01 Sequencing and Microarray Facility

University Of Tx Md Anderson Can Ctr, Houston TX

Investigators

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Abstract

PROJECT SUMMARY: THE SEQUENCING AND MICROARRAY FACILITY (SMF) The mission of the Sequencing and Microarray Facility (SMF) is to use state-of-the-art instrumentation and innovative technical expertise to provide investigators with the highest quality genomic data from a comprehensive range of genomic services, which include Illumina platform-based next-generation sequencing (NGS) services (whole genome, whole exome, RNA-Seq, ChIP-Seq, and single-cell analysis), Sanger- and Illumina-based gene resequencing, and microarray platforms (gene expression, microRNA, methylation, single- nucleotide polymorphism, and copy number analyses). For these services, the SMF innovates and develops customized protocols, as needed, to enable investigators to obtain reliable genomic data on specimens that are commonly found in cancer center tissue banks such as FFPE tissues, serum, plasma, and urine, the analytes from which are often of low quality and/or quantity. Demand for SMF's NGS service has increased 1374% over the prior grant cycle. The SMF director is Dr. Vicki Huff, co-directors are Drs. Sharon Dent and Nicholas Navin, and the Facility Manager is Ms. Erika Thompson. Instrumentation includes two NovaSeqs, a HighSeq4000, two HiSeq2000s, a NextSeq500, a MiSeq, two ABI 3730s, a digital droplet PCR System, a Fluidigm C1 Single-Cell Auto Prep and EVOS FL Auto Imaging Systems, a Nanostring nCounter MAX Analysis System, a 10X Genomics Chromium System, an Affymetrix Fluidics Station, and two robotic workstations (Agilent Bravo and Eppendorf epMotion 5075 TMX). Many of these were purchased using the $3,171,019 the institution has provided the SMF for equipment since 2013. One of the NovaSeq6000s was purchased with an NIH S10 HEI grant award. The SMF supported the research of 482 MD Anderson investigators, 361 of whom are CCSG program members representing all 16 CCSG programs. In the past grant cycle, SMF contributed to 649 publications, 78% of which were published in journals with IF >5 and 29% of which were published in journals with IF >10. Chargeback fees provided 93% of the SMF budget of $7,138,252. CCSG support was 6.8% ($486,766). Because 93% of the samples processed by the SMF were from peer-reviewed users, CCSG funds were well leveraged. In grant Yr44, the SMF is requesting $497,812 from the CCSG (estimated 6.6% of its budget). In the coming grant cycle, the SMF will continue to build on its record of providing cutting-edge genomic services to support high-impact science. Current plans include 1) continuing the development of specialized protocols and services, including immune profiling, single-cell copy number analysis, single-cell ATAC-Seq, and single- cell CRISPR sequencing, as well as phased exomes and whole genomes, accurate large structural variant identification, and digital spatial profiling, and 2) expanding SMF services to include enhanced data processing. With these measures, we will continue to provide investigators with the unique and exceptional genomic services they have come to expect from the SMF.