Genomics

Dataset Information

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Ena-DATASET-MDACC-02-02-2018-10:54:47:473-560 - samples


ABSTRACT: The oral and gut microbiomes of melanoma patients were characterized before the initiation of ant-PD1 immunotherapy, and compared to treatment response. Validation studies were performed in germ-free mice using stool from patients who responded/did not respond to ant-PD1 immunotherapy. All baseline oral(n=86) and gut (n=43) microbiome samples were subject to 16S sequencing - V4 region ( merged fastq files have been made available through this portal). Whole genome shotgun sequencing (WGS) was performed on a subset of fecal samples (n=25)- these files are also available( paired end reads). Also available are 16S sequencing results of stool samples from donors (n=2) used in fecal microbiota transplant and murine samples (n=12) from germ-free mice transplanted with stool from responder/non-responder patients.

PROVIDER: EGAD00001003943 | EGA |

REPOSITORIES: EGA

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Publications

Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.

Gopalakrishnan V V   Spencer C N CN   Nezi L L   Reuben A A   Andrews M C MC   Karpinets T V TV   Prieto P A PA   Vicente D D   Hoffman K K   Wei S C SC   Cogdill A P AP   Zhao L L   Hudgens C W CW   Hutchinson D S DS   Manzo T T   Petaccia de Macedo M M   Cotechini T T   Kumar T T   Chen W S WS   Reddy S M SM   Szczepaniak Sloane R R   Galloway-Pena J J   Jiang H H   Chen P L PL   Shpall E J EJ   Rezvani K K   Alousi A M AM   Chemaly R F RF   Shelburne S S   Vence L M LM   Okhuysen P C PC   Jensen V B VB   Swennes A G AG   McAllister F F   Marcelo Riquelme Sanchez E E   Zhang Y Y   Le Chatelier E E   Zitvogel L L   Pons N N   Austin-Breneman J L JL   Haydu L E LE   Burton E M EM   Gardner J M JM   Sirmans E E   Hu J J   Lazar A J AJ   Tsujikawa T T   Diab A A   Tawbi H H   Glitza I C IC   Hwu W J WJ   Patel S P SP   Woodman S E SE   Amaria R N RN   Davies M A MA   Gershenwald J E JE   Hwu P P   Lee J E JE   Zhang J J   Coussens L M LM   Cooper Z A ZA   Futreal P A PA   Daniel C R CR   Ajami N J NJ   Petrosino J F JF   Tetzlaff M T MT   Sharma P P   Allison J P JP   Jenq R R RR   Wargo J A JA  

Science (New York, N.Y.) 20171102 6371


Preclinical mouse models suggest that the gut microbiome modulates tumor response to checkpoint blockade immunotherapy; however, this has not been well-characterized in human cancer patients. Here we examined the oral and gut microbiome of melanoma patients undergoing anti-programmed cell death 1 protein (PD-1) immunotherapy (<i>n</i> = 112). Significant differences were observed in the diversity and composition of the patient gut microbiome of responders versus nonresponders. Analysis of patien  ...[more]

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