e.g. EGA for Genomic Data) * Requests for data from any non-BMS entity as a part of the standard clinical trial transparency requirement

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001003661 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00002463866 fastq.gz 4.1 GB
EGAF00002463867 fastq.gz 4.0 GB
EGAF00002463868 fastq.gz 3.5 GB
EGAF00002463869 fastq.gz 3.4 GB
EGAF00002463870 fastq.gz 3.6 GB
EGAF00002463871 fastq.gz 3.7 GB
EGAF00002463872 fastq.gz 3.7 GB
EGAF00002463873 fastq.gz 3.6 GB
EGAF00002463874 fastq.gz 3.6 GB
EGAF00002463875 fastq.gz 3.9 GB
EGAF00002463876 fastq.gz 3.4 GB
EGAF00002463877 fastq.gz 3.4 GB
EGAF00002463878 fastq.gz 3.7 GB
EGAF00002463879 fastq.gz 3.9 GB
EGAF00002463880 fastq.gz 3.6 GB
EGAF00002463881 fastq.gz 3.7 GB
EGAF00002463882 fastq.gz 3.8 GB
EGAF00002463883 fastq.gz 3.9 GB
EGAF00002463884 fastq.gz 4.0 GB
EGAF00002463885 fastq.gz 4.2 GB
EGAF00002463886 fastq.gz 3.8 GB
EGAF00002463887 fastq.gz 3.9 GB
EGAF00002463888 fastq.gz 3.5 GB
EGAF00002463889 fastq.gz 3.6 GB
EGAF00002463890 fastq.gz 3.5 GB
EGAF00002463891 fastq.gz 3.4 GB
EGAF00002463892 fastq.gz 3.6 GB
EGAF00002463893 fastq.gz 3.6 GB
EGAF00002463894 fastq.gz 3.4 GB
EGAF00002463895 fastq.gz 3.5 GB
EGAF00002463896 fastq.gz 4.3 GB
EGAF00002463897 fastq.gz 4.2 GB
EGAF00002463898 fastq.gz 4.6 GB
EGAF00002463899 fastq.gz 4.9 GB
EGAF00002463900 fastq.gz 3.7 GB
EGAF00002463901 fastq.gz 4.0 GB
EGAF00002463902 fastq.gz 3.7 GB
EGAF00002463903 fastq.gz 3.8 GB
EGAF00002463904 fastq.gz 3.8 GB
EGAF00002463905 fastq.gz 3.9 GB
EGAF00002463906 fastq.gz 3.5 GB
EGAF00002463907 fastq.gz 3.4 GB
EGAF00002463908 fastq.gz 3.2 GB
EGAF00002463909 fastq.gz 3.2 GB
EGAF00002463910 fastq.gz 3.6 GB
EGAF00002463911 fastq.gz 3.6 GB
EGAF00002463912 fastq.gz 3.6 GB
EGAF00002463913 fastq.gz 3.6 GB
EGAF00002463914 fastq.gz 4.0 GB
EGAF00002463915 fastq.gz 4.3 GB
EGAF00002463916 fastq.gz 4.1 GB
EGAF00002463917 fastq.gz 4.2 GB
EGAF00002463918 fastq.gz 3.9 GB
EGAF00002463919 fastq.gz 4.3 GB
EGAF00002463920 fastq.gz 3.5 GB
EGAF00002463921 fastq.gz 3.6 GB
EGAF00002463922 fastq.gz 3.6 GB
EGAF00002463923 fastq.gz 3.8 GB
EGAF00002463924 fastq.gz 4.2 GB
EGAF00002463925 fastq.gz 4.4 GB
EGAF00002463926 fastq.gz 4.0 GB
EGAF00002463927 fastq.gz 4.0 GB
EGAF00002463928 fastq.gz 3.7 GB
EGAF00002463929 fastq.gz 3.8 GB
EGAF00002463930 fastq.gz 4.3 GB
EGAF00002463931 fastq.gz 4.4 GB
EGAF00002463932 fastq.gz 3.3 GB
EGAF00002463933 fastq.gz 3.4 GB
EGAF00002463934 fastq.gz 3.3 GB
EGAF00002463935 fastq.gz 3.6 GB
EGAF00002463936 fastq.gz 3.5 GB
EGAF00002463937 fastq.gz 3.7 GB
EGAF00002463938 fastq.gz 4.1 GB
EGAF00002463939 fastq.gz 4.1 GB
EGAF00002463940 fastq.gz 3.5 GB
EGAF00002463941 fastq.gz 3.8 GB
EGAF00002463942 fastq.gz 4.8 GB
EGAF00002463943 fastq.gz 5.0 GB
EGAF00002463944 fastq.gz 4.0 GB
EGAF00002463945 fastq.gz 4.2 GB
EGAF00002463946 fastq.gz 4.2 GB
EGAF00002463947 fastq.gz 4.1 GB
EGAF00002463948 fastq.gz 3.7 GB
EGAF00002463949 fastq.gz 3.7 GB
EGAF00002463950 fastq.gz 3.1 GB
EGAF00002463951 fastq.gz 3.4 GB
EGAF00002463952 fastq.gz 3.6 GB
EGAF00002463953 fastq.gz 4.0 GB
EGAF00002463954 fastq.gz 4.1 GB
EGAF00002463955 fastq.gz 4.3 GB
EGAF00002463956 fastq.gz 4.0 GB
EGAF00002463957 fastq.gz 3.9 GB
EGAF00002463958 fastq.gz 4.2 GB
EGAF00002463959 fastq.gz 4.4 GB
EGAF00002463960 fastq.gz 3.9 GB
EGAF00002463961 fastq.gz 4.1 GB
EGAF00002463962 fastq.gz 3.6 GB
EGAF00002463963 fastq.gz 3.8 GB
EGAF00002463964 fastq.gz 4.1 GB
EGAF00002463965 fastq.gz 4.0 GB
EGAF00002463966 fastq.gz 4.4 GB
EGAF00002463967 fastq.gz 4.5 GB
EGAF00002463968 fastq.gz 4.8 GB
EGAF00002463969 fastq.gz 5.0 GB
EGAF00002463970 fastq.gz 3.6 GB
EGAF00002463971 fastq.gz 3.9 GB
EGAF00002463972 fastq.gz 4.9 GB
EGAF00002463973 fastq.gz 5.1 GB
EGAF00002463974 fastq.gz 4.0 GB
EGAF00002463975 fastq.gz 4.3 GB
EGAF00002463976 fastq.gz 4.5 GB
EGAF00002463977 fastq.gz 4.6 GB
EGAF00002463978 fastq.gz 5.3 GB
EGAF00002463979 fastq.gz 5.6 GB
EGAF00002463980 fastq.gz 4.7 GB
EGAF00002463981 fastq.gz 5.0 GB
EGAF00002463982 fastq.gz 4.7 GB
EGAF00002463983 fastq.gz 4.9 GB
EGAF00002463984 fastq.gz 3.0 GB
EGAF00002463985 fastq.gz 3.2 GB
EGAF00002463986 fastq.gz 3.4 GB
EGAF00002463987 fastq.gz 3.6 GB
EGAF00002463988 fastq.gz 4.1 GB
EGAF00002463989 fastq.gz 4.3 GB
EGAF00002463990 fastq.gz 3.8 GB
EGAF00002463991 fastq.gz 4.0 GB
EGAF00002463992 fastq.gz 3.5 GB
EGAF00002463993 fastq.gz 3.8 GB
EGAF00002463994 fastq.gz 3.3 GB
EGAF00002463995 fastq.gz 3.5 GB
EGAF00002463996 fastq.gz 3.7 GB
EGAF00002463997 fastq.gz 3.8 GB
EGAF00002463998 fastq.gz 3.7 GB
EGAF00002463999 fastq.gz 3.9 GB
EGAF00002464000 fastq.gz 4.2 GB
EGAF00002464001 fastq.gz 4.4 GB
EGAF00002464002 fastq.gz 3.9 GB
EGAF00002464003 fastq.gz 4.1 GB
EGAF00002464004 fastq.gz 4.3 GB
EGAF00002464005 fastq.gz 4.6 GB
EGAF00002464006 fastq.gz 3.2 GB
EGAF00002464007 fastq.gz 3.4 GB
EGAF00002464008 fastq.gz 3.1 GB
EGAF00002464009 fastq.gz 3.3 GB
EGAF00002464010 fastq.gz 4.2 GB
EGAF00002464011 fastq.gz 4.4 GB
EGAF00002464012 fastq.gz 3.2 GB
EGAF00002464013 fastq.gz 3.4 GB
EGAF00002464014 fastq.gz 4.3 GB
EGAF00002464015 fastq.gz 4.7 GB
EGAF00002464016 fastq.gz 3.4 GB
EGAF00002464017 fastq.gz 3.8 GB
EGAF00002464018 fastq.gz 3.7 GB
EGAF00002464019 fastq.gz 4.0 GB
EGAF00002464020 fastq.gz 3.6 GB
EGAF00002464021 fastq.gz 3.6 GB
EGAF00002464022 fastq.gz 4.0 GB
EGAF00002464023 fastq.gz 4.3 GB
EGAF00002464024 fastq.gz 3.9 GB
EGAF00002464025 fastq.gz 4.1 GB
EGAF00002464026 fastq.gz 3.9 GB
EGAF00002464027 fastq.gz 3.8 GB
EGAF00002464028 fastq.gz 3.5 GB
EGAF00002464029 fastq.gz 3.6 GB
EGAF00002464030 fastq.gz 3.6 GB
EGAF00002464031 fastq.gz 3.7 GB
EGAF00002464032 fastq.gz 3.2 GB
EGAF00002464033 fastq.gz 3.4 GB
EGAF00002464034 fastq.gz 4.0 GB
EGAF00002464035 fastq.gz 3.9 GB
EGAF00002464036 fastq.gz 3.9 GB
EGAF00002464037 fastq.gz 3.8 GB
EGAF00002464038 fastq.gz 3.7 GB
EGAF00002464039 fastq.gz 3.7 GB
EGAF00002464040 fastq.gz 3.5 GB
EGAF00002464041 fastq.gz 3.5 GB
EGAF00002464042 fastq.gz 3.1 GB
EGAF00002464043 fastq.gz 3.1 GB
EGAF00002464044 fastq.gz 3.8 GB
EGAF00002464045 fastq.gz 3.9 GB
EGAF00002464046 fastq.gz 3.4 GB
EGAF00002464047 fastq.gz 3.6 GB
EGAF00002464048 fastq.gz 3.8 GB
EGAF00002464049 fastq.gz 3.8 GB
EGAF00002464050 fastq.gz 3.9 GB
EGAF00002464051 fastq.gz 4.2 GB
EGAF00002464052 fastq.gz 4.0 GB
EGAF00002464053 fastq.gz 4.1 GB
EGAF00002464054 fastq.gz 3.5 GB
EGAF00002464055 fastq.gz 3.8 GB
EGAF00002464056 fastq.gz 3.8 GB
EGAF00002464057 fastq.gz 3.9 GB
EGAF00002464058 fastq.gz 3.7 GB
EGAF00002464059 fastq.gz 4.0 GB
EGAF00002464060 fastq.gz 3.6 GB
EGAF00002464061 fastq.gz 3.6 GB
EGAF00002464062 fastq.gz 3.9 GB
EGAF00002464063 fastq.gz 4.2 GB
EGAF00002464064 fastq.gz 3.4 GB
EGAF00002464065 fastq.gz 3.6 GB
EGAF00002464066 fastq.gz 4.4 GB
EGAF00002464067 fastq.gz 4.5 GB
EGAF00002464068 fastq.gz 4.0 GB
EGAF00002464069 fastq.gz 3.9 GB
EGAF00002464070 fastq.gz 4.8 GB
EGAF00002464071 fastq.gz 4.7 GB
EGAF00002464072 fastq.gz 3.3 GB
EGAF00002464073 fastq.gz 3.5 GB
EGAF00002464074 fastq.gz 3.2 GB
EGAF00002464075 fastq.gz 3.4 GB
EGAF00002464076 fastq.gz 4.1 GB
EGAF00002464077 fastq.gz 4.4 GB
EGAF00002464078 fastq.gz 4.3 GB
EGAF00002464079 fastq.gz 4.4 GB
EGAF00002464080 fastq.gz 4.4 GB
EGAF00002464081 fastq.gz 4.7 GB
EGAF00002464082 fastq.gz 4.5 GB
EGAF00002464083 fastq.gz 4.6 GB
EGAF00002464084 fastq.gz 4.2 GB
EGAF00002464085 fastq.gz 4.5 GB
EGAF00002464086 fastq.gz 3.4 GB
EGAF00002464087 fastq.gz 3.7 GB
EGAF00002464088 fastq.gz 4.1 GB
EGAF00002464089 fastq.gz 4.0 GB
EGAF00002464090 fastq.gz 4.2 GB
EGAF00002464091 fastq.gz 4.5 GB
EGAF00002464092 fastq.gz 4.2 GB
EGAF00002464093 fastq.gz 4.5 GB
EGAF00002464094 fastq.gz 3.4 GB
EGAF00002464095 fastq.gz 3.4 GB
EGAF00002464096 fastq.gz 3.9 GB
EGAF00002464097 fastq.gz 4.0 GB
EGAF00002464098 fastq.gz 3.9 GB
EGAF00002464099 fastq.gz 3.8 GB
EGAF00002464100 fastq.gz 3.9 GB
EGAF00002464101 fastq.gz 3.9 GB
EGAF00002464102 fastq.gz 4.1 GB
EGAF00002464103 fastq.gz 4.0 GB
EGAF00002464104 fastq.gz 4.4 GB
EGAF00002464105 fastq.gz 4.3 GB
EGAF00002464106 fastq.gz 3.5 GB
EGAF00002464107 fastq.gz 3.8 GB
EGAF00002464108 fastq.gz 3.6 GB
EGAF00002464109 fastq.gz 3.6 GB
EGAF00002464110 fastq.gz 3.5 GB
EGAF00002464111 fastq.gz 3.7 GB
EGAF00002464112 fastq.gz 3.7 GB
EGAF00002464113 fastq.gz 4.0 GB
EGAF00002464114 fastq.gz 3.4 GB
EGAF00002464115 fastq.gz 3.6 GB
EGAF00002464116 fastq.gz 4.0 GB
EGAF00002464117 fastq.gz 4.2 GB
EGAF00002464118 fastq.gz 3.6 GB
EGAF00002464119 fastq.gz 3.8 GB
EGAF00002464120 fastq.gz 4.9 GB
EGAF00002464121 fastq.gz 5.1 GB
EGAF00002464122 fastq.gz 3.7 GB
EGAF00002464123 fastq.gz 3.7 GB
EGAF00002464124 fastq.gz 3.4 GB
EGAF00002464125 fastq.gz 3.7 GB
EGAF00002464126 fastq.gz 4.0 GB
EGAF00002464127 fastq.gz 3.9 GB
EGAF00002464128 fastq.gz 4.2 GB
EGAF00002464129 fastq.gz 4.5 GB
EGAF00002464130 fastq.gz 3.9 GB
EGAF00002464131 fastq.gz 4.1 GB
EGAF00002464132 fastq.gz 4.4 GB
EGAF00002464133 fastq.gz 4.6 GB
EGAF00002464134 fastq.gz 3.7 GB
EGAF00002464135 fastq.gz 3.9 GB
EGAF00002464136 fastq.gz 5.5 GB
EGAF00002464137 fastq.gz 5.7 GB
EGAF00002464138 fastq.gz 4.6 GB
EGAF00002464139 fastq.gz 4.6 GB
EGAF00002464140 fastq.gz 4.4 GB
EGAF00002464141 fastq.gz 4.5 GB
EGAF00002464142 fastq.gz 4.2 GB
EGAF00002464143 fastq.gz 4.3 GB
EGAF00002464144 fastq.gz 3.5 GB
EGAF00002464145 fastq.gz 3.7 GB
EGAF00002464146 fastq.gz 4.3 GB
EGAF00002464147 fastq.gz 4.6 GB
EGAF00002464148 fastq.gz 4.1 GB
EGAF00002464149 fastq.gz 4.3 GB
EGAF00002464150 fastq.gz 3.9 GB
EGAF00002464151 fastq.gz 4.1 GB
EGAF00002464152 fastq.gz 4.4 GB
EGAF00002464153 fastq.gz 4.4 GB
EGAF00002464154 fastq.gz 4.2 GB
EGAF00002464155 fastq.gz 4.4 GB
EGAF00002464156 fastq.gz 3.5 GB
EGAF00002464157 fastq.gz 3.8 GB
EGAF00002464158 fastq.gz 4.2 GB
EGAF00002464159 fastq.gz 4.2 GB
EGAF00002464160 fastq.gz 4.9 GB
EGAF00002464161 fastq.gz 4.9 GB
EGAF00002464162 fastq.gz 3.9 GB
EGAF00002464163 fastq.gz 4.2 GB
EGAF00002464164 fastq.gz 4.2 GB
EGAF00002464165 fastq.gz 4.4 GB
EGAF00002464166 fastq.gz 3.9 GB
EGAF00002464167 fastq.gz 4.2 GB
EGAF00002464168 fastq.gz 4.1 GB
EGAF00002464169 fastq.gz 4.3 GB
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EGAF00002464171 fastq.gz 4.4 GB
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736 Files (3.0 TB)