We provide consultation on all aspects of study design and sample collection. We also foster informal discussions of microbiome investigators from varied backgrounds to enhance research studies at MSKCC. Our interdisciplinary group ranges from immunologists, infectious disease experts, gastroenterologists, and bone-marrow transplant specialists to virologists and bioinformaticians.
We have a variety of methodologies adapted to extract and enrich for high-quality DNA/RNA of tough microbes (archaea, bacteria, yeast) commonly present in the human gut. We are specialized in techniques with bead-beating instrumentation and semi-automatic workflows adaptable to robotics for higher throughput.
We perform custom barcoded PCR amplification of the bacterial 16S ribosomal RNA (rRNA) gene sequences targeting the region V4-V5 with primers 515F-926R. Similarly, we also perform barcoded PCR amplification of the ITS gene sequences of fungal species. The MMF has the capacity of multiplexing hundreds of samples during library preparation facilitating high-throughput bulk sequencing and compatibility with bioinformatic computational analysis. Pool libraries will be sequenced as PE250 reads on MiSeq or NovaSeq Illumina platforms at IGO.
Depending on the depth of coverage desired and species of interest, we can perform library preparation for deep sequencing of full microbial genomes. Libraries can be sequenced as PE100 or PE150 at NovaSeq Illumina platforms at IGO.
We extensively vet sequencing data files to ensure high-quality data is delivered to the investigator. On a per-project basis we may be able to provide support during computational analysis. Please inquire via email to Ana Gradissimo at [email protected] .