Laboratory Capabilities and Resources

Capabilities:  The Institute of Population and Precision Health (IPPH) lab has standardized protocols and workflows for sample collection, transportation, initial sample processing, storage and bio-banking and a range of molecular genomics and proteomics related assays.

Initial sample processing: Includes but not limited to separation of plasma/serum, cell separation including peripheral blood mononuclear cells (PBMC) and granulocytes and make appropriate aliquots.

 DNA extraction: High throughput extraction from different sources including whole blood, blood cells (PBMC, granulocytes), cf-DNA, tumor and normal tissue from fresh frozen and formalin fixed paraffin embedded (FFPE) blocks. QC is done using appropriate technology like Nanodrop (ND), Quantas, Agilent BioAnalyzer and qPCR.

RNA extraction: High throughput extraction from different sources including whole blood, PBMC, tumor and normal tissue from fresh frozen, RNA Later-preserved, and formalin fixed paraffin embedded (FFPE) blocks. QC is done using appropriate technology like Nanodrop (ND), Quantas, Agilent BioAnalyzer and qPCR.

DNA based assays: PCR, Real-Time qPCR, High Resolution melt (HRM) for microsatellite instability (MSI), low throughput (by qPCR) to genome-wide ultra-high throughput genotyping using different microarray platform, genome-wide DNA methylation using microarray-based ultra-high density infinium chips, targeted DNA sequencing using next generation sequencing (NGS) platform – MiSeq, somatic mutation detection using deep sequencing in MiSeq  exome and whole genome sequencing using NGS. The lab has generated high quality genome-wide SNP genotype data from more than sixteen thousand DNA samples with different microarray chips including Affymetrix 10K, 100 K, Illumina 610Quad, Cyto12, Exome chip, MultiEthnic 850K, custom designed CHICAGO MEGA etc. For genome-wide methylation, the lab has generated data from two thousand samples using different chips including 27 K, 450K and EPIC arrays.

Next Generation Sequencing (NGS): Targeted DNA sequencing is done from six thousand samples.

RNA based assays: Candidate based gene expression study using qPCR, genome wide gene expression using microarray platform, targeted gene expression on NGS using MiSeq and transcriptome-wide sequencing on HiSeq.

Protein based assays: Simultaneous detection of multiple analytes like cytokines, auto-antibodies, different cardiac and metabolic biomarkers in different body fluids using multiplex Luminex platform.

Telomere assay: Our lab has developed a novel cost-effective highthroughput assay for Relative Telomere Length (RTL) measurement from DNA using probe-based Luminex assay that does not need DNA amplification by PCR. The assay has been used in a number of large-scale epidemiological studies including HEALS and GTEx to determine RTL in more than ten thousand samples.

Facilities: The IPPH lab is located on the sixth floor of the KCBD building. The lab space includes 2646 sq-ft of core laboratory space, 385 sq-ft of space for a sample repository and other storage area, and 780 sq-ft of contiguous office space, all on the same floor. Currently the lab has six full-time staffs.

Major Equipment: The laboratory has modern infrastructure and equipment including four refrigerated centrifuges, four nonrefrigerated centrifuges, five thermolyclers, one Real-time q-PCR machine (BioRad ), Agilent BioAnalyzer , NanoDrop 1000, NanoDrop 8000, Quantas fluorometer, PE counter, two barcode printers, Illumina scanner with auto-loader, two TeCan Evo robots for automated liquid handling, hybridization ovens, NGS MiSeq instrument and Luminex 200 platform and other standard equipments for molecular genomics laboratory.

The laboratory also has access to Applied Biosystems 7900HT real-time PCR system, Sanger sequencing, iScan, HiSeq in the core facility in the same building.

Computer:  The laboratory is equipped with 13 personal computers, network printers, barcode printer and a powerful Filesever (Dell PowerEdge 2900, Quad Core Intel Xeon 2.66GHz, 8GB RAM) connected to multiple Disk Storage Arrays (RAID) with 85 TB usable disk via two Dell PowerVault MD1000, Dell PowerVault MD3200i, and a Dell PowerVault MD 1200 which is capable of processing huge amount of microarray data. We also have tape back-up system – Dell PowerVault 110T, LTO2-L, 200/400GB). An efficient local area network has been established to connect the MiSeq sequencer, BeadArray Readers, BeadXpress reader, Autoloader, Tecan robots and barcode scanning PCs. (Please see the figure 1) A gigabit switch connects each scanner to the Fileserver via a non-routable, private network. The FileServer has an additional network card that is connected to the public network (internet). The FTP server machine is connected to the public network (internet). All data acquired is only saved to the FileServer. All other desktop computers are connected through internet to the University of Chicago hospital network.